see
https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.4/Version%2014.4.4
New features include:
-- more SMILES/SMARTS options, including OpenSMILES, Strict Hueckel 4+2,
and MMFF94 options.
show smiles/open
show smiles/strict
show smiles/mmff94
show smiles/noaromatic
InChI.js library for JSmol
-- more polyhedra options
-- very simple CIF format
Jmol.___JmolVersion="14.5.4_2016.03.13"
new feature: polyhedra POINTS x.y
-- adds variable size spherical points at corners of polyhedra
-- color is that of element, or black
new feature: show SMILES/xxxx
-- xxxx = open, strict, openstrict, mmff94
new feature: show chemical NAME
-- singular "name" gives just the first name; "names" gives full list
new feature: full implementation of OpenSMILES aromatic model
new feature: {*}.find("SMILES/open")
-- generates OpenSMILES string for selected atoms
-- applies OpenSMILES aromaticity rules for 5-, 6-, and 7-membered rings
-- not chemical -- allows exocyclic c=C bonds and [nH] in 6-membered rings
-- also adds atom class if property_atomClass is nonzero
-- for example:
$ load $2-butanol
$ @2.property_atomclass=2
$ @3.property_atomclass=3
$ @5.property_atomclass=5
$ print {*}.find("smiles/open")
C[C@H:2]([OH:5])[CH2:3]C
new feature: /open option for smiles.find("SMILES", pattern)
-- applies OpenSMILES model of aromaticity
-- finds aromaticity-normalized pattern "in" aromaticity-normalized smiles
-- can be after SMILES or as beginning of pattern
$ print "OC1=CC(N)=CC=C1".find("SMILES","NC1=CC(O)=CC=C1")
0
$ print "OC1=CC(N)=CC=C1".find("SMILES/open","NC1=CC(O)=CC=C1")
8
$ print "OC1=CC(N)=CC=C1".find("SMILES","/open/NC1=CC(O)=CC=C1")
8
new feature: compare("smile1","/open/smiles2")
-- applies OpenSMILES model of aromaticity
-- checks for match of atom class if present (default value 0 matches "not
present")
-- does aromaticity normalization on both strings
$ print compare("OC1=CC(N)=CC=C1", "NC1=CC(O)=CC=C1", "isomer")
CONSTITUTIONAL ISOMERS
$ print compare("OC1=CC(N)=CC=C1", "/open/NC1=CC(O)=CC=C1", "isomer")
IDENTICAL
new feature: {*}.find("SMILES/strict")
-- generates OpenSMILES string for selected atoms
-- applies standard Hueckel aromaticity rules for 5-, 6-, and 7-membered
rings
-- does not allow exocyclic c=C bonds or [nH] in 6-membered rings
-- does not create atom classes
-- also for compare() and search()
new feature: {*}.find("SMILES/open strict")
-- same as just /strict, but also generates atom classes if present as
property_atomClass
-- also for compare() and search()
new feature: {*}.find("SMILES/mmff94")
-- applies a very STRICT, chemically meaningful Hueckel 4+2 Rule
-- adds allowance for only a 1-electron contribution to 6-membered rings
(three double bonds)
-- also for compare() and search()
new feature: optional processing of OpenSMILES [CH2:002] ":<n>" atom class.
-- positive integer value only
-- checks the atom property property_atomclass
-- for SMARTS, [:0] means "without an atomclass"
-- for SMARTS, [!:0] means "any non-zero atomclass"
-- for SMARTS, same as [$(select property_atomclass=n)]
-- only enabled with Jmol SMILES directive "/open/"; otherwise ignored
-- for example:
$ load $2-butanol
$ show smiles
C[C@H](O)CC
$ @2.property_atomclass=2
$ @3.property_atomclass=3
$ @5.property_atomclass=5
$ select *
15 atoms selected
$ select on search("/open/[:3]")
1 atoms selected
$ select on search("/open/[!:3]")
14 atoms selected
$ select on search("/open/[:0]")
12 atoms selected
$ select on search("/open/[!:0]")
3 atoms selected
$ select on search("/open/[!:3 & !:0]")
2 atoms selected
new feature: UNITCELL TRANSFORM @m4x4
-- direct 4x4 matrix transformation of a unit cell
new feature: calculate symmetry polyhedra {atomset}
-- selectively calculates polyhedra.
-- for example: calculate symmetry polyhedra {polyhedra(4)}
new feature: calculate symmetry polyhedra id
-- selectively calculates polyhedra for a given ID.
-- for example: calculate symmetry polyhedra "poly1"
new feature: atom set can be specified in polyhedra() function:
-- print {2.1}.polyhedra(3)
-- print {2.1}.polyhedra("....polySMILES string...")
new feature: WRITE MOL67 xxx.mol
-- writes MOL format with bonds of type 6 or 7 (aromatic single/double;
rarely significant)
new feature: (JSmol) standard InChI generator (see inchi.htm, inchi/*)
-- JavaScript library for generation of InChIs
-- runs completely in JavaScript
-- equivalent to SHOW CHEMICAL stdinchi
-- about 900 KB
bug fix: CIF reader _atom_site_cartn_x incompatible with _geom_bond
-- this fix now allows Jmol to read very simple CIF files that are
equivalent to unlimited-atom MOL files
-- _ccdc_geom_bond_type is not required, defaulting to S
-- _ccdc_geom_bond_types include S, D, T, Q (quadruple), and A (aromatic)
data_icosahedron
loop_
_atom_site_label
_atom_site_Cartn_x
_atom_site_Cartn_y
_atom_site_Cartn_z
C01 0.0000000000 0.0000000000 9.5105651630
C02 8.5065080835 0.0000000000 4.2532540418
C03 2.6286555606 8.0901699437 4.2532540418
C04 -6.8819096024 5.0000000000 4.2532540418
C05 -6.8819096024 -5.0000000000 4.2532540418
C06 2.6286555606 -8.0901699437 4.2532540418
C07 6.8819096024 5.0000000000 -4.2532540418
C08 -2.6286555606 8.0901699437 -4.2532540418
C09 -8.5065080835 0.0000000000 -4.2532540418
C10 -2.6286555606 -8.0901699437 -4.2532540418
C11 6.8819096024 -5.0000000000 -4.2532540418
C12 0.0000000000 0.0000000000 -9.5105651630
loop_
_geom_bond_atom_site_label_1
_geom_bond_atom_site_label_2
_ccdc_geom_bond_type
C01 C02 S
C01 C03 S
C01 C04 S
C01 C05 S
C01 C06 S
C02 C03 S
C03 C04 S
C04 C05 S
C05 C06 S
...etc...
bug fix: SMILES should not be returned with comments for internal
processing or sending to PubChem or others
bug fix: SHOW chemical SMILES can be off because it was using the name, not
the SMILES string
-- sometimes - e.g. "menthol" - the name has no chirality, but the
structure does (of course).
bug fix: Jmol 14.3.16_2015.09.15 broke first-match-only flag in SMILES
mapping
bug fix: POLYHEDRA when selection halos are on, all have edges
bug fix: moving of polyhedron will fail if corner of polyhedron is an atom
bug fix: macro functions cannot be used later in same script as a MACRO
command
-- presence of MACRO command now removes check for unknown command name
exception
bug fix: Tripos MOL2 reader does not read element symbols properly
bug fix: default write MOL file should not indicate aromatic bond types 6
and 7
-- corrects the fact that these bonds are reserved for queries
-- only affects cases where that bond type has been set (after calculate
aromatic or loading of ligand CIF files
-- examples (reporting "DIASTEREOMERS")
print compare("F/C=C=C=C/F","F/C=C=C=C\\F","isomer")
load $F-C=C=C=C-F;print compare("F/C=C=C=C\\F",{1.1},"isomer")
bug fix: SMILES generator unnecessarily over-expressing double-bond / and
\.
bug fix: Inconsistent use of "DIASTEREOMERS" (preferred) and
"DIASTERIOMERS" (incorrect)
JmolVersion="14.5.3_2016.03.05"
bug fix: SMILES TB trigonal bipyramidal stereochemistry not functional
bug fix: SMILES [@TBn] not recognizing n > 2
bug fix: SMILES OH octahedral stereochemistry error
bug fix: SMILES [@OHn] not recognizing n > 2
bug fix: SMILES SP square planar stereochemistry will report ENANTIOMERS
rather than DIASTEREOMERS
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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