jmcastagnetto Tue Apr 10 11:44:25 2001 EDT
Added files:
/pear/Science/Chemistry/doc Science_Chemistry_Atom.html
Science_Chemistry_Atom_PDB.html
Science_Chemistry_Coordinates.html
Science_Chemistry_Element.html
Science_Chemistry_Macromolecule.html
Science_Chemistry_Macromolecule_PDB.html
Science_Chemistry_Molecule.html
Science_Chemistry_Molecule_XYZ.html
Science_Chemistry_PDBFile.html
Science_Chemistry_PDBParser.html
Science_Chemistry_Periodic_Table.html
Science_Chemistry_Residue_PDB.html
class_Science_Chemistry_Atom.xml
class_Science_Chemistry_Atom_PDB.xml
class_Science_Chemistry_Coordinates.xml
class_Science_Chemistry_Element.xml
class_Science_Chemistry_Macromolecule.xml
class_Science_Chemistry_Macromolecule_PDB.xml
class_Science_Chemistry_Molecule.xml
class_Science_Chemistry_Molecule_XYZ.xml
class_Science_Chemistry_PDBFile.xml
class_Science_Chemistry_PDBParser.xml
class_Science_Chemistry_Periodic_Table.xml
class_Science_Chemistry_Residue_PDB.xml
classtree_Science_Chemistry_Atom.xml
classtree_Science_Chemistry_Coordinates.xml
classtree_Science_Chemistry_Element.xml
classtree_Science_Chemistry_Macromolecule.xml
classtree_Science_Chemistry_Molecule.xml
classtree_Science_Chemistry_PDBFile.xml
classtree_Science_Chemistry_PDBParser.xml
classtree_Science_Chemistry_Periodic_Table.xml
packageelementlist_Science_Chemistry.html
Modified files:
/pear/Science/Chemistry/doc elementlist.xml packagelist.xml
phpdoc_classtree.html
phpdoc_elementlist.html
phpdoc_packagelist.html
phpdoc_warnings.html
phpdoc_xmlfiles.html
warnings_classanalyser.xml
warnings_parser.xml
Log:
New docs after renaming of classes from Chem_* to Science_Chemistry_*
a good solution, until PHP gets some sort of namespace
Index: pear/Science/Chemistry/doc/elementlist.xml
diff -u pear/Science/Chemistry/doc/elementlist.xml:1.1
pear/Science/Chemistry/doc/elementlist.xml:1.2
--- pear/Science/Chemistry/doc/elementlist.xml:1.1 Tue Apr 10 09:44:39 2001
+++ pear/Science/Chemistry/doc/elementlist.xml Tue Apr 10 11:44:24 2001
@@ -1 +1 @@
-<?xml version="1.0"?><phpdoc><index><chapter char="C"><element type="class" source=""
sourcetype="class" name="Chem_Atom_PDB">Represents a PDB atom record</element><element
type="functions" source="Chem_Atom_PDB" sourcetype="class"
name="Chem_Atom_PDB"/><element type="class" source="" sourcetype="class"
name="Chem_Atom">Base class representing an Atom</element><element type="functions"
source="Chem_Atom" sourcetype="class" name="Chem_Atom">Constructor for the class,
requires the element symbol</element><element type="class" source=""
sourcetype="class" name="Chem_Coordinates">Utility class for defining 3D coordinates
and</element><element type="functions" source="Chem_Coordinates" sourcetype="class"
name="Chem_Coordinates">Constructor for the class, returns null if parameter
is</element><element type="class" source="" sourcetype="class"
name="Chem_Element">Utility class that defines a chemical element
object</element><element type="functions" source="Chem_Element" sourcetype="class"
name="Chem_Element">Constructor for the class</element><element type="class" source=""
sourcetype="class" name="Chem_Macromolecule_PDB">Represents a PDB macromolecule,
composed of several</element><element type="functions" source="Chem_Macromolecule_PDB"
sourcetype="class" name="Chem_Macromolecule_PDB">Constructor for the
class</element><element type="class" source="" sourcetype="class"
name="Chem_Macromolecule">Represents a macromolecule, composed of
several</element><element type="functions" source="Chem_Macromolecule"
sourcetype="class" name="Chem_Macromolecule">Constructor for the class, requires a
macromolecule name</element><element type="class" source="" sourcetype="class"
name="Chem_Molecule_XYZ">Base class representing a Molecule from a XYZ format
file</element><element type="functions" source="Chem_Molecule_XYZ" sourcetype="class"
name="Chem_Molecule_XYZ">Constructor for the class, accepts 2 optional
parameters:</element><element type="class" source="" sourcetype="class"
name="Chem_Residue_PDB">Represents a PDB residue</element><element type="functions"
source="Chem_Residue_PDB" sourcetype="class" name="Chem_Residue_PDB">Constructor for
the class</element><element type="class" source="" sourcetype="class"
name="Chem_Molecule">Base class representing a Molecule</element><element
type="functions" source="Chem_Molecule" sourcetype="class"
name="Chem_Molecule">Constructor for the class, requires a molecule
name</element><element type="class" source="" sourcetype="class"
name="Chem_PDBFile">Represents a PDB file, composed of one or more
Chem_Macromolecule_PDB objects</element><element type="functions"
source="Chem_PDBFile" sourcetype="class" name="Chem_PDBFile">Constructor for the
class, requires a PDB filename</element><element type="class" source=""
sourcetype="class" name="Chem_PDBParser">A self-contained class to parse a PDB file
into an array of residues</element><element type="functions" source="Chem_PDBParser"
sourcetype="class" name="Chem_PDBParser">Constructor for the class, requires a PDB
filename</element><element type="class" source="" sourcetype="class"
name="Chem_Periodic_Table">Utility class that defines a Periodic Table of
elements</element></chapter><chapter char="g"><element type="functions"
source="Chem_Atom_PDB" sourcetype="class" name="getField"/><element type="functions"
source="Chem_Atom" sourcetype="class" name="getElement">Returns the chemical symbol
for the atom</element><element type="functions" source="Chem_Periodic_Table"
sourcetype="class" name="getElement">Returns a Chem_Element object correspoding to the
symbol (case sensitive)</element><element type="functions" source="Chem_Atom"
sourcetype="class" name="getCoordinates">Returns the coordinates object for the
atom</element><element type="functions" source="Chem_Coordinates" sourcetype="class"
name="getCoordinates">Returns the array of coordinates</element><element
type="functions" source="Chem_Macromolecule" sourcetype="class"
name="getMolecules">Returns an array of Chem_Molecule objects</element><element
type="functions" source="Chem_Residue_PDB" sourcetype="class"
name="getGeomParams"/><element type="functions" source="Chem_Molecule"
sourcetype="class" name="getAtoms">Returns an array of Atom objects</element><element
type="functions" source="Chem_Molecule" sourcetype="class"
name="getBondCutoff">Returns the bond cutoff uses to determine bonds</element><element
type="functions" source="Chem_Molecule" sourcetype="class"
name="getDistanceMatrix">Returns the atom-atom distance matrix</element><element
type="functions" source="Chem_Molecule" sourcetype="class"
name="getConnectionTable">Returns an array of connected atoms and their bond
distance</element><element type="functions" source="Chem_PDBParser" sourcetype="class"
name="getResidueList">Returns an array of residues with a particular
name</element><element type="functions" source="Chem_Periodic_Table"
sourcetype="class" name="getElementFamily">Returns an array of Chem_Element objects
belonging to an element family</element></chapter><chapter char="r"><element
type="variables" source="Chem_Atom_PDB" sourcetype="class" name="$rec_name">PDB Atom
record type, one of ATOM or HETATM</element><element type="variables"
source="Chem_Atom_PDB" sourcetype="class" name="$res_name">PDB Atom&apos;s Residue
name</element><element type="variables" source="Chem_Atom_PDB" sourcetype="class"
name="$res_seq_num">PDB Atom&apos;s Residue sequential
numnber</element></chapter><chapter char="s"><element type="variables"
source="Chem_Atom_PDB" sourcetype="class" name="$ser_num">PDB Atom serial
number</element><element type="variables" source="Chem_Atom_PDB" sourcetype="class"
name="$segment_id">PDB Atom segment identifier</element><element type="functions"
source="Chem_Atom" sourcetype="class" name="setCoordinates">Sets the coordinates for
the atom object</element><element type="variables" source="Chem_Element"
sourcetype="class" name="$symbol">Element&apos;s symbol, one or two characters,
case sensitive</element><element type="variables" source="Chem_Residue_PDB"
sourcetype="class" name="$seq_num">PDB Residue sequence number</element><element
type="functions" source="Chem_Molecule" sourcetype="class" name="setBondCutoff">Sets
the distance cutoff for bond determination</element></chapter><chapter
char="a"><element type="variables" source="Chem_Atom_PDB" sourcetype="class"
name="$atom_name">PDB Atom name</element><element type="variables"
source="Chem_Atom_PDB" sourcetype="class" name="$alt_loc">PDB Atom alternative
location</element><element type="functions" source="Chem_Coordinates"
sourcetype="class" name="areCoordinates">Checks if the object is an instance of
Chem_Coordinates</element><element type="functions" source="Chem_Macromolecule"
sourcetype="class" name="addMolecule">Adds a Chem_Molecule object to the list of
molecules in the macromolecule</element><element type="functions"
source="Chem_Molecule" sourcetype="class" name="addAtom">Adds a Chem_Atom object to
the list of atoms in the molecule</element><element type="variables"
source="Chem_Molecule" sourcetype="class" name="$atoms">Array of atom objects in the
molecule</element></chapter><chapter char="c"><element type="variables"
source="Chem_Atom_PDB" sourcetype="class" name="$chain_id">PDB Atom&apos;s Residue
chain ID</element><element type="variables" source="Chem_Atom_PDB" sourcetype="class"
name="$charge">PDB Atom electronic charge</element><element type="variables"
source="Chem_Coordinates" sourcetype="class" name="$coords">Array of tridimensional
coordinates: (x, y, z)</element><element type="functions" source="Chem_Residue_PDB"
sourcetype="class" name="calcGeomParams"/><element type="variables"
source="Chem_Residue_PDB" sourcetype="class" name="$chain">PDB Residue
chain</element><element type="functions" source="Chem_Molecule" sourcetype="class"
name="calcDistanceMatrix">Calculates the atom-atom distance matrix in
Angstroms</element><element type="functions" source="Chem_Molecule" sourcetype="class"
name="calcConnectionTable">Calculates the connection table for the
molecule</element><element type="variables" source="Chem_Molecule" sourcetype="class"
name="$conn_table">Atom-Atom connection (bond) table</element><element
type="variables" source="Chem_PDBFile" sourcetype="class" name="$class">PDB
macromolecule(s) class</element><element type="variables" source="Chem_PDBParser"
sourcetype="class" name="$class">PDB macromolecule(s)
class</element></chapter><chapter char="i"><element type="variables"
source="Chem_Atom_PDB" sourcetype="class" name="$ins_code">PDB Atom insert
code</element><element type="functions" source="Chem_Atom" sourcetype="class"
name="isAtom">Checks if the object is an instance of Chem_Atom</element><element
type="functions" source="Chem_Element" sourcetype="class" name="isElement">Checks if
an object is a Chem_Element instance</element><element type="functions"
source="Chem_Macromolecule" sourcetype="class" name="initMacromolecule">Initializes
the array of Chem_Molecule objects</element><element type="functions"
source="Chem_Macromolecule" sourcetype="class" name="isMacromolecule">Checks if the
object is an instance of Chem_Macromolecule</element><element type="variables"
source="Chem_Residue_PDB" sourcetype="class" name="$id">PDB Residue
ID</element><element type="functions" source="Chem_Molecule" sourcetype="class"
name="initMolecule">Initializes the array of Chem_Atom objects</element><element
type="functions" source="Chem_Molecule" sourcetype="class" name="isMolecule">Checks if
the object is an instance of Chem_Molecule</element><element type="functions"
source="Chem_Periodic_Table" sourcetype="class" name="initTable">Initializes the
Periodic Table array</element></chapter><chapter char="o"><element type="variables"
source="Chem_Atom_PDB" sourcetype="class" name="$occupancy">PDB Atom
occupancy</element></chapter><chapter char="t"><element type="variables"
source="Chem_Atom_PDB" sourcetype="class" name="$temp_factor">PDB Atom temperature
factor</element><element type="functions" source="Chem_Atom" sourcetype="class"
name="toString">Returns a string representation of the Chem_Atom
object</element><element type="functions" source="Chem_Coordinates" sourcetype="class"
name="toString">Returns a string representation of the coordinates: x y
z</element><element type="functions" source="Chem_Macromolecule" sourcetype="class"
name="toString">Returns a string representation of the macromolecule</element><element
type="functions" source="Chem_Molecule_XYZ" sourcetype="class"
name="toString">Generates a string representation of the XYZ
molecule</element><element type="functions" source="Chem_Molecule" sourcetype="class"
name="toString">Returns a string representation of the molecule</element><element
type="functions" source="Chem_Atom" sourcetype="class" name="toCML">Returns a CML
representation of the Chem_Atom object</element><element type="functions"
source="Chem_Coordinates" sourcetype="class" name="toCML">Returns a CML representation
of the coordinates</element><element type="functions" source="Chem_Macromolecule"
sourcetype="class" name="toCML">Returns a CML representation of the
molecule</element><element type="functions" source="Chem_Molecule" sourcetype="class"
name="toCML">Returns a CML representation of the molecule</element><element
type="functions" source="Chem_PDBFile" sourcetype="class" name="toCML">Returns a CML
representation of the PDB file</element></chapter><chapter char="V"><element
type="variables" source="Chem_Atom_PDB" sourcetype="class" name="$VALID">If the atom
object has been initialized</element><element type="variables"
source="Chem_Residue_PDB" sourcetype="class" name="$VALID">If the PDB residue object
has been initialized</element></chapter><chapter char="p"><element type="variables"
source="Chem_Atom_PDB" sourcetype="class" name="$parent_residue">Reference to the
containing Residue object</element><element type="functions"
source="Chem_Macromolecule_PDB" sourcetype="class" name="parseResidues">Makes the
array of residues in the macromolecule</element><element type="functions"
source="Chem_PDBParser" sourcetype="class" name="parseResidues">Makes the array of
residues in the macromolecule</element><element type="functions"
source="Chem_Molecule_XYZ" sourcetype="class" name="parseXYZ">method that does the
parsing of the XYZ data itself</element><element type="functions"
source="Chem_Molecule_XYZ" sourcetype="class" name="parseAtom">Parses an XYZ atom
record</element><element type="functions" source="Chem_PDBParser" sourcetype="class"
name="parseAtom">Parses an atom record into an associative array</element><element
type="variables" source="Chem_Residue_PDB" sourcetype="class" name="$pdb">PDB ID for
the protein that contains</element><element type="variables" source="Chem_PDBFile"
sourcetype="class" name="$pdb">PDB ID</element><element type="variables"
source="Chem_PDBParser" sourcetype="class" name="$pdb">PDB ID</element><element
type="functions" source="Chem_Molecule" sourcetype="class"
name="printDistanceMatrix">Prints the atom-atom distance matrix</element><element
type="functions" source="Chem_Molecule" sourcetype="class"
name="printConnectionTable">Prints the molecule&apos;s connection
table</element><element type="functions" source="Chem_PDBFile" sourcetype="class"
name="parseFile">Makes the arrays of all present PDB record types</element><element
type="variables" source="Chem_Periodic_Table" sourcetype="class"
name="$periodic_table">The associative array containing the chemical
elements</element></chapter><chapter char="d"><element type="functions"
source="Chem_Atom" sourcetype="class" name="distance">Calculates the cartesian
distance from this atom</element><element type="functions" source="Chem_Coordinates"
sourcetype="class" name="distance">Castesian distance calculation
method</element><element type="variables" source="Chem_Molecule" sourcetype="class"
name="$dist_matrix">Atom-Atom distance matrix</element><element type="variables"
source="Chem_PDBFile" sourcetype="class" name="$date">PDB file&apos;s
date</element><element type="variables" source="Chem_PDBParser" sourcetype="class"
name="$date">PDB file&apos;s date</element></chapter><chapter char="e"><element
type="variables" source="Chem_Atom" sourcetype="class" name="$element">Element
symbol</element><element type="variables" source="Chem_Molecule_XYZ"
sourcetype="class" name="$energy">Energy of the molecule. Optional value in XYZ file
format.</element></chapter><chapter char="x"><element type="variables"
source="Chem_Atom" sourcetype="class" name="$xyz">Chem_Coordinates
object</element></chapter><chapter char="n"><element type="variables"
source="Chem_Element" sourcetype="class" name="$name">Element&apos;s
name</element><element type="variables" source="Chem_Macromolecule" sourcetype="class"
name="$name">Macromolecule&apos;s name</element><element type="variables"
source="Chem_Molecule" sourcetype="class" name="$name">Molecule name</element><element
type="variables" source="Chem_Element" sourcetype="class"
name="$number">Element&apos;s atomic number</element><element type="variables"
source="Chem_Macromolecule" sourcetype="class" name="$num_molecules">Number of
molecules/subunits</element><element type="variables" source="Chem_Molecule"
sourcetype="class" name="$num_atoms">Number of atoms in the molecule</element><element
type="variables" source="Chem_PDBFile" sourcetype="class"
name="$num_macromolecules">Number of molecules/subunits</element><element
type="variables" source="Chem_PDBParser" sourcetype="class"
name="$num_macromolecules">Number of macromolecules</element></chapter><chapter
char="w"><element type="variables" source="Chem_Element" sourcetype="class"
name="$weight">Element&apos;s atomic weight in a.m.u (atomic mass
units)</element></chapter><chapter char="m"><element type="variables"
source="Chem_Element" sourcetype="class" name="$melting_point">Element&apos;s
melting point, with comments</element><element type="variables"
source="Chem_Macromolecule" sourcetype="class" name="$molecules">Array of molecular
objects</element><element type="variables" source="Chem_Residue_PDB"
sourcetype="class" name="$macromol">Reference to the protein</element><element
type="variables" source="Chem_PDBFile" sourcetype="class" name="$meta">Array of meta
records</element><element type="variables" source="Chem_PDBFile" sourcetype="class"
name="$macromolecules">Array of macromolecular objects</element><element
type="variables" source="Chem_PDBParser" sourcetype="class"
name="$macromolecules">Array of macromolecules</element></chapter><chapter
char="b"><element type="variables" source="Chem_Element" sourcetype="class"
name="$boiling_point">Element&apos;s boiling point, with
comments</element></chapter><chapter char="f"><element type="variables"
source="Chem_Element" sourcetype="class" name="$family">Element&apos;s
family</element><element type="variables" source="Chem_PDBFile" sourcetype="class"
name="$file">Full path to PDB file</element><element type="variables"
source="Chem_PDBParser" sourcetype="class" name="$file">Full path to PDB
file</element></chapter><chapter char="B"><element type="variables"
source="Chem_Molecule" sourcetype="class" name="$BONDCUTOFF">Distance cutoff for bond
estimation</element></chapter><chapter char="S"><element type="package" source=""
sourcetype="" name="Science_Chemistry"/></chapter></index></phpdoc>
\ No newline at end of file
+<?xml version="1.0"?><phpdoc><index><chapter char="S"><element type="class" source=""
+sourcetype="class" name="Science_Chemistry_Atom_PDB">Represents a PDB atom
+record</element><element type="functions" source="Science_Chemistry_Atom_PDB"
+sourcetype="class" name="Science_Chemistry_Atom_PDB"/><element type="class" source=""
+sourcetype="class" name="Science_Chemistry_Atom">Base class representing an
+Atom</element><element type="functions" source="Science_Chemistry_Atom"
+sourcetype="class" name="Science_Chemistry_Atom">Constructor for the class, requires
+the element symbol</element><element type="class" source="" sourcetype="class"
+name="Science_Chemistry_Coordinates">Utility class for defining 3D coordinates
+and</element><element type="functions" source="Science_Chemistry_Coordinates"
+sourcetype="class" name="Science_Chemistry_Coordinates">Constructor for the class,
+returns null if parameter is</element><element type="class" source=""
+sourcetype="class" name="Science_Chemistry_Element">Utility class that defines a
+chemical element object</element><element type="functions"
+source="Science_Chemistry_Element" sourcetype="class"
+name="Science_Chemistry_Element">Constructor for the class</element><element
+type="class" source="" sourcetype="class"
+name="Science_Chemistry_Macromolecule_PDB">Represents a PDB macromolecule, composed
+of several</element><element type="functions"
+source="Science_Chemistry_Macromolecule_PDB" sourcetype="class"
+name="Science_Chemistry_Macromolecule_PDB">Constructor for the
+class</element><element type="class" source="" sourcetype="class"
+name="Science_Chemistry_Macromolecule">Represents a macromolecule, composed of
+several</element><element type="functions" source="Science_Chemistry_Macromolecule"
+sourcetype="class" name="Science_Chemistry_Macromolecule">Constructor for the class,
+requires a macromolecule name</element><element type="class" source=""
+sourcetype="class" name="Science_Chemistry_Molecule_XYZ">Base class representing a
+Molecule from a XYZ format file</element><element type="functions"
+source="Science_Chemistry_Molecule_XYZ" sourcetype="class"
+name="Science_Chemistry_Molecule_XYZ">Constructor for the class, accepts 2 optional
+parameters:</element><element type="class" source="" sourcetype="class"
+name="Science_Chemistry_Residue_PDB">Represents a PDB residue</element><element
+type="functions" source="Science_Chemistry_Residue_PDB" sourcetype="class"
+name="Science_Chemistry_Residue_PDB">Constructor for the class</element><element
+type="class" source="" sourcetype="class" name="Science_Chemistry_Molecule">Base
+class representing a Molecule</element><element type="functions"
+source="Science_Chemistry_Molecule" sourcetype="class"
+name="Science_Chemistry_Molecule">Constructor for the class, requires a molecule
+name</element><element type="class" source="" sourcetype="class"
+name="Science_Chemistry_PDBFile">Represents a PDB file, composed of one or more
+Science_Chemistry_Macromolecule_PDB objects</element><element type="functions"
+source="Science_Chemistry_PDBFile" sourcetype="class"
+name="Science_Chemistry_PDBFile">Constructor for the class, requires a PDB
+filename</element><element type="class" source="" sourcetype="class"
+name="Science_Chemistry_PDBParser">A self-contained class to parse a PDB file into an
+array of residues</element><element type="functions"
+source="Science_Chemistry_PDBParser" sourcetype="class"
+name="Science_Chemistry_PDBParser">Constructor for the class, requires a PDB
+filename</element><element type="class" source="" sourcetype="class"
+name="Science_Chemistry_Periodic_Table">Utility class that defines a Periodic Table
+of elements</element><element type="package" source="" sourcetype=""
+name="Science_Chemistry"/></chapter><chapter char="g"><element type="functions"
+source="Science_Chemistry_Atom_PDB" sourcetype="class" name="getField"/><element
+type="functions" source="Science_Chemistry_Atom" sourcetype="class"
+name="getElement">Returns the chemical symbol for the atom</element><element
+type="functions" source="Science_Chemistry_Periodic_Table" sourcetype="class"
+name="getElement">Returns a Science_Chemistry_Element object correspoding to the
+symbol (case sensitive)</element><element type="functions"
+source="Science_Chemistry_Atom" sourcetype="class" name="getCoordinates">Returns the
+coordinates object for the atom</element><element type="functions"
+source="Science_Chemistry_Coordinates" sourcetype="class"
+name="getCoordinates">Returns the array of coordinates</element><element
+type="functions" source="Science_Chemistry_Macromolecule" sourcetype="class"
+name="getMolecules">Returns an array of Science_Chemistry_Molecule
+objects</element><element type="functions" source="Science_Chemistry_Residue_PDB"
+sourcetype="class" name="getGeomParams"/><element type="functions"
+source="Science_Chemistry_Molecule" sourcetype="class" name="getAtoms">Returns an
+array of Atom objects</element><element type="functions"
+source="Science_Chemistry_Molecule" sourcetype="class" name="getBondCutoff">Returns
+the bond cutoff uses to determine bonds</element><element type="functions"
+source="Science_Chemistry_Molecule" sourcetype="class"
+name="getDistanceMatrix">Returns the atom-atom distance matrix</element><element
+type="functions" source="Science_Chemistry_Molecule" sourcetype="class"
+name="getConnectionTable">Returns an array of connected atoms and their bond
+distance</element><element type="functions" source="Science_Chemistry_PDBParser"
+sourcetype="class" name="getResidueList">Returns an array of residues with a
+particular name</element><element type="functions"
+source="Science_Chemistry_Periodic_Table" sourcetype="class"
+name="getElementFamily">Returns an array of Science_Chemistry_Element objects
+belonging to an element family</element></chapter><chapter char="r"><element
+type="variables" source="Science_Chemistry_Atom_PDB" sourcetype="class"
+name="$rec_name">PDB Atom record type, one of ATOM or HETATM</element><element
+type="variables" source="Science_Chemistry_Atom_PDB" sourcetype="class"
+name="$res_name">PDB Atom&apos;s Residue name</element><element type="variables"
+source="Science_Chemistry_Atom_PDB" sourcetype="class" name="$res_seq_num">PDB
+Atom&apos;s Residue sequential numnber</element></chapter><chapter
+char="s"><element type="variables" source="Science_Chemistry_Atom_PDB"
+sourcetype="class" name="$ser_num">PDB Atom serial number</element><element
+type="variables" source="Science_Chemistry_Atom_PDB" sourcetype="class"
+name="$segment_id">PDB Atom segment identifier</element><element type="functions"
+source="Science_Chemistry_Atom" sourcetype="class" name="setCoordinates">Sets the
+coordinates for the atom object</element><element type="variables"
+source="Science_Chemistry_Element" sourcetype="class"
+name="$symbol">Element&apos;s symbol, one or two characters, case
+sensitive</element><element type="variables" source="Science_Chemistry_Residue_PDB"
+sourcetype="class" name="$seq_num">PDB Residue sequence number</element><element
+type="functions" source="Science_Chemistry_Molecule" sourcetype="class"
+name="setBondCutoff">Sets the distance cutoff for bond
+determination</element></chapter><chapter char="a"><element type="variables"
+source="Science_Chemistry_Atom_PDB" sourcetype="class" name="$atom_name">PDB Atom
+name</element><element type="variables" source="Science_Chemistry_Atom_PDB"
+sourcetype="class" name="$alt_loc">PDB Atom alternative location</element><element
+type="functions" source="Science_Chemistry_Coordinates" sourcetype="class"
+name="areCoordinates">Checks if the object is an instance of
+Science_Chemistry_Coordinates</element><element type="functions"
+source="Science_Chemistry_Macromolecule" sourcetype="class" name="addMolecule">Adds a
+Science_Chemistry_Molecule object to the list of molecules in the
+macromolecule</element><element type="functions" source="Science_Chemistry_Molecule"
+sourcetype="class" name="addAtom">Adds a Science_Chemistry_Atom object to the list of
+atoms in the molecule</element><element type="variables"
+source="Science_Chemistry_Molecule" sourcetype="class" name="$atoms">Array of atom
+objects in the molecule</element></chapter><chapter char="c"><element
+type="variables" source="Science_Chemistry_Atom_PDB" sourcetype="class"
+name="$chain_id">PDB Atom&apos;s Residue chain ID</element><element
+type="variables" source="Science_Chemistry_Atom_PDB" sourcetype="class"
+name="$charge">PDB Atom electronic charge</element><element type="variables"
+source="Science_Chemistry_Coordinates" sourcetype="class" name="$coords">Array of
+tridimensional coordinates: (x, y, z)</element><element type="functions"
+source="Science_Chemistry_Residue_PDB" sourcetype="class"
+name="calcGeomParams"/><element type="variables"
+source="Science_Chemistry_Residue_PDB" sourcetype="class" name="$chain">PDB Residue
+chain</element><element type="functions" source="Science_Chemistry_Molecule"
+sourcetype="class" name="calcDistanceMatrix">Calculates the atom-atom distance matrix
+in Angstroms</element><element type="functions" source="Science_Chemistry_Molecule"
+sourcetype="class" name="calcConnectionTable">Calculates the connection table for the
+molecule</element><element type="variables" source="Science_Chemistry_Molecule"
+sourcetype="class" name="$conn_table">Atom-Atom connection (bond)
+table</element><element type="variables" source="Science_Chemistry_PDBFile"
+sourcetype="class" name="$class">PDB macromolecule(s) class</element><element
+type="variables" source="Science_Chemistry_PDBParser" sourcetype="class"
+name="$class">PDB macromolecule(s) class</element></chapter><chapter
+char="i"><element type="variables" source="Science_Chemistry_Atom_PDB"
+sourcetype="class" name="$ins_code">PDB Atom insert code</element><element
+type="functions" source="Science_Chemistry_Atom" sourcetype="class"
+name="isAtom">Checks if the object is an instance of
+Science_Chemistry_Atom</element><element type="functions"
+source="Science_Chemistry_Element" sourcetype="class" name="isElement">Checks if an
+object is a Science_Chemistry_Element instance</element><element type="functions"
+source="Science_Chemistry_Macromolecule" sourcetype="class"
+name="initMacromolecule">Initializes the array of Science_Chemistry_Molecule
+objects</element><element type="functions" source="Science_Chemistry_Macromolecule"
+sourcetype="class" name="isMacromolecule">Checks if the object is an instance of
+Science_Chemistry_Macromolecule</element><element type="variables"
+source="Science_Chemistry_Residue_PDB" sourcetype="class" name="$id">PDB Residue
+ID</element><element type="functions" source="Science_Chemistry_Molecule"
+sourcetype="class" name="initMolecule">Initializes the array of
+Science_Chemistry_Atom objects</element><element type="functions"
+source="Science_Chemistry_Molecule" sourcetype="class" name="isMolecule">Checks if
+the object is an instance of Science_Chemistry_Molecule</element><element
+type="functions" source="Science_Chemistry_Periodic_Table" sourcetype="class"
+name="initTable">Initializes the Periodic Table array</element></chapter><chapter
+char="o"><element type="variables" source="Science_Chemistry_Atom_PDB"
+sourcetype="class" name="$occupancy">PDB Atom occupancy</element></chapter><chapter
+char="t"><element type="variables" source="Science_Chemistry_Atom_PDB"
+sourcetype="class" name="$temp_factor">PDB Atom temperature factor</element><element
+type="functions" source="Science_Chemistry_Atom" sourcetype="class"
+name="toString">Returns a string representation of the Science_Chemistry_Atom
+object</element><element type="functions" source="Science_Chemistry_Coordinates"
+sourcetype="class" name="toString">Returns a string representation of the
+coordinates: x y z</element><element type="functions"
+source="Science_Chemistry_Macromolecule" sourcetype="class" name="toString">Returns a
+string representation of the macromolecule</element><element type="functions"
+source="Science_Chemistry_Molecule_XYZ" sourcetype="class" name="toString">Generates
+a string representation of the XYZ molecule</element><element type="functions"
+source="Science_Chemistry_Molecule" sourcetype="class" name="toString">Returns a
+string representation of the molecule</element><element type="functions"
+source="Science_Chemistry_Atom" sourcetype="class" name="toCML">Returns a CML
+representation of the Science_Chemistry_Atom object</element><element
+type="functions" source="Science_Chemistry_Coordinates" sourcetype="class"
+name="toCML">Returns a CML representation of the coordinates</element><element
+type="functions" source="Science_Chemistry_Macromolecule" sourcetype="class"
+name="toCML">Returns a CML representation of the molecule</element><element
+type="functions" source="Science_Chemistry_Molecule" sourcetype="class"
+name="toCML">Returns a CML representation of the molecule</element><element
+type="functions" source="Science_Chemistry_PDBFile" sourcetype="class"
+name="toCML">Returns a CML representation of the PDB file</element></chapter><chapter
+char="V"><element type="variables" source="Science_Chemistry_Atom_PDB"
+sourcetype="class" name="$VALID">If the atom object has been
+initialized</element><element type="variables" source="Science_Chemistry_Residue_PDB"
+sourcetype="class" name="$VALID">If the PDB residue object has been
+initialized</element></chapter><chapter char="p"><element type="variables"
+source="Science_Chemistry_Atom_PDB" sourcetype="class"
+name="$parent_residue">Reference to the containing Residue object</element><element
+type="functions" source="Science_Chemistry_Macromolecule_PDB" sourcetype="class"
+name="parseResidues">Makes the array of residues in the
+macromolecule</element><element type="functions" source="Science_Chemistry_PDBParser"
+sourcetype="class" name="parseResidues">Makes the array of residues in the
+macromolecule</element><element type="functions"
+source="Science_Chemistry_Molecule_XYZ" sourcetype="class" name="parseXYZ">method
+that does the parsing of the XYZ data itself</element><element type="functions"
+source="Science_Chemistry_Molecule_XYZ" sourcetype="class" name="parseAtom">Parses an
+XYZ atom record</element><element type="functions"
+source="Science_Chemistry_PDBParser" sourcetype="class" name="parseAtom">Parses an
+atom record into an associative array</element><element type="variables"
+source="Science_Chemistry_Residue_PDB" sourcetype="class" name="$pdb">PDB ID for the
+protein that contains</element><element type="variables"
+source="Science_Chemistry_PDBFile" sourcetype="class" name="$pdb">PDB
+ID</element><element type="variables" source="Science_Chemistry_PDBParser"
+sourcetype="class" name="$pdb">PDB ID</element><element type="functions"
+source="Science_Chemistry_Molecule" sourcetype="class"
+name="printDistanceMatrix">Prints the atom-atom distance matrix</element><element
+type="functions" source="Science_Chemistry_Molecule" sourcetype="class"
+name="printConnectionTable">Prints the molecule&apos;s connection
+table</element><element type="functions" source="Science_Chemistry_PDBFile"
+sourcetype="class" name="parseFile">Makes the arrays of all present PDB record
+types</element><element type="variables" source="Science_Chemistry_Periodic_Table"
+sourcetype="class" name="$periodic_table">The associative array containing the
+chemical elements</element></chapter><chapter char="d"><element type="functions"
+source="Science_Chemistry_Atom" sourcetype="class" name="distance">Calculates the
+cartesian distance from this atom</element><element type="functions"
+source="Science_Chemistry_Coordinates" sourcetype="class" name="distance">Castesian
+distance calculation method</element><element type="variables"
+source="Science_Chemistry_Molecule" sourcetype="class" name="$dist_matrix">Atom-Atom
+distance matrix</element><element type="variables" source="Science_Chemistry_PDBFile"
+sourcetype="class" name="$date">PDB file&apos;s date</element><element
+type="variables" source="Science_Chemistry_PDBParser" sourcetype="class"
+name="$date">PDB file&apos;s date</element></chapter><chapter char="e"><element
+type="variables" source="Science_Chemistry_Atom" sourcetype="class"
+name="$element">Element symbol</element><element type="variables"
+source="Science_Chemistry_Molecule_XYZ" sourcetype="class" name="$energy">Energy of
+the molecule. Optional value in XYZ file format.</element></chapter><chapter
+char="x"><element type="variables" source="Science_Chemistry_Atom" sourcetype="class"
+name="$xyz">Science_Chemistry_Coordinates object</element></chapter><chapter
+char="n"><element type="variables" source="Science_Chemistry_Element"
+sourcetype="class" name="$name">Element&apos;s name</element><element
+type="variables" source="Science_Chemistry_Macromolecule" sourcetype="class"
+name="$name">Macromolecule&apos;s name</element><element type="variables"
+source="Science_Chemistry_Molecule" sourcetype="class" name="$name">Molecule
+name</element><element type="variables" source="Science_Chemistry_Element"
+sourcetype="class" name="$number">Element&apos;s atomic number</element><element
+type="variables" source="Science_Chemistry_Macromolecule" sourcetype="class"
+name="$num_molecules">Number of molecules/subunits</element><element type="variables"
+source="Science_Chemistry_Molecule" sourcetype="class" name="$num_atoms">Number of
+atoms in the molecule</element><element type="variables"
+source="Science_Chemistry_PDBFile" sourcetype="class"
+name="$num_macromolecules">Number of molecules/subunits</element><element
+type="variables" source="Science_Chemistry_PDBParser" sourcetype="class"
+name="$num_macromolecules">Number of macromolecules</element></chapter><chapter
+char="w"><element type="variables" source="Science_Chemistry_Element"
+sourcetype="class" name="$weight">Element&apos;s atomic weight in a.m.u (atomic
+mass units)</element></chapter><chapter char="m"><element type="variables"
+source="Science_Chemistry_Element" sourcetype="class"
+name="$melting_point">Element&apos;s melting point, with
+comments</element><element type="variables" source="Science_Chemistry_Macromolecule"
+sourcetype="class" name="$molecules">Array of molecular objects</element><element
+type="variables" source="Science_Chemistry_Residue_PDB" sourcetype="class"
+name="$macromol">Reference to the protein</element><element type="variables"
+source="Science_Chemistry_PDBFile" sourcetype="class" name="$meta">Array of meta
+records</element><element type="variables" source="Science_Chemistry_PDBFile"
+sourcetype="class" name="$macromolecules">Array of macromolecular
+objects</element><element type="variables" source="Science_Chemistry_PDBParser"
+sourcetype="class" name="$macromolecules">Array of
+macromolecules</element></chapter><chapter char="b"><element type="variables"
+source="Science_Chemistry_Element" sourcetype="class"
+name="$boiling_point">Element&apos;s boiling point, with
+comments</element></chapter><chapter char="f"><element type="variables"
+source="Science_Chemistry_Element" sourcetype="class"
+name="$family">Element&apos;s family</element><element type="variables"
+source="Science_Chemistry_PDBFile" sourcetype="class" name="$file">Full path to PDB
+file</element><element type="variables" source="Science_Chemistry_PDBParser"
+sourcetype="class" name="$file">Full path to PDB file</element></chapter><chapter
+char="B"><element type="variables" source="Science_Chemistry_Molecule"
+sourcetype="class" name="$BONDCUTOFF">Distance cutoff for bond
+estimation</element></chapter></index></phpdoc>
\ No newline at end of file
Index: pear/Science/Chemistry/doc/packagelist.xml
diff -u pear/Science/Chemistry/doc/packagelist.xml:1.1
pear/Science/Chemistry/doc/packagelist.xml:1.2
--- pear/Science/Chemistry/doc/packagelist.xml:1.1 Tue Apr 10 09:44:39 2001
+++ pear/Science/Chemistry/doc/packagelist.xml Tue Apr 10 11:44:24 2001
@@ -1 +1 @@
-<?xml version="1.0"?><phpdoc><packagelist><package name="Science_Chemistry"><class
name="Chem_Atom_PDB"/><class name="Chem_Atom"/><class name="Chem_Coordinates"/><class
name="Chem_Element"/><class name="Chem_Macromolecule_PDB"/><class
name="Chem_Macromolecule"/><class name="Chem_Molecule_XYZ"/><class
name="Chem_Residue_PDB"/><class name="Chem_Molecule"/><class
name="Chem_PDBFile"/><class name="Chem_PDBParser"/><class
name="Chem_Periodic_Table"/></package></packagelist></phpdoc>
\ No newline at end of file
+<?xml version="1.0"?><phpdoc><packagelist><package name="Science_Chemistry"><class
+name="Science_Chemistry_Atom_PDB"/><class name="Science_Chemistry_Atom"/><class
+name="Science_Chemistry_Coordinates"/><class name="Science_Chemistry_Element"/><class
+name="Science_Chemistry_Macromolecule_PDB"/><class
+name="Science_Chemistry_Macromolecule"/><class
+name="Science_Chemistry_Molecule_XYZ"/><class
+name="Science_Chemistry_Residue_PDB"/><class
+name="Science_Chemistry_Molecule"/><class name="Science_Chemistry_PDBFile"/><class
+name="Science_Chemistry_PDBParser"/><class
+name="Science_Chemistry_Periodic_Table"/></package></packagelist></phpdoc>
\ No newline at end of file
Index: pear/Science/Chemistry/doc/phpdoc_classtree.html
diff -u pear/Science/Chemistry/doc/phpdoc_classtree.html:1.1
pear/Science/Chemistry/doc/phpdoc_classtree.html:1.2
--- pear/Science/Chemistry/doc/phpdoc_classtree.html:1.1 Tue Apr 10 09:44:39
2001
+++ pear/Science/Chemistry/doc/phpdoc_classtree.html Tue Apr 10 11:44:24 2001
@@ -34,8 +34,8 @@
</tr>
<tr>
<td align="left" valign="top">
- <h4>Chem_Atom</h4>
- <ul><li><a href="Chem_Atom.html">Chem_Atom</a><ul><li><a
href="Chem_Atom_PDB.html">Chem_Atom_PDB</a></ul></ul>
+ <h4>Science_Chemistry_Atom</h4>
+ <ul><li><a
+href="Science_Chemistry_Atom.html">Science_Chemistry_Atom</a><ul><li><a
+href="Science_Chemistry_Atom_PDB.html">Science_Chemistry_Atom_PDB</a></ul></ul>
</td>
</tr>
@@ -44,8 +44,8 @@
</tr>
<tr>
<td align="left" valign="top">
- <h4>Chem_Coordinates</h4>
- <ul><li><a
href="Chem_Coordinates.html">Chem_Coordinates</a></ul>
+ <h4>Science_Chemistry_Coordinates</h4>
+ <ul><li><a
+href="Science_Chemistry_Coordinates.html">Science_Chemistry_Coordinates</a></ul>
</td>
</tr>
@@ -54,8 +54,8 @@
</tr>
<tr>
<td align="left" valign="top">
- <h4>Chem_Element</h4>
- <ul><li><a href="Chem_Element.html">Chem_Element</a></ul>
+ <h4>Science_Chemistry_Element</h4>
+ <ul><li><a
+href="Science_Chemistry_Element.html">Science_Chemistry_Element</a></ul>
</td>
</tr>
@@ -64,8 +64,8 @@
</tr>
<tr>
<td align="left" valign="top">
- <h4>Chem_Macromolecule</h4>
- <ul><li><a
href="Chem_Macromolecule.html">Chem_Macromolecule</a><ul><li><a
href="Chem_Macromolecule_PDB.html">Chem_Macromolecule_PDB</a></ul></ul>
+ <h4>Science_Chemistry_Macromolecule</h4>
+ <ul><li><a
+href="Science_Chemistry_Macromolecule.html">Science_Chemistry_Macromolecule</a><ul><li><a
+
+href="Science_Chemistry_Macromolecule_PDB.html">Science_Chemistry_Macromolecule_PDB</a></ul></ul>
</td>
</tr>
@@ -74,8 +74,8 @@
</tr>
<tr>
<td align="left" valign="top">
- <h4>Chem_Molecule</h4>
- <ul><li><a
href="Chem_Molecule.html">Chem_Molecule</a><ul><li><a
href="Chem_Molecule_XYZ.html">Chem_Molecule_XYZ</a><li><a
href="Chem_Residue_PDB.html">Chem_Residue_PDB</a></ul></ul>
+ <h4>Science_Chemistry_Molecule</h4>
+ <ul><li><a
+href="Science_Chemistry_Molecule.html">Science_Chemistry_Molecule</a><ul><li><a
+href="Science_Chemistry_Molecule_XYZ.html">Science_Chemistry_Molecule_XYZ</a><li><a
+href="Science_Chemistry_Residue_PDB.html">Science_Chemistry_Residue_PDB</a></ul></ul>
</td>
</tr>
@@ -84,8 +84,8 @@
</tr>
<tr>
<td align="left" valign="top">
- <h4>Chem_PDBFile</h4>
- <ul><li><a href="Chem_PDBFile.html">Chem_PDBFile</a></ul>
+ <h4>Science_Chemistry_PDBFile</h4>
+ <ul><li><a
+href="Science_Chemistry_PDBFile.html">Science_Chemistry_PDBFile</a></ul>
</td>
</tr>
@@ -94,8 +94,8 @@
</tr>
<tr>
<td align="left" valign="top">
- <h4>Chem_PDBParser</h4>
- <ul><li><a href="Chem_PDBParser.html">Chem_PDBParser</a></ul>
+ <h4>Science_Chemistry_PDBParser</h4>
+ <ul><li><a
+href="Science_Chemistry_PDBParser.html">Science_Chemistry_PDBParser</a></ul>
</td>
</tr>
@@ -104,8 +104,8 @@
</tr>
<tr>
<td align="left" valign="top">
- <h4>Chem_Periodic_Table</h4>
- <ul><li><a
href="Chem_Periodic_Table.html">Chem_Periodic_Table</a></ul>
+ <h4>Science_Chemistry_Periodic_Table</h4>
+ <ul><li><a
+href="Science_Chemistry_Periodic_Table.html">Science_Chemistry_Periodic_Table</a></ul>
</td>
</tr>
Index: pear/Science/Chemistry/doc/phpdoc_elementlist.html
diff -u pear/Science/Chemistry/doc/phpdoc_elementlist.html:1.1
pear/Science/Chemistry/doc/phpdoc_elementlist.html:1.2
--- pear/Science/Chemistry/doc/phpdoc_elementlist.html:1.1 Tue Apr 10 09:44:39
2001
+++ pear/Science/Chemistry/doc/phpdoc_elementlist.html Tue Apr 10 11:44:24 2001
@@ -24,7 +24,7 @@
</tr>
<tr>
<td colspan="2" align="left" valign="top">
- <a href="#a">a</a> <a href="#b">b</a> <a href="#B">B</a> <a
href="#C">C</a> <a href="#c">c</a> <a href="#d">d</a> <a href="#e">e</a> <a
href="#f">f</a> <a href="#g">g</a> <a href="#i">i</a> <a href="#m">m</a> <a
href="#n">n</a> <a href="#o">o</a> <a href="#p">p</a> <a href="#r">r</a> <a
href="#s">s</a> <a href="#S">S</a> <a href="#t">t</a> <a href="#V">V</a> <a
href="#w">w</a> <a href="#x">x</a>
+ <a href="#a">a</a> <a href="#b">b</a> <a href="#B">B</a> <a
+href="#c">c</a> <a href="#d">d</a> <a href="#e">e</a> <a href="#f">f</a> <a
+href="#g">g</a> <a href="#i">i</a> <a href="#m">m</a> <a href="#n">n</a> <a
+href="#o">o</a> <a href="#p">p</a> <a href="#r">r</a> <a href="#S">S</a> <a
+href="#s">s</a> <a href="#t">t</a> <a href="#V">V</a> <a href="#w">w</a> <a
+href="#x">x</a>
</td>
</tr>
@@ -35,7 +35,7 @@
<tr>
<td>$atom_name</td>
<td width="100%" align="left" valign="top">
- Variable in Class <a
href="Chem_Atom_PDB.html">Chem_Atom_PDB</a><br>
+ Variable in Class <a
+href="Science_Chemistry_Atom_PDB.html">Science_Chemistry_Atom_PDB</a><br>
PDB Atom name
</td>
</tr>
@@ -43,7 +43,7 @@
<tr>
<td>$alt_loc</td>
<td width="100%" align="left" valign="top">
- Variable in Class <a
href="Chem_Atom_PDB.html">Chem_Atom_PDB</a><br>
+ Variable in Class <a
+href="Science_Chemistry_Atom_PDB.html">Science_Chemistry_Atom_PDB</a><br>
PDB Atom alternative location
</td>
</tr>
@@ -51,31 +51,31 @@
<tr>
<td>areCoordinates</td>
<td width="100%" align="left" valign="top">
- Function in class <a
href="Chem_Coordinates.html">Chem_Coordinates</a><br>
- Checks if the object is an instance of Chem_Coordinates
+ Function in class <a
+href="Science_Chemistry_Coordinates.html">Science_Chemistry_Coordinates</a><br>
+ Checks if the object is an instance of
+Science_Chemistry_Coordinates
</td>
</tr>
<tr>
<td>addMolecule</td>
<td width="100%" align="left" valign="top">
- Function in class <a
href="Chem_Macromolecule.html">Chem_Macromolecule</a><br>
- Adds a Chem_Molecule object to the list of molecules in the
macromolecule
+ Function in class <a
+href="Science_Chemistry_Macromolecule.html">Science_Chemistry_Macromolecule</a><br>
+ Adds a Science_Chemistry_Molecule object to the list of
+molecules in the macromolecule
</td>
</tr>
<tr>
<td>addAtom</td>
<td width="100%" align="left" valign="top">
- Function in class <a
href="Chem_Molecule.html">Chem_Molecule</a><br>
- Adds a Chem_Atom object to the list of atoms in the molecule
+ Function in class <a
+href="Science_Chemistry_Molecule.html">Science_Chemistry_Molecule</a><br>
+ Adds a Science_Chemistry_Atom object to the list of atoms in
+the molecule
</td>
</tr>
<tr>
<td>$atoms</td>
<td width="100%" align="left" valign="top">
- Variable in Class <a
href="Chem_Molecule.html">Chem_Molecule</a><br>
+ Variable in Class <a
+href="Science_Chemistry_Molecule.html">Science_Chemistry_Molecule</a><br>
Array of atom objects in the molecule
</td>
</tr>
@@ -88,7 +88,7 @@
<tr>
<td>$boiling_point</td>
<td width="100%" align="left" valign="top">
- Variable in Class <a
href="Chem_Element.html">Chem_Element</a><br>
+ Variable in Class <a
+href="Science_Chemistry_Element.html">Science_Chemistry_Element</a><br>
Element's boiling point, with comments
</td>
</tr>
@@ -101,209 +101,20 @@
<tr>
<td>$BONDCUTOFF</td>
<td width="100%" align="left" valign="top">
- Variable in Class <a
href="Chem_Molecule.html">Chem_Molecule</a><br>
+ Variable in Class <a
+href="Science_Chemistry_Molecule.html">Science_Chemistry_Molecule</a><br>
Distance cutoff for bond estimation
</td>
</tr>
<tr>
- <td colspan="2" align="left" valign="top"><h4><a
name="C">C</a></h4></td>
- </tr>
-
- <tr>
- <td>Chem_Atom_PDB</td>
- <td width="100%" align="left" valign="top">
- Class <a href="Chem_Atom_PDB.html">Chem_Atom_PDB</a>.<br>
- Represents a PDB atom record
- </td>
- </tr>
-
- <tr>
- <td>Chem_Atom_PDB</td>
- <td width="100%" align="left" valign="top">
- Function in class <a
href="Chem_Atom_PDB.html">Chem_Atom_PDB</a><br>
-
- </td>
- </tr>
-
- <tr>
- <td>Chem_Atom</td>
- <td width="100%" align="left" valign="top">
- Class <a href="Chem_Atom.html">Chem_Atom</a>.<br>
- Base class representing an Atom
- </td>
- </tr>
-
- <tr>
- <td>Chem_Atom</td>
- <td width="100%" align="left" valign="top">
- Function in class <a href="Chem_Atom.html">Chem_Atom</a><br>
- Constructor for the class, requires the element symbol
- </td>
- </tr>
-
- <tr>
- <td>Chem_Coordinates</td>
- <td width="100%" align="left" valign="top">
- Class <a
href="Chem_Coordinates.html">Chem_Coordinates</a>.<br>
- Utility class for defining 3D coordinates and
- </td>
- </tr>
-
- <tr>
- <td>Chem_Coordinates</td>
- <td width="100%" align="left" valign="top">
- Function in class <a
href="Chem_Coordinates.html">Chem_Coordinates</a><br>
- Constructor for the class, returns null if parameter is
- </td>
- </tr>
-
- <tr>
- <td>Chem_Element</td>
- <td width="100%" align="left" valign="top">
- Class <a href="Chem_Element.html">Chem_Element</a>.<br>
- Utility class that defines a chemical element object
- </td>
- </tr>
-
- <tr>
- <td>Chem_Element</td>
- <td width="100%" align="left" valign="top">
- Function in class <a
href="Chem_Element.html">Chem_Element</a><br>
- Constructor for the class
- </td>
- </tr>
-
- <tr>
- <td>Chem_Macromolecule_PDB</td>
- <td width="100%" align="left" valign="top">
- Class <a
href="Chem_Macromolecule_PDB.html">Chem_Macromolecule_PDB</a>.<br>
- Represents a PDB macromolecule, composed of several
- </td>
- </tr>
-
- <tr>
- <td>Chem_Macromolecule_PDB</td>
- <td width="100%" align="left" valign="top">
- Function in class <a
href="Chem_Macromolecule_PDB.html">Chem_Macromolecule_PDB</a><br>
- Constructor for the class
- </td>
- </tr>
-
- <tr>
- <td>Chem_Macromolecule</td>
- <td width="100%" align="left" valign="top">
- Class <a
href="Chem_Macromolecule.html">Chem_Macromolecule</a>.<br>
- Represents a macromolecule, composed of several
- </td>
- </tr>
-
- <tr>
- <td>Chem_Macromolecule</td>
- <td width="100%" align="left" valign="top">
- Function in class <a
href="Chem_Macromolecule.html">Chem_Macromolecule</a><br>
- Constructor for the class, requires a macromolecule name
- </td>
- </tr>
-
- <tr>
- <td>Chem_Molecule_XYZ</td>
- <td width="100%" align="left" valign="top">
- Class <a
href="Chem_Molecule_XYZ.html">Chem_Molecule_XYZ</a>.<br>
- Base class representing a Molecule from a XYZ format file
- </td>
- </tr>
-
- <tr>
- <td>Chem_Molecule_XYZ</td>
- <td width="100%" align="left" valign="top">
- Function in class <a
href="Chem_Molecule_XYZ.html">Chem_Molecule_XYZ</a><br>
- Constructor for the class, accepts 2 optional parameters:
- </td>
- </tr>
-
- <tr>
- <td>Chem_Residue_PDB</td>
- <td width="100%" align="left" valign="top">
- Class <a
href="Chem_Residue_PDB.html">Chem_Residue_PDB</a>.<br>
- Represents a PDB residue
- </td>
- </tr>
-
- <tr>
- <td>Chem_Residue_PDB</td>
- <td width="100%" align="left" valign="top">
- Function in class <a
href="Chem_Residue_PDB.html">Chem_Residue_PDB</a><br>
- Constructor for the class
- </td>
- </tr>
-
- <tr>
- <td>Chem_Molecule</td>
- <td width="100%" align="left" valign="top">
- Class <a href="Chem_Molecule.html">Chem_Molecule</a>.<br>
- Base class representing a Molecule
- </td>
- </tr>
-
- <tr>
- <td>Chem_Molecule</td>
- <td width="100%" align="left" valign="top">
- Function in class <a
href="Chem_Molecule.html">Chem_Molecule</a><br>
- Constructor for the class, requires a molecule name
- </td>
- </tr>
-
- <tr>
- <td>Chem_PDBFile</td>
- <td width="100%" align="left" valign="top">
- Class <a href="Chem_PDBFile.html">Chem_PDBFile</a>.<br>
- Represents a PDB file, composed of one or more
Chem_Macromolecule_PDB objects
- </td>
- </tr>
-
- <tr>
- <td>Chem_PDBFile</td>
- <td width="100%" align="left" valign="top">
- Function in class <a
href="Chem_PDBFile.html">Chem_PDBFile</a><br>
- Constructor for the class, requires a PDB filename
- </td>
- </tr>
-
- <tr>
- <td>Chem_PDBParser</td>
- <td width="100%" align="left" valign="top">
- Class <a href="Chem_PDBParser.html">Chem_PDBParser</a>.<br>
- A self-contained class to parse a PDB file into an array of
residues
- </td>
- </tr>
-
- <tr>
- <td>Chem_PDBParser</td>
- <td width="100%" align="left" valign="top">
- Function in class <a
href="Chem_PDBParser.html">Chem_PDBParser</a><br>
- Constructor for the class, requires a PDB filename
- </td>
- </tr>
-
- <tr>
- <td>Chem_Periodic_Table</td>
- <td width="100%" align="left" valign="top">
- Class <a
href="Chem_Periodic_Table.html">Chem_Periodic_Table</a>.<br>
- Utility class that defines a Periodic Table of elements
- </td>
- </tr>
-
-
- <tr>
<td colspan="2" align="left" valign="top"><h4><a
name="c">c</a></h4></td>
</tr>
<tr>
<td>$chain_id</td>
<td width="100%" align="left" valign="top">
- Variable in Class <a
href="Chem_Atom_PDB.html">Chem_Atom_PDB</a><br>
+ Variable in Class <a
+href="Science_Chemistry_Atom_PDB.html">Science_Chemistry_Atom_PDB</a><br>
PDB Atom's Residue chain ID
</td>
</tr>
@@ -311,7 +122,7 @@
<tr>
<td>$charge</td>
<td width="100%" align="left" valign="top">
- Variable in Class <a
href="Chem_Atom_PDB.html">Chem_Atom_PDB</a><br>
+ Variable in Class <a
+href="Science_Chemistry_Atom_PDB.html">Science_Chemistry_Atom_PDB</a><br>
PDB Atom electronic charge
</td>
</tr>
@@ -319,7 +130,7 @@
<tr>
<td>$coords</td>
<td width="100%" align="left" valign="top">
- Variable in Class <a
href="Chem_Coordinates.html">Chem_Coordinates</a><br>
+ Variable in Class <a
+href="Science_Chemistry_Coordinates.html">Science_Chemistry_Coordinates</a><br>
Array of tridimensional coordinates: (x, y, z)
</td>
</tr>
@@ -327,7 +138,7 @@
<tr>
<td>calcGeomParams</td>
<td width="100%" align="left" valign="top">
- Function in class <a
href="Chem_Residue_PDB.html">Chem_Residue_PDB</a><br>
+ Function in class <a
+href="Science_Chemistry_Residue_PDB.html">Science_Chemistry_Residue_PDB</a><br>
</td>
</tr>
@@ -335,7 +146,7 @@
<tr>
<td>$chain</td>
<td width="100%" align="left" valign="top">
- Variable in Class <a
href="Chem_Residue_PDB.html">Chem_Residue_PDB</a><br>
+ Variable in Class <a
+href="Science_Chemistry_Residue_PDB.html">Science_Chemistry_Residue_PDB</a><br>
PDB Residue chain
</td>
</tr>
@@ -343,7 +154,7 @@
<tr>
<td>calcDistanceMatrix</td>
<td width="100%" align="left" valign="top">
- Function in class <a
href="Chem_Molecule.html">Chem_Molecule</a><br>
+ Function in class <a
+href="Science_Chemistry_Molecule.html">Science_Chemistry_Molecule</a><br>
Calculates the atom-atom distance matrix in Angstroms
</td>
</tr>
@@ -351,7 +162,7 @@
<tr>
<td>calcConnectionTable</td>
<td width="100%" align="left" valign="top">
- Function in class <a
href="Chem_Molecule.html">Chem_Molecule</a><br>
+ Function in class <a
+href="Science_Chemistry_Molecule.html">Science_Chemistry_Molecule</a><br>
Calculates the connection table for the molecule
</td>
</tr>
@@ -359,7 +170,7 @@
<tr>
<td>$conn_table</td>
<td width="100%" align="left" valign="top">
- Variable in Class <a
href="Chem_Molecule.html">Chem_Molecule</a><br>
+ Variable in Class <a
+href="Science_Chemistry_Molecule.html">Science_Chemistry_Molecule</a><br>
Atom-Atom connection (bond) table
</td>
</tr>
@@ -367,7 +178,7 @@
<tr>
<td>$class</td>
<td width="100%" align="left" valign="top">
- Variable in Class <a
href="Chem_PDBFile.html">Chem_PDBFile</a><br>
+ Variable in Class <a
+href="Science_Chemistry_PDBFile.html">Science_Chemistry_PDBFile</a><br>
PDB macromolecule(s) class
</td>
</tr>
@@ -375,7 +186,7 @@
<tr>
<td>$class</td>
<td width="100%" align="left" valign="top">
- Variable in Class <a
href="Chem_PDBParser.html">Chem_PDBParser</a><br>
+ Variable in Class <a
+href="Science_Chemistry_PDBParser.html">Science_Chemistry_PDBParser</a><br>
PDB macromolecule(s) class
</td>
</tr>
@@ -388,7 +199,7 @@
<tr>
<td>distance</td>
<td width="100%" align="left" valign="top">
- Function in class <a href="Chem_Atom.html">Chem_Atom</a><br>
+ Function in class <a
+href="Science_Chemistry_Atom.html">Science_Chemistry_Atom</a><br>
Calculates the cartesian distance from this atom
</td>
</tr>
@@ -396,7 +207,7 @@
<tr>
<td>distance</td>
<td width="100%" align="left" valign="top">
- Function in class <a
href="Chem_Coordinates.html">Chem_Coordinates</a><br>
+ Function in class <a
+href="Science_Chemistry_Coordinates.html">Science_Chemistry_Coordinates</a><br>
Castesian distance calculation method
</td>
</tr>
@@ -404,7 +215,7 @@
<tr>
<td>$dist_matrix</td>
<td width="100%" align="left" valign="top">
- Variable in Class <a
href="Chem_Molecule.html">Chem_Molecule</a><br>
+ Variable in Class <a
+href="Science_Chemistry_Molecule.html">Science_Chemistry_Molecule</a><br>
Atom-Atom distance matrix
</td>
</tr>
@@ -412,7 +223,7 @@
<tr>
<td>$date</td>
<td width="100%" align="left" valign="top">
- Variable in Class <a
href="Chem_PDBFile.html">Chem_PDBFile</a><br>
+ Variable in Class <a
+href="Science_Chemistry_PDBFile.html">Science_Chemistry_PDBFile</a><br>
PDB file's date
</td>
</tr>
@@ -420,7 +231,7 @@
<tr>
<td>$date</td>
<td width="100%" align="left" valign="top">
- Variable in Class <a
href="Chem_PDBParser.html">Chem_PDBParser</a><br>
+ Variable in Class <a
+href="Science_Chemistry_PDBParser.html">Science_Chemistry_PDBParser</a><br>
PDB file's date
</td>
</tr>
@@ -433,7 +244,7 @@
<tr>
<td>$element</td>
<td width="100%" align="left" valign="top">
- Variable in Class <a href="Chem_Atom.html">Chem_Atom</a><br>
+ Variable in Class <a
+href="Science_Chemistry_Atom.html">Science_Chemistry_Atom</a><br>
Element symbol
</td>
</tr>
@@ -441,7 +252,7 @@
<tr>
<td>$energy</td>
<td width="100%" align="left" valign="top">
- Variable in Class <a
href="Chem_Molecule_XYZ.html">Chem_Molecule_XYZ</a><br>
+ Variable in Class <a
+href="Science_Chemistry_Molecule_XYZ.html">Science_Chemistry_Molecule_XYZ</a><br>
Energy of the molecule. Optional value in XYZ file format.
</td>
</tr>
@@ -454,7 +265,7 @@
<tr>
<td>$family</td>
<td width="100%" align="left" valign="top">
- Variable in Class <a
href="Chem_Element.html">Chem_Element</a><br>
+ Variable in Class <a
+href="Science_Chemistry_Element.html">Science_Chemistry_Element</a><br>
Element's family
</td>
</tr>
@@ -462,7 +273,7 @@
<tr>
<td>$file</td>
<td width="100%" align="left" valign="top">
- Variable in Class <a
href="Chem_PDBFile.html">Chem_PDBFile</a><br>
+ Variable in Class <a
+href="Science_Chemistry_PDBFile.html">Science_Chemistry_PDBFile</a><br>
Full path to PDB file
</td>
</tr>
@@ -470,7 +281,7 @@
<tr>
<td>$file</td>
<td width="100%" align="left" valign="top">
- Variable in Class <a
href="Chem_PDBParser.html">Chem_PDBParser</a><br>
+ Variable in Class <a
+href="Science_Chemistry_PDBParser.html">Science_Chemistry_PDBParser</a><br>
Full path to PDB file
</td>
</tr>
@@ -483,7 +294,7 @@
<tr>
<td>getField</td>
<td width="100%" align="left" valign="top">
- Function in class <a
href="Chem_Atom_PDB.html">Chem_Atom_PDB</a><br>
+ Function in class <a
+href="Science_Chemistry_Atom_PDB.html">Science_Chemistry_Atom_PDB</a><br>
</td>
</tr>
@@ -491,7 +302,7 @@
<tr>
<td>getElement</td>
<td width="100%" align="left" valign="top">
- Function in class <a href="Chem_Atom.html">Chem_Atom</a><br>
+ Function in class <a
+href="Science_Chemistry_Atom.html">Science_Chemistry_Atom</a><br>
Returns the chemical symbol for the atom
</td>
</tr>
@@ -499,15 +310,15 @@
<tr>
<td>getElement</td>
<td width="100%" align="left" valign="top">
- Function in class <a
href="Chem_Periodic_Table.html">Chem_Periodic_Table</a><br>
- Returns a Chem_Element object correspoding to the symbol (case
sensitive)
+ Function in class <a
+href="Science_Chemistry_Periodic_Table.html">Science_Chemistry_Periodic_Table</a><br>
+ Returns a Science_Chemistry_Element object correspoding to the
+symbol (case sensitive)
</td>
</tr>
<tr>
<td>getCoordinates</td>
<td width="100%" align="left" valign="top">
- Function in class <a href="Chem_Atom.html">Chem_Atom</a><br>
+ Function in class <a
+href="Science_Chemistry_Atom.html">Science_Chemistry_Atom</a><br>
Returns the coordinates object for the atom
</td>
</tr>
@@ -515,7 +326,7 @@
<tr>
<td>getCoordinates</td>
<td width="100%" align="left" valign="top">
- Function in class <a
href="Chem_Coordinates.html">Chem_Coordinates</a><br>
+ Function in class <a
+href="Science_Chemistry_Coordinates.html">Science_Chemistry_Coordinates</a><br>
Returns the array of coordinates
</td>
</tr>
@@ -523,15 +334,15 @@
<tr>
<td>getMolecules</td>
<td width="100%" align="left" valign="top">
- Function in class <a
href="Chem_Macromolecule.html">Chem_Macromolecule</a><br>
- Returns an array of Chem_Molecule objects
+ Function in class <a
+href="Science_Chemistry_Macromolecule.html">Science_Chemistry_Macromolecule</a><br>
+ Returns an array of Science_Chemistry_Molecule objects
</td>
</tr>
<tr>
<td>getGeomParams</td>
<td width="100%" align="left" valign="top">
- Function in class <a
href="Chem_Residue_PDB.html">Chem_Residue_PDB</a><br>
+ Function in class <a
+href="Science_Chemistry_Residue_PDB.html">Science_Chemistry_Residue_PDB</a><br>
</td>
</tr>
@@ -539,7 +350,7 @@
<tr>
<td>getAtoms</td>
<td width="100%" align="left" valign="top">
- Function in class <a
href="Chem_Molecule.html">Chem_Molecule</a><br>
+ Function in class <a
+href="Science_Chemistry_Molecule.html">Science_Chemistry_Molecule</a><br>
Returns an array of Atom objects
</td>
</tr>
@@ -547,7 +358,7 @@
<tr>
<td>getBondCutoff</td>
<td width="100%" align="left" valign="top">
- Function in class <a
href="Chem_Molecule.html">Chem_Molecule</a><br>
+ Function in class <a
+href="Science_Chemistry_Molecule.html">Science_Chemistry_Molecule</a><br>
Returns the bond cutoff uses to determine bonds
</td>
</tr>
@@ -555,7 +366,7 @@
<tr>
<td>getDistanceMatrix</td>
<td width="100%" align="left" valign="top">
- Function in class <a
href="Chem_Molecule.html">Chem_Molecule</a><br>
+ Function in class <a
+href="Science_Chemistry_Molecule.html">Science_Chemistry_Molecule</a><br>
Returns the atom-atom distance matrix
</td>
</tr>
@@ -563,7 +374,7 @@
<tr>
<td>getConnectionTable</td>
<td width="100%" align="left" valign="top">
- Function in class <a
href="Chem_Molecule.html">Chem_Molecule</a><br>
+ Function in class <a
+href="Science_Chemistry_Molecule.html">Science_Chemistry_Molecule</a><br>
Returns an array of connected atoms and their bond distance
</td>
</tr>
@@ -571,7 +382,7 @@
<tr>
<td>getResidueList</td>
<td width="100%" align="left" valign="top">
- Function in class <a
href="Chem_PDBParser.html">Chem_PDBParser</a><br>
+ Function in class <a
+href="Science_Chemistry_PDBParser.html">Science_Chemistry_PDBParser</a><br>
Returns an array of residues with a particular name
</td>
</tr>
@@ -579,8 +390,8 @@
<tr>
<td>getElementFamily</td>
<td width="100%" align="left" valign="top">
- Function in class <a
href="Chem_Periodic_Table.html">Chem_Periodic_Table</a><br>
- Returns an array of Chem_Element objects belonging to an
element family
+ Function in class <a
+href="Science_Chemistry_Periodic_Table.html">Science_Chemistry_Periodic_Table</a><br>
+ Returns an array of Science_Chemistry_Element objects
+belonging to an element family
</td>
</tr>
@@ -592,7 +403,7 @@
<tr>
<td>$ins_code</td>
<td width="100%" align="left" valign="top">
- Variable in Class <a
href="Chem_Atom_PDB.html">Chem_Atom_PDB</a><br>
+ Variable in Class <a
+href="Science_Chemistry_Atom_PDB.html">Science_Chemistry_Atom_PDB</a><br>
PDB Atom insert code
</td>
</tr>
@@ -600,39 +411,39 @@
<tr>
<td>isAtom</td>
<td width="100%" align="left" valign="top">
- Function in class <a href="Chem_Atom.html">Chem_Atom</a><br>
- Checks if the object is an instance of Chem_Atom
+ Function in class <a
+href="Science_Chemistry_Atom.html">Science_Chemistry_Atom</a><br>
+ Checks if the object is an instance of Science_Chemistry_Atom
</td>
</tr>
<tr>
<td>isElement</td>
<td width="100%" align="left" valign="top">
- Function in class <a
href="Chem_Element.html">Chem_Element</a><br>
- Checks if an object is a Chem_Element instance
+ Function in class <a
+href="Science_Chemistry_Element.html">Science_Chemistry_Element</a><br>
+ Checks if an object is a Science_Chemistry_Element instance
</td>
</tr>
<tr>
<td>initMacromolecule</td>
<td width="100%" align="left" valign="top">
- Function in class <a
href="Chem_Macromolecule.html">Chem_Macromolecule</a><br>
- Initializes the array of Chem_Molecule objects
+ Function in class <a
+href="Science_Chemistry_Macromolecule.html">Science_Chemistry_Macromolecule</a><br>
+ Initializes the array of Science_Chemistry_Molecule objects
</td>
</tr>
<tr>
<td>isMacromolecule</td>
<td width="100%" align="left" valign="top">
- Function in class <a
href="Chem_Macromolecule.html">Chem_Macromolecule</a><br>
- Checks if the object is an instance of Chem_Macromolecule
+ Function in class <a
+href="Science_Chemistry_Macromolecule.html">Science_Chemistry_Macromolecule</a><br>
+ Checks if the object is an instance of
+Science_Chemistry_Macromolecule
</td>
</tr>
<tr>
<td>$id</td>
<td width="100%" align="left" valign="top">
- Variable in Class <a
href="Chem_Residue_PDB.html">Chem_Residue_PDB</a><br>
+ Variable in Class <a
+href="Science_Chemistry_Residue_PDB.html">Science_Chemistry_Residue_PDB</a><br>
PDB Residue ID
</td>
</tr>
@@ -640,23 +451,23 @@
<tr>
<td>initMolecule</td>
<td width="100%" align="left" valign="top">
- Function in class <a
href="Chem_Molecule.html">Chem_Molecule</a><br>
- Initializes the array of Chem_Atom objects
+ Function in class <a
+href="Science_Chemistry_Molecule.html">Science_Chemistry_Molecule</a><br>
+ Initializes the array of Science_Chemistry_Atom objects
</td>
</tr>
<tr>
<td>isMolecule</td>
<td width="100%" align="left" valign="top">
- Function in class <a
href="Chem_Molecule.html">Chem_Molecule</a><br>
- Checks if the object is an instance of Chem_Molecule
+ Function in class <a
+href="Science_Chemistry_Molecule.html">Science_Chemistry_Molecule</a><br>
+ Checks if the object is an instance of
+Science_Chemistry_Molecule
</td>
</tr>
<tr>
<td>initTable</td>
<td width="100%" align="left" valign="top">
- Function in class <a
href="Chem_Periodic_Table.html">Chem_Periodic_Table</a><br>
+ Function in class <a
+href="Science_Chemistry_Periodic_Table.html">Science_Chemistry_Periodic_Table</a><br>
Initializes the Periodic Table array
</td>
</tr>
@@ -669,7 +480,7 @@
<tr>
<td>$melting_point</td>
<td width="100%" align="left" valign="top">
- Variable in Class <a
href="Chem_Element.html">Chem_Element</a><br>
+ Variable in Class <a
+href="Science_Chemistry_Element.html">Science_Chemistry_Element</a><br>
Element's melting point, with comments
</td>
</tr>
@@ -677,7 +488,7 @@
<tr>
<td>$molecules</td>
<td width="100%" align="left" valign="top">
- Variable in Class <a
href="Chem_Macromolecule.html">Chem_Macromolecule</a><br>
+ Variable in Class <a
+href="Science_Chemistry_Macromolecule.html">Science_Chemistry_Macromolecule</a><br>
Array of molecular objects
</td>
</tr>
@@ -685,7 +496,7 @@
<tr>
<td>$macromol</td>
<td width="100%" align="left" valign="top">
- Variable in Class <a
href="Chem_Residue_PDB.html">Chem_Residue_PDB</a><br>
+ Variable in Class <a
+href="Science_Chemistry_Residue_PDB.html">Science_Chemistry_Residue_PDB</a><br>
Reference to the protein
</td>
</tr>
@@ -693,7 +504,7 @@
<tr>
<td>$meta</td>
<td width="100%" align="left" valign="top">
- Variable in Class <a
href="Chem_PDBFile.html">Chem_PDBFile</a><br>
+ Variable in Class <a
+href="Science_Chemistry_PDBFile.html">Science_Chemistry_PDBFile</a><br>
Array of meta records
</td>
</tr>
@@ -701,7 +512,7 @@
<tr>
<td>$macromolecules</td>
<td width="100%" align="left" valign="top">
- Variable in Class <a
href="Chem_PDBFile.html">Chem_PDBFile</a><br>
+ Variable in Class <a
+href="Science_Chemistry_PDBFile.html">Science_Chemistry_PDBFile</a><br>
Array of macromolecular objects
</td>
</tr>
@@ -709,7 +520,7 @@
<tr>
<td>$macromolecules</td>
<td width="100%" align="left" valign="top">
- Variable in Class <a
href="Chem_PDBParser.html">Chem_PDBParser</a><br>
+ Variable in Class <a
+href="Science_Chemistry_PDBParser.html">Science_Chemistry_PDBParser</a><br>
Array of macromolecules
</td>
</tr>
@@ -722,7 +533,7 @@
<tr>
<td>$name</td>
<td width="100%" align="left" valign="top">
- Variable in Class <a
href="Chem_Element.html">Chem_Element</a><br>
+ Variable in Class <a
+href="Science_Chemistry_Element.html">Science_Chemistry_Element</a><br>
Element's name
</td>
</tr>
@@ -730,7 +541,7 @@
<tr>
<td>$name</td>
<td width="100%" align="left" valign="top">
- Variable in Class <a
href="Chem_Macromolecule.html">Chem_Macromolecule</a><br>
+ Variable in Class <a
+href="Science_Chemistry_Macromolecule.html">Science_Chemistry_Macromolecule</a><br>
Macromolecule's name
</td>
</tr>
@@ -738,7 +549,7 @@
<tr>
<td>$name</td>
<td width="100%" align="left" valign="top">
- Variable in Class <a
href="Chem_Molecule.html">Chem_Molecule</a><br>
+ Variable in Class <a
+href="Science_Chemistry_Molecule.html">Science_Chemistry_Molecule</a><br>
Molecule name
</td>
</tr>
@@ -746,7 +557,7 @@
<tr>
<td>$number</td>
<td width="100%" align="left" valign="top">
- Variable in Class <a
href="Chem_Element.html">Chem_Element</a><br>
+ Variable in Class <a
+href="Science_Chemistry_Element.html">Science_Chemistry_Element</a><br>
Element's atomic number
</td>
</tr>
@@ -754,7 +565,7 @@
<tr>
<td>$num_molecules</td>
<td width="100%" align="left" valign="top">
- Variable in Class <a
href="Chem_Macromolecule.html">Chem_Macromolecule</a><br>
+ Variable in Class <a
+href="Science_Chemistry_Macromolecule.html">Science_Chemistry_Macromolecule</a><br>
Number of molecules/subunits
</td>
</tr>
@@ -762,7 +573,7 @@
<tr>
<td>$num_atoms</td>
<td width="100%" align="left" valign="top">
- Variable in Class <a
href="Chem_Molecule.html">Chem_Molecule</a><br>
+ Variable in Class <a
+href="Science_Chemistry_Molecule.html">Science_Chemistry_Molecule</a><br>
Number of atoms in the molecule
</td>
</tr>
@@ -770,7 +581,7 @@
<tr>
<td>$num_macromolecules</td>
<td width="100%" align="left" valign="top">
- Variable in Class <a
href="Chem_PDBFile.html">Chem_PDBFile</a><br>
+ Variable in Class <a
+href="Science_Chemistry_PDBFile.html">Science_Chemistry_PDBFile</a><br>
Number of molecules/subunits
</td>
</tr>
@@ -778,7 +589,7 @@
<tr>
<td>$num_macromolecules</td>
<td width="100%" align="left" valign="top">
- Variable in Class <a
href="Chem_PDBParser.html">Chem_PDBParser</a><br>
+ Variable in Class <a
+href="Science_Chemistry_PDBParser.html">Science_Chemistry_PDBParser</a><br>
Number of macromolecules
</td>
</tr>
@@ -791,7 +602,7 @@
<tr>
<td>$occupancy</td>
<td width="100%" align="left" valign="top">
- Variable in Class <a
href="Chem_Atom_PDB.html">Chem_Atom_PDB</a><br>
+ Variable in Class <a
+href="Science_Chemistry_Atom_PDB.html">Science_Chemistry_Atom_PDB</a><br>
PDB Atom occupancy
</td>
</tr>
@@ -804,7 +615,7 @@
<tr>
<td>$parent_residue</td>
<td width="100%" align="left" valign="top">
- Variable in Class <a
href="Chem_Atom_PDB.html">Chem_Atom_PDB</a><br>
+ Variable in Class <a
+href="Science_Chemistry_Atom_PDB.html">Science_Chemistry_Atom_PDB</a><br>
Reference to the containing Residue object
</td>
</tr>
@@ -812,7 +623,7 @@
<tr>
<td>parseResidues</td>
<td width="100%" align="left" valign="top">
- Function in class <a
href="Chem_Macromolecule_PDB.html">Chem_Macromolecule_PDB</a><br>
+ Function in class <a
+href="Science_Chemistry_Macromolecule_PDB.html">Science_Chemistry_Macromolecule_PDB</a><br>
Makes the array of residues in the macromolecule
</td>
</tr>
@@ -820,7 +631,7 @@
<tr>
<td>parseResidues</td>
<td width="100%" align="left" valign="top">
- Function in class <a
href="Chem_PDBParser.html">Chem_PDBParser</a><br>
+ Function in class <a
+href="Science_Chemistry_PDBParser.html">Science_Chemistry_PDBParser</a><br>
Makes the array of residues in the macromolecule
</td>
</tr>
@@ -828,7 +639,7 @@
<tr>
<td>parseXYZ</td>
<td width="100%" align="left" valign="top">
- Function in class <a
href="Chem_Molecule_XYZ.html">Chem_Molecule_XYZ</a><br>
+ Function in class <a
+href="Science_Chemistry_Molecule_XYZ.html">Science_Chemistry_Molecule_XYZ</a><br>
method that does the parsing of the XYZ data itself
</td>
</tr>
@@ -836,7 +647,7 @@
<tr>
<td>parseAtom</td>
<td width="100%" align="left" valign="top">
- Function in class <a
href="Chem_Molecule_XYZ.html">Chem_Molecule_XYZ</a><br>
+ Function in class <a
+href="Science_Chemistry_Molecule_XYZ.html">Science_Chemistry_Molecule_XYZ</a><br>
Parses an XYZ atom record
</td>
</tr>
@@ -844,7 +655,7 @@
<tr>
<td>parseAtom</td>
<td width="100%" align="left" valign="top">
- Function in class <a
href="Chem_PDBParser.html">Chem_PDBParser</a><br>
+ Function in class <a
+href="Science_Chemistry_PDBParser.html">Science_Chemistry_PDBParser</a><br>
Parses an atom record into an associative array
</td>
</tr>
@@ -852,7 +663,7 @@
<tr>
<td>$pdb</td>
<td width="100%" align="left" valign="top">
- Variable in Class <a
href="Chem_Residue_PDB.html">Chem_Residue_PDB</a><br>
+ Variable in Class <a
+href="Science_Chemistry_Residue_PDB.html">Science_Chemistry_Residue_PDB</a><br>
PDB ID for the protein that contains
</td>
</tr>
@@ -860,7 +671,7 @@
<tr>
<td>$pdb</td>
<td width="100%" align="left" valign="top">
- Variable in Class <a
href="Chem_PDBFile.html">Chem_PDBFile</a><br>
+ Variable in Class <a
+href="Science_Chemistry_PDBFile.html">Science_Chemistry_PDBFile</a><br>
PDB ID
</td>
</tr>
@@ -868,7 +679,7 @@
<tr>
<td>$pdb</td>
<td width="100%" align="left" valign="top">
- Variable in Class <a
href="Chem_PDBParser.html">Chem_PDBParser</a><br>
+ Variable in Class <a
+href="Science_Chemistry_PDBParser.html">Science_Chemistry_PDBParser</a><br>
PDB ID
</td>
</tr>
@@ -876,7 +687,7 @@
<tr>
<td>printDistanceMatrix</td>
<td width="100%" align="left" valign="top">
- Function in class <a
href="Chem_Molecule.html">Chem_Molecule</a><br>
+ Function in class <a
+href="Science_Chemistry_Molecule.html">Science_Chemistry_Molecule</a><br>
Prints the atom-atom distance matrix
</td>
</tr>
@@ -884,7 +695,7 @@
<tr>
<td>printConnectionTable</td>
<td width="100%" align="left" valign="top">
- Function in class <a
href="Chem_Molecule.html">Chem_Molecule</a><br>
+ Function in class <a
+href="Science_Chemistry_Molecule.html">Science_Chemistry_Molecule</a><br>
Prints the molecule's connection table
</td>
</tr>
@@ -892,7 +703,7 @@
<tr>
<td>parseFile</td>
<td width="100%" align="left" valign="top">
- Function in class <a
href="Chem_PDBFile.html">Chem_PDBFile</a><br>
+ Function in class <a
+href="Science_Chemistry_PDBFile.html">Science_Chemistry_PDBFile</a><br>
Makes the arrays of all present PDB record types
</td>
</tr>
@@ -900,7 +711,7 @@
<tr>
<td>$periodic_table</td>
<td width="100%" align="left" valign="top">
- Variable in Class <a
href="Chem_Periodic_Table.html">Chem_Periodic_Table</a><br>
+ Variable in Class <a
+href="Science_Chemistry_Periodic_Table.html">Science_Chemistry_Periodic_Table</a><br>
The associative array containing the chemical elements
</td>
</tr>
@@ -913,7 +724,7 @@
<tr>
<td>$rec_name</td>
<td width="100%" align="left" valign="top">
- Variable in Class <a
href="Chem_Atom_PDB.html">Chem_Atom_PDB</a><br>
+ Variable in Class <a
+href="Science_Chemistry_Atom_PDB.html">Science_Chemistry_Atom_PDB</a><br>
PDB Atom record type, one of ATOM or HETATM
</td>
</tr>
@@ -921,7 +732,7 @@
<tr>
<td>$res_name</td>
<td width="100%" align="left" valign="top">
- Variable in Class <a
href="Chem_Atom_PDB.html">Chem_Atom_PDB</a><br>
+ Variable in Class <a
+href="Science_Chemistry_Atom_PDB.html">Science_Chemistry_Atom_PDB</a><br>
PDB Atom's Residue name
</td>
</tr>
@@ -929,20 +740,217 @@
<tr>
<td>$res_seq_num</td>
<td width="100%" align="left" valign="top">
- Variable in Class <a
href="Chem_Atom_PDB.html">Chem_Atom_PDB</a><br>
+ Variable in Class <a
+href="Science_Chemistry_Atom_PDB.html">Science_Chemistry_Atom_PDB</a><br>
PDB Atom's Residue sequential numnber
</td>
</tr>
<tr>
+ <td colspan="2" align="left" valign="top"><h4><a
+name="S">S</a></h4></td>
+ </tr>
+
+ <tr>
+ <td>Science_Chemistry_Atom_PDB</td>
+ <td width="100%" align="left" valign="top">
+
+ Class <a
+href="Science_Chemistry_Atom_PDB.html">Science_Chemistry_Atom_PDB</a>.<br>
+ Represents a PDB atom record
+ </td>
+ </tr>
+
+ <tr>
+ <td>Science_Chemistry_Atom_PDB</td>
+ <td width="100%" align="left" valign="top">
+
+ Function in class <a
+href="Science_Chemistry_Atom_PDB.html">Science_Chemistry_Atom_PDB</a><br>
+
+ </td>
+ </tr>
+
+ <tr>
+ <td>Science_Chemistry_Atom</td>
+ <td width="100%" align="left" valign="top">
+
+ Class <a
+href="Science_Chemistry_Atom.html">Science_Chemistry_Atom</a>.<br>
+ Base class representing an Atom
+ </td>
+ </tr>
+
+ <tr>
+ <td>Science_Chemistry_Atom</td>
+ <td width="100%" align="left" valign="top">
+
+ Function in class <a
+href="Science_Chemistry_Atom.html">Science_Chemistry_Atom</a><br>
+ Constructor for the class, requires the element symbol
+ </td>
+ </tr>
+
+ <tr>
+ <td>Science_Chemistry_Coordinates</td>
+ <td width="100%" align="left" valign="top">
+
+ Class <a
+href="Science_Chemistry_Coordinates.html">Science_Chemistry_Coordinates</a>.<br>
+ Utility class for defining 3D coordinates and
+ </td>
+ </tr>
+
+ <tr>
+ <td>Science_Chemistry_Coordinates</td>
+ <td width="100%" align="left" valign="top">
+
+ Function in class <a
+href="Science_Chemistry_Coordinates.html">Science_Chemistry_Coordinates</a><br>
+ Constructor for the class, returns null if parameter is
+ </td>
+ </tr>
+
+ <tr>
+ <td>Science_Chemistry_Element</td>
+ <td width="100%" align="left" valign="top">
+
+ Class <a
+href="Science_Chemistry_Element.html">Science_Chemistry_Element</a>.<br>
+ Utility class that defines a chemical element object
+ </td>
+ </tr>
+
+ <tr>
+ <td>Science_Chemistry_Element</td>
+ <td width="100%" align="left" valign="top">
+
+ Function in class <a
+href="Science_Chemistry_Element.html">Science_Chemistry_Element</a><br>
+ Constructor for the class
+ </td>
+ </tr>
+
+ <tr>
+ <td>Science_Chemistry_Macromolecule_PDB</td>
+ <td width="100%" align="left" valign="top">
+
+ Class <a
+href="Science_Chemistry_Macromolecule_PDB.html">Science_Chemistry_Macromolecule_PDB</a>.<br>
+ Represents a PDB macromolecule, composed of several
+ </td>
+ </tr>
+
+ <tr>
+ <td>Science_Chemistry_Macromolecule_PDB</td>
+ <td width="100%" align="left" valign="top">
+
+ Function in class <a
+href="Science_Chemistry_Macromolecule_PDB.html">Science_Chemistry_Macromolecule_PDB</a><br>
+ Constructor for the class
+ </td>
+ </tr>
+
+ <tr>
+ <td>Science_Chemistry_Macromolecule</td>
+ <td width="100%" align="left" valign="top">
+
+ Class <a
+href="Science_Chemistry_Macromolecule.html">Science_Chemistry_Macromolecule</a>.<br>
+ Represents a macromolecule, composed of several
+ </td>
+ </tr>
+
+ <tr>
+ <td>Science_Chemistry_Macromolecule</td>
+ <td width="100%" align="left" valign="top">
+
+ Function in class <a
+href="Science_Chemistry_Macromolecule.html">Science_Chemistry_Macromolecule</a><br>
+ Constructor for the class, requires a macromolecule name
+ </td>
+ </tr>
+
+ <tr>
+ <td>Science_Chemistry_Molecule_XYZ</td>
+ <td width="100%" align="left" valign="top">
+
+ Class <a
+href="Science_Chemistry_Molecule_XYZ.html">Science_Chemistry_Molecule_XYZ</a>.<br>
+ Base class representing a Molecule from a XYZ format file
+ </td>
+ </tr>
+
+ <tr>
+ <td>Science_Chemistry_Molecule_XYZ</td>
+ <td width="100%" align="left" valign="top">
+
+ Function in class <a
+href="Science_Chemistry_Molecule_XYZ.html">Science_Chemistry_Molecule_XYZ</a><br>
+ Constructor for the class, accepts 2 optional parameters:
+ </td>
+ </tr>
+
+ <tr>
+ <td>Science_Chemistry_Residue_PDB</td>
+ <td width="100%" align="left" valign="top">
+
+ Class <a
+href="Science_Chemistry_Residue_PDB.html">Science_Chemistry_Residue_PDB</a>.<br>
+ Represents a PDB residue
+ </td>
+ </tr>
+
+ <tr>
+ <td>Science_Chemistry_Residue_PDB</td>
+ <td width="100%" align="left" valign="top">
+
+ Function in class <a
+href="Science_Chemistry_Residue_PDB.html">Science_Chemistry_Residue_PDB</a><br>
+ Constructor for the class
+ </td>
+ </tr>
+
+ <tr>
+ <td>Science_Chemistry_Molecule</td>
+ <td width="100%" align="left" valign="top">
+
+ Class <a
+href="Science_Chemistry_Molecule.html">Science_Chemistry_Molecule</a>.<br>
+ Base class representing a Molecule
+ </td>
+ </tr>
+
+ <tr>
+ <td>Science_Chemistry_Molecule</td>
+ <td width="100%" align="left" valign="top">
+
+ Function in class <a
+href="Science_Chemistry_Molecule.html">Science_Chemistry_Molecule</a><br>
+ Constructor for the class, requires a molecule name
+ </td>
+ </tr>
+
+ <tr>
+ <td>Science_Chemistry_PDBFile</td>
+ <td width="100%" align="left" valign="top">
+
+ Class <a
+href="Science_Chemistry_PDBFile.html">Science_Chemistry_PDBFile</a>.<br>
+ Represents a PDB file, composed of one or more
+Science_Chemistry_Macromolecule_PDB objects
+ </td>
+ </tr>
+
+ <tr>
+ <td>Science_Chemistry_PDBFile</td>
+ <td width="100%" align="left" valign="top">
+
+ Function in class <a
+href="Science_Chemistry_PDBFile.html">Science_Chemistry_PDBFile</a><br>
+ Constructor for the class, requires a PDB filename
+ </td>
+ </tr>
+
+ <tr>
+ <td>Science_Chemistry_PDBParser</td>
+ <td width="100%" align="left" valign="top">
+
+ Class <a
+href="Science_Chemistry_PDBParser.html">Science_Chemistry_PDBParser</a>.<br>
+ A self-contained class to parse a PDB file into an array of
+residues
+ </td>
+ </tr>
+
+ <tr>
+ <td>Science_Chemistry_PDBParser</td>
+ <td width="100%" align="left" valign="top">
+
+ Function in class <a
+href="Science_Chemistry_PDBParser.html">Science_Chemistry_PDBParser</a><br>
+ Constructor for the class, requires a PDB filename
+ </td>
+ </tr>
+
+ <tr>
+ <td>Science_Chemistry_Periodic_Table</td>
+ <td width="100%" align="left" valign="top">
+
+ Class <a
+href="Science_Chemistry_Periodic_Table.html">Science_Chemistry_Periodic_Table</a>.<br>
+ Utility class that defines a Periodic Table of elements
+ </td>
+ </tr>
+
+ <tr>
+ <td>Science_Chemistry</td>
+ <td width="100%" align="left" valign="top">
+
+ Package<br>
+
+ </td>
+ </tr>
+
+
+ <tr>
<td colspan="2" align="left" valign="top"><h4><a
name="s">s</a></h4></td>
</tr>
<tr>
<td>$ser_num</td>
<td width="100%" align="left" valign="top">
- Variable in Class <a
href="Chem_Atom_PDB.html">Chem_Atom_PDB</a><br>
+ Variable in Class <a
+href="Science_Chemistry_Atom_PDB.html">Science_Chemistry_Atom_PDB</a><br>
PDB Atom serial number
</td>
</tr>
@@ -950,7 +958,7 @@
<tr>
<td>$segment_id</td>
<td width="100%" align="left" valign="top">
- Variable in Class <a
href="Chem_Atom_PDB.html">Chem_Atom_PDB</a><br>
+ Variable in Class <a
+href="Science_Chemistry_Atom_PDB.html">Science_Chemistry_Atom_PDB</a><br>
PDB Atom segment identifier
</td>
</tr>
@@ -958,7 +966,7 @@
<tr>
<td>setCoordinates</td>
<td width="100%" align="left" valign="top">
- Function in class <a href="Chem_Atom.html">Chem_Atom</a><br>
+ Function in class <a
+href="Science_Chemistry_Atom.html">Science_Chemistry_Atom</a><br>
Sets the coordinates for the atom object
</td>
</tr>
@@ -966,7 +974,7 @@
<tr>
<td>$symbol</td>
<td width="100%" align="left" valign="top">
- Variable in Class <a
href="Chem_Element.html">Chem_Element</a><br>
+ Variable in Class <a
+href="Science_Chemistry_Element.html">Science_Chemistry_Element</a><br>
Element's symbol, one or two characters, case sensitive
</td>
</tr>
@@ -974,7 +982,7 @@
<tr>
<td>$seq_num</td>
<td width="100%" align="left" valign="top">
- Variable in Class <a
href="Chem_Residue_PDB.html">Chem_Residue_PDB</a><br>
+ Variable in Class <a
+href="Science_Chemistry_Residue_PDB.html">Science_Chemistry_Residue_PDB</a><br>
PDB Residue sequence number
</td>
</tr>
@@ -982,33 +990,20 @@
<tr>
<td>setBondCutoff</td>
<td width="100%" align="left" valign="top">
- Function in class <a
href="Chem_Molecule.html">Chem_Molecule</a><br>
+ Function in class <a
+href="Science_Chemistry_Molecule.html">Science_Chemistry_Molecule</a><br>
Sets the distance cutoff for bond determination
</td>
</tr>
<tr>
- <td colspan="2" align="left" valign="top"><h4><a
name="S">S</a></h4></td>
- </tr>
-
- <tr>
- <td>Science_Chemistry</td>
- <td width="100%" align="left" valign="top">
- Package<br>
-
- </td>
- </tr>
-
-
- <tr>
<td colspan="2" align="left" valign="top"><h4><a
name="t">t</a></h4></td>
</tr>
<tr>
<td>$temp_factor</td>
<td width="100%" align="left" valign="top">
- Variable in Class <a
href="Chem_Atom_PDB.html">Chem_Atom_PDB</a><br>
+ Variable in Class <a
+href="Science_Chemistry_Atom_PDB.html">Science_Chemistry_Atom_PDB</a><br>
PDB Atom temperature factor
</td>
</tr>
@@ -1016,15 +1011,15 @@
<tr>
<td>toString</td>
<td width="100%" align="left" valign="top">
- Function in class <a href="Chem_Atom.html">Chem_Atom</a><br>
- Returns a string representation of the Chem_Atom object
+ Function in class <a
+href="Science_Chemistry_Atom.html">Science_Chemistry_Atom</a><br>
+ Returns a string representation of the Science_Chemistry_Atom
+object
</td>
</tr>
<tr>
<td>toString</td>
<td width="100%" align="left" valign="top">
- Function in class <a
href="Chem_Coordinates.html">Chem_Coordinates</a><br>
+ Function in class <a
+href="Science_Chemistry_Coordinates.html">Science_Chemistry_Coordinates</a><br>
Returns a string representation of the coordinates: x y z
</td>
</tr>
@@ -1032,7 +1027,7 @@
<tr>
<td>toString</td>
<td width="100%" align="left" valign="top">
- Function in class <a
href="Chem_Macromolecule.html">Chem_Macromolecule</a><br>
+ Function in class <a
+href="Science_Chemistry_Macromolecule.html">Science_Chemistry_Macromolecule</a><br>
Returns a string representation of the macromolecule
</td>
</tr>
@@ -1040,7 +1035,7 @@
<tr>
<td>toString</td>
<td width="100%" align="left" valign="top">
- Function in class <a
href="Chem_Molecule_XYZ.html">Chem_Molecule_XYZ</a><br>
+ Function in class <a
+href="Science_Chemistry_Molecule_XYZ.html">Science_Chemistry_Molecule_XYZ</a><br>
Generates a string representation of the XYZ molecule
</td>
</tr>
@@ -1048,7 +1043,7 @@
<tr>
<td>toString</td>
<td width="100%" align="left" valign="top">
- Function in class <a
href="Chem_Molecule.html">Chem_Molecule</a><br>
+ Function in class <a
+href="Science_Chemistry_Molecule.html">Science_Chemistry_Molecule</a><br>
Returns a string representation of the molecule
</td>
</tr>
@@ -1056,15 +1051,15 @@
<tr>
<td>toCML</td>
<td width="100%" align="left" valign="top">
- Function in class <a href="Chem_Atom.html">Chem_Atom</a><br>
- Returns a CML representation of the Chem_Atom object
+ Function in class <a
+href="Science_Chemistry_Atom.html">Science_Chemistry_Atom</a><br>
+ Returns a CML representation of the Science_Chemistry_Atom
+object
</td>
</tr>
<tr>
<td>toCML</td>
<td width="100%" align="left" valign="top">
- Function in class <a
href="Chem_Coordinates.html">Chem_Coordinates</a><br>
+ Function in class <a
+href="Science_Chemistry_Coordinates.html">Science_Chemistry_Coordinates</a><br>
Returns a CML representation of the coordinates
</td>
</tr>
@@ -1072,7 +1067,7 @@
<tr>
<td>toCML</td>
<td width="100%" align="left" valign="top">
- Function in class <a
href="Chem_Macromolecule.html">Chem_Macromolecule</a><br>
+ Function in class <a
+href="Science_Chemistry_Macromolecule.html">Science_Chemistry_Macromolecule</a><br>
Returns a CML representation of the molecule
</td>
</tr>
@@ -1080,7 +1075,7 @@
<tr>
<td>toCML</td>
<td width="100%" align="left" valign="top">
- Function in class <a
href="Chem_Molecule.html">Chem_Molecule</a><br>
+ Function in class <a
+href="Science_Chemistry_Molecule.html">Science_Chemistry_Molecule</a><br>
Returns a CML representation of the molecule
</td>
</tr>
@@ -1088,7 +1083,7 @@
<tr>
<td>toCML</td>
<td width="100%" align="left" valign="top">
- Function in class <a
href="Chem_PDBFile.html">Chem_PDBFile</a><br>
+ Function in class <a
+href="Science_Chemistry_PDBFile.html">Science_Chemistry_PDBFile</a><br>
Returns a CML representation of the PDB file
</td>
</tr>
@@ -1101,7 +1096,7 @@
<tr>
<td>$VALID</td>
<td width="100%" align="left" valign="top">
- Variable in Class <a
href="Chem_Atom_PDB.html">Chem_Atom_PDB</a><br>
+ Variable in Class <a
+href="Science_Chemistry_Atom_PDB.html">Science_Chemistry_Atom_PDB</a><br>
If the atom object has been initialized
</td>
</tr>
@@ -1109,7 +1104,7 @@
<tr>
<td>$VALID</td>
<td width="100%" align="left" valign="top">
- Variable in Class <a
href="Chem_Residue_PDB.html">Chem_Residue_PDB</a><br>
+ Variable in Class <a
+href="Science_Chemistry_Residue_PDB.html">Science_Chemistry_Residue_PDB</a><br>
If the PDB residue object has been initialized
</td>
</tr>
@@ -1122,7 +1117,7 @@
<tr>
<td>$weight</td>
<td width="100%" align="left" valign="top">
- Variable in Class <a
href="Chem_Element.html">Chem_Element</a><br>
+ Variable in Class <a
+href="Science_Chemistry_Element.html">Science_Chemistry_Element</a><br>
Element's atomic weight in a.m.u (atomic mass units)
</td>
</tr>
@@ -1135,8 +1130,8 @@
<tr>
<td>$xyz</td>
<td width="100%" align="left" valign="top">
- Variable in Class <a href="Chem_Atom.html">Chem_Atom</a><br>
- Chem_Coordinates object
+ Variable in Class <a
+href="Science_Chemistry_Atom.html">Science_Chemistry_Atom</a><br>
+ Science_Chemistry_Coordinates object
</td>
</tr>
Index: pear/Science/Chemistry/doc/phpdoc_packagelist.html
diff -u pear/Science/Chemistry/doc/phpdoc_packagelist.html:1.1
pear/Science/Chemistry/doc/phpdoc_packagelist.html:1.2
--- pear/Science/Chemistry/doc/phpdoc_packagelist.html:1.1 Tue Apr 10 09:44:39
2001
+++ pear/Science/Chemistry/doc/phpdoc_packagelist.html Tue Apr 10 11:44:24 2001
@@ -48,62 +48,62 @@
<tr>
<td colspan="2" align="left"
valign="top"> </td>
- <td align="left" valign="top"><a
href="Chem_Atom_PDB.html">Chem_Atom_PDB</a></td>
+ <td align="left" valign="top"><a
+href="Science_Chemistry_Atom_PDB.html">Science_Chemistry_Atom_PDB</a></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"> </td>
- <td align="left" valign="top"><a
href="Chem_Atom.html">Chem_Atom</a></td>
+ <td align="left" valign="top"><a
+href="Science_Chemistry_Atom.html">Science_Chemistry_Atom</a></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"> </td>
- <td align="left" valign="top"><a
href="Chem_Coordinates.html">Chem_Coordinates</a></td>
+ <td align="left" valign="top"><a
+href="Science_Chemistry_Coordinates.html">Science_Chemistry_Coordinates</a></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"> </td>
- <td align="left" valign="top"><a
href="Chem_Element.html">Chem_Element</a></td>
+ <td align="left" valign="top"><a
+href="Science_Chemistry_Element.html">Science_Chemistry_Element</a></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"> </td>
- <td align="left" valign="top"><a
href="Chem_Macromolecule_PDB.html">Chem_Macromolecule_PDB</a></td>
+ <td align="left" valign="top"><a
+href="Science_Chemistry_Macromolecule_PDB.html">Science_Chemistry_Macromolecule_PDB</a></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"> </td>
- <td align="left" valign="top"><a
href="Chem_Macromolecule.html">Chem_Macromolecule</a></td>
+ <td align="left" valign="top"><a
+href="Science_Chemistry_Macromolecule.html">Science_Chemistry_Macromolecule</a></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"> </td>
- <td align="left" valign="top"><a
href="Chem_Molecule_XYZ.html">Chem_Molecule_XYZ</a></td>
+ <td align="left" valign="top"><a
+href="Science_Chemistry_Molecule_XYZ.html">Science_Chemistry_Molecule_XYZ</a></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"> </td>
- <td align="left" valign="top"><a
href="Chem_Residue_PDB.html">Chem_Residue_PDB</a></td>
+ <td align="left" valign="top"><a
+href="Science_Chemistry_Residue_PDB.html">Science_Chemistry_Residue_PDB</a></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"> </td>
- <td align="left" valign="top"><a
href="Chem_Molecule.html">Chem_Molecule</a></td>
+ <td align="left" valign="top"><a
+href="Science_Chemistry_Molecule.html">Science_Chemistry_Molecule</a></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"> </td>
- <td align="left" valign="top"><a
href="Chem_PDBFile.html">Chem_PDBFile</a></td>
+ <td align="left" valign="top"><a
+href="Science_Chemistry_PDBFile.html">Science_Chemistry_PDBFile</a></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"> </td>
- <td align="left" valign="top"><a
href="Chem_PDBParser.html">Chem_PDBParser</a></td>
+ <td align="left" valign="top"><a
+href="Science_Chemistry_PDBParser.html">Science_Chemistry_PDBParser</a></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"> </td>
- <td align="left" valign="top"><a
href="Chem_Periodic_Table.html">Chem_Periodic_Table</a></td>
+ <td align="left" valign="top"><a
+href="Science_Chemistry_Periodic_Table.html">Science_Chemistry_Periodic_Table</a></td>
</tr>
Index: pear/Science/Chemistry/doc/phpdoc_warnings.html
diff -u pear/Science/Chemistry/doc/phpdoc_warnings.html:1.1
pear/Science/Chemistry/doc/phpdoc_warnings.html:1.2
--- pear/Science/Chemistry/doc/phpdoc_warnings.html:1.1 Tue Apr 10 09:44:39 2001
+++ pear/Science/Chemistry/doc/phpdoc_warnings.html Tue Apr 10 11:44:24 2001
@@ -34,7 +34,7 @@
</tr>
<tr>
<td align="left" valign="top">
-
<h4>/home/jesus/devel/php/PEAR_local/Science/Chemistry/PDBFile.php</h4>
+
+<h4>/home/jesus/devel/php/pear/Science/Chemistry/PDBFile.php</h4>
1 Warning(s).
</td>
</tr>
@@ -46,11 +46,11 @@
<table border="0" cellspacing="4" cellpadding="4"
bordercolor="Silver">
<tr>
- <td align="left" valign="top"><b>[class]
Chem_PDBFile</b></td>
+ <td align="left" valign="top"><b>[class]
+Science_Chemistry_PDBFile</b></td>
<td align="left" valign="top">mismatch</td>
</tr>
<tr>
- <td colspan="2" align="left"
valign="top">PHPDoc found 1 syntax error(s) in the tag list. Tag: '@see
Chem_PDBParser' - Could not understand all references. Use function() to referr to
functions and to referr to variables - don't know what 'Chem_PDBParser' referrs to..
Syntax: '([^\s]+(?:::))?([^:][a-zA-Z_\x7f-\xff][a-zA-Z0-9_\xzf-\xff]*\(\s*\))'
(function), '([^\s]+(?:::))?([$][^:][a-zA-Z_\x7f-\xff][a-zA-Z0-9_\xzf-\xff]*)'
(variable), '([^\s]+)' (module or class)..</td>
+ <td colspan="2" align="left"
+valign="top">PHPDoc found 1 syntax error(s) in the tag list. Tag: '@see
+Science_Chemistry_PDBParser' - Could not understand all references. Use function() to
+referr to functions and to referr to variables - don't know what
+'Science_Chemistry_PDBParser' referrs to.. Syntax:
+'([^\s]+(?:::))?([^:][a-zA-Z_\x7f-\xff][a-zA-Z0-9_\xzf-\xff]*\(\s*\))' (function),
+'([^\s]+(?:::))?([$][^:][a-zA-Z_\x7f-\xff][a-zA-Z0-9_\xzf-\xff]*)' (variable),
+'([^\s]+)' (module or class)..</td>
</tr>
<tr>
<td height="5" colspan="2" align="left"
valign="top"> </td>
@@ -65,7 +65,7 @@
</tr>
<tr>
<td align="left" valign="top">
-
<h4>/home/jesus/devel/php/PEAR_local/Science/Chemistry/PDBParser.php</h4>
+
+<h4>/home/jesus/devel/php/pear/Science/Chemistry/PDBParser.php</h4>
2 Warning(s).
</td>
</tr>
@@ -77,11 +77,11 @@
<table border="0" cellspacing="4" cellpadding="4"
bordercolor="Silver">
<tr>
- <td align="left" valign="top"><b>[class]
Chem_PDBParser</b></td>
+ <td align="left" valign="top"><b>[class]
+Science_Chemistry_PDBParser</b></td>
<td align="left" valign="top">mismatch</td>
</tr>
<tr>
- <td colspan="2" align="left"
valign="top">PHPDoc found 1 syntax error(s) in the tag list. Tag: '@see Chem_PDBFile'
- Could not understand all references. Use function() to referr to functions and to
referr to variables - don't know what 'Chem_PDBFile' referrs to.. Syntax:
'([^\s]+(?:::))?([^:][a-zA-Z_\x7f-\xff][a-zA-Z0-9_\xzf-\xff]*\(\s*\))' (function),
'([^\s]+(?:::))?([$][^:][a-zA-Z_\x7f-\xff][a-zA-Z0-9_\xzf-\xff]*)' (variable),
'([^\s]+)' (module or class)..</td>
+ <td colspan="2" align="left"
+valign="top">PHPDoc found 1 syntax error(s) in the tag list. Tag: '@see
+Science_Chemistry_PDBFile' - Could not understand all references. Use function() to
+referr to functions and to referr to variables - don't know what
+'Science_Chemistry_PDBFile' referrs to.. Syntax:
+'([^\s]+(?:::))?([^:][a-zA-Z_\x7f-\xff][a-zA-Z0-9_\xzf-\xff]*\(\s*\))' (function),
+'([^\s]+(?:::))?([$][^:][a-zA-Z_\x7f-\xff][a-zA-Z0-9_\xzf-\xff]*)' (variable),
+'([^\s]+)' (module or class)..</td>
</tr>
<tr>
<td height="5" colspan="2" align="left"
valign="top"> </td>
@@ -107,7 +107,7 @@
</tr>
<tr>
<td align="left" valign="top">
-
<h4>/home/jesus/devel/php/PEAR_local/Science/Chemistry/Atom_PDB.php</h4>
+
+<h4>/home/jesus/devel/php/pear/Science/Chemistry/Atom_PDB.php</h4>
4 Warning(s).
</td>
</tr>
@@ -130,7 +130,7 @@
</tr>
<tr>
- <td align="left" valign="top"><b>[function]
chem_atom_pdb</b></td>
+ <td align="left" valign="top"><b>[function]
+science_chemistry_atom_pdb</b></td>
<td align="left" valign="top">missing</td>
</tr>
<tr>
@@ -141,7 +141,7 @@
</tr>
<tr>
- <td align="left" valign="top"><b>[function]
chem_atom_pdb</b></td>
+ <td align="left" valign="top"><b>[function]
+science_chemistry_atom_pdb</b></td>
<td align="left" valign="top">missing</td>
</tr>
<tr>
@@ -171,7 +171,7 @@
</tr>
<tr>
<td align="left" valign="top">
-
<h4>/home/jesus/devel/php/PEAR_local/Science/Chemistry/Atom.php</h4>
+ <h4>/home/jesus/devel/php/pear/Science/Chemistry/Atom.php</h4>
2 Warning(s).
</td>
</tr>
@@ -183,7 +183,7 @@
<table border="0" cellspacing="4" cellpadding="4"
bordercolor="Silver">
<tr>
- <td align="left" valign="top"><b>[function]
chem_atom</b></td>
+ <td align="left" valign="top"><b>[function]
+science_chemistry_atom</b></td>
<td align="left" valign="top">mismatch</td>
</tr>
<tr>
@@ -213,7 +213,7 @@
</tr>
<tr>
<td align="left" valign="top">
-
<h4>/home/jesus/devel/php/PEAR_local/Science/Chemistry/Macromolecule_PDB.php</h4>
+
+<h4>/home/jesus/devel/php/pear/Science/Chemistry/Macromolecule_PDB.php</h4>
2 Warning(s).
</td>
</tr>
@@ -225,7 +225,7 @@
<table border="0" cellspacing="4" cellpadding="4"
bordercolor="Silver">
<tr>
- <td align="left" valign="top"><b>[variables]
chem_macromolecule_pdb</b></td>
+ <td align="left" valign="top"><b>[variables]
+science_chemistry_macromolecule_pdb</b></td>
<td align="left" valign="top">mismatch</td>
</tr>
<tr>
@@ -236,7 +236,7 @@
</tr>
<tr>
- <td align="left" valign="top"><b>[function]
chem_macromolecule_pdb</b></td>
+ <td align="left" valign="top"><b>[function]
+science_chemistry_macromolecule_pdb</b></td>
<td align="left" valign="top">mismatch</td>
</tr>
<tr>
@@ -255,7 +255,7 @@
</tr>
<tr>
<td align="left" valign="top">
-
<h4>/home/jesus/devel/php/PEAR_local/Science/Chemistry/Macromolecule.php</h4>
+
+<h4>/home/jesus/devel/php/pear/Science/Chemistry/Macromolecule.php</h4>
5 Warning(s).
</td>
</tr>
@@ -267,7 +267,7 @@
<table border="0" cellspacing="4" cellpadding="4"
bordercolor="Silver">
<tr>
- <td align="left" valign="top"><b>[function]
chem_macromolecule</b></td>
+ <td align="left" valign="top"><b>[function]
+science_chemistry_macromolecule</b></td>
<td align="left" valign="top">mismatch</td>
</tr>
<tr>
@@ -330,7 +330,7 @@
</tr>
<tr>
<td align="left" valign="top">
-
<h4>/home/jesus/devel/php/PEAR_local/Science/Chemistry/Residue_PDB.php</h4>
+
+<h4>/home/jesus/devel/php/pear/Science/Chemistry/Residue_PDB.php</h4>
2 Warning(s).
</td>
</tr>
@@ -342,11 +342,11 @@
<table border="0" cellspacing="4" cellpadding="4"
bordercolor="Silver">
<tr>
- <td align="left" valign="top"><b>[function]
chem_residue_pdb</b></td>
+ <td align="left" valign="top"><b>[function]
+science_chemistry_residue_pdb</b></td>
<td align="left" valign="top">mismatch</td>
</tr>
<tr>
- <td colspan="2" align="left" valign="top">3th
parameter type '$macromol' does match the the documented type 'object
Chem_Macromolecule_PDB', possible error consider an update to '@param string $macromol
reference to the containing macromolecule' or '@param string reference to the
containing macromolecule', the variable name is optional.</td>
+ <td colspan="2" align="left" valign="top">3th
+parameter type '$macromol' does match the the documented type 'object
+Science_Chemistry_Macromolecule_PDB', possible error consider an update to '@param
+string $macromol reference to the containing macromolecule' or '@param string
+reference to the containing macromolecule', the variable name is optional.</td>
</tr>
<tr>
<td height="5" colspan="2" align="left"
valign="top"> </td>
@@ -372,7 +372,7 @@
</tr>
<tr>
<td align="left" valign="top">
-
<h4>/home/jesus/devel/php/PEAR_local/Science/Chemistry/Molecule.php</h4>
+
+<h4>/home/jesus/devel/php/pear/Science/Chemistry/Molecule.php</h4>
5 Warning(s).
</td>
</tr>
@@ -384,7 +384,7 @@
<table border="0" cellspacing="4" cellpadding="4"
bordercolor="Silver">
<tr>
- <td align="left" valign="top"><b>[function]
chem_molecule</b></td>
+ <td align="left" valign="top"><b>[function]
+science_chemistry_molecule</b></td>
<td align="left" valign="top">mismatch</td>
</tr>
<tr>
@@ -447,7 +447,7 @@
</tr>
<tr>
<td align="left" valign="top">
-
<h4>/home/jesus/devel/php/PEAR_local/Science/Chemistry/PDBFile.php</h4>
+
+<h4>/home/jesus/devel/php/pear/Science/Chemistry/PDBFile.php</h4>
2 Warning(s).
</td>
</tr>
@@ -459,7 +459,7 @@
<table border="0" cellspacing="4" cellpadding="4"
bordercolor="Silver">
<tr>
- <td align="left" valign="top"><b>[functions]
chem_pdbfile</b></td>
+ <td align="left" valign="top"><b>[functions]
+science_chemistry_pdbfile</b></td>
<td align="left" valign="top">mismatch</td>
</tr>
<tr>
@@ -474,7 +474,7 @@
<td align="left" valign="top">mismatch</td>
</tr>
<tr>
- <td colspan="2" align="left" valign="top">@see
referrs to the function 'Chem_Macromolecule_PDB()' which is not defined in the class.
Entry gets ignored.</td>
+ <td colspan="2" align="left" valign="top">@see
+referrs to the function 'Science_Chemistry_Macromolecule_PDB()' which is not defined
+in the class. Entry gets ignored.</td>
</tr>
<tr>
<td height="5" colspan="2" align="left"
valign="top"> </td>
@@ -489,7 +489,7 @@
</tr>
<tr>
<td align="left" valign="top">
-
<h4>/home/jesus/devel/php/PEAR_local/Science/Chemistry/PDBParser.php</h4>
+
+<h4>/home/jesus/devel/php/pear/Science/Chemistry/PDBParser.php</h4>
3 Warning(s).
</td>
</tr>
Index: pear/Science/Chemistry/doc/phpdoc_xmlfiles.html
diff -u pear/Science/Chemistry/doc/phpdoc_xmlfiles.html:1.1
pear/Science/Chemistry/doc/phpdoc_xmlfiles.html:1.2
--- pear/Science/Chemistry/doc/phpdoc_xmlfiles.html:1.1 Tue Apr 10 09:44:39 2001
+++ pear/Science/Chemistry/doc/phpdoc_xmlfiles.html Tue Apr 10 11:44:24 2001
@@ -34,7 +34,7 @@
<tr>
<td align="left" valign="top">
<ul>
- <li><a
href="class_Chem_Atom_PDB.xml">class_Chem_Atom_PDB.xml</a><li><a
href="class_Chem_Atom.xml">class_Chem_Atom.xml</a><li><a
href="classtree_Chem_Atom.xml">classtree_Chem_Atom.xml</a><li><a
href="class_Chem_Coordinates.xml">class_Chem_Coordinates.xml</a><li><a
href="classtree_Chem_Coordinates.xml">classtree_Chem_Coordinates.xml</a><li><a
href="class_Chem_Element.xml">class_Chem_Element.xml</a><li><a
href="classtree_Chem_Element.xml">classtree_Chem_Element.xml</a><li><a
href="class_Chem_Macromolecule_PDB.xml">class_Chem_Macromolecule_PDB.xml</a><li><a
href="class_Chem_Macromolecule.xml">class_Chem_Macromolecule.xml</a><li><a
href="classtree_Chem_Macromolecule.xml">classtree_Chem_Macromolecule.xml</a><li><a
href="class_Chem_Molecule_XYZ.xml">class_Chem_Molecule_XYZ.xml</a><li><a
href="class_Chem_Residue_PDB.xml">class_Chem_Residue_PDB.xml</a><li><a
href="class_Chem_Molecule.xml">class_Chem_Molecule.xml</a><li><a
href="classtree_Chem_Molecule.xml">classtree_Chem_Molecule.xml</a><li><a
href="class_Chem_PDBFile.xml">class_Chem_PDBFile.xml</a><li><a
href="classtree_Chem_PDBFile.xml">classtree_Chem_PDBFile.xml</a><li><a
href="class_Chem_PDBParser.xml">class_Chem_PDBParser.xml</a><li><a
href="classtree_Chem_PDBParser.xml">classtree_Chem_PDBParser.xml</a><li><a
href="class_Chem_Periodic_Table.xml">class_Chem_Periodic_Table.xml</a><li><a
href="classtree_Chem_Periodic_Table.xml">classtree_Chem_Periodic_Table.xml</a><li><a
href="packagelist.xml">packagelist.xml</a><li><a
href="elementlist.xml">elementlist.xml</a><li><a
href="warnings_parser.xml">warnings_parser.xml</a><li><a
href="warnings_classanalyser.xml">warnings_classanalyser.xml</a>
+ <li><a
+href="class_Science_Chemistry_Atom_PDB.xml">class_Science_Chemistry_Atom_PDB.xml</a><li><a
+ href="class_Science_Chemistry_Atom.xml">class_Science_Chemistry_Atom.xml</a><li><a
+href="classtree_Science_Chemistry_Atom.xml">classtree_Science_Chemistry_Atom.xml</a><li><a
+
+href="class_Science_Chemistry_Coordinates.xml">class_Science_Chemistry_Coordinates.xml</a><li><a
+
+href="classtree_Science_Chemistry_Coordinates.xml">classtree_Science_Chemistry_Coordinates.xml</a><li><a
+
+href="class_Science_Chemistry_Element.xml">class_Science_Chemistry_Element.xml</a><li><a
+
+href="classtree_Science_Chemistry_Element.xml">classtree_Science_Chemistry_Element.xml</a><li><a
+
+href="class_Science_Chemistry_Macromolecule_PDB.xml">class_Science_Chemistry_Macromolecule_PDB.xml</a><li><a
+
+href="class_Science_Chemistry_Macromolecule.xml">class_Science_Chemistry_Macromolecule.xml</a><li><a
+
+href="classtree_Science_Chemistry_Macromolecule.xml">classtree_Science_Chemistry_Macromolecule.xml</a><li><a
+
+href="class_Science_Chemistry_Molecule_XYZ.xml">class_Science_Chemistry_Molecule_XYZ.xml</a><li><a
+
+href="class_Science_Chemistry_Residue_PDB.xml">class_Science_Chemistry_Residue_PDB.xml</a><li><a
+
+href="class_Science_Chemistry_Molecule.xml">class_Science_Chemistry_Molecule.xml</a><li><a
+
+href="classtree_Science_Chemistry_Molecule.xml">classtree_Science_Chemistry_Molecule.xml</a><li><a
+
+href="class_Science_Chemistry_PDBFile.xml">class_Science_Chemistry_PDBFile.xml</a><li><a
+
+href="classtree_Science_Chemistry_PDBFile.xml">classtree_Science_Chemistry_PDBFile.xml</a><li><a
+
+href="class_Science_Chemistry_PDBParser.xml">class_Science_Chemistry_PDBParser.xml</a><li><a
+
+href="classtree_Science_Chemistry_PDBParser.xml">classtree_Science_Chemistry_PDBParser.xml</a><li><a
+
+href="class_Science_Chemistry_Periodic_Table.xml">class_Science_Chemistry_Periodic_Table.xml</a><li><a
+
+href="classtree_Science_Chemistry_Periodic_Table.xml">classtree_Science_Chemistry_Periodic_Table.xml</a><li><a
+ href="packagelist.xml">packagelist.xml</a><li><a
+href="elementlist.xml">elementlist.xml</a><li><a
+href="warnings_parser.xml">warnings_parser.xml</a><li><a
+href="warnings_classanalyser.xml">warnings_classanalyser.xml</a>
</ul>
</td>
</tr>
Index: pear/Science/Chemistry/doc/warnings_classanalyser.xml
diff -u pear/Science/Chemistry/doc/warnings_classanalyser.xml:1.1
pear/Science/Chemistry/doc/warnings_classanalyser.xml:1.2
--- pear/Science/Chemistry/doc/warnings_classanalyser.xml:1.1 Tue Apr 10 09:44:39
2001
+++ pear/Science/Chemistry/doc/warnings_classanalyser.xml Tue Apr 10 11:44:24
+2001
@@ -1 +1 @@
-<?xml version="1.0"?><phpdoc><warnings
file="/home/jesus/devel/php/PEAR_local/Science/Chemistry/Atom_PDB.php"><warning
name="$valid" type="mismatch" elementtype="functions">@see referrs to the function
&apos;initAtom()&apos; which is not defined in the class. Entry gets
ignored.</warning><warning name="chem_atom_pdb" type="missing"
elementtype="function">1st parameter &apos;$atomrec&apos; is not documented
add &apos;@param (object objectname|type) [description]&apos; to the end of
the @param[eter] list.</warning><warning name="chem_atom_pdb" type="missing"
elementtype="function">2nd parameter &apos;$residue&apos; is not documented
add &apos;@param string [description]&apos; to the end of the @param[eter]
list.</warning><warning name="getfield" type="missing" elementtype="function">1st
parameter &apos;$field&apos; is not documented add &apos;@param (object
objectname|type) [description]&apos; to the end of the @param[eter]
list.</warning></warnings><warnings
file="/home/jesus/devel/php/PEAR_local/Science/Chemistry/Atom.php"><warning
name="chem_atom" type="mismatch" elementtype="function">2nd parameter type
&apos;$coords&apos; does match the the documented type
&apos;array&apos;, possible error consider an update to &apos;@param
string $coords array of coordinates (x, y, z)&apos; or &apos;@param string
array of coordinates (x, y, z)&apos;, the variable name is
optional.</warning><warning name="tocml" type="mismatch" elementtype="function">1st
parameter type &apos;$id&apos; does match the the documented type
&apos;string&apos;, possible error consider an update to &apos;@param
integer $id (description)&apos; or &apos;@param integer
(description)&apos;, the variable name is optional.</warning></warnings><warnings
file="/home/jesus/devel/php/PEAR_local/Science/Chemistry/Macromolecule_PDB.php"><warning
name="chem_macromolecule_pdb" type="mismatch" elementtype="variables">@see referrs to
the variable &apos;$pdb&apos; which is not defined in the class. Entry gets
ignored.</warning><warning name="chem_macromolecule_pdb" type="mismatch"
elementtype="function">3th parameter type &apos;$pdbfile&apos; does match the
the documented type &apos;object PDBFile&apos;, possible error consider an
update to &apos;@param string $pdbfile reference to the PDB file object&apos;
or &apos;@param string reference to the PDB file object&apos;, the variable
name is optional.</warning></warnings><warnings
file="/home/jesus/devel/php/PEAR_local/Science/Chemistry/Macromolecule.php"><warning
name="chem_macromolecule" type="mismatch" elementtype="function">2nd parameter type
&apos;$molecules&apos; does match the the documented type
&apos;array&apos;, possible error consider an update to &apos;@param
string $molecules (description)&apos; or &apos;@param string
(description)&apos;, the variable name is optional.</warning><warning name="tocml"
type="mismatch" elementtype="function">1st parameter &apos;$title&apos; does
not match the documented name &apos;$id&apos;, update the tag to
&apos;@param string $title (description)&apos; or &apos;@param string
(description)&apos;, the variable name is optional.</warning><warning name="tocml"
type="mismatch" elementtype="function">2nd parameter type &apos;$id&apos; does
match the the documented type &apos;boolean&apos;, possible error consider an
update to &apos;@param string $id (description)&apos; or &apos;@param
string (description)&apos;, the variable name is optional.</warning><warning
name="tocml" type="mismatch" elementtype="function">2nd parameter
&apos;$id&apos; does not match the documented name
&apos;$connect&apos;, update the tag to &apos;@param string $id
(description)&apos; or &apos;@param string (description)&apos;, the
variable name is optional.</warning><warning name="tocml" type="missing"
elementtype="function">3th parameter &apos;$connect&apos; is not documented
add &apos;@param boolean [description]&apos; to the end of the @param[eter]
list.</warning></warnings><warnings
file="/home/jesus/devel/php/PEAR_local/Science/Chemistry/Residue_PDB.php"><warning
name="chem_residue_pdb" type="mismatch" elementtype="function">3th parameter type
&apos;$macromol&apos; does match the the documented type &apos;object
Chem_Macromolecule_PDB&apos;, possible error consider an update to
&apos;@param string $macromol reference to the containing macromolecule&apos;
or &apos;@param string reference to the containing macromolecule&apos;, the
variable name is optional.</warning><warning name="getgeomparams" type="missing"
elementtype="function">1st parameter &apos;$param&apos; is not documented add
&apos;@param (object objectname|type) [description]&apos; to the end of the
@param[eter] list.</warning></warnings><warnings
file="/home/jesus/devel/php/PEAR_local/Science/Chemistry/Molecule.php"><warning
name="chem_molecule" type="mismatch" elementtype="function">2nd parameter type
&apos;$atoms&apos; does match the the documented type
&apos;array&apos;, possible error consider an update to &apos;@param
string $atoms (description)&apos; or &apos;@param string
(description)&apos;, the variable name is optional.</warning><warning name="tocml"
type="mismatch" elementtype="function">1st parameter &apos;$title&apos; does
not match the documented name &apos;$id&apos;, update the tag to
&apos;@param string $title (description)&apos; or &apos;@param string
(description)&apos;, the variable name is optional.</warning><warning name="tocml"
type="mismatch" elementtype="function">2nd parameter type &apos;$id&apos; does
match the the documented type &apos;boolean&apos;, possible error consider an
update to &apos;@param string $id (description)&apos; or &apos;@param
string (description)&apos;, the variable name is optional.</warning><warning
name="tocml" type="mismatch" elementtype="function">2nd parameter
&apos;$id&apos; does not match the documented name
&apos;$connect&apos;, update the tag to &apos;@param string $id
(description)&apos; or &apos;@param string (description)&apos;, the
variable name is optional.</warning><warning name="tocml" type="missing"
elementtype="function">3th parameter &apos;$connect&apos; is not documented
add &apos;@param boolean [description]&apos; to the end of the @param[eter]
list.</warning></warnings><warnings
file="/home/jesus/devel/php/PEAR_local/Science/Chemistry/PDBFile.php"><warning
name="chem_pdbfile" type="mismatch" elementtype="functions">@see referrs to the
function &apos;mkArrays()&apos; which is not defined in the class. Entry gets
ignored.</warning><warning name="parsefile" type="mismatch"
elementtype="functions">@see referrs to the function
&apos;Chem_Macromolecule_PDB()&apos; which is not defined in the class. Entry
gets ignored.</warning></warnings><warnings
file="/home/jesus/devel/php/PEAR_local/Science/Chemistry/PDBParser.php"><warning
name="parseresidues" type="mismatch" elementtype="functions">@see referrs to the
function &apos;parseFile()&apos; which is not defined in the class. Entry gets
ignored.</warning><warning name="parseatom" type="missing" elementtype="function">3th
parameter &apos;&$atomname&apos; is not documented add &apos;@param
(object objectname|type) [description]&apos; to the end of the @param[eter]
list.</warning><warning name="getresiduelist" type="mismatch"
elementtype="function">2nd parameter &apos;$resname&apos; does not match the
documented name &apos;$resnam&apos;, update the tag to &apos;@param string
$resname Residue name, e.g. HIS, CYS, etc.&apos; or &apos;@param string
Residue name, e.g. HIS, CYS, etc.&apos;, the variable name is
optional.</warning></warnings></phpdoc>
\ No newline at end of file
+<?xml version="1.0"?><phpdoc><warnings
+file="/home/jesus/devel/php/pear/Science/Chemistry/Atom_PDB.php"><warning
+name="$valid" type="mismatch" elementtype="functions">@see referrs to the function
+&apos;initAtom()&apos; which is not defined in the class. Entry gets
+ignored.</warning><warning name="science_chemistry_atom_pdb" type="missing"
+elementtype="function">1st parameter &apos;$atomrec&apos; is not documented
+add &apos;@param (object objectname|type) [description]&apos; to the end of
+the @param[eter] list.</warning><warning name="science_chemistry_atom_pdb"
+type="missing" elementtype="function">2nd parameter &apos;$residue&apos; is
+not documented add &apos;@param string [description]&apos; to the end of the
+@param[eter] list.</warning><warning name="getfield" type="missing"
+elementtype="function">1st parameter &apos;$field&apos; is not documented add
+&apos;@param (object objectname|type) [description]&apos; to the end of the
+@param[eter] list.</warning></warnings><warnings
+file="/home/jesus/devel/php/pear/Science/Chemistry/Atom.php"><warning
+name="science_chemistry_atom" type="mismatch" elementtype="function">2nd parameter
+type &apos;$coords&apos; does match the the documented type
+&apos;array&apos;, possible error consider an update to &apos;@param
+string $coords array of coordinates (x, y, z)&apos; or &apos;@param string
+array of coordinates (x, y, z)&apos;, the variable name is
+optional.</warning><warning name="tocml" type="mismatch" elementtype="function">1st
+parameter type &apos;$id&apos; does match the the documented type
+&apos;string&apos;, possible error consider an update to &apos;@param
+integer $id (description)&apos; or &apos;@param integer
+(description)&apos;, the variable name is optional.</warning></warnings><warnings
+file="/home/jesus/devel/php/pear/Science/Chemistry/Macromolecule_PDB.php"><warning
+name="science_chemistry_macromolecule_pdb" type="mismatch"
+elementtype="variables">@see referrs to the variable &apos;$pdb&apos; which
+is not defined in the class. Entry gets ignored.</warning><warning
+name="science_chemistry_macromolecule_pdb" type="mismatch" elementtype="function">3th
+parameter type &apos;$pdbfile&apos; does match the the documented type
+&apos;object PDBFile&apos;, possible error consider an update to
+&apos;@param string $pdbfile reference to the PDB file object&apos; or
+&apos;@param string reference to the PDB file object&apos;, the variable name
+is optional.</warning></warnings><warnings
+file="/home/jesus/devel/php/pear/Science/Chemistry/Macromolecule.php"><warning
+name="science_chemistry_macromolecule" type="mismatch" elementtype="function">2nd
+parameter type &apos;$molecules&apos; does match the the documented type
+&apos;array&apos;, possible error consider an update to &apos;@param
+string $molecules (description)&apos; or &apos;@param string
+(description)&apos;, the variable name is optional.</warning><warning
+name="tocml" type="mismatch" elementtype="function">1st parameter
+&apos;$title&apos; does not match the documented name
+&apos;$id&apos;, update the tag to &apos;@param string $title
+(description)&apos; or &apos;@param string (description)&apos;, the
+variable name is optional.</warning><warning name="tocml" type="mismatch"
+elementtype="function">2nd parameter type &apos;$id&apos; does match the the
+documented type &apos;boolean&apos;, possible error consider an update to
+&apos;@param string $id (description)&apos; or &apos;@param string
+(description)&apos;, the variable name is optional.</warning><warning
+name="tocml" type="mismatch" elementtype="function">2nd parameter
+&apos;$id&apos; does not match the documented name
+&apos;$connect&apos;, update the tag to &apos;@param string $id
+(description)&apos; or &apos;@param string (description)&apos;, the
+variable name is optional.</warning><warning name="tocml" type="missing"
+elementtype="function">3th parameter &apos;$connect&apos; is not documented
+add &apos;@param boolean [description]&apos; to the end of the @param[eter]
+list.</warning></warnings><warnings
+file="/home/jesus/devel/php/pear/Science/Chemistry/Residue_PDB.php"><warning
+name="science_chemistry_residue_pdb" type="mismatch" elementtype="function">3th
+parameter type &apos;$macromol&apos; does match the the documented type
+&apos;object Science_Chemistry_Macromolecule_PDB&apos;, possible error
+consider an update to &apos;@param string $macromol reference to the containing
+macromolecule&apos; or &apos;@param string reference to the containing
+macromolecule&apos;, the variable name is optional.</warning><warning
+name="getgeomparams" type="missing" elementtype="function">1st parameter
+&apos;$param&apos; is not documented add &apos;@param (object
+objectname|type) [description]&apos; to the end of the @param[eter]
+list.</warning></warnings><warnings
+file="/home/jesus/devel/php/pear/Science/Chemistry/Molecule.php"><warning
+name="science_chemistry_molecule" type="mismatch" elementtype="function">2nd
+parameter type &apos;$atoms&apos; does match the the documented type
+&apos;array&apos;, possible error consider an update to &apos;@param
+string $atoms (description)&apos; or &apos;@param string
+(description)&apos;, the variable name is optional.</warning><warning
+name="tocml" type="mismatch" elementtype="function">1st parameter
+&apos;$title&apos; does not match the documented name
+&apos;$id&apos;, update the tag to &apos;@param string $title
+(description)&apos; or &apos;@param string (description)&apos;, the
+variable name is optional.</warning><warning name="tocml" type="mismatch"
+elementtype="function">2nd parameter type &apos;$id&apos; does match the the
+documented type &apos;boolean&apos;, possible error consider an update to
+&apos;@param string $id (description)&apos; or &apos;@param string
+(description)&apos;, the variable name is optional.</warning><warning
+name="tocml" type="mismatch" elementtype="function">2nd parameter
+&apos;$id&apos; does not match the documented name
+&apos;$connect&apos;, update the tag to &apos;@param string $id
+(description)&apos; or &apos;@param string (description)&apos;, the
+variable name is optional.</warning><warning name="tocml" type="missing"
+elementtype="function">3th parameter &apos;$connect&apos; is not documented
+add &apos;@param boolean [description]&apos; to the end of the @param[eter]
+list.</warning></warnings><warnings
+file="/home/jesus/devel/php/pear/Science/Chemistry/PDBFile.php"><warning
+name="science_chemistry_pdbfile" type="mismatch" elementtype="functions">@see referrs
+to the function &apos;mkArrays()&apos; which is not defined in the class.
+Entry gets ignored.</warning><warning name="parsefile" type="mismatch"
+elementtype="functions">@see referrs to the function
+&apos;Science_Chemistry_Macromolecule_PDB()&apos; which is not defined in the
+class. Entry gets ignored.</warning></warnings><warnings
+file="/home/jesus/devel/php/pear/Science/Chemistry/PDBParser.php"><warning
+name="parseresidues" type="mismatch" elementtype="functions">@see referrs to the
+function &apos;parseFile()&apos; which is not defined in the class. Entry
+gets ignored.</warning><warning name="parseatom" type="missing"
+elementtype="function">3th parameter &apos;&$atomname&apos; is not
+documented add &apos;@param (object objectname|type) [description]&apos; to
+the end of the @param[eter] list.</warning><warning name="getresiduelist"
+type="mismatch" elementtype="function">2nd parameter &apos;$resname&apos;
+does not match the documented name &apos;$resnam&apos;, update the tag to
+&apos;@param string $resname Residue name, e.g. HIS, CYS, etc.&apos; or
+&apos;@param string Residue name, e.g. HIS, CYS, etc.&apos;, the variable
+name is optional.</warning></warnings></phpdoc>
\ No newline at end of file
Index: pear/Science/Chemistry/doc/warnings_parser.xml
diff -u pear/Science/Chemistry/doc/warnings_parser.xml:1.1
pear/Science/Chemistry/doc/warnings_parser.xml:1.2
--- pear/Science/Chemistry/doc/warnings_parser.xml:1.1 Tue Apr 10 09:44:39 2001
+++ pear/Science/Chemistry/doc/warnings_parser.xml Tue Apr 10 11:44:24 2001
@@ -1 +1 @@
-<?xml version="1.0"?><phpdoc><warnings
file="/home/jesus/devel/php/PEAR_local/Science/Chemistry/PDBFile.php"><warning
name="Chem_PDBFile" type="mismatch" elementtype="class">PHPDoc found 1 syntax error(s)
in the tag list. Tag: &apos;@see Chem_PDBParser&apos; - Could not understand
all references. Use function() to referr to functions and to referr to variables -
don&apos;t know what &apos;Chem_PDBParser&apos; referrs to.. Syntax:
&apos;([^\s]+(?:::))?([^:][a-zA-Z_\x7f-\xff][a-zA-Z0-9_\xzf-\xff]*\(\s*\))&apos;
(function),
&apos;([^\s]+(?:::))?([$][^:][a-zA-Z_\x7f-\xff][a-zA-Z0-9_\xzf-\xff]*)&apos;
(variable), &apos;([^\s]+)&apos; (module or
class)..</warning></warnings><warnings
file="/home/jesus/devel/php/PEAR_local/Science/Chemistry/PDBParser.php"><warning
name="Chem_PDBParser" type="mismatch" elementtype="class">PHPDoc found 1 syntax
error(s) in the tag list. Tag: &apos;@see Chem_PDBFile&apos; - Could not
understand all references. Use function() to referr to functions and to referr to
variables - don&apos;t know what &apos;Chem_PDBFile&apos; referrs to..
Syntax:
&apos;([^\s]+(?:::))?([^:][a-zA-Z_\x7f-\xff][a-zA-Z0-9_\xzf-\xff]*\(\s*\))&apos;
(function),
&apos;([^\s]+(?:::))?([$][^:][a-zA-Z_\x7f-\xff][a-zA-Z0-9_\xzf-\xff]*)&apos;
(variable), &apos;([^\s]+)&apos; (module or class)..</warning><warning
name="$date" type="mismatch" elementtype="variable">PHPDoc found 1 syntax error(s) in
the tag list. Tag: &apos;@var date&apos; - General syntax error, syntax:
&apos;@var (object objectname|type)
[$varname]&apos;./(string|integer|int|long|real|double|float|boolean|bool|mixed|array|object)(?:\s+([a-zA-Z_\x7f-\xff][a-zA-Z0-9_\xzf-\xff]*))?(?:\s+([&]?[$][a-zA-Z_\x7f-\xff][a-zA-Z0-9_\xzf-\xff]*))?\s*(.*)?/is.</warning></warnings></phpdoc>
\ No newline at end of file
+<?xml version="1.0"?><phpdoc><warnings
+file="/home/jesus/devel/php/pear/Science/Chemistry/PDBFile.php"><warning
+name="Science_Chemistry_PDBFile" type="mismatch" elementtype="class">PHPDoc found 1
+syntax error(s) in the tag list. Tag: &apos;@see
+Science_Chemistry_PDBParser&apos; - Could not understand all references. Use
+function() to referr to functions and to referr to variables - don&apos;t know
+what &apos;Science_Chemistry_PDBParser&apos; referrs to.. Syntax:
+&apos;([^\s]+(?:::))?([^:][a-zA-Z_\x7f-\xff][a-zA-Z0-9_\xzf-\xff]*\(\s*\))&apos;
+ (function),
+&apos;([^\s]+(?:::))?([$][^:][a-zA-Z_\x7f-\xff][a-zA-Z0-9_\xzf-\xff]*)&apos;
+(variable), &apos;([^\s]+)&apos; (module or
+class)..</warning></warnings><warnings
+file="/home/jesus/devel/php/pear/Science/Chemistry/PDBParser.php"><warning
+name="Science_Chemistry_PDBParser" type="mismatch" elementtype="class">PHPDoc found 1
+syntax error(s) in the tag list. Tag: &apos;@see
+Science_Chemistry_PDBFile&apos; - Could not understand all references. Use
+function() to referr to functions and to referr to variables - don&apos;t know
+what &apos;Science_Chemistry_PDBFile&apos; referrs to.. Syntax:
+&apos;([^\s]+(?:::))?([^:][a-zA-Z_\x7f-\xff][a-zA-Z0-9_\xzf-\xff]*\(\s*\))&apos;
+ (function),
+&apos;([^\s]+(?:::))?([$][^:][a-zA-Z_\x7f-\xff][a-zA-Z0-9_\xzf-\xff]*)&apos;
+(variable), &apos;([^\s]+)&apos; (module or class)..</warning><warning
+name="$date" type="mismatch" elementtype="variable">PHPDoc found 1 syntax error(s) in
+the tag list. Tag: &apos;@var date&apos; - General syntax error, syntax:
+&apos;@var (object objectname|type)
+[$varname]&apos;./(string|integer|int|long|real|double|float|boolean|bool|mixed|array|object)(?:\s+([a-zA-Z_\x7f-\xff][a-zA-Z0-9_\xzf-\xff]*))?(?:\s+([&]?[$][a-zA-Z_\x7f-\xff][a-zA-Z0-9_\xzf-\xff]*))?\s*(.*)?/is.</warning></warnings></phpdoc>
\ No newline at end of file
Index: pear/Science/Chemistry/doc/Science_Chemistry_Atom.html
+++ pear/Science/Chemistry/doc/Science_Chemistry_Atom.html
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<!-- Generated with PHPDoc, http://www.phpdoc.de -->
<html>
<head>
<title>Chemical classes - Science_Chemistry - Class:
Science_Chemistry_Atom</title>
<link href="phpdoc.css" rel="stylesheet" type="text/css">
</head>
<body>
<table width="100%" border="0">
<tr>
<td align="left" valign="top" bgcolor="#B0BAFF">
<table width="100%">
<tr>
<td align="left" valign="top"><a
href="phpdoc_packagelist.html">Packageindex</a></td>
<td align="left" valign="top"><a
href="phpdoc_classtree.html">Classtrees</a></td>
<td align="left" valign="top"><a
href="phpdoc_modulegroup.html">Modulegroups</a></td>
<td align="left" valign="top"><a
href="phpdoc_elementlist.html">Elementlist</a></td>
<td align="left" valign="top"><a
href="phpdoc_warnings.html">Report</a></td>
<td align="left" valign="top"><a
href="phpdoc_xmlfiles.html">XML Files</a></td>
</tr>
</table>
</td>
</tr>
<tr>
<td height="20" align="left" valign="top"><hr></td>
</tr>
<tr>
<td align="left" valign="top">
File: <a
href="file:///home/jesus/devel/php/pear/Science/Chemistry/Atom.php"
target="_new">/home/jesus/devel/php/pear/Science/Chemistry/Atom.php</a>
<h5>Chemical classes - Science_Chemistry</h5>
<h1>Science_Chemistry_Atom</h1>
Science_Chemistry_Atom<br>
<p>
Base class representing an Atom
<p>
</td>
</tr>
<tr>
<td align="left" valign="top">
<h4>public class Science_Chemistry_Atom </h4>
Base class representing an Atom
<br>
<p>
<table>
<tr><td align="left" valign="top">Authors</td><td
align="left" valign="top">Jesus M. Castagnetto <<a
href="mailto:[EMAIL PROTECTED]">[EMAIL PROTECTED]</a>></td></tr>
<tr><td align="left" valign="top">Version</td><td
align="left" valign="top">1.0</td></tr>
</table>
</td>
</tr>
<tr>
<td height="10" align="left" valign="top"> </td>
</tr>
<tr>
<td align="left" valign="top">
<b>Direct known subclasses:</b> <a
href="Science_Chemistry_Atom_PDB.html">Science_Chemistry_Atom_PDB</a>
</td>
</tr>
<tr>
<td height="20" align="left" valign="top"><hr></td>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Public Method Summary</h2></td>
</tr>
<tr>
<td align="right" valign="top">object
Science_Chemistry_Atom</td>
<td align="left" valign="top" width="100%"><a
href="#function_Science_Chemistry_Atom()"><h4>Science_Chemistry_Atom(string $element,
[ string $coords ])</h4></a>Constructor for the class, requires the element symbol</td>
</tr>
<tr>
<td align="right" valign="top">boolean</td>
<td align="left" valign="top" width="100%"><a
href="#function_setCoordinates()"><h4>setCoordinates(array $coords)</h4></a>Sets the
coordinates for the atom object</td>
</tr>
<tr>
<td align="right" valign="top">string</td>
<td align="left" valign="top" width="100%"><a
href="#function_getElement()"><h4>getElement()</h4></a>Returns the chemical symbol for
the atom</td>
</tr>
<tr>
<td align="right" valign="top">object
Science_Chemistry_Coordinates</td>
<td align="left" valign="top" width="100%"><a
href="#function_getCoordinates()"><h4>getCoordinates()</h4></a>Returns the coordinates
object for the atom</td>
</tr>
<tr>
<td align="right" valign="top">float</td>
<td align="left" valign="top" width="100%"><a
href="#function_distance()"><h4>distance(object Science_Chemistry_Atom
$atom2)</h4></a>Calculates the cartesian distance from this atom</td>
</tr>
<tr>
<td align="right" valign="top">boolean</td>
<td align="left" valign="top" width="100%"><a
href="#function_isAtom()"><h4>isAtom(object Science_Chemistry_Atom
$obj)</h4></a>Checks if the object is an instance of Science_Chemistry_Atom</td>
</tr>
<tr>
<td align="right" valign="top">string</td>
<td align="left" valign="top" width="100%"><a
href="#function_toString()"><h4>toString()</h4></a>Returns a string representation of
the Science_Chemistry_Atom object</td>
</tr>
<tr>
<td align="right" valign="top">string</td>
<td align="left" valign="top" width="100%"><a
href="#function_toCML()"><h4>toCML([ integer $id ])</h4></a>Returns a CML
representation of the Science_Chemistry_Atom object</td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Private Field Summary</h2></td>
</tr>
<tr>
<td align="right" valign="top">string</td>
<td align="left" valign="top" width="100%"><a
href="#variable_$element"><h4>$element</h4></a>Element symbol</td>
</tr>
<tr>
<td align="right" valign="top">object
Science_Chemistry_Coordinates</td>
<td align="left" valign="top" width="100%"><a
href="#variable_$xyz"><h4>$xyz</h4></a>Science_Chemistry_Coordinates object</td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Public Method Details</h2></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_Science_Chemistry_Atom()"><h4>Science_Chemistry_Atom</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public object
Science_Chemistry_Atom Science_Chemistry_Atom( string $element, [ string $coords ]
)</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
Constructor for the class, requires
the element symbol
<br>
and an optional array of coordinates
<p>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top">Parameter</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">string</td>
<td align="left"
valign="top">$element</td>
<td align="left"
valign="top"><code></code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top">chemical symbol</td>
</tr>
</table>
</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">string</td>
<td align="left"
valign="top">$coords</td>
<td align="left"
valign="top"><code>= >>""<<</code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top">array of coordinates (x, y, z)</td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>object Science_Chemistry_Atom <p></td>
</tr>
<tr>
<td align="left" valign="top">See Also</td>
<td align="left" valign="top"><a
href="#function_setCoordinates()">setCoordinates()</a></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_setCoordinates()"><h4>setCoordinates</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public boolean setCoordinates(
array $coords )</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
Sets the coordinates for the atom
object
<br>
<p>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top">Parameter</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">array</td>
<td align="left"
valign="top">$coords</td>
<td align="left"
valign="top"><code></code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top">array of coordinates (x, y, z)</td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>boolean <p></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_getElement()"><h4>getElement</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public string getElement(
)</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
Returns the chemical symbol for the
atom
<br>
<p>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>string <p></td>
</tr>
<tr>
<td align="left" valign="top">See Also</td>
<td align="left" valign="top"><a
href="#var_$element">$element</a></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_getCoordinates()"><h4>getCoordinates</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public object
Science_Chemistry_Coordinates getCoordinates( )</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
Returns the coordinates object for the
atom
<br>
<p>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>object Science_Chemistry_Coordinates
<p></td>
</tr>
<tr>
<td align="left" valign="top">See Also</td>
<td align="left" valign="top"><a
href="#var_$xyz">$xyz</a></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_distance()"><h4>distance</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public float distance( object
Science_Chemistry_Atom $atom2 )</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
Calculates the cartesian distance from
this atom
<br>
instance to another
<p>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top">Parameter</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">object Science_Chemistry_Atom</td>
<td align="left"
valign="top">$atom2</td>
<td align="left"
valign="top"><code></code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top"></td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>float <p>distance </td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_isAtom()"><h4>isAtom</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public boolean isAtom( object
Science_Chemistry_Atom $obj )</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
Checks if the object is an instance of
Science_Chemistry_Atom
<br>
<p>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top">Parameter</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">object Science_Chemistry_Atom</td>
<td align="left"
valign="top">$obj</td>
<td align="left"
valign="top"><code></code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top"></td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>boolean <p></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_toString()"><h4>toString</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public string toString( )</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
Returns a string representation of the
Science_Chemistry_Atom object
<br>
<p>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>string <p></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_toCML()"><h4>toCML</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public string toCML( [ integer
$id ] )</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
Returns a CML representation of the
Science_Chemistry_Atom object
<br>
Accepts an optional id
<p>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top">Parameter</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">integer</td>
<td align="left"
valign="top">$id</td>
<td align="left"
valign="top"><code>= >>1<<</code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top"></td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>string <p></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
</table>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Private Field Details</h2></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="variable_$element"><h4>$element</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>private string $element</b>
<p>
>><code>""</code><<
<p>
Element symbol
<br>
</td>
</tr>
<tr>
<td align="left" valign="top">See Also</td>
<td align="left" valign="top"><a
href="#function_getElement()">getElement()</a></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="variable_$xyz"><h4>$xyz</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>private object
Science_Chemistry_Coordinates $xyz</b>
<p>
>><code></code><<
<p>
Science_Chemistry_Coordinates object
<br>
</td>
</tr>
<tr>
<td align="left" valign="top">See Also</td>
<td align="left" valign="top"><a
href="#function_getCoordinates()">getCoordinates()</a></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
</table>
</tr>
<tr>
<td height="10" align="left" valign="top"><hr></td>
</tr>
<tr>
<td align="left" valign="top" bgcolor="#C0C0C0">
<table>
<tr>
<td align="left" valign="top"><a
href="phpdoc_packagelist.html">Packageindex</a></td>
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href="phpdoc_warnings.html">Report</a></td>
<td align="left" valign="top"><a
href="phpdoc_xmlfiles.html">XML Files</a></td>
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<tr>
<td align="left" valign="top">PHPDoc 1.0beta</td>
</tr>
</table>
</body>
</html>
Index: pear/Science/Chemistry/doc/Science_Chemistry_Atom_PDB.html
+++ pear/Science/Chemistry/doc/Science_Chemistry_Atom_PDB.html
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<!-- Generated with PHPDoc, http://www.phpdoc.de -->
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<head>
<title>Chemical classes - Science_Chemistry - Class:
Science_Chemistry_Atom_PDB</title>
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</head>
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<table width="100%" border="0">
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File: <a
href="file:///home/jesus/devel/php/pear/Science/Chemistry/Atom_PDB.php"
target="_new">/home/jesus/devel/php/pear/Science/Chemistry/Atom_PDB.php</a>
<h5>Chemical classes - Science_Chemistry</h5>
<h1>Science_Chemistry_Atom_PDB</h1>
<a
href="Science_Chemistry_Atom.html">Science_Chemistry_Atom</a><br>
|<br> +-- Science_Chemistry_Atom_PDB<br>
<p>
Represents a PDB atom record
<p>
</td>
</tr>
<tr>
<td align="left" valign="top">
<h4>public class Science_Chemistry_Atom_PDB extends <a
href="Science_Chemistry_Atom.html">Science_Chemistry_Atom</a></h4>
Represents a PDB atom record
<br>
and contains a reference to the PDB residue to which it belongs
<p>
<table>
<tr><td align="left" valign="top">Authors</td><td
align="left" valign="top">Jesus M. Castagnetto <<a
href="mailto:[EMAIL PROTECTED]">[EMAIL PROTECTED]</a>></td></tr>
<tr><td align="left" valign="top">Version</td><td
align="left" valign="top">1.0</td></tr>
</table>
</td>
</tr>
<tr>
<td height="10" align="left" valign="top"> </td>
</tr>
<tr>
<td height="20" align="left" valign="top"><hr></td>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td align="left" valign="top"><h3>Methods
inherited from Science_Chemistry_Atom</h3></td>
</tr>
<tr>
<td align="left" valign="top"><a
href="Science_Chemistry_Atom.html#function_science_chemistry_atom">science_chemistry_atom</a>,
<a href="Science_Chemistry_Atom.html#function_setcoordinates">setcoordinates</a>, <a
href="Science_Chemistry_Atom.html#function_getelement">getelement</a>, <a
href="Science_Chemistry_Atom.html#function_getcoordinates">getcoordinates</a>, <a
href="Science_Chemistry_Atom.html#function_distance">distance</a>, <a
href="Science_Chemistry_Atom.html#function_isatom">isatom</a>, <a
href="Science_Chemistry_Atom.html#function_tostring">tostring</a>, <a
href="Science_Chemistry_Atom.html#function_tocml">tocml</a></td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Public Method Summary</h2></td>
</tr>
<tr>
<td align="right" valign="top">void</td>
<td align="left" valign="top" width="100%"><a
href="#function_Science_Chemistry_Atom_PDB()"><h4>Science_Chemistry_Atom_PDB(
$atomrec, string $residue)</h4></a>Warning: documentation is missing.</td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Private Method Summary</h2></td>
</tr>
<tr>
<td align="right" valign="top">void</td>
<td align="left" valign="top" width="100%"><a
href="#function_getField()"><h4>getField( $field)</h4></a>Warning: documentation is
missing.</td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td align="left" valign="top"><h3>Fields
inherited from Science_Chemistry_Atom</h3></td>
</tr>
<tr>
<td align="left" valign="top"><a
href="Science_Chemistry_Atom.html#variable_$element">$element</a>, <a
href="Science_Chemistry_Atom.html#variable_$xyz">$xyz</a></td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Public Field Summary</h2></td>
</tr>
<tr>
<td align="right" valign="top">boolean</td>
<td align="left" valign="top" width="100%"><a
href="#variable_$VALID"><h4>$VALID</h4></a>If the atom object has been initialized</td>
</tr>
<tr>
<td align="right" valign="top">object
Residue_PDB</td>
<td align="left" valign="top" width="100%"><a
href="#variable_$parent_residue"><h4>$parent_residue</h4></a>Reference to the
containing Residue object</td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Private Field Summary</h2></td>
</tr>
<tr>
<td align="right" valign="top">string</td>
<td align="left" valign="top" width="100%"><a
href="#variable_$rec_name"><h4>$rec_name</h4></a>PDB Atom record type, one of ATOM or
HETATM</td>
</tr>
<tr>
<td align="right" valign="top">integer</td>
<td align="left" valign="top" width="100%"><a
href="#variable_$ser_num"><h4>$ser_num</h4></a>PDB Atom serial number</td>
</tr>
<tr>
<td align="right" valign="top">string</td>
<td align="left" valign="top" width="100%"><a
href="#variable_$atom_name"><h4>$atom_name</h4></a>PDB Atom name</td>
</tr>
<tr>
<td align="right" valign="top">string</td>
<td align="left" valign="top" width="100%"><a
href="#variable_$alt_loc"><h4>$alt_loc</h4></a>PDB Atom alternative location</td>
</tr>
<tr>
<td align="right" valign="top">string</td>
<td align="left" valign="top" width="100%"><a
href="#variable_$res_name"><h4>$res_name</h4></a>PDB Atom's Residue name</td>
</tr>
<tr>
<td align="right" valign="top">string</td>
<td align="left" valign="top" width="100%"><a
href="#variable_$chain_id"><h4>$chain_id</h4></a>PDB Atom's Residue chain ID</td>
</tr>
<tr>
<td align="right" valign="top">string</td>
<td align="left" valign="top" width="100%"><a
href="#variable_$res_seq_num"><h4>$res_seq_num</h4></a>PDB Atom's Residue sequential
numnber</td>
</tr>
<tr>
<td align="right" valign="top">string</td>
<td align="left" valign="top" width="100%"><a
href="#variable_$ins_code"><h4>$ins_code</h4></a>PDB Atom insert code</td>
</tr>
<tr>
<td align="right" valign="top">float</td>
<td align="left" valign="top" width="100%"><a
href="#variable_$occupancy"><h4>$occupancy</h4></a>PDB Atom occupancy</td>
</tr>
<tr>
<td align="right" valign="top">float</td>
<td align="left" valign="top" width="100%"><a
href="#variable_$temp_factor"><h4>$temp_factor</h4></a>PDB Atom temperature factor</td>
</tr>
<tr>
<td align="right" valign="top">string</td>
<td align="left" valign="top" width="100%"><a
href="#variable_$segment_id"><h4>$segment_id</h4></a>PDB Atom segment identifier</td>
</tr>
<tr>
<td align="right" valign="top">float</td>
<td align="left" valign="top" width="100%"><a
href="#variable_$charge"><h4>$charge</h4></a>PDB Atom electronic charge</td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Public Method Details</h2></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_Science_Chemistry_Atom_PDB()"><h4>Science_Chemistry_Atom_PDB</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public void
Science_Chemistry_Atom_PDB( $atomrec, string $residue )</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
<br>
<p>
Warning: documentation is missing.
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top">Parameter</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top"></td>
<td align="left"
valign="top">$atomrec</td>
<td align="left"
valign="top"><code></code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top">Warning: documentation is missing.</td>
</tr>
</table>
</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">string</td>
<td align="left"
valign="top">$residue</td>
<td align="left"
valign="top"><code></code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top">Warning: documentation is missing.</td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>void <p></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
</table>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Private Method Details</h2></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_getField()"><h4>getField</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>private void getField( $field
)</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
<br>
<p>
Warning: documentation is missing.
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top">Parameter</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top"></td>
<td align="left"
valign="top">$field</td>
<td align="left"
valign="top"><code></code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top">Warning: documentation is missing.</td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>void <p></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
</table>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Public Field Details</h2></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="variable_$VALID"><h4>$VALID</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public boolean $VALID</b>
<p>
>><code>false</code><<
<p>
If the atom object has been initialized
<br>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="variable_$parent_residue"><h4>$parent_residue</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public object Residue_PDB
$parent_residue</b>
<p>
>><code></code><<
<p>
Reference to the containing Residue
object
<br>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
</table>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Private Field Details</h2></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="variable_$rec_name"><h4>$rec_name</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>private string $rec_name</b>
<p>
>><code></code><<
<p>
PDB Atom record type, one of ATOM or
HETATM
<br>
</td>
</tr>
<tr>
<td align="left" valign="top">See Also</td>
<td align="left" valign="top"><a
href="#function_getField()">getField()</a></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="variable_$ser_num"><h4>$ser_num</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>private integer $ser_num</b>
<p>
>><code></code><<
<p>
PDB Atom serial number
<br>
</td>
</tr>
<tr>
<td align="left" valign="top">See Also</td>
<td align="left" valign="top"><a
href="#function_getField()">getField()</a></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="variable_$atom_name"><h4>$atom_name</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>private string $atom_name</b>
<p>
>><code></code><<
<p>
PDB Atom name
<br>
</td>
</tr>
<tr>
<td align="left" valign="top">See Also</td>
<td align="left" valign="top"><a
href="#function_getField()">getField()</a></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="variable_$alt_loc"><h4>$alt_loc</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>private string $alt_loc</b>
<p>
>><code></code><<
<p>
PDB Atom alternative location
<br>
</td>
</tr>
<tr>
<td align="left" valign="top">See Also</td>
<td align="left" valign="top"><a
href="#function_getField()">getField()</a></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="variable_$res_name"><h4>$res_name</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>private string $res_name</b>
<p>
>><code></code><<
<p>
PDB Atom's Residue name
<br>
</td>
</tr>
<tr>
<td align="left" valign="top">See Also</td>
<td align="left" valign="top"><a
href="#function_getField()">getField()</a></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="variable_$chain_id"><h4>$chain_id</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>private string $chain_id</b>
<p>
>><code></code><<
<p>
PDB Atom's Residue chain ID
<br>
</td>
</tr>
<tr>
<td align="left" valign="top">See Also</td>
<td align="left" valign="top"><a
href="#function_getField()">getField()</a></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="variable_$res_seq_num"><h4>$res_seq_num</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>private string $res_seq_num</b>
<p>
>><code></code><<
<p>
PDB Atom's Residue sequential numnber
<br>
</td>
</tr>
<tr>
<td align="left" valign="top">See Also</td>
<td align="left" valign="top"><a
href="#function_getField()">getField()</a></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="variable_$ins_code"><h4>$ins_code</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>private string $ins_code</b>
<p>
>><code></code><<
<p>
PDB Atom insert code
<br>
</td>
</tr>
<tr>
<td align="left" valign="top">See Also</td>
<td align="left" valign="top"><a
href="#function_getField()">getField()</a></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="variable_$occupancy"><h4>$occupancy</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>private float $occupancy</b>
<p>
>><code></code><<
<p>
PDB Atom occupancy
<br>
</td>
</tr>
<tr>
<td align="left" valign="top">See Also</td>
<td align="left" valign="top"><a
href="#function_getField()">getField()</a></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="variable_$temp_factor"><h4>$temp_factor</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>private float $temp_factor</b>
<p>
>><code></code><<
<p>
PDB Atom temperature factor
<br>
</td>
</tr>
<tr>
<td align="left" valign="top">See Also</td>
<td align="left" valign="top"><a
href="#function_getField()">getField()</a></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="variable_$segment_id"><h4>$segment_id</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>private string $segment_id</b>
<p>
>><code></code><<
<p>
PDB Atom segment identifier
<br>
</td>
</tr>
<tr>
<td align="left" valign="top">See Also</td>
<td align="left" valign="top"><a
href="#function_getField()">getField()</a></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="variable_$charge"><h4>$charge</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>private float $charge</b>
<p>
>><code></code><<
<p>
PDB Atom electronic charge
<br>
</td>
</tr>
<tr>
<td align="left" valign="top">See Also</td>
<td align="left" valign="top"><a
href="#function_getField()">getField()</a></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
</table>
</tr>
<tr>
<td height="10" align="left" valign="top"><hr></td>
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Index: pear/Science/Chemistry/doc/Science_Chemistry_Coordinates.html
+++ pear/Science/Chemistry/doc/Science_Chemistry_Coordinates.html
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Science_Chemistry_Coordinates</title>
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File: <a
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target="_new">/home/jesus/devel/php/pear/Science/Chemistry/Coordinates.php</a>
<h5>Chemical classes - Science_Chemistry</h5>
<h1>Science_Chemistry_Coordinates</h1>
Science_Chemistry_Coordinates<br>
<p>
Utility class for defining 3D coordinates and
<p>
</td>
</tr>
<tr>
<td align="left" valign="top">
<h4>public class Science_Chemistry_Coordinates </h4>
Utility class for defining 3D coordinates and
<br>
its associated distance() method
<p>
<table>
<tr><td align="left" valign="top">Authors</td><td
align="left" valign="top">Jesus M. Castagnetto <<a
href="mailto:[EMAIL PROTECTED]">[EMAIL PROTECTED]</a>></td></tr>
<tr><td align="left" valign="top">Version</td><td
align="left" valign="top">1.0</td></tr>
</table>
</td>
</tr>
<tr>
<td height="10" align="left" valign="top"> </td>
</tr>
<tr>
<td height="20" align="left" valign="top"><hr></td>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Public Method Summary</h2></td>
</tr>
<tr>
<td align="right" valign="top">object
Science_Chemistry_Coordinates</td>
<td align="left" valign="top" width="100%"><a
href="#function_Science_Chemistry_Coordinates()"><h4>Science_Chemistry_Coordinates(array
$coords)</h4></a>Constructor for the class, returns null if parameter is</td>
</tr>
<tr>
<td align="right" valign="top">float</td>
<td align="left" valign="top" width="100%"><a
href="#function_distance()"><h4>distance(object Science_Chemistry_Coordinates
$coord)</h4></a>Castesian distance calculation method</td>
</tr>
<tr>
<td align="right" valign="top">boolean</td>
<td align="left" valign="top" width="100%"><a
href="#function_areCoordinates()"><h4>areCoordinates(object
Science_Chemistry_Coordinates $obj)</h4></a>Checks if the object is an instance of
Science_Chemistry_Coordinates</td>
</tr>
<tr>
<td align="right" valign="top">array</td>
<td align="left" valign="top" width="100%"><a
href="#function_getCoordinates()"><h4>getCoordinates()</h4></a>Returns the array of
coordinates</td>
</tr>
<tr>
<td align="right" valign="top">string</td>
<td align="left" valign="top" width="100%"><a
href="#function_toString()"><h4>toString()</h4></a>Returns a string representation of
the coordinates: x y z</td>
</tr>
<tr>
<td align="right" valign="top">string</td>
<td align="left" valign="top" width="100%"><a
href="#function_toCML()"><h4>toCML()</h4></a>Returns a CML representation of the
coordinates</td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Private Field Summary</h2></td>
</tr>
<tr>
<td align="right" valign="top">array</td>
<td align="left" valign="top" width="100%"><a
href="#variable_$coords"><h4>$coords</h4></a>Array of tridimensional coordinates: (x,
y, z)</td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Public Method Details</h2></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_Science_Chemistry_Coordinates()"><h4>Science_Chemistry_Coordinates</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public object
Science_Chemistry_Coordinates Science_Chemistry_Coordinates( array $coords )</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
Constructor for the class, returns
null if parameter is
<br>
not an array with 3 entries
<p>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top">Parameter</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">array</td>
<td align="left"
valign="top">$coords</td>
<td align="left"
valign="top"><code></code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top">array of three floats (x, y, z)</td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>object Science_Chemistry_Coordinates
<p></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_distance()"><h4>distance</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public float distance( object
Science_Chemistry_Coordinates $coord )</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
Castesian distance calculation method
<br>
<p>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top">Parameter</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">object Science_Chemistry_Coordinates</td>
<td align="left"
valign="top">$coord</td>
<td align="left"
valign="top"><code></code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top"></td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>float <p>distance </td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_areCoordinates()"><h4>areCoordinates</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public boolean areCoordinates(
object Science_Chemistry_Coordinates $obj )</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
Checks if the object is an instance of
Science_Chemistry_Coordinates
<br>
<p>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top">Parameter</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">object Science_Chemistry_Coordinates</td>
<td align="left"
valign="top">$obj</td>
<td align="left"
valign="top"><code></code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top"></td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>boolean <p></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_getCoordinates()"><h4>getCoordinates</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public array getCoordinates(
)</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
Returns the array of coordinates
<br>
<p>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>array <p>array (x, y, z)</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_toString()"><h4>toString</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public string toString( )</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
Returns a string representation of the
coordinates: x y z
<br>
<p>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>string <p></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_toCML()"><h4>toCML</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public string toCML( )</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
Returns a CML representation of the
coordinates
<br>
<p>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>string <p></td>
</tr>
<tr>
<td colspan="2" align="left"
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<tr><td colspan="2" align="left" valign="top"><a
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<b>private array $coords</b>
<p>
>><code></code><<
<p>
Array of tridimensional coordinates:
(x, y, z)
<br>
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Index: pear/Science/Chemistry/doc/Science_Chemistry_Element.html
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File: <a
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<h5>Chemical classes - Science_Chemistry</h5>
<h1>Science_Chemistry_Element</h1>
Science_Chemistry_Element<br>
<p>
Utility class that defines a chemical element object
<p>
</td>
</tr>
<tr>
<td align="left" valign="top">
<h4>public class Science_Chemistry_Element </h4>
Utility class that defines a chemical element object
<br>
<p>
<table>
<tr><td align="left" valign="top">Authors</td><td
align="left" valign="top">Jesus M. Castagnetto <<a
href="mailto:[EMAIL PROTECTED]">[EMAIL PROTECTED]</a>></td></tr>
<tr><td align="left" valign="top">Version</td><td
align="left" valign="top">1.0</td></tr>
</table>
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<td height="10" align="left" valign="top"> </td>
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</tr>
<tr>
<td align="right" valign="top">object
Science_Chemistry_Element</td>
<td align="left" valign="top" width="100%"><a
href="#function_Science_Chemistry_Element()"><h4>Science_Chemistry_Element(string
$sym, string $name, integer $num, float $wgt, string $mp, string $bp, string
$fam)</h4></a>Constructor for the class</td>
</tr>
<tr>
<td align="right" valign="top">boolean</td>
<td align="left" valign="top" width="100%"><a
href="#function_isElement()"><h4>isElement(object Science_Chemistry_Element
$obj)</h4></a>Checks if an object is a Science_Chemistry_Element instance</td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Public Field Summary</h2></td>
</tr>
<tr>
<td align="right" valign="top">string</td>
<td align="left" valign="top" width="100%"><a
href="#variable_$symbol"><h4>$symbol</h4></a>Element's symbol, one or two characters,
case sensitive</td>
</tr>
<tr>
<td align="right" valign="top">string</td>
<td align="left" valign="top" width="100%"><a
href="#variable_$name"><h4>$name</h4></a>Element's name</td>
</tr>
<tr>
<td align="right" valign="top">integer</td>
<td align="left" valign="top" width="100%"><a
href="#variable_$number"><h4>$number</h4></a>Element's atomic number</td>
</tr>
<tr>
<td align="right" valign="top">float</td>
<td align="left" valign="top" width="100%"><a
href="#variable_$weight"><h4>$weight</h4></a>Element's atomic weight in a.m.u (atomic
mass units)</td>
</tr>
<tr>
<td align="right" valign="top">string</td>
<td align="left" valign="top" width="100%"><a
href="#variable_$melting_point"><h4>$melting_point</h4></a>Element's melting point,
with comments</td>
</tr>
<tr>
<td align="right" valign="top">string</td>
<td align="left" valign="top" width="100%"><a
href="#variable_$boiling_point"><h4>$boiling_point</h4></a>Element's boiling point,
with comments</td>
</tr>
<tr>
<td align="right" valign="top">string</td>
<td align="left" valign="top" width="100%"><a
href="#variable_$family"><h4>$family</h4></a>Element's family</td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Public Method Details</h2></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_Science_Chemistry_Element()"><h4>Science_Chemistry_Element</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public object
Science_Chemistry_Element Science_Chemistry_Element( string $sym, string $name,
integer $num, float $wgt, string $mp, string $bp, string $fam )</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
Constructor for the class
<br>
<p>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top">Parameter</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">string</td>
<td align="left"
valign="top">$sym</td>
<td align="left"
valign="top"><code></code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top">element symbol</td>
</tr>
</table>
</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">string</td>
<td align="left"
valign="top">$name</td>
<td align="left"
valign="top"><code></code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top">element name</td>
</tr>
</table>
</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">integer</td>
<td align="left"
valign="top">$num</td>
<td align="left"
valign="top"><code></code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top">atomic number</td>
</tr>
</table>
</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">float</td>
<td align="left"
valign="top">$wgt</td>
<td align="left"
valign="top"><code></code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top">atomic weight</td>
</tr>
</table>
</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">string</td>
<td align="left"
valign="top">$mp</td>
<td align="left"
valign="top"><code></code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top">melting point (with comments)</td>
</tr>
</table>
</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">string</td>
<td align="left"
valign="top">$bp</td>
<td align="left"
valign="top"><code></code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top">boiling point (with comments)</td>
</tr>
</table>
</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">string</td>
<td align="left"
valign="top">$fam</td>
<td align="left"
valign="top"><code></code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top">family</td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>object Science_Chemistry_Element <p></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_isElement()"><h4>isElement</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public boolean isElement( object
Science_Chemistry_Element $obj )</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
Checks if an object is a
Science_Chemistry_Element instance
<br>
<p>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top">Parameter</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">object Science_Chemistry_Element</td>
<td align="left"
valign="top">$obj</td>
<td align="left"
valign="top"><code></code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top"></td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>boolean <p></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
</table>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Public Field Details</h2></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="variable_$symbol"><h4>$symbol</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public string $symbol</b>
<p>
>><code></code><<
<p>
Element's symbol, one or two
characters, case sensitive
<br>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="variable_$name"><h4>$name</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public string $name</b>
<p>
>><code></code><<
<p>
Element's name
<br>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="variable_$number"><h4>$number</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public integer $number</b>
<p>
>><code></code><<
<p>
Element's atomic number
<br>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="variable_$weight"><h4>$weight</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public float $weight</b>
<p>
>><code></code><<
<p>
Element's atomic weight in a.m.u
(atomic mass units)
<br>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="variable_$melting_point"><h4>$melting_point</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public string $melting_point</b>
<p>
>><code></code><<
<p>
Element's melting point, with comments
<br>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="variable_$boiling_point"><h4>$boiling_point</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public string $boiling_point</b>
<p>
>><code></code><<
<p>
Element's boiling point, with comments
<br>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="variable_$family"><h4>$family</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public string $family</b>
<p>
>><code></code><<
<p>
Element's family
<br>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
</table>
</tr>
<tr>
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Index: pear/Science/Chemistry/doc/Science_Chemistry_Macromolecule.html
+++ pear/Science/Chemistry/doc/Science_Chemistry_Macromolecule.html
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File: <a
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target="_new">/home/jesus/devel/php/pear/Science/Chemistry/Macromolecule.php</a>
<h5>Chemical classes - Science_Chemistry</h5>
<h1>Science_Chemistry_Macromolecule</h1>
Science_Chemistry_Macromolecule<br>
<p>
Represents a macromolecule, composed of several
<p>
</td>
</tr>
<tr>
<td align="left" valign="top">
<h4>public class Science_Chemistry_Macromolecule </h4>
Represents a macromolecule, composed of several
<br>
Science_Chemistry_Molecule objects
<p>
<table>
<tr><td align="left" valign="top">Authors</td><td
align="left" valign="top">Jesus M. Castagnetto <<a
href="mailto:[EMAIL PROTECTED]">[EMAIL PROTECTED]</a>></td></tr>
<tr><td align="left" valign="top">Version</td><td
align="left" valign="top">1.0</td></tr>
</table>
</td>
</tr>
<tr>
<td height="10" align="left" valign="top"> </td>
</tr>
<tr>
<td align="left" valign="top">
<b>Direct known subclasses:</b> <a
href="Science_Chemistry_Macromolecule_PDB.html">Science_Chemistry_Macromolecule_PDB</a>
</td>
</tr>
<tr>
<td height="20" align="left" valign="top"><hr></td>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Public Method Summary</h2></td>
</tr>
<tr>
<td align="right" valign="top">object
Science_Chemistry_Macromolecule</td>
<td align="left" valign="top" width="100%"><a
href="#function_Science_Chemistry_Macromolecule()"><h4>Science_Chemistry_Macromolecule(string
$name, [ string $molecules ])</h4></a>Constructor for the class, requires a
macromolecule name</td>
</tr>
<tr>
<td align="right" valign="top">boolean</td>
<td align="left" valign="top" width="100%"><a
href="#function_initMacromolecule()"><h4>initMacromolecule(array
$molecules)</h4></a>Initializes the array of Science_Chemistry_Molecule objects</td>
</tr>
<tr>
<td align="right" valign="top">boolean</td>
<td align="left" valign="top" width="100%"><a
href="#function_addMolecule()"><h4>addMolecule(object Science_Chemistry_Molecule
$mol)</h4></a>Adds a Science_Chemistry_Molecule object to the list of molecules in the
macromolecule</td>
</tr>
<tr>
<td align="right" valign="top">array</td>
<td align="left" valign="top" width="100%"><a
href="#function_getMolecules()"><h4>getMolecules()</h4></a>Returns an array of
Science_Chemistry_Molecule objects</td>
</tr>
<tr>
<td align="right" valign="top">boolean</td>
<td align="left" valign="top" width="100%"><a
href="#function_isMacromolecule()"><h4>isMacromolecule(object
Science_Chemistry_Macromolecule $obj)</h4></a>Checks if the object is an instance of
Science_Chemistry_Macromolecule</td>
</tr>
<tr>
<td align="right" valign="top">string</td>
<td align="left" valign="top" width="100%"><a
href="#function_toString()"><h4>toString()</h4></a>Returns a string representation of
the macromolecule</td>
</tr>
<tr>
<td align="right" valign="top">string</td>
<td align="left" valign="top" width="100%"><a
href="#function_toCML()"><h4>toCML([ string $title, string $id ], boolean
$connect)</h4></a>Returns a CML representation of the molecule</td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Private Field Summary</h2></td>
</tr>
<tr>
<td align="right" valign="top">string</td>
<td align="left" valign="top" width="100%"><a
href="#variable_$name"><h4>$name</h4></a>Macromolecule's name</td>
</tr>
<tr>
<td align="right" valign="top">array</td>
<td align="left" valign="top" width="100%"><a
href="#variable_$molecules"><h4>$molecules</h4></a>Array of molecular objects</td>
</tr>
<tr>
<td align="right" valign="top">int</td>
<td align="left" valign="top" width="100%"><a
href="#variable_$num_molecules"><h4>$num_molecules</h4></a>Number of
molecules/subunits</td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Public Method Details</h2></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_Science_Chemistry_Macromolecule()"><h4>Science_Chemistry_Macromolecule</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public object
Science_Chemistry_Macromolecule Science_Chemistry_Macromolecule( string $name, [
string $molecules ] )</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
Constructor for the class, requires a
macromolecule name
<br>
and an optional array of
Science_Chemistry_Molecule objects
<p>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top">Parameter</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">string</td>
<td align="left"
valign="top">$name</td>
<td align="left"
valign="top"><code></code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top"></td>
</tr>
</table>
</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">string</td>
<td align="left"
valign="top">$molecules</td>
<td align="left"
valign="top"><code>= >>""<<</code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top"></td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>object Science_Chemistry_Macromolecule
<p></td>
</tr>
<tr>
<td align="left" valign="top">See Also</td>
<td align="left" valign="top"><a
href="#var_$name">$name</a>, <a
href="#function_initMacromolecule()">initMacromolecule()</a></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_initMacromolecule()"><h4>initMacromolecule</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public boolean
initMacromolecule( array $molecules )</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
Initializes the array of
Science_Chemistry_Molecule objects
<br>
<p>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top">Parameter</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">array</td>
<td align="left"
valign="top">$molecules</td>
<td align="left"
valign="top"><code></code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top"></td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>boolean <p></td>
</tr>
<tr>
<td align="left" valign="top">See Also</td>
<td align="left" valign="top"><a
href="#var_$num_molecules">$num_molecules</a>, <a
href="#var_$molecules">$molecules</a>, <a
href="#function_addMolecule()">addMolecule()</a></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_addMolecule()"><h4>addMolecule</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public boolean addMolecule(
object Science_Chemistry_Molecule $mol )</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
Adds a Science_Chemistry_Molecule
object to the list of molecules in the macromolecule
<br>
<p>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top">Parameter</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">object Science_Chemistry_Molecule</td>
<td align="left"
valign="top">$mol</td>
<td align="left"
valign="top"><code></code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top"></td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>boolean <p></td>
</tr>
<tr>
<td align="left" valign="top">See Also</td>
<td align="left" valign="top"><a
href="#function_initMacromolecule()">initMacromolecule()</a></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_getMolecules()"><h4>getMolecules</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public array getMolecules(
)</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
Returns an array of
Science_Chemistry_Molecule objects
<br>
<p>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>array <p></td>
</tr>
<tr>
<td align="left" valign="top">See Also</td>
<td align="left" valign="top"><a
href="#var_$molecules">$molecules</a></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_isMacromolecule()"><h4>isMacromolecule</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public boolean isMacromolecule(
object Science_Chemistry_Macromolecule $obj )</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
Checks if the object is an instance of
Science_Chemistry_Macromolecule
<br>
<p>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top">Parameter</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">object Science_Chemistry_Macromolecule</td>
<td align="left"
valign="top">$obj</td>
<td align="left"
valign="top"><code></code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top"></td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>boolean <p></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_toString()"><h4>toString</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public string toString( )</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
Returns a string representation of the
macromolecule
<br>
as a multiple molecule XYZ-format file
<p>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>string <p></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_toCML()"><h4>toCML</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public string toCML( [ string
$title, string $id ], boolean $connect )</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
Returns a CML representation of the
molecule
<br>
Accepts an optional id, and a flag to
signalprinting of the connection table
<p>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top">Parameter</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">string</td>
<td align="left"
valign="top">$title</td>
<td align="left"
valign="top"><code>= >>"macromolecule"<<</code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top"></td>
</tr>
</table>
</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">string</td>
<td align="left"
valign="top">$id</td>
<td align="left"
valign="top"><code>= >>"macromol1"<<</code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top"></td>
</tr>
</table>
</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">boolean</td>
<td align="left"
valign="top">$connect</td>
<td align="left"
valign="top"><code></code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top">Warning: documentation is missing.</td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>string <p></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
</table>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Private Field Details</h2></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="variable_$name"><h4>$name</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>private string $name</b>
<p>
>><code></code><<
<p>
Macromolecule's name
<br>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="variable_$molecules"><h4>$molecules</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>private array $molecules</b>
<p>
>><code></code><<
<p>
Array of molecular objects
<br>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="variable_$num_molecules"><h4>$num_molecules</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>private int $num_molecules</b>
<p>
>><code></code><<
<p>
Number of molecules/subunits
<br>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
</table>
</tr>
<tr>
<td height="10" align="left" valign="top"><hr></td>
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Index: pear/Science/Chemistry/doc/Science_Chemistry_Macromolecule_PDB.html
+++ pear/Science/Chemistry/doc/Science_Chemistry_Macromolecule_PDB.html
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File: <a
href="file:///home/jesus/devel/php/pear/Science/Chemistry/Macromolecule_PDB.php"
target="_new">/home/jesus/devel/php/pear/Science/Chemistry/Macromolecule_PDB.php</a>
<h5>Chemical classes - Science_Chemistry</h5>
<h1>Science_Chemistry_Macromolecule_PDB</h1>
<a
href="Science_Chemistry_Macromolecule.html">Science_Chemistry_Macromolecule</a><br>
|<br> +-- Science_Chemistry_Macromolecule_PDB<br>
<p>
Represents a PDB macromolecule, composed of several
<p>
</td>
</tr>
<tr>
<td align="left" valign="top">
<h4>public class Science_Chemistry_Macromolecule_PDB
extends <a
href="Science_Chemistry_Macromolecule.html">Science_Chemistry_Macromolecule</a></h4>
Represents a PDB macromolecule, composed of several
<br>
Science_Chemistry_Residue_PDB objects
<p>
<table>
<tr><td align="left" valign="top">Authors</td><td
align="left" valign="top">Jesus M. Castagnetto <<a
href="mailto:[EMAIL PROTECTED]">[EMAIL PROTECTED]</a>></td></tr>
<tr><td align="left" valign="top">Version</td><td
align="left" valign="top">1.0</td></tr>
</table>
</td>
</tr>
<tr>
<td height="10" align="left" valign="top"> </td>
</tr>
<tr>
<td height="20" align="left" valign="top"><hr></td>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td align="left" valign="top"><h3>Methods
inherited from Science_Chemistry_Macromolecule</h3></td>
</tr>
<tr>
<td align="left" valign="top"><a
href="Science_Chemistry_Macromolecule.html#function_science_chemistry_macromolecule">science_chemistry_macromolecule</a>,
<a
href="Science_Chemistry_Macromolecule.html#function_initmacromolecule">initmacromolecule</a>,
<a href="Science_Chemistry_Macromolecule.html#function_addmolecule">addmolecule</a>,
<a href="Science_Chemistry_Macromolecule.html#function_getmolecules">getmolecules</a>,
<a
href="Science_Chemistry_Macromolecule.html#function_ismacromolecule">ismacromolecule</a>,
<a href="Science_Chemistry_Macromolecule.html#function_tostring">tostring</a>, <a
href="Science_Chemistry_Macromolecule.html#function_tocml">tocml</a></td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Public Method Summary</h2></td>
</tr>
<tr>
<td align="right" valign="top">object
Science_Chemistry_Macromolecule_PDB</td>
<td align="left" valign="top" width="100%"><a
href="#function_Science_Chemistry_Macromolecule_PDB()"><h4>Science_Chemistry_Macromolecule_PDB(string
$pdb, array $records, [ string $pdbfile ])</h4></a>Constructor for the class</td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Private Method Summary</h2></td>
</tr>
<tr>
<td align="right" valign="top">void</td>
<td align="left" valign="top" width="100%"><a
href="#function_parseResidues()"><h4>parseResidues(array $records)</h4></a>Makes the
array of residues in the macromolecule</td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td align="left" valign="top"><h3>Fields
inherited from Science_Chemistry_Macromolecule</h3></td>
</tr>
<tr>
<td align="left" valign="top"><a
href="Science_Chemistry_Macromolecule.html#variable_$name">$name</a>, <a
href="Science_Chemistry_Macromolecule.html#variable_$molecules">$molecules</a>, <a
href="Science_Chemistry_Macromolecule.html#variable_$num_molecules">$num_molecules</a></td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Public Method Details</h2></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_Science_Chemistry_Macromolecule_PDB()"><h4>Science_Chemistry_Macromolecule_PDB</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public object
Science_Chemistry_Macromolecule_PDB Science_Chemistry_Macromolecule_PDB( string $pdb,
array $records, [ string $pdbfile ] )</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
Constructor for the class
<br>
<p>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top">Parameter</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">string</td>
<td align="left"
valign="top">$pdb</td>
<td align="left"
valign="top"><code></code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top">PDB ID of the containing file</td>
</tr>
</table>
</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">array</td>
<td align="left"
valign="top">$records</td>
<td align="left"
valign="top"><code></code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top">Array of lines comprising the macromolecule</td>
</tr>
</table>
</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">string</td>
<td align="left"
valign="top">$pdbfile</td>
<td align="left"
valign="top"><code>= >>""<<</code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top">reference to the PDB file object</td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>object Science_Chemistry_Macromolecule_PDB
<p></td>
</tr>
<tr>
<td align="left" valign="top">See Also</td>
<td align="left" valign="top"><a
href="#function_parseResidues()">parseResidues()</a></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
</table>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Private Method Details</h2></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_parseResidues()"><h4>parseResidues</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>private void parseResidues(
array $records )</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
Makes the array of residues in the
macromolecule
<br>
<p>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top">Parameter</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">array</td>
<td align="left"
valign="top">$records</td>
<td align="left"
valign="top"><code></code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top"></td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>void <p></td>
</tr>
<tr>
<td align="left" valign="top">See Also</td>
<td align="left" valign="top"><a
href="#function_Science_Chemistry_Macromolecule_PDB()">Science_Chemistry_Macromolecule_PDB()</a></td>
</tr>
<tr>
<td colspan="2" align="left"
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</tr>
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File: <a
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<h5>Chemical classes - Science_Chemistry</h5>
<h1>Science_Chemistry_Molecule</h1>
Science_Chemistry_Molecule<br>
<p>
Base class representing a Molecule
<p>
</td>
</tr>
<tr>
<td align="left" valign="top">
<h4>public class Science_Chemistry_Molecule </h4>
Base class representing a Molecule
<br>
<p>
<table>
<tr><td align="left" valign="top">Authors</td><td
align="left" valign="top">Jesus M. Castagnetto <<a
href="mailto:[EMAIL PROTECTED]">[EMAIL PROTECTED]</a>></td></tr>
<tr><td align="left" valign="top">Version</td><td
align="left" valign="top">1.0</td></tr>
</table>
</td>
</tr>
<tr>
<td height="10" align="left" valign="top"> </td>
</tr>
<tr>
<td align="left" valign="top">
<b>Direct known subclasses:</b> <a
href="Science_Chemistry_Molecule_XYZ.html">Science_Chemistry_Molecule_XYZ</a>, <a
href="Science_Chemistry_Residue_PDB.html">Science_Chemistry_Residue_PDB</a>
</td>
</tr>
<tr>
<td height="20" align="left" valign="top"><hr></td>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Public Method Summary</h2></td>
</tr>
<tr>
<td align="right" valign="top">object
Science_Chemistry_Molecule</td>
<td align="left" valign="top" width="100%"><a
href="#function_Science_Chemistry_Molecule()"><h4>Science_Chemistry_Molecule(string
$name, [ string $atoms ])</h4></a>Constructor for the class, requires a molecule
name</td>
</tr>
<tr>
<td align="right" valign="top">boolean</td>
<td align="left" valign="top" width="100%"><a
href="#function_initMolecule()"><h4>initMolecule(array $atoms)</h4></a>Initializes the
array of Science_Chemistry_Atom objects</td>
</tr>
<tr>
<td align="right" valign="top">boolean</td>
<td align="left" valign="top" width="100%"><a
href="#function_addAtom()"><h4>addAtom(object Science_Chemistry_Atom
$atom)</h4></a>Adds a Science_Chemistry_Atom object to the list of atoms in the
molecule</td>
</tr>
<tr>
<td align="right" valign="top">array</td>
<td align="left" valign="top" width="100%"><a
href="#function_getAtoms()"><h4>getAtoms()</h4></a>Returns an array of Atom
objects</td>
</tr>
<tr>
<td align="right" valign="top">boolean</td>
<td align="left" valign="top" width="100%"><a
href="#function_isMolecule()"><h4>isMolecule(object Science_Chemistry_Molecule
$obj)</h4></a>Checks if the object is an instance of Science_Chemistry_Molecule</td>
</tr>
<tr>
<td align="right" valign="top">string</td>
<td align="left" valign="top" width="100%"><a
href="#function_toString()"><h4>toString()</h4></a>Returns a string representation of
the molecule</td>
</tr>
<tr>
<td align="right" valign="top">string</td>
<td align="left" valign="top" width="100%"><a
href="#function_toCML()"><h4>toCML([ string $title, string $id ], boolean
$connect)</h4></a>Returns a CML representation of the molecule</td>
</tr>
<tr>
<td align="right" valign="top">boolean</td>
<td align="left" valign="top" width="100%"><a
href="#function_setBondCutoff()"><h4>setBondCutoff(float $cutoff)</h4></a>Sets the
distance cutoff for bond determination</td>
</tr>
<tr>
<td align="right" valign="top">float</td>
<td align="left" valign="top" width="100%"><a
href="#function_getBondCutoff()"><h4>getBondCutoff()</h4></a>Returns the bond cutoff
uses to determine bonds</td>
</tr>
<tr>
<td align="right" valign="top">boolean</td>
<td align="left" valign="top" width="100%"><a
href="#function_calcDistanceMatrix()"><h4>calcDistanceMatrix()</h4></a>Calculates the
atom-atom distance matrix in Angstroms</td>
</tr>
<tr>
<td align="right" valign="top">string</td>
<td align="left" valign="top" width="100%"><a
href="#function_printDistanceMatrix()"><h4>printDistanceMatrix()</h4></a>Prints the
atom-atom distance matrix</td>
</tr>
<tr>
<td align="right" valign="top">array</td>
<td align="left" valign="top" width="100%"><a
href="#function_getDistanceMatrix()"><h4>getDistanceMatrix()</h4></a>Returns the
atom-atom distance matrix</td>
</tr>
<tr>
<td align="right" valign="top">boolean</td>
<td align="left" valign="top" width="100%"><a
href="#function_calcConnectionTable()"><h4>calcConnectionTable()</h4></a>Calculates
the connection table for the molecule</td>
</tr>
<tr>
<td align="right" valign="top">boolean</td>
<td align="left" valign="top" width="100%"><a
href="#function_printConnectionTable()"><h4>printConnectionTable()</h4></a>Prints the
molecule's connection table</td>
</tr>
<tr>
<td align="right" valign="top">array</td>
<td align="left" valign="top" width="100%"><a
href="#function_getConnectionTable()"><h4>getConnectionTable()</h4></a>Returns an
array of connected atoms and their bond distance</td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Public Field Summary</h2></td>
</tr>
<tr>
<td align="right" valign="top">string</td>
<td align="left" valign="top" width="100%"><a
href="#variable_$name"><h4>$name</h4></a>Molecule name</td>
</tr>
<tr>
<td align="right" valign="top">integer</td>
<td align="left" valign="top" width="100%"><a
href="#variable_$num_atoms"><h4>$num_atoms</h4></a>Number of atoms in the molecule</td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Private Field Summary</h2></td>
</tr>
<tr>
<td align="right" valign="top">array</td>
<td align="left" valign="top" width="100%"><a
href="#variable_$atoms"><h4>$atoms</h4></a>Array of atom objects in the molecule</td>
</tr>
<tr>
<td align="right" valign="top">array</td>
<td align="left" valign="top" width="100%"><a
href="#variable_$dist_matrix"><h4>$dist_matrix</h4></a>Atom-Atom distance matrix</td>
</tr>
<tr>
<td align="right" valign="top">array</td>
<td align="left" valign="top" width="100%"><a
href="#variable_$conn_table"><h4>$conn_table</h4></a>Atom-Atom connection (bond)
table</td>
</tr>
<tr>
<td align="right" valign="top">float</td>
<td align="left" valign="top" width="100%"><a
href="#variable_$BONDCUTOFF"><h4>$BONDCUTOFF</h4></a>Distance cutoff for bond
estimation</td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Public Method Details</h2></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_Science_Chemistry_Molecule()"><h4>Science_Chemistry_Molecule</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public object
Science_Chemistry_Molecule Science_Chemistry_Molecule( string $name, [ string $atoms ]
)</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
Constructor for the class, requires a
molecule name
<br>
and an optional array of
Science_Chemistry_Atom objects
<p>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top">Parameter</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">string</td>
<td align="left"
valign="top">$name</td>
<td align="left"
valign="top"><code></code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top"></td>
</tr>
</table>
</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">string</td>
<td align="left"
valign="top">$atoms</td>
<td align="left"
valign="top"><code>= >>""<<</code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top"></td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>object Science_Chemistry_Molecule <p></td>
</tr>
<tr>
<td align="left" valign="top">See Also</td>
<td align="left" valign="top"><a
href="#var_$name">$name</a>, <a href="#function_initMolecule()">initMolecule()</a></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_initMolecule()"><h4>initMolecule</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public boolean initMolecule(
array $atoms )</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
Initializes the array of
Science_Chemistry_Atom objects
<br>
<p>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top">Parameter</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">array</td>
<td align="left"
valign="top">$atoms</td>
<td align="left"
valign="top"><code></code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top"></td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>boolean <p></td>
</tr>
<tr>
<td align="left" valign="top">See Also</td>
<td align="left" valign="top"><a
href="#var_$num_atoms">$num_atoms</a>, <a href="#var_$atoms">$atoms</a>, <a
href="#function_addAtom()">addAtom()</a></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_addAtom()"><h4>addAtom</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public boolean addAtom( object
Science_Chemistry_Atom $atom )</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
Adds a Science_Chemistry_Atom object
to the list of atoms in the molecule
<br>
<p>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top">Parameter</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">object Science_Chemistry_Atom</td>
<td align="left"
valign="top">$atom</td>
<td align="left"
valign="top"><code></code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top"></td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>boolean <p></td>
</tr>
<tr>
<td align="left" valign="top">See Also</td>
<td align="left" valign="top"><a
href="#function_initMolecule()">initMolecule()</a></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_getAtoms()"><h4>getAtoms</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public array getAtoms( )</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
Returns an array of Atom objects
<br>
<p>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>array <p></td>
</tr>
<tr>
<td align="left" valign="top">See Also</td>
<td align="left" valign="top"><a
href="#var_$atoms">$atoms</a></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_isMolecule()"><h4>isMolecule</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public boolean isMolecule(
object Science_Chemistry_Molecule $obj )</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
Checks if the object is an instance of
Science_Chemistry_Molecule
<br>
<p>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top">Parameter</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">object Science_Chemistry_Molecule</td>
<td align="left"
valign="top">$obj</td>
<td align="left"
valign="top"><code></code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top"></td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>boolean <p></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_toString()"><h4>toString</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public string toString( )</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
Returns a string representation of the
molecule
<br>
as a XYZ-format file
<p>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>string <p></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_toCML()"><h4>toCML</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public string toCML( [ string
$title, string $id ], boolean $connect )</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
Returns a CML representation of the
molecule
<br>
Accepts an optional id, and a flag to
signalprinting of the connection table
<p>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top">Parameter</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">string</td>
<td align="left"
valign="top">$title</td>
<td align="left"
valign="top"><code>= >>"molecule"<<</code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top"></td>
</tr>
</table>
</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">string</td>
<td align="left"
valign="top">$id</td>
<td align="left"
valign="top"><code>= >>"mol1"<<</code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top"></td>
</tr>
</table>
</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">boolean</td>
<td align="left"
valign="top">$connect</td>
<td align="left"
valign="top"><code></code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top">Warning: documentation is missing.</td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>string <p></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_setBondCutoff()"><h4>setBondCutoff</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public boolean setBondCutoff(
float $cutoff )</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
Sets the distance cutoff for bond
determination
<br>
<p>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top">Parameter</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">float</td>
<td align="left"
valign="top">$cutoff</td>
<td align="left"
valign="top"><code></code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top"></td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>boolean <p></td>
</tr>
<tr>
<td align="left" valign="top">See Also</td>
<td align="left" valign="top"><a
href="#var_$BONDCUTOFF">$BONDCUTOFF</a>, <a
href="#function_getBondCutoff()">getBondCutoff()</a>, <a
href="#function_calcConnectionTable()">calcConnectionTable()</a></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_getBondCutoff()"><h4>getBondCutoff</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public float getBondCutoff(
)</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
Returns the bond cutoff uses to
determine bonds
<br>
<p>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>float <p></td>
</tr>
<tr>
<td align="left" valign="top">See Also</td>
<td align="left" valign="top"><a
href="#var_$BONDCUTOFF">$BONDCUTOFF</a>, <a
href="#function_setBondCutoff()">setBondCutoff()</a>, <a
href="#function_calcConnectionTable()">calcConnectionTable()</a></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_calcDistanceMatrix()"><h4>calcDistanceMatrix</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public boolean
calcDistanceMatrix( )</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
Calculates the atom-atom distance
matrix in Angstroms
<br>
<p>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>boolean <p></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_printDistanceMatrix()"><h4>printDistanceMatrix</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public string
printDistanceMatrix( )</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
Prints the atom-atom distance matrix
<br>
<p>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>string <p></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_getDistanceMatrix()"><h4>getDistanceMatrix</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public array getDistanceMatrix(
)</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
Returns the atom-atom distance matrix
<br>
<p>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>array <p></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_calcConnectionTable()"><h4>calcConnectionTable</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public boolean
calcConnectionTable( )</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
Calculates the connection table for
the molecule
<br>
<p>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>boolean <p></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_printConnectionTable()"><h4>printConnectionTable</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public boolean
printConnectionTable( )</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
Prints the molecule's connection table
<br>
<p>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>boolean <p></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_getConnectionTable()"><h4>getConnectionTable</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public array getConnectionTable(
)</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
Returns an array of connected atoms
and their bond distance
<br>
e.g. array ( array ($atomobj1,
$atomobj2, $distance ), ... )
<p>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>array <p></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
</table>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Public Field Details</h2></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="variable_$name"><h4>$name</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public string $name</b>
<p>
>><code>""</code><<
<p>
Molecule name
<br>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="variable_$num_atoms"><h4>$num_atoms</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public integer $num_atoms</b>
<p>
>><code></code><<
<p>
Number of atoms in the molecule
<br>
</td>
</tr>
<tr>
<td align="left" valign="top">See Also</td>
<td align="left" valign="top"><a
href="#function_initMolecule()">initMolecule()</a></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
</table>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Private Field Details</h2></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="variable_$atoms"><h4>$atoms</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>private array $atoms</b>
<p>
>><code>array()</code><<
<p>
Array of atom objects in the molecule
<br>
</td>
</tr>
<tr>
<td align="left" valign="top">See Also</td>
<td align="left" valign="top"><a
href="#function_initMolecule()">initMolecule()</a></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="variable_$dist_matrix"><h4>$dist_matrix</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>private array $dist_matrix</b>
<p>
>><code>array()</code><<
<p>
Atom-Atom distance matrix
<br>
</td>
</tr>
<tr>
<td align="left" valign="top">See Also</td>
<td align="left" valign="top"><a
href="#function_calcDistanceMatrix()">calcDistanceMatrix()</a></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="variable_$conn_table"><h4>$conn_table</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>private array $conn_table</b>
<p>
>><code>array()</code><<
<p>
Atom-Atom connection (bond) table
<br>
</td>
</tr>
<tr>
<td align="left" valign="top">See Also</td>
<td align="left" valign="top"><a
href="#function_calcConnectionTable()">calcConnectionTable()</a></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="variable_$BONDCUTOFF"><h4>$BONDCUTOFF</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>private float $BONDCUTOFF</b>
<p>
>><code>1.8</code><<
<p>
Distance cutoff for bond estimation
<br>
</td>
</tr>
<tr>
<td align="left" valign="top">See Also</td>
<td align="left" valign="top"><a
href="#function_setBondCutoff()">setBondCutoff()</a>, <a
href="#function_getBondCutoff()">getBondCutoff()</a>, <a
href="#function_calcConnectionTable()">calcConnectionTable()</a></td>
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Index: pear/Science/Chemistry/doc/Science_Chemistry_Molecule_XYZ.html
+++ pear/Science/Chemistry/doc/Science_Chemistry_Molecule_XYZ.html
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
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File: <a
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target="_new">/home/jesus/devel/php/pear/Science/Chemistry/Molecule_XYZ.php</a>
<h5>Chemical classes - Science_Chemistry</h5>
<h1>Science_Chemistry_Molecule_XYZ</h1>
<a
href="Science_Chemistry_Molecule.html">Science_Chemistry_Molecule</a><br>
|<br> +-- Science_Chemistry_Molecule_XYZ<br>
<p>
Base class representing a Molecule from a XYZ format file
<p>
</td>
</tr>
<tr>
<td align="left" valign="top">
<h4>public class Science_Chemistry_Molecule_XYZ extends <a
href="Science_Chemistry_Molecule.html">Science_Chemistry_Molecule</a></h4>
Base class representing a Molecule from a XYZ format file
<br>
<p>
<table>
<tr><td align="left" valign="top">Authors</td><td
align="left" valign="top">Jesus M. Castagnetto <<a
href="mailto:[EMAIL PROTECTED]">[EMAIL PROTECTED]</a>></td></tr>
<tr><td align="left" valign="top">Version</td><td
align="left" valign="top">1.0</td></tr>
</table>
</td>
</tr>
<tr>
<td height="10" align="left" valign="top"> </td>
</tr>
<tr>
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</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td align="left" valign="top"><h3>Methods
inherited from Science_Chemistry_Molecule</h3></td>
</tr>
<tr>
<td align="left" valign="top"><a
href="Science_Chemistry_Molecule.html#function_science_chemistry_molecule">science_chemistry_molecule</a>,
<a href="Science_Chemistry_Molecule.html#function_initmolecule">initmolecule</a>, <a
href="Science_Chemistry_Molecule.html#function_addatom">addatom</a>, <a
href="Science_Chemistry_Molecule.html#function_getatoms">getatoms</a>, <a
href="Science_Chemistry_Molecule.html#function_ismolecule">ismolecule</a>, <a
href="Science_Chemistry_Molecule.html#function_tocml">tocml</a>, <a
href="Science_Chemistry_Molecule.html#function_setbondcutoff">setbondcutoff</a>, <a
href="Science_Chemistry_Molecule.html#function_getbondcutoff">getbondcutoff</a>, <a
href="Science_Chemistry_Molecule.html#function_calcdistancematrix">calcdistancematrix</a>,
<a
href="Science_Chemistry_Molecule.html#function_printdistancematrix">printdistancematrix</a>,
<a
href="Science_Chemistry_Molecule.html#function_getdistancematrix">getdistancematrix</a>,
<a
href="Science_Chemistry_Molecule.html#function_calcconnectiontable">calcconnectiontable</a>,
<a
href="Science_Chemistry_Molecule.html#function_printconnectiontable">printconnectiontable</a>,
<a
href="Science_Chemistry_Molecule.html#function_getconnectiontable">getconnectiontable</a></td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Public Method Summary</h2></td>
</tr>
<tr>
<td align="right" valign="top">object
Science_Chemistry_Molecule_XYZ</td>
<td align="left" valign="top" width="100%"><a
href="#function_Science_Chemistry_Molecule_XYZ()"><h4>Science_Chemistry_Molecule_XYZ([
string $xyzdata, string $src ])</h4></a>Constructor for the class, accepts 2 optional
parameters:</td>
</tr>
<tr>
<td align="right" valign="top">boolean</td>
<td align="left" valign="top" width="100%"><a
href="#function_parseXYZ()"><h4>parseXYZ(string $xyzdata, string $src)</h4></a>method
that does the parsing of the XYZ data itself</td>
</tr>
<tr>
<td align="right" valign="top">string</td>
<td align="left" valign="top" width="100%"><a
href="#function_toString()"><h4>toString()</h4></a>Generates a string representation
of the XYZ moleculeWarning: documentation is missing.</td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Private Method Summary</h2></td>
</tr>
<tr>
<td align="right" valign="top">object
Science_Chemistry_Atom</td>
<td align="left" valign="top" width="100%"><a
href="#function_parseAtom()"><h4>parseAtom(string $line)</h4></a>Parses an XYZ atom
record</td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td align="left" valign="top"><h3>Fields
inherited from Science_Chemistry_Molecule</h3></td>
</tr>
<tr>
<td align="left" valign="top"><a
href="Science_Chemistry_Molecule.html#variable_$name">$name</a>, <a
href="Science_Chemistry_Molecule.html#variable_$num_atoms">$num_atoms</a>, <a
href="Science_Chemistry_Molecule.html#variable_$atoms">$atoms</a>, <a
href="Science_Chemistry_Molecule.html#variable_$dist_matrix">$dist_matrix</a>, <a
href="Science_Chemistry_Molecule.html#variable_$conn_table">$conn_table</a>, <a
href="Science_Chemistry_Molecule.html#variable_$bondcutoff">$bondcutoff</a></td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Public Field Summary</h2></td>
</tr>
<tr>
<td align="right" valign="top">float</td>
<td align="left" valign="top" width="100%"><a
href="#variable_$energy"><h4>$energy</h4></a>Energy of the molecule. Optional value in
XYZ file format.</td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Public Method Details</h2></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_Science_Chemistry_Molecule_XYZ()"><h4>Science_Chemistry_Molecule_XYZ</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public object
Science_Chemistry_Molecule_XYZ Science_Chemistry_Molecule_XYZ( [ string $xyzdata,
string $src ] )</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
Constructor for the class, accepts 2
optional parameters:
<br>
the data and its source. Possible
values for $src: "file", "string"
<p>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top">Parameter</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">string</td>
<td align="left"
valign="top">$xyzdata</td>
<td align="left"
valign="top"><code>= >>""<<</code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top"></td>
</tr>
</table>
</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">string</td>
<td align="left"
valign="top">$src</td>
<td align="left"
valign="top"><code>= >>"file"<<</code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top">one of "file" or "string"</td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>object Science_Chemistry_Molecule_XYZ
<p></td>
</tr>
<tr>
<td align="left" valign="top">See Also</td>
<td align="left" valign="top"><a
href="#function_parseXYZ()">parseXYZ()</a></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_parseXYZ()"><h4>parseXYZ</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public boolean parseXYZ( string
$xyzdata, string $src )</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
method that does the parsing of the
XYZ data itself
<br>
<p>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top">Parameter</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">string</td>
<td align="left"
valign="top">$xyzdata</td>
<td align="left"
valign="top"><code></code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top"></td>
</tr>
</table>
</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">string</td>
<td align="left"
valign="top">$src</td>
<td align="left"
valign="top"><code></code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top"></td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>boolean <p></td>
</tr>
<tr>
<td align="left" valign="top">See Also</td>
<td align="left" valign="top"><a
href="#function_Science_Chemistry_Molecule_XYZ()">Science_Chemistry_Molecule_XYZ()</a></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_toString()"><h4>toString</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public string toString( )</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
Generates a string representation of
the XYZ molecule
<br>
Overrides parent
Science_Chemistry_Molecule::toString() method
<p>
Warning: documentation is missing.
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>string <p></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
</table>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Private Method Details</h2></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_parseAtom()"><h4>parseAtom</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>private object
Science_Chemistry_Atom parseAtom( string $line )</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
Parses an XYZ atom record
<br>
<p>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top">Parameter</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">string</td>
<td align="left"
valign="top">$line</td>
<td align="left"
valign="top"><code></code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top"></td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>object Science_Chemistry_Atom <p>@acess
public</td>
</tr>
<tr>
<td align="left" valign="top">See Also</td>
<td align="left" valign="top"><a
href="#function_parseXYZ()">parseXYZ()</a></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
</table>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Public Field Details</h2></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="variable_$energy"><h4>$energy</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public float $energy</b>
<p>
>><code></code><<
<p>
Energy of the molecule. Optional value
in XYZ file format.
<br>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
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Index: pear/Science/Chemistry/doc/Science_Chemistry_PDBFile.html
+++ pear/Science/Chemistry/doc/Science_Chemistry_PDBFile.html
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<h5>Chemical classes - Science_Chemistry</h5>
<h1>Science_Chemistry_PDBFile</h1>
Science_Chemistry_PDBFile<br>
<p>
Represents a PDB file, composed of one or more
Science_Chemistry_Macromolecule_PDB objects
<p>
</td>
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<td align="left" valign="top">
<h4>public class Science_Chemistry_PDBFile </h4>
Represents a PDB file, composed of one or more
Science_Chemistry_Macromolecule_PDB objects
<br>
<p>
<table>
<tr><td align="left" valign="top">Authors</td><td
align="left" valign="top">Jesus M. Castagnetto <<a
href="mailto:[EMAIL PROTECTED]">[EMAIL PROTECTED]</a>></td></tr>
<tr><td align="left" valign="top">Version</td><td
align="left" valign="top">1.0</td></tr>
</table>
</td>
</tr>
<tr>
<td height="10" align="left" valign="top"> </td>
</tr>
<tr>
<td height="20" align="left" valign="top"><hr></td>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Public Method Summary</h2></td>
</tr>
<tr>
<td align="right" valign="top">object
PDBFile</td>
<td align="left" valign="top" width="100%"><a
href="#function_Science_Chemistry_PDBFile()"><h4>Science_Chemistry_PDBFile(string
$filename)</h4></a>Constructor for the class, requires a PDB filename</td>
</tr>
<tr>
<td align="right" valign="top">string</td>
<td align="left" valign="top" width="100%"><a
href="#function_toCML()"><h4>toCML()</h4></a>Returns a CML representation of the PDB
file</td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Private Method Summary</h2></td>
</tr>
<tr>
<td align="right" valign="top">void</td>
<td align="left" valign="top" width="100%"><a
href="#function_parseFile()"><h4>parseFile(array $arr)</h4></a>Makes the arrays of all
present PDB record types</td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Private Field Summary</h2></td>
</tr>
<tr>
<td align="right" valign="top">string</td>
<td align="left" valign="top" width="100%"><a
href="#variable_$pdb"><h4>$pdb</h4></a>PDB ID</td>
</tr>
<tr>
<td align="right" valign="top">string</td>
<td align="left" valign="top" width="100%"><a
href="#variable_$file"><h4>$file</h4></a>Full path to PDB file</td>
</tr>
<tr>
<td align="right" valign="top">string</td>
<td align="left" valign="top" width="100%"><a
href="#variable_$date"><h4>$date</h4></a>PDB file's date</td>
</tr>
<tr>
<td align="right" valign="top">string</td>
<td align="left" valign="top" width="100%"><a
href="#variable_$class"><h4>$class</h4></a>PDB macromolecule(s) class</td>
</tr>
<tr>
<td align="right" valign="top">array</td>
<td align="left" valign="top" width="100%"><a
href="#variable_$meta"><h4>$meta</h4></a>Array of meta records</td>
</tr>
<tr>
<td align="right" valign="top">array</td>
<td align="left" valign="top" width="100%"><a
href="#variable_$macromolecules"><h4>$macromolecules</h4></a>Array of macromolecular
objects</td>
</tr>
<tr>
<td align="right" valign="top">int</td>
<td align="left" valign="top" width="100%"><a
href="#variable_$num_macromolecules"><h4>$num_macromolecules</h4></a>Number of
molecules/subunits</td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Public Method Details</h2></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_Science_Chemistry_PDBFile()"><h4>Science_Chemistry_PDBFile</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public object PDBFile
Science_Chemistry_PDBFile( string $filename )</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
Constructor for the class, requires a
PDB filename
<br>
<p>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top">Parameter</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">string</td>
<td align="left"
valign="top">$filename</td>
<td align="left"
valign="top"><code></code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top"></td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>object PDBFile <p>;</td>
</tr>
<tr>
<td align="left" valign="top">See Also</td>
<td align="left" valign="top"><a
href="#var_$pdb">$pdb</a>, <a href="#var_$file">$file</a></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_toCML()"><h4>toCML</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public string toCML( )</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
Returns a CML representation of the
PDB file
<br>
TODO
<p>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>string <p></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
</table>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Private Method Details</h2></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_parseFile()"><h4>parseFile</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>private void parseFile( array
$arr )</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
Makes the arrays of all present PDB
record types
<br>
<p>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top">Parameter</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">array</td>
<td align="left"
valign="top">$arr</td>
<td align="left"
valign="top"><code></code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top">array of lines</td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>void <p></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
</table>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Private Field Details</h2></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="variable_$pdb"><h4>$pdb</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>private string $pdb</b>
<p>
>><code></code><<
<p>
PDB ID
<br>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="variable_$file"><h4>$file</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>private string $file</b>
<p>
>><code></code><<
<p>
Full path to PDB file
<br>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="variable_$date"><h4>$date</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>private string $date</b>
<p>
>><code></code><<
<p>
PDB file's date
<br>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="variable_$class"><h4>$class</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>private string $class</b>
<p>
>><code></code><<
<p>
PDB macromolecule(s) class
<br>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="variable_$meta"><h4>$meta</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>private array $meta</b>
<p>
>><code></code><<
<p>
Array of meta records
<br>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="variable_$macromolecules"><h4>$macromolecules</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>private array $macromolecules</b>
<p>
>><code></code><<
<p>
Array of macromolecular objects
<br>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="variable_$num_macromolecules"><h4>$num_macromolecules</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>private int
$num_macromolecules</b>
<p>
>><code></code><<
<p>
Number of molecules/subunits
<br>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
</table>
</tr>
<tr>
<td height="10" align="left" valign="top"><hr></td>
</tr>
<tr>
<td align="left" valign="top" bgcolor="#C0C0C0">
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href="phpdoc_packagelist.html">Packageindex</a></td>
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File: <a
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target="_new">/home/jesus/devel/php/pear/Science/Chemistry/PDBParser.php</a>
<h5>Chemical classes - Science_Chemistry</h5>
<h1>Science_Chemistry_PDBParser</h1>
Science_Chemistry_PDBParser<br>
<p>
A self-contained class to parse a PDB file into an array of
residues
<p>
</td>
</tr>
<tr>
<td align="left" valign="top">
<h4>public class Science_Chemistry_PDBParser </h4>
A self-contained class to parse a PDB file into an array of
residues
<br>
each containing an array of atoms<br>Useful when dealing
with big PDB files, where using the Science_Chemistry_PDBFileclass will generate out
of memory errors.
<p>
<table>
<tr><td align="left" valign="top">Authors</td><td
align="left" valign="top">Jesus M. Castagnetto <<a
href="mailto:[EMAIL PROTECTED]">[EMAIL PROTECTED]</a>></td></tr>
<tr><td align="left" valign="top">Version</td><td
align="left" valign="top">1.0</td></tr>
</table>
</td>
</tr>
<tr>
<td height="10" align="left" valign="top"> </td>
</tr>
<tr>
<td height="20" align="left" valign="top"><hr></td>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Public Method Summary</h2></td>
</tr>
<tr>
<td align="right" valign="top">object
PDBParser</td>
<td align="left" valign="top" width="100%"><a
href="#function_Science_Chemistry_PDBParser()"><h4>Science_Chemistry_PDBParser(string
$filename, [ boolean $multi, boolean $meta, boolean $full ])</h4></a>Constructor for
the class, requires a PDB filename</td>
</tr>
<tr>
<td align="right" valign="top">array</td>
<td align="left" valign="top" width="100%"><a
href="#function_getResidueList()"><h4>getResidueList(integer $macromol, string
$resname)</h4></a>Returns an array of residues with a particular name</td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Private Method Summary</h2></td>
</tr>
<tr>
<td align="right" valign="top">void</td>
<td align="left" valign="top" width="100%"><a
href="#function_parseResidues()"><h4>parseResidues(array $records, boolean
$full)</h4></a>Makes the array of residues in the macromolecule</td>
</tr>
<tr>
<td align="right" valign="top">void</td>
<td align="left" valign="top" width="100%"><a
href="#function_parseAtom()"><h4>parseAtom(string $atomrec, boolean $full,
&$atomname)</h4></a>Parses an atom record into an associative array</td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Private Field Summary</h2></td>
</tr>
<tr>
<td align="right" valign="top">string</td>
<td align="left" valign="top" width="100%"><a
href="#variable_$pdb"><h4>$pdb</h4></a>PDB ID</td>
</tr>
<tr>
<td align="right" valign="top">string</td>
<td align="left" valign="top" width="100%"><a
href="#variable_$file"><h4>$file</h4></a>Full path to PDB file</td>
</tr>
<tr>
<td align="right" valign="top">unknown</td>
<td align="left" valign="top" width="100%"><a
href="#variable_$date"><h4>$date</h4></a>PDB file's date</td>
</tr>
<tr>
<td align="right" valign="top">string</td>
<td align="left" valign="top" width="100%"><a
href="#variable_$class"><h4>$class</h4></a>PDB macromolecule(s) class</td>
</tr>
<tr>
<td align="right" valign="top">array</td>
<td align="left" valign="top" width="100%"><a
href="#variable_$macromolecules"><h4>$macromolecules</h4></a>Array of
macromolecules</td>
</tr>
<tr>
<td align="right" valign="top">int</td>
<td align="left" valign="top" width="100%"><a
href="#variable_$num_macromolecules"><h4>$num_macromolecules</h4></a>Number of
macromolecules</td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Public Method Details</h2></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_Science_Chemistry_PDBParser()"><h4>Science_Chemistry_PDBParser</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public object PDBParser
Science_Chemistry_PDBParser( string $filename, [ boolean $multi, boolean $meta,
boolean $full ] )</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
Constructor for the class, requires a
PDB filename
<br>
<p>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top">Parameter</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">string</td>
<td align="left"
valign="top">$filename</td>
<td align="left"
valign="top"><code></code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top">PDB filename</td>
</tr>
</table>
</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">boolean</td>
<td align="left"
valign="top">$multi</td>
<td align="left"
valign="top"><code>= >>false<<</code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top">whether to parse all models in a multi-model file</td>
</tr>
</table>
</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">boolean</td>
<td align="left"
valign="top">$meta</td>
<td align="left"
valign="top"><code>= >>false<<</code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top">whether to store the PDB file meta information</td>
</tr>
</table>
</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">boolean</td>
<td align="left"
valign="top">$full</td>
<td align="left"
valign="top"><code>= >>false<<</code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top">whether to store the full set of fields per atom</td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>object PDBParser <p></td>
</tr>
<tr>
<td align="left" valign="top">See Also</td>
<td align="left" valign="top"><a
href="#function_parseResidues()">parseResidues()</a></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_getResidueList()"><h4>getResidueList</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public array getResidueList(
integer $macromol, string $resname )</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
Returns an array of residues with a
particular name
<br>
from the indicated macromolecule index
<p>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top">Parameter</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">integer</td>
<td align="left"
valign="top">$macromol</td>
<td align="left"
valign="top"><code></code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top">Index of the macromolecule in the $macromolecules array</td>
</tr>
</table>
</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">string</td>
<td align="left"
valign="top">$resname</td>
<td align="left"
valign="top"><code></code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top">Residue name, e.g. HIS, CYS, etc.</td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>array <p>list of residues with the
requested name</td>
</tr>
<tr>
<td align="left" valign="top">See Also</td>
<td align="left" valign="top"><a
href="#var_$macromolecules">$macromolecules</a></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
</table>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Private Method Details</h2></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_parseResidues()"><h4>parseResidues</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>private void parseResidues(
array $records, boolean $full )</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
Makes the array of residues in the
macromolecule
<br>
<p>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top">Parameter</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">array</td>
<td align="left"
valign="top">$records</td>
<td align="left"
valign="top"><code></code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top"></td>
</tr>
</table>
</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">boolean</td>
<td align="left"
valign="top">$full</td>
<td align="left"
valign="top"><code></code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top">whether to store the full set of fields per atom</td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>void <p></td>
</tr>
<tr>
<td align="left" valign="top">See Also</td>
<td align="left" valign="top"><a
href="#function_parseAtom()">parseAtom()</a></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_parseAtom()"><h4>parseAtom</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>private void parseAtom( string
$atomrec, boolean $full, &$atomname )</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
Parses an atom record into an
associative array
<br>
<p>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top">Parameter</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">string</td>
<td align="left"
valign="top">$atomrec</td>
<td align="left"
valign="top"><code></code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top">PDB atom record</td>
</tr>
</table>
</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">boolean</td>
<td align="left"
valign="top">$full</td>
<td align="left"
valign="top"><code></code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top">whether to store the full set of fields per atom</td>
</tr>
</table>
</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top"></td>
<td align="left"
valign="top">&$atomname</td>
<td align="left"
valign="top"><code></code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top">Warning: documentation is missing.</td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>void <p></td>
</tr>
<tr>
<td align="left" valign="top">See Also</td>
<td align="left" valign="top"><a
href="#function_parseResidues()">parseResidues()</a></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
</table>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Private Field Details</h2></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="variable_$pdb"><h4>$pdb</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>private string $pdb</b>
<p>
>><code></code><<
<p>
PDB ID
<br>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="variable_$file"><h4>$file</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>private string $file</b>
<p>
>><code></code><<
<p>
Full path to PDB file
<br>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="variable_$date"><h4>$date</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>private unknown $date</b>
<p>
>><code></code><<
<p>
PDB file's date
<br>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
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<tr>
<td colspan="2" align="left" valign="top">
<b>private string $class</b>
<p>
>><code></code><<
<p>
PDB macromolecule(s) class
<br>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="variable_$macromolecules"><h4>$macromolecules</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>private array $macromolecules</b>
<p>
>><code></code><<
<p>
Array of macromolecules
<br>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="variable_$num_macromolecules"><h4>$num_macromolecules</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>private int
$num_macromolecules</b>
<p>
>><code></code><<
<p>
Number of macromolecules
<br>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
</table>
</tr>
<tr>
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Index: pear/Science/Chemistry/doc/Science_Chemistry_Periodic_Table.html
+++ pear/Science/Chemistry/doc/Science_Chemistry_Periodic_Table.html
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Science_Chemistry_Periodic_Table</title>
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File: <a
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target="_new">/home/jesus/devel/php/pear/Science/Chemistry/Periodic_Table.php</a>
<h5>Chemical classes - Science_Chemistry</h5>
<h1>Science_Chemistry_Periodic_Table</h1>
Science_Chemistry_Periodic_Table<br>
<p>
Utility class that defines a Periodic Table of elements
<p>
</td>
</tr>
<tr>
<td align="left" valign="top">
<h4>public class Science_Chemistry_Periodic_Table </h4>
Utility class that defines a Periodic Table of elements
<br>
<p>
<table>
<tr><td align="left" valign="top">Authors</td><td
align="left" valign="top">Jesus M. Castagnetto <<a
href="mailto:[EMAIL PROTECTED]">[EMAIL PROTECTED]</a>></td></tr>
<tr><td align="left" valign="top">Version</td><td
align="left" valign="top">1.0</td></tr>
</table>
</td>
</tr>
<tr>
<td height="10" align="left" valign="top"> </td>
</tr>
<tr>
<td height="20" align="left" valign="top"><hr></td>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Public Method Summary</h2></td>
</tr>
<tr>
<td align="right" valign="top">object
Science_Chemistry_Element</td>
<td align="left" valign="top" width="100%"><a
href="#function_getElement()"><h4>getElement(string $symbol)</h4></a>Returns a
Science_Chemistry_Element object correspoding to the symbol (case sensitive)</td>
</tr>
<tr>
<td align="right" valign="top">array</td>
<td align="left" valign="top" width="100%"><a
href="#function_getElementFamily()"><h4>getElementFamily(string
$family)</h4></a>Returns an array of Science_Chemistry_Element objects belonging to an
element family</td>
</tr>
<tr>
<td align="right" valign="top">void</td>
<td align="left" valign="top" width="100%"><a
href="#function_initTable()"><h4>initTable()</h4></a>Initializes the Periodic Table
array</td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Public Field Summary</h2></td>
</tr>
<tr>
<td align="right" valign="top">array</td>
<td align="left" valign="top" width="100%"><a
href="#variable_$periodic_table"><h4>$periodic_table</h4></a>The associative array
containing the chemical elements</td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Public Method Details</h2></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_getElement()"><h4>getElement</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public object
Science_Chemistry_Element getElement( string $symbol )</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
Returns a Science_Chemistry_Element
object correspoding to the symbol (case sensitive)
<br>
<p>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top">Parameter</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">string</td>
<td align="left"
valign="top">$symbol</td>
<td align="left"
valign="top"><code></code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top"></td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>object Science_Chemistry_Element <p></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_getElementFamily()"><h4>getElementFamily</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public array getElementFamily(
string $family )</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
Returns an array of
Science_Chemistry_Element objects belonging to an element family
<br>
<p>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top">Parameter</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">string</td>
<td align="left"
valign="top">$family</td>
<td align="left"
valign="top"><code></code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top"></td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>array <p>Science_Chemistry_Element
objects</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_initTable()"><h4>initTable</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public void initTable( )</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
Initializes the Periodic Table array
<br>
<p>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>void <p></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
</table>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Public Field Details</h2></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="variable_$periodic_table"><h4>$periodic_table</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public array $periodic_table</b>
<p>
>><code>array()</code><<
<p>
The associative array containing the
chemical elements
<br>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
</table>
</tr>
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Index: pear/Science/Chemistry/doc/Science_Chemistry_Residue_PDB.html
+++ pear/Science/Chemistry/doc/Science_Chemistry_Residue_PDB.html
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File: <a
href="file:///home/jesus/devel/php/pear/Science/Chemistry/Residue_PDB.php"
target="_new">/home/jesus/devel/php/pear/Science/Chemistry/Residue_PDB.php</a>
<h5>Chemical classes - Science_Chemistry</h5>
<h1>Science_Chemistry_Residue_PDB</h1>
<a
href="Science_Chemistry_Molecule.html">Science_Chemistry_Molecule</a><br>
|<br> +-- Science_Chemistry_Residue_PDB<br>
<p>
Represents a PDB residue
<p>
</td>
</tr>
<tr>
<td align="left" valign="top">
<h4>public class Science_Chemistry_Residue_PDB extends <a
href="Science_Chemistry_Molecule.html">Science_Chemistry_Molecule</a></h4>
Represents a PDB residue
<br>
<p>
<table>
<tr><td align="left" valign="top">Authors</td><td
align="left" valign="top">Jesus M. Castagnetto <<a
href="mailto:[EMAIL PROTECTED]">[EMAIL PROTECTED]</a>></td></tr>
<tr><td align="left" valign="top">Version</td><td
align="left" valign="top">1.0</td></tr>
</table>
</td>
</tr>
<tr>
<td height="10" align="left" valign="top"> </td>
</tr>
<tr>
<td height="20" align="left" valign="top"><hr></td>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td align="left" valign="top"><h3>Methods
inherited from Science_Chemistry_Molecule</h3></td>
</tr>
<tr>
<td align="left" valign="top"><a
href="Science_Chemistry_Molecule.html#function_science_chemistry_molecule">science_chemistry_molecule</a>,
<a href="Science_Chemistry_Molecule.html#function_initmolecule">initmolecule</a>, <a
href="Science_Chemistry_Molecule.html#function_addatom">addatom</a>, <a
href="Science_Chemistry_Molecule.html#function_getatoms">getatoms</a>, <a
href="Science_Chemistry_Molecule.html#function_ismolecule">ismolecule</a>, <a
href="Science_Chemistry_Molecule.html#function_tostring">tostring</a>, <a
href="Science_Chemistry_Molecule.html#function_tocml">tocml</a>, <a
href="Science_Chemistry_Molecule.html#function_setbondcutoff">setbondcutoff</a>, <a
href="Science_Chemistry_Molecule.html#function_getbondcutoff">getbondcutoff</a>, <a
href="Science_Chemistry_Molecule.html#function_calcdistancematrix">calcdistancematrix</a>,
<a
href="Science_Chemistry_Molecule.html#function_printdistancematrix">printdistancematrix</a>,
<a
href="Science_Chemistry_Molecule.html#function_getdistancematrix">getdistancematrix</a>,
<a
href="Science_Chemistry_Molecule.html#function_calcconnectiontable">calcconnectiontable</a>,
<a
href="Science_Chemistry_Molecule.html#function_printconnectiontable">printconnectiontable</a>,
<a
href="Science_Chemistry_Molecule.html#function_getconnectiontable">getconnectiontable</a></td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Public Method Summary</h2></td>
</tr>
<tr>
<td align="right" valign="top">object
Science_Chemistry_Residue_PDB</td>
<td align="left" valign="top" width="100%"><a
href="#function_Science_Chemistry_Residue_PDB()"><h4>Science_Chemistry_Residue_PDB(string
$pdb, array $atomrec_arr, [ string $macromol ])</h4></a>Constructor for the class</td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Private Method Summary</h2></td>
</tr>
<tr>
<td align="right" valign="top">void</td>
<td align="left" valign="top" width="100%"><a
href="#function_calcGeomParams()"><h4>calcGeomParams()</h4></a>Warning: documentation
is missing.</td>
</tr>
<tr>
<td align="right" valign="top">void</td>
<td align="left" valign="top" width="100%"><a
href="#function_getGeomParams()"><h4>getGeomParams( $param)</h4></a>Warning:
documentation is missing.</td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td align="left" valign="top"><h3>Fields
inherited from Science_Chemistry_Molecule</h3></td>
</tr>
<tr>
<td align="left" valign="top"><a
href="Science_Chemistry_Molecule.html#variable_$name">$name</a>, <a
href="Science_Chemistry_Molecule.html#variable_$num_atoms">$num_atoms</a>, <a
href="Science_Chemistry_Molecule.html#variable_$atoms">$atoms</a>, <a
href="Science_Chemistry_Molecule.html#variable_$dist_matrix">$dist_matrix</a>, <a
href="Science_Chemistry_Molecule.html#variable_$conn_table">$conn_table</a>, <a
href="Science_Chemistry_Molecule.html#variable_$bondcutoff">$bondcutoff</a></td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Public Field Summary</h2></td>
</tr>
<tr>
<td align="right" valign="top">boolean</td>
<td align="left" valign="top" width="100%"><a
href="#variable_$VALID"><h4>$VALID</h4></a>If the PDB residue object has been
initialized</td>
</tr>
<tr>
<td align="right" valign="top">object
Science_Chemistry_Macromolecule_PDB</td>
<td align="left" valign="top" width="100%"><a
href="#variable_$macromol"><h4>$macromol</h4></a>Reference to the protein</td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Private Field Summary</h2></td>
</tr>
<tr>
<td align="right" valign="top">integer</td>
<td align="left" valign="top" width="100%"><a
href="#variable_$seq_num"><h4>$seq_num</h4></a>PDB Residue sequence number</td>
</tr>
<tr>
<td align="right" valign="top">string</td>
<td align="left" valign="top" width="100%"><a
href="#variable_$chain"><h4>$chain</h4></a>PDB Residue chain</td>
</tr>
<tr>
<td align="right" valign="top">string</td>
<td align="left" valign="top" width="100%"><a
href="#variable_$id"><h4>$id</h4></a>PDB Residue ID</td>
</tr>
<tr>
<td align="right" valign="top">string</td>
<td align="left" valign="top" width="100%"><a
href="#variable_$pdb"><h4>$pdb</h4></a>PDB ID for the protein that contains</td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Public Method Details</h2></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_Science_Chemistry_Residue_PDB()"><h4>Science_Chemistry_Residue_PDB</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public object
Science_Chemistry_Residue_PDB Science_Chemistry_Residue_PDB( string $pdb, array
$atomrec_arr, [ string $macromol ] )</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
Constructor for the class
<br>
<p>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top">Parameter</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">string</td>
<td align="left"
valign="top">$pdb</td>
<td align="left"
valign="top"><code></code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top">PDB if of the protein/nucleic acid/etc.</td>
</tr>
</table>
</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">array</td>
<td align="left"
valign="top">$atomrec_arr</td>
<td align="left"
valign="top"><code></code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top">Array of PDB atom record lines</td>
</tr>
</table>
</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top">string</td>
<td align="left"
valign="top">$macromol</td>
<td align="left"
valign="top"><code>= >>""<<</code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top">reference to the containing macromolecule</td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>object Science_Chemistry_Residue_PDB
<p></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
</table>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Private Method Details</h2></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_calcGeomParams()"><h4>calcGeomParams</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>private void calcGeomParams(
)</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
<br>
<p>
Warning: documentation is missing.
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>void <p></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="function_getGeomParams()"><h4>getGeomParams</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>private void getGeomParams(
$param )</b><p>
</td>
</tr>
<tr>
<td width="10" align="left"
valign="top"> </td>
<td align="left" valign="top">
<br>
<p>
Warning: documentation is missing.
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top">Parameter</td>
</tr>
<tr>
<td></td>
<td align="left" valign="top">
<table>
<tr>
<td align="left"
valign="top"></td>
<td align="left"
valign="top">$param</td>
<td align="left"
valign="top"><code></code></td>
</tr>
<tr>
<td></td>
<td colspan="2"
align="left" valign="top">Warning: documentation is missing.</td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">Returns</td>
<td>void <p></td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
</table>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Public Field Details</h2></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="variable_$VALID"><h4>$VALID</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public boolean $VALID</b>
<p>
>><code>false</code><<
<p>
If the PDB residue object has been
initialized
<br>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="variable_$macromol"><h4>$macromol</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>public object
Science_Chemistry_Macromolecule_PDB $macromol</b>
<p>
>><code></code><<
<p>
Reference to the protein
<br>
to which this residue belongs
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
</table>
</tr>
<tr>
<td align="left" valign="top">
<table width="100%" border="0">
<tr>
<td colspan="2" align="left"
valign="top"><h2>Private Field Details</h2></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="variable_$seq_num"><h4>$seq_num</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>private integer $seq_num</b>
<p>
>><code></code><<
<p>
PDB Residue sequence number
<br>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="variable_$chain"><h4>$chain</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>private string $chain</b>
<p>
>><code></code><<
<p>
PDB Residue chain
<br>
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="variable_$id"><h4>$id</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>private string $id</b>
<p>
>><code></code><<
<p>
PDB Residue ID
<br>
$id = "$name:$seq_num:$chain"
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
<tr><td colspan="2" align="left" valign="top"><a
name="variable_$pdb"><h4>$pdb</h4></a></td></tr>
<tr>
<td colspan="2" align="left" valign="top">
<b>private string $pdb</b>
<p>
>><code></code><<
<p>
PDB ID for the protein that contains
<br>
this residue
</td>
</tr>
<tr>
<td colspan="2" align="left"
valign="top"><hr></td>
</tr>
</table>
</tr>
<tr>
<td height="10" align="left" valign="top"><hr></td>
</tr>
<tr>
<td align="left" valign="top" bgcolor="#C0C0C0">
<table>
<tr>
<td align="left" valign="top"><a
href="phpdoc_packagelist.html">Packageindex</a></td>
<td align="left" valign="top"><a
href="phpdoc_classtree.html">Classtrees</a></td>
<td align="left" valign="top"><a
href="phpdoc_modulegroup.html">Modulegroups</a></td>
<td align="left" valign="top"><a
href="phpdoc_elementlist.html">Elementlist</a></td>
<td align="left" valign="top"><a
href="phpdoc_warnings.html">Report</a></td>
<td align="left" valign="top"><a
href="phpdoc_xmlfiles.html">XML Files</a></td>
</tr>
</table>
</td>
</tr>
<tr>
<td align="left" valign="top">PHPDoc 1.0beta</td>
</tr>
</table>
</body>
</html>
Index: pear/Science/Chemistry/doc/class_Science_Chemistry_Atom.xml
+++ pear/Science/Chemistry/doc/class_Science_Chemistry_Atom.xml
<?xml version="1.0"?><phpdoc><class name="Science_Chemistry_Atom" extends=""
undoc="false" access="public"
package="Science_Chemistry"><file>/home/jesus/devel/php/pear/Science/Chemistry/Atom.php</file><doc><author
email="[EMAIL PROTECTED]">Jesus M.
Castagnetto</author><description/><shortdescription>Base class representing an
Atom</shortdescription><version>1.0</version></doc><function
name="Science_Chemistry_Atom" undoc="false" access="public"><doc><see
type="function">setCoordinates()</see><parameter name="$element"
type="string">chemical symbol</parameter><parameter name="$coords"
default="&quot;&quot;" type="string">array of coordinates (x, y,
z)</parameter><return name="" type="object Science_Chemistry_Atom"/><description>and
an optional array of coordinates</description><shortdescription>Constructor for the
class, requires the element symbol</shortdescription></doc></function><function
name="setCoordinates" undoc="false" access="public"><doc><parameter name="$coords"
type="array">array of coordinates (x, y, z)</parameter><return name=""
type="boolean"/><description/><shortdescription>Sets the coordinates for the atom
object</shortdescription></doc></function><function name="getElement" undoc="false"
access="public"><doc><see type="var">$element</see><return name=""
type="string"/><description/><shortdescription>Returns the chemical symbol for the
atom</shortdescription></doc></function><function name="getCoordinates" undoc="false"
access="public"><doc><see type="var">$xyz</see><return name="" type="object
Science_Chemistry_Coordinates"/><description/><shortdescription>Returns the
coordinates object for the atom</shortdescription></doc></function><function
name="distance" undoc="false" access="public"><doc><parameter name="$atom2"
type="object Science_Chemistry_Atom"/><return name="" type="float">distance
</return><description>instance to another</description><shortdescription>Calculates
the cartesian distance from this atom</shortdescription></doc></function><function
name="isAtom" undoc="false" access="public"><doc><parameter name="$obj" type="object
Science_Chemistry_Atom"/><return name=""
type="boolean"/><description/><shortdescription>Checks if the object is an instance of
Science_Chemistry_Atom</shortdescription></doc></function><function name="toString"
undoc="false" access="public"><doc><return name=""
type="string"/><description/><shortdescription>Returns a string representation of the
Science_Chemistry_Atom object</shortdescription></doc></function><function
name="toCML" undoc="false" access="public"><doc><parameter name="$id" default="1"
type="integer"/><return name="" type="string"/><description>Accepts an optional
id</description><shortdescription>Returns a CML representation of the
Science_Chemistry_Atom object</shortdescription></doc></function><variable
name="$element" access="private" type="string">&quot;&quot;<doc><see
type="function">getElement()</see><description/><shortdescription>Element
symbol</shortdescription></doc></variable><variable name="$xyz" access="private"
type="object Science_Chemistry_Coordinates"><doc><see
type="function">getCoordinates()</see><description/><shortdescription>Science_Chemistry_Coordinates
object</shortdescription></doc></variable><subclasses><subclass>Science_Chemistry_Atom_PDB</subclass></subclasses></class></phpdoc>
Index: pear/Science/Chemistry/doc/class_Science_Chemistry_Atom_PDB.xml
+++ pear/Science/Chemistry/doc/class_Science_Chemistry_Atom_PDB.xml
<?xml version="1.0"?><phpdoc><class name="Science_Chemistry_Atom_PDB"
extends="Science_Chemistry_Atom" undoc="false" access="public"
package="Science_Chemistry"><file>/home/jesus/devel/php/pear/Science/Chemistry/Atom_PDB.php</file><doc><author
email="[EMAIL PROTECTED]">Jesus M. Castagnetto</author><inherited
src="Array"/><description>and contains a reference to the PDB residue to which it
belongs</description><shortdescription>Represents a PDB atom
record</shortdescription><version>1.0</version></doc><function
name="Science_Chemistry_Atom_PDB" undoc="true" access="public"><doc><parameter
name="$atomrec" undoc="true"/><parameter name="$residue" type="string"
undoc="true"/><return type="void"/></doc></function><function name="getField"
undoc="true" access="private"><doc><parameter name="$field" undoc="true"/><return
type="void"/></doc></function><variable name="$rec_name" access="private"
type="string"><doc><see
type="function">getField()</see><description/><shortdescription>PDB Atom record type,
one of ATOM or HETATM</shortdescription></doc></variable><variable name="$ser_num"
access="private" type="integer"><doc><see
type="function">getField()</see><description/><shortdescription>PDB Atom serial
number</shortdescription></doc></variable><variable name="$atom_name" access="private"
type="string"><doc><see
type="function">getField()</see><description/><shortdescription>PDB Atom
name</shortdescription></doc></variable><variable name="$alt_loc" access="private"
type="string"><doc><see
type="function">getField()</see><description/><shortdescription>PDB Atom alternative
location</shortdescription></doc></variable><variable name="$res_name"
access="private" type="string"><doc><see
type="function">getField()</see><description/><shortdescription>PDB Atom&apos;s
Residue name</shortdescription></doc></variable><variable name="$chain_id"
access="private" type="string"><doc><see
type="function">getField()</see><description/><shortdescription>PDB Atom&apos;s
Residue chain ID</shortdescription></doc></variable><variable name="$res_seq_num"
access="private" type="string"><doc><see
type="function">getField()</see><description/><shortdescription>PDB Atom&apos;s
Residue sequential numnber</shortdescription></doc></variable><variable
name="$ins_code" access="private" type="string"><doc><see
type="function">getField()</see><description/><shortdescription>PDB Atom insert
code</shortdescription></doc></variable><variable name="$occupancy" access="private"
type="float"><doc><see
type="function">getField()</see><description/><shortdescription>PDB Atom
occupancy</shortdescription></doc></variable><variable name="$temp_factor"
access="private" type="float"><doc><see
type="function">getField()</see><description/><shortdescription>PDB Atom temperature
factor</shortdescription></doc></variable><variable name="$segment_id"
access="private" type="string"><doc><see
type="function">getField()</see><description/><shortdescription>PDB Atom segment
identifier</shortdescription></doc></variable><variable name="$charge"
access="private" type="float"><doc><see
type="function">getField()</see><description/><shortdescription>PDB Atom electronic
charge</shortdescription></doc></variable><variable name="$VALID" access="public"
type="boolean">false<doc><description/><shortdescription>If the atom object has been
initialized</shortdescription></doc></variable><variable name="$parent_residue"
access="public" type="object
Residue_PDB"><doc><description/><shortdescription>Reference to the containing Residue
object</shortdescription></doc></variable><inherited src="Science_Chemistry_Atom"
type="functions"><element>science_chemistry_atom</element><element>setcoordinates</element><element>getelement</element><element>getcoordinates</element><element>distance</element><element>isatom</element><element>tostring</element><element>tocml</element></inherited><inherited
src="Science_Chemistry_Atom"
type="variables"><element>$element</element><element>$xyz</element></inherited><path><parent>Science_Chemistry_Atom</parent></path><baseclass>Science_Chemistry_Atom</baseclass></class></phpdoc>
Index: pear/Science/Chemistry/doc/class_Science_Chemistry_Coordinates.xml
+++ pear/Science/Chemistry/doc/class_Science_Chemistry_Coordinates.xml
<?xml version="1.0"?><phpdoc><class name="Science_Chemistry_Coordinates" extends=""
undoc="false" access="public"
package="Science_Chemistry"><file>/home/jesus/devel/php/pear/Science/Chemistry/Coordinates.php</file><doc><author
email="[EMAIL PROTECTED]">Jesus M. Castagnetto</author><description>its
associated distance() method</description><shortdescription>Utility class for defining
3D coordinates and</shortdescription><version>1.0</version></doc><function
name="Science_Chemistry_Coordinates" undoc="false" access="public"><doc><parameter
name="$coords" type="array">array of three floats (x, y, z)</parameter><return name=""
type="object Science_Chemistry_Coordinates"/><description>not an array with 3
entries</description><shortdescription>Constructor for the class, returns null if
parameter is</shortdescription></doc></function><function name="distance"
undoc="false" access="public"><doc><parameter name="$coord" type="object
Science_Chemistry_Coordinates"/><return name="" type="float">distance
</return><description/><shortdescription>Castesian distance calculation
method</shortdescription></doc></function><function name="areCoordinates"
undoc="false" access="public"><doc><parameter name="$obj" type="object
Science_Chemistry_Coordinates"/><return name=""
type="boolean"/><description/><shortdescription>Checks if the object is an instance of
Science_Chemistry_Coordinates</shortdescription></doc></function><function
name="getCoordinates" undoc="false" access="public"><doc><return name=""
type="array">array (x, y, z)</return><description/><shortdescription>Returns the array
of coordinates</shortdescription></doc></function><function name="toString"
undoc="false" access="public"><doc><return name=""
type="string"/><description/><shortdescription>Returns a string representation of the
coordinates: x y z</shortdescription></doc></function><function name="toCML"
undoc="false" access="public"><doc><return name=""
type="string"/><description/><shortdescription>Returns a CML representation of the
coordinates</shortdescription></doc></function><variable name="$coords"
access="private" type="array"><doc><description/><shortdescription>Array of
tridimensional coordinates: (x, y,
z)</shortdescription></doc></variable></class></phpdoc>
Index: pear/Science/Chemistry/doc/class_Science_Chemistry_Element.xml
+++ pear/Science/Chemistry/doc/class_Science_Chemistry_Element.xml
<?xml version="1.0"?><phpdoc><class name="Science_Chemistry_Element" extends=""
undoc="false" access="public"
package="Science_Chemistry"><file>/home/jesus/devel/php/pear/Science/Chemistry/Element.php</file><doc><author
email="[EMAIL PROTECTED]">Jesus M.
Castagnetto</author><description/><shortdescription>Utility class that defines a
chemical element object</shortdescription><version>1.0</version></doc><function
name="Science_Chemistry_Element" undoc="false" access="public"><doc><parameter
name="$sym" type="string">element symbol</parameter><parameter name="$name"
type="string">element name</parameter><parameter name="$num" type="integer">atomic
number</parameter><parameter name="$wgt" type="float">atomic
weight</parameter><parameter name="$mp" type="string">melting point (with
comments)</parameter><parameter name="$bp" type="string">boiling point (with
comments)</parameter><parameter name="$fam" type="string">family</parameter><return
name="" type="object
Science_Chemistry_Element"/><description/><shortdescription>Constructor for the
class</shortdescription></doc></function><function name="isElement" undoc="false"
access="public"><doc><parameter name="$obj" type="object
Science_Chemistry_Element"/><return name=""
type="boolean"/><description/><shortdescription>Checks if an object is a
Science_Chemistry_Element instance</shortdescription></doc></function><variable
name="$symbol" access="public"
type="string"><doc><description/><shortdescription>Element&apos;s symbol, one or
two characters, case sensitive</shortdescription></doc></variable><variable
name="$name" access="public"
type="string"><doc><description/><shortdescription>Element&apos;s
name</shortdescription></doc></variable><variable name="$number" access="public"
type="integer"><doc><description/><shortdescription>Element&apos;s atomic
number</shortdescription></doc></variable><variable name="$weight" access="public"
type="float"><doc><description/><shortdescription>Element&apos;s atomic weight in
a.m.u (atomic mass units)</shortdescription></doc></variable><variable
name="$melting_point" access="public"
type="string"><doc><description/><shortdescription>Element&apos;s melting point,
with comments</shortdescription></doc></variable><variable name="$boiling_point"
access="public" type="string"><doc><description/><shortdescription>Element&apos;s
boiling point, with comments</shortdescription></doc></variable><variable
name="$family" access="public"
type="string"><doc><description/><shortdescription>Element&apos;s
family</shortdescription></doc></variable></class></phpdoc>
Index: pear/Science/Chemistry/doc/class_Science_Chemistry_Macromolecule.xml
+++ pear/Science/Chemistry/doc/class_Science_Chemistry_Macromolecule.xml
<?xml version="1.0"?><phpdoc><class name="Science_Chemistry_Macromolecule" extends=""
undoc="false" access="public"
package="Science_Chemistry"><file>/home/jesus/devel/php/pear/Science/Chemistry/Macromolecule.php</file><doc><author
email="[EMAIL PROTECTED]">Jesus M.
Castagnetto</author><description>Science_Chemistry_Molecule
objects</description><shortdescription>Represents a macromolecule, composed of
several</shortdescription><version>1.0</version></doc><function
name="Science_Chemistry_Macromolecule" undoc="false" access="public"><doc><see
type="var">$name</see><see type="function">initMacromolecule()</see><parameter
name="$name" type="string"/><parameter name="$molecules"
default="&quot;&quot;" type="string"/><return name="" type="object
Science_Chemistry_Macromolecule"/><description>and an optional array of
Science_Chemistry_Molecule objects</description><shortdescription>Constructor for the
class, requires a macromolecule name</shortdescription></doc></function><function
name="initMacromolecule" undoc="false" access="public"><doc><see
type="var">$num_molecules</see><see type="var">$molecules</see><see
type="function">addMolecule()</see><parameter name="$molecules" type="array"/><return
name="" type="boolean"/><description/><shortdescription>Initializes the array of
Science_Chemistry_Molecule objects</shortdescription></doc></function><function
name="addMolecule" undoc="false" access="public"><doc><see
type="function">initMacromolecule()</see><parameter name="$mol" type="object
Science_Chemistry_Molecule"/><return name=""
type="boolean"/><description/><shortdescription>Adds a Science_Chemistry_Molecule
object to the list of molecules in the
macromolecule</shortdescription></doc></function><function name="getMolecules"
undoc="false" access="public"><doc><see type="var">$molecules</see><return name=""
type="array"/><description/><shortdescription>Returns an array of
Science_Chemistry_Molecule objects</shortdescription></doc></function><function
name="isMacromolecule" undoc="false" access="public"><doc><parameter name="$obj"
type="object Science_Chemistry_Macromolecule"/><return name=""
type="boolean"/><description/><shortdescription>Checks if the object is an instance of
Science_Chemistry_Macromolecule</shortdescription></doc></function><function
name="toString" undoc="false" access="public"><doc><return name=""
type="string"/><description>as a multiple molecule XYZ-format
file</description><shortdescription>Returns a string representation of the
macromolecule</shortdescription></doc></function><function name="toCML" undoc="false"
access="public"><doc><parameter name="$title"
default="&quot;macromolecule&quot;" type="string"/><parameter name="$id"
default="&quot;macromol1&quot;" type="string"/><parameter name="$connect"
type="boolean" undoc="true"/><return name="" type="string"/><description>Accepts an
optional id, and a flag to signalprinting of the connection
table</description><shortdescription>Returns a CML representation of the
molecule</shortdescription></doc></function><variable name="$name" access="private"
type="string"><doc><description/><shortdescription>Macromolecule&apos;s
name</shortdescription></doc></variable><variable name="$molecules" access="private"
type="array"><doc><description/><shortdescription>Array of molecular
objects</shortdescription></doc></variable><variable name="$num_molecules"
access="private" type="int"><doc><description/><shortdescription>Number of
molecules/subunits</shortdescription></doc></variable><subclasses><subclass>Science_Chemistry_Macromolecule_PDB</subclass></subclasses></class></phpdoc>
Index: pear/Science/Chemistry/doc/class_Science_Chemistry_Macromolecule_PDB.xml
+++ pear/Science/Chemistry/doc/class_Science_Chemistry_Macromolecule_PDB.xml
<?xml version="1.0"?><phpdoc><class name="Science_Chemistry_Macromolecule_PDB"
extends="Science_Chemistry_Macromolecule" undoc="false" access="public"
package="Science_Chemistry"><file>/home/jesus/devel/php/pear/Science/Chemistry/Macromolecule_PDB.php</file><doc><author
email="[EMAIL PROTECTED]">Jesus M. Castagnetto</author><inherited
src="Array"/><description>Science_Chemistry_Residue_PDB
objects</description><shortdescription>Represents a PDB macromolecule, composed of
several</shortdescription><version>1.0</version></doc><function
name="Science_Chemistry_Macromolecule_PDB" undoc="false" access="public"><doc><see
type="function">parseResidues()</see><parameter name="$pdb" type="string">PDB ID of
the containing file</parameter><parameter name="$records" type="array">Array of lines
comprising the macromolecule</parameter><parameter name="$pdbfile"
default="&quot;&quot;" type="string">reference to the PDB file
object</parameter><return name="" type="object
Science_Chemistry_Macromolecule_PDB"/><description/><shortdescription>Constructor for
the class</shortdescription></doc></function><function name="parseResidues"
undoc="false" access="private"><doc><see
type="function">Science_Chemistry_Macromolecule_PDB()</see><parameter name="$records"
type="array"/><return type="void"/><description/><shortdescription>Makes the array of
residues in the macromolecule</shortdescription></doc></function><inherited
src="Science_Chemistry_Macromolecule"
type="functions"><element>science_chemistry_macromolecule</element><element>initmacromolecule</element><element>addmolecule</element><element>getmolecules</element><element>ismacromolecule</element><element>tostring</element><element>tocml</element></inherited><inherited
src="Science_Chemistry_Macromolecule"
type="variables"><element>$name</element><element>$molecules</element><element>$num_molecules</element></inherited><path><parent>Science_Chemistry_Macromolecule</parent></path><baseclass>Science_Chemistry_Macromolecule</baseclass></class></phpdoc>
Index: pear/Science/Chemistry/doc/class_Science_Chemistry_Molecule.xml
+++ pear/Science/Chemistry/doc/class_Science_Chemistry_Molecule.xml
<?xml version="1.0"?><phpdoc><class name="Science_Chemistry_Molecule" extends=""
undoc="false" access="public"
package="Science_Chemistry"><file>/home/jesus/devel/php/pear/Science/Chemistry/Molecule.php</file><doc><author
email="[EMAIL PROTECTED]">Jesus M.
Castagnetto</author><description/><shortdescription>Base class representing a
Molecule</shortdescription><version>1.0</version></doc><function
name="Science_Chemistry_Molecule" undoc="false" access="public"><doc><see
type="var">$name</see><see type="function">initMolecule()</see><parameter name="$name"
type="string"/><parameter name="$atoms" default="&quot;&quot;"
type="string"/><return name="" type="object
Science_Chemistry_Molecule"/><description>and an optional array of
Science_Chemistry_Atom objects</description><shortdescription>Constructor for the
class, requires a molecule name</shortdescription></doc></function><function
name="initMolecule" undoc="false" access="public"><doc><see
type="var">$num_atoms</see><see type="var">$atoms</see><see
type="function">addAtom()</see><parameter name="$atoms" type="array"/><return name=""
type="boolean"/><description/><shortdescription>Initializes the array of
Science_Chemistry_Atom objects</shortdescription></doc></function><function
name="addAtom" undoc="false" access="public"><doc><see
type="function">initMolecule()</see><parameter name="$atom" type="object
Science_Chemistry_Atom"/><return name=""
type="boolean"/><description/><shortdescription>Adds a Science_Chemistry_Atom object
to the list of atoms in the molecule</shortdescription></doc></function><function
name="getAtoms" undoc="false" access="public"><doc><see type="var">$atoms</see><return
name="" type="array"/><description/><shortdescription>Returns an array of Atom
objects</shortdescription></doc></function><function name="isMolecule" undoc="false"
access="public"><doc><parameter name="$obj" type="object
Science_Chemistry_Molecule"/><return name=""
type="boolean"/><description/><shortdescription>Checks if the object is an instance of
Science_Chemistry_Molecule</shortdescription></doc></function><function
name="toString" undoc="false" access="public"><doc><return name=""
type="string"/><description>as a XYZ-format
file</description><shortdescription>Returns a string representation of the
molecule</shortdescription></doc></function><function name="toCML" undoc="false"
access="public"><doc><parameter name="$title" default="&quot;molecule&quot;"
type="string"/><parameter name="$id" default="&quot;mol1&quot;"
type="string"/><parameter name="$connect" type="boolean" undoc="true"/><return name=""
type="string"/><description>Accepts an optional id, and a flag to signalprinting of
the connection table</description><shortdescription>Returns a CML representation of
the molecule</shortdescription></doc></function><function name="setBondCutoff"
undoc="false" access="public"><doc><see type="var">$BONDCUTOFF</see><see
type="function">getBondCutoff()</see><see
type="function">calcConnectionTable()</see><parameter name="$cutoff"
type="float"/><return name="" type="boolean"/><description/><shortdescription>Sets the
distance cutoff for bond determination</shortdescription></doc></function><function
name="getBondCutoff" undoc="false" access="public"><doc><see
type="var">$BONDCUTOFF</see><see type="function">setBondCutoff()</see><see
type="function">calcConnectionTable()</see><return name=""
type="float"/><description/><shortdescription>Returns the bond cutoff uses to
determine bonds</shortdescription></doc></function><function name="calcDistanceMatrix"
undoc="false" access="public"><doc><return name=""
type="boolean"/><description/><shortdescription>Calculates the atom-atom distance
matrix in Angstroms</shortdescription></doc></function><function
name="printDistanceMatrix" undoc="false" access="public"><doc><return name=""
type="string"/><description/><shortdescription>Prints the atom-atom distance
matrix</shortdescription></doc></function><function name="getDistanceMatrix"
undoc="false" access="public"><doc><return name=""
type="array"/><description/><shortdescription>Returns the atom-atom distance
matrix</shortdescription></doc></function><function name="calcConnectionTable"
undoc="false" access="public"><doc><return name=""
type="boolean"/><description/><shortdescription>Calculates the connection table for
the molecule</shortdescription></doc></function><function name="printConnectionTable"
undoc="false" access="public"><doc><return name=""
type="boolean"/><description/><shortdescription>Prints the molecule&apos;s
connection table</shortdescription></doc></function><function
name="getConnectionTable" undoc="false" access="public"><doc><return name=""
type="array"/><description>e.g. array ( array ($atomobj1, $atomobj2, $distance ), ...
)</description><shortdescription>Returns an array of connected atoms and their bond
distance</shortdescription></doc></function><variable name="$name" access="public"
type="string">&quot;&quot;<doc><description/><shortdescription>Molecule
name</shortdescription></doc></variable><variable name="$num_atoms" access="public"
type="integer"><doc><see
type="function">initMolecule()</see><description/><shortdescription>Number of atoms in
the molecule</shortdescription></doc></variable><variable name="$atoms"
access="private" type="array">array()<doc><see
type="function">initMolecule()</see><description/><shortdescription>Array of atom
objects in the molecule</shortdescription></doc></variable><variable
name="$dist_matrix" access="private" type="array">array()<doc><see
type="function">calcDistanceMatrix()</see><description/><shortdescription>Atom-Atom
distance matrix</shortdescription></doc></variable><variable name="$conn_table"
access="private" type="array">array()<doc><see
type="function">calcConnectionTable()</see><description/><shortdescription>Atom-Atom
connection (bond) table</shortdescription></doc></variable><variable
name="$BONDCUTOFF" access="private" type="float">1.8<doc><see
type="function">setBondCutoff()</see><see type="function">getBondCutoff()</see><see
type="function">calcConnectionTable()</see><description/><shortdescription>Distance
cutoff for bond
estimation</shortdescription></doc></variable><subclasses><subclass>Science_Chemistry_Molecule_XYZ</subclass><subclass>Science_Chemistry_Residue_PDB</subclass></subclasses></class></phpdoc>
Index: pear/Science/Chemistry/doc/class_Science_Chemistry_Molecule_XYZ.xml
+++ pear/Science/Chemistry/doc/class_Science_Chemistry_Molecule_XYZ.xml
<?xml version="1.0"?><phpdoc><class name="Science_Chemistry_Molecule_XYZ"
extends="Science_Chemistry_Molecule" undoc="false" access="public"
package="Science_Chemistry"><file>/home/jesus/devel/php/pear/Science/Chemistry/Molecule_XYZ.php</file><doc><author
email="[EMAIL PROTECTED]">Jesus M. Castagnetto</author><inherited
src="Array"/><overriden src="Array"/><description/><shortdescription>Base class
representing a Molecule from a XYZ format
file</shortdescription><version>1.0</version></doc><function
name="Science_Chemistry_Molecule_XYZ" undoc="false" access="public"><doc><see
type="function">parseXYZ()</see><parameter name="$xyzdata"
default="&quot;&quot;" type="string"/><parameter name="$src"
default="&quot;file&quot;" type="string">one of &quot;file&quot; or
&quot;string&quot;</parameter><return name="" type="object
Science_Chemistry_Molecule_XYZ"/><description>the data and its source. Possible values
for $src: &quot;file&quot;,
&quot;string&quot;</description><shortdescription>Constructor for the class,
accepts 2 optional parameters:</shortdescription></doc></function><function
name="parseXYZ" undoc="false" access="public"><doc><see
type="function">Science_Chemistry_Molecule_XYZ()</see><parameter name="$xyzdata"
type="string"/><parameter name="$src" type="string"/><return name=""
type="boolean"/><description/><shortdescription>method that does the parsing of the
XYZ data itself</shortdescription></doc></function><function name="parseAtom"
undoc="false" access="private"><doc><see type="function">parseXYZ()</see><parameter
name="$line" type="string"/><return name="" type="object
Science_Chemistry_Atom">@acess public</return><description/><shortdescription>Parses
an XYZ atom record</shortdescription></doc></function><function name="toString"
undoc="true" access="public"><doc><return name="" type="string"/><overriden
src="Science_Chemistry_Molecule"/><description>Overrides parent
Science_Chemistry_Molecule::toString() method</description><shortdescription>Generates
a string representation of the XYZ
molecule</shortdescription></doc></function><variable name="$energy" access="public"
type="float"><doc><description/><shortdescription>Energy of the molecule. Optional
value in XYZ file format.</shortdescription></doc></variable><inherited
src="Science_Chemistry_Molecule"
type="functions"><element>science_chemistry_molecule</element><element>initmolecule</element><element>addatom</element><element>getatoms</element><element>ismolecule</element><element>tocml</element><element>setbondcutoff</element><element>getbondcutoff</element><element>calcdistancematrix</element><element>printdistancematrix</element><element>getdistancematrix</element><element>calcconnectiontable</element><element>printconnectiontable</element><element>getconnectiontable</element></inherited><inherited
src="Science_Chemistry_Molecule"
type="variables"><element>$name</element><element>$num_atoms</element><element>$atoms</element><element>$dist_matrix</element><element>$conn_table</element><element>$bondcutoff</element></inherited><path><parent>Science_Chemistry_Molecule</parent></path><baseclass>Science_Chemistry_Molecule</baseclass></class></phpdoc>
Index: pear/Science/Chemistry/doc/class_Science_Chemistry_PDBFile.xml
+++ pear/Science/Chemistry/doc/class_Science_Chemistry_PDBFile.xml
<?xml version="1.0"?><phpdoc><class name="Science_Chemistry_PDBFile" extends=""
undoc="false" access="public"
package="Science_Chemistry"><file>/home/jesus/devel/php/pear/Science/Chemistry/PDBFile.php</file><doc><author
email="[EMAIL PROTECTED]">Jesus M.
Castagnetto</author><description/><shortdescription>Represents a PDB file, composed of
one or more Science_Chemistry_Macromolecule_PDB
objects</shortdescription><version>1.0</version></doc><function
name="Science_Chemistry_PDBFile" undoc="false" access="public"><doc><see
type="var">$pdb</see><see type="var">$file</see><parameter name="$filename"
type="string"/><return name="" type="object
PDBFile">;</return><description/><shortdescription>Constructor for the class, requires
a PDB filename</shortdescription></doc></function><function name="parseFile"
undoc="false" access="private"><doc><parameter name="$arr" type="array">array of
lines</parameter><return type="void"/><description/><shortdescription>Makes the arrays
of all present PDB record types</shortdescription></doc></function><function
name="toCML" undoc="false" access="public"><doc><return name=""
type="string"/><description>TODO</description><shortdescription>Returns a CML
representation of the PDB file</shortdescription></doc></function><variable
name="$pdb" access="private" type="string"><doc><description/><shortdescription>PDB
ID</shortdescription></doc></variable><variable name="$file" access="private"
type="string"><doc><description/><shortdescription>Full path to PDB
file</shortdescription></doc></variable><variable name="$date" access="private"
type="string"><doc><description/><shortdescription>PDB file&apos;s
date</shortdescription></doc></variable><variable name="$class" access="private"
type="string"><doc><description/><shortdescription>PDB macromolecule(s)
class</shortdescription></doc></variable><variable name="$meta" access="private"
type="array"><doc><description/><shortdescription>Array of meta
records</shortdescription></doc></variable><variable name="$macromolecules"
access="private" type="array"><doc><description/><shortdescription>Array of
macromolecular objects</shortdescription></doc></variable><variable
name="$num_macromolecules" access="private"
type="int"><doc><description/><shortdescription>Number of
molecules/subunits</shortdescription></doc></variable></class></phpdoc>
Index: pear/Science/Chemistry/doc/class_Science_Chemistry_PDBParser.xml
+++ pear/Science/Chemistry/doc/class_Science_Chemistry_PDBParser.xml
<?xml version="1.0"?><phpdoc><class name="Science_Chemistry_PDBParser" extends=""
undoc="false" access="public"
package="Science_Chemistry"><file>/home/jesus/devel/php/pear/Science/Chemistry/PDBParser.php</file><doc><author
email="[EMAIL PROTECTED]">Jesus M. Castagnetto</author><description>each
containing an array of atoms&lt;br&gt;Useful when dealing with big PDB files,
where using the Science_Chemistry_PDBFileclass will generate out of memory
errors.</description><shortdescription>A self-contained class to parse a PDB file into
an array of residues</shortdescription><version>1.0</version></doc><function
name="Science_Chemistry_PDBParser" undoc="false" access="public"><doc><see
type="function">parseResidues()</see><parameter name="$filename" type="string">PDB
filename</parameter><parameter name="$multi" default="false" type="boolean">whether to
parse all models in a multi-model file</parameter><parameter name="$meta"
default="false" type="boolean">whether to store the PDB file meta
information</parameter><parameter name="$full" default="false" type="boolean">whether
to store the full set of fields per atom</parameter><return name="" type="object
PDBParser"/><description/><shortdescription>Constructor for the class, requires a PDB
filename</shortdescription></doc></function><function name="parseResidues"
undoc="false" access="private"><doc><see type="function">parseAtom()</see><parameter
name="$records" type="array"/><parameter name="$full" type="boolean">whether to store
the full set of fields per atom</parameter><return
type="void"/><description/><shortdescription>Makes the array of residues in the
macromolecule</shortdescription></doc></function><function name="parseAtom"
undoc="false" access="private"><doc><see
type="function">parseResidues()</see><parameter name="$atomrec" type="string">PDB atom
record</parameter><parameter name="$full" type="boolean">whether to store the full set
of fields per atom</parameter><parameter name="&$atomname" undoc="true"/><return
type="void"/><description/><shortdescription>Parses an atom record into an associative
array</shortdescription></doc></function><function name="getResidueList" undoc="false"
access="public"><doc><see type="var">$macromolecules</see><parameter name="$macromol"
type="integer">Index of the macromolecule in the $macromolecules
array</parameter><parameter name="$resname" type="string">Residue name, e.g. HIS, CYS,
etc.</parameter><return name="" type="array">list of residues with the requested
name</return><description>from the indicated macromolecule
index</description><shortdescription>Returns an array of residues with a particular
name</shortdescription></doc></function><variable name="$pdb" access="private"
type="string"><doc><description/><shortdescription>PDB
ID</shortdescription></doc></variable><variable name="$file" access="private"
type="string"><doc><description/><shortdescription>Full path to PDB
file</shortdescription></doc></variable><variable name="$date" access="private"
type="unknown"><doc><description/><shortdescription>PDB file&apos;s
date</shortdescription></doc></variable><variable name="$class" access="private"
type="string"><doc><description/><shortdescription>PDB macromolecule(s)
class</shortdescription></doc></variable><variable name="$macromolecules"
access="private" type="array"><doc><description/><shortdescription>Array of
macromolecules</shortdescription></doc></variable><variable name="$num_macromolecules"
access="private" type="int"><doc><description/><shortdescription>Number of
macromolecules</shortdescription></doc></variable></class></phpdoc>
Index: pear/Science/Chemistry/doc/class_Science_Chemistry_Periodic_Table.xml
+++ pear/Science/Chemistry/doc/class_Science_Chemistry_Periodic_Table.xml
<?xml version="1.0"?><phpdoc><class name="Science_Chemistry_Periodic_Table" extends=""
undoc="false" access="public"
package="Science_Chemistry"><file>/home/jesus/devel/php/pear/Science/Chemistry/Periodic_Table.php</file><doc><author
email="[EMAIL PROTECTED]">Jesus M.
Castagnetto</author><description/><shortdescription>Utility class that defines a
Periodic Table of elements</shortdescription><version>1.0</version></doc><function
name="getElement" undoc="false" access="public"><doc><parameter name="$symbol"
type="string"/><return name="" type="object
Science_Chemistry_Element"/><description/><shortdescription>Returns a
Science_Chemistry_Element object correspoding to the symbol (case
sensitive)</shortdescription></doc></function><function name="getElementFamily"
undoc="false" access="public"><doc><parameter name="$family" type="string"/><return
name="" type="array">Science_Chemistry_Element
objects</return><description/><shortdescription>Returns an array of
Science_Chemistry_Element objects belonging to an element
family</shortdescription></doc></function><function name="initTable" undoc="false"
access="public"><doc><return type="void"/><description/><shortdescription>Initializes
the Periodic Table array</shortdescription></doc></function><variable
name="$periodic_table" access="public"
type="array">array()<doc><description/><shortdescription>The associative array
containing the chemical elements</shortdescription></doc></variable></class></phpdoc>
Index: pear/Science/Chemistry/doc/class_Science_Chemistry_Residue_PDB.xml
+++ pear/Science/Chemistry/doc/class_Science_Chemistry_Residue_PDB.xml
<?xml version="1.0"?><phpdoc><class name="Science_Chemistry_Residue_PDB"
extends="Science_Chemistry_Molecule" undoc="false" access="public"
package="Science_Chemistry"><file>/home/jesus/devel/php/pear/Science/Chemistry/Residue_PDB.php</file><doc><author
email="[EMAIL PROTECTED]">Jesus M. Castagnetto</author><inherited
src="Array"/><description/><shortdescription>Represents a PDB
residue</shortdescription><version>1.0</version></doc><function
name="Science_Chemistry_Residue_PDB" undoc="false" access="public"><doc><parameter
name="$pdb" type="string">PDB if of the protein/nucleic
acid/etc.</parameter><parameter name="$atomrec_arr" type="array">Array of PDB atom
record lines</parameter><parameter name="$macromol" default="&quot;&quot;"
type="string">reference to the containing macromolecule</parameter><return name=""
type="object
Science_Chemistry_Residue_PDB"/><description/><shortdescription>Constructor for the
class</shortdescription></doc></function><function name="calcGeomParams" undoc="true"
access="private"><doc><return type="void"/></doc></function><function
name="getGeomParams" undoc="true" access="private"><doc><parameter name="$param"
undoc="true"/><return type="void"/></doc></function><variable name="$seq_num"
access="private" type="integer"><doc><description/><shortdescription>PDB Residue
sequence number</shortdescription></doc></variable><variable name="$chain"
access="private" type="string"><doc><description/><shortdescription>PDB Residue
chain</shortdescription></doc></variable><variable name="$id" access="private"
type="string"><doc><description>$id =
&quot;$name:$seq_num:$chain&quot;</description><shortdescription>PDB Residue
ID</shortdescription></doc></variable><variable name="$pdb" access="private"
type="string"><doc><description>this residue</description><shortdescription>PDB ID for
the protein that contains</shortdescription></doc></variable><variable name="$VALID"
access="public" type="boolean">false<doc><description/><shortdescription>If the PDB
residue object has been initialized</shortdescription></doc></variable><variable
name="$macromol" access="public" type="object
Science_Chemistry_Macromolecule_PDB"><doc><description>to which this residue
belongs</description><shortdescription>Reference to the
protein</shortdescription></doc></variable><inherited src="Science_Chemistry_Molecule"
type="functions"><element>science_chemistry_molecule</element><element>initmolecule</element><element>addatom</element><element>getatoms</element><element>ismolecule</element><element>tostring</element><element>tocml</element><element>setbondcutoff</element><element>getbondcutoff</element><element>calcdistancematrix</element><element>printdistancematrix</element><element>getdistancematrix</element><element>calcconnectiontable</element><element>printconnectiontable</element><element>getconnectiontable</element></inherited><inherited
src="Science_Chemistry_Molecule"
type="variables"><element>$name</element><element>$num_atoms</element><element>$atoms</element><element>$dist_matrix</element><element>$conn_table</element><element>$bondcutoff</element></inherited><path><parent>Science_Chemistry_Molecule</parent></path><baseclass>Science_Chemistry_Molecule</baseclass></class></phpdoc>
Index: pear/Science/Chemistry/doc/classtree_Science_Chemistry_Atom.xml
+++ pear/Science/Chemistry/doc/classtree_Science_Chemistry_Atom.xml
<?xml version="1.0"?><phpdoc><classtree baseclass="Science_Chemistry_Atom"><class
name="Science_Chemistry_Atom_PDB"></class><class
name="Science_Chemistry_Atom"><subclass>Science_Chemistry_Atom_PDB</subclass></class></classtree></phpdoc>
Index: pear/Science/Chemistry/doc/classtree_Science_Chemistry_Coordinates.xml
+++ pear/Science/Chemistry/doc/classtree_Science_Chemistry_Coordinates.xml
<?xml version="1.0"?><phpdoc><classtree
baseclass="Science_Chemistry_Coordinates"><class
name="Science_Chemistry_Coordinates"></class></classtree></phpdoc>
Index: pear/Science/Chemistry/doc/classtree_Science_Chemistry_Element.xml
+++ pear/Science/Chemistry/doc/classtree_Science_Chemistry_Element.xml
<?xml version="1.0"?><phpdoc><classtree baseclass="Science_Chemistry_Element"><class
name="Science_Chemistry_Element"></class></classtree></phpdoc>
Index: pear/Science/Chemistry/doc/classtree_Science_Chemistry_Macromolecule.xml
+++ pear/Science/Chemistry/doc/classtree_Science_Chemistry_Macromolecule.xml
<?xml version="1.0"?><phpdoc><classtree
baseclass="Science_Chemistry_Macromolecule"><class
name="Science_Chemistry_Macromolecule_PDB"></class><class
name="Science_Chemistry_Macromolecule"><subclass>Science_Chemistry_Macromolecule_PDB</subclass></class></classtree></phpdoc>
Index: pear/Science/Chemistry/doc/classtree_Science_Chemistry_Molecule.xml
+++ pear/Science/Chemistry/doc/classtree_Science_Chemistry_Molecule.xml
<?xml version="1.0"?><phpdoc><classtree baseclass="Science_Chemistry_Molecule"><class
name="Science_Chemistry_Molecule_XYZ"></class><class
name="Science_Chemistry_Residue_PDB"></class><class
name="Science_Chemistry_Molecule"><subclass>Science_Chemistry_Molecule_XYZ</subclass><subclass>Science_Chemistry_Residue_PDB</subclass></class></classtree></phpdoc>
Index: pear/Science/Chemistry/doc/classtree_Science_Chemistry_PDBFile.xml
+++ pear/Science/Chemistry/doc/classtree_Science_Chemistry_PDBFile.xml
<?xml version="1.0"?><phpdoc><classtree baseclass="Science_Chemistry_PDBFile"><class
name="Science_Chemistry_PDBFile"></class></classtree></phpdoc>
Index: pear/Science/Chemistry/doc/classtree_Science_Chemistry_PDBParser.xml
+++ pear/Science/Chemistry/doc/classtree_Science_Chemistry_PDBParser.xml
<?xml version="1.0"?><phpdoc><classtree baseclass="Science_Chemistry_PDBParser"><class
name="Science_Chemistry_PDBParser"></class></classtree></phpdoc>
Index: pear/Science/Chemistry/doc/classtree_Science_Chemistry_Periodic_Table.xml
+++ pear/Science/Chemistry/doc/classtree_Science_Chemistry_Periodic_Table.xml
<?xml version="1.0"?><phpdoc><classtree
baseclass="Science_Chemistry_Periodic_Table"><class
name="Science_Chemistry_Periodic_Table"></class></classtree></phpdoc>
Index: pear/Science/Chemistry/doc/packageelementlist_Science_Chemistry.html
+++ pear/Science/Chemistry/doc/packageelementlist_Science_Chemistry.html
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<title>Chemical classes - Frameset Packageelements</title>
</head>
<body>
<table width="100%">
<tr>
<td colspan=3 align="left" valign="top">
<h3>Packagelist</h3>
</td>
</tr>
<tr>
<td colspan="3" align="left"
valign="top"><h4>Science_Chemistry</h4></td>
</tr>
<tr>
<td align="left" valign="top"> </td>
<td colspan="2" align="left" valign="top"><h5>Classes</h5></td>
</tr>
<tr>
<td colspan="2" align="left" valign="top"> </td>
<td align="left" valign="top"><a href="Chem_Atom_PDB.html"
target="main">Chem_Atom_PDB</a></td>
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