Nico has released Jmol 11.3.44. This release and related releases 41-43
introduce several new features and fix loads of bugs.
New features:
Jmol Math getProperty() function
--------------------------------
The Jmol math getProperty() function allows access to all getProperty
information fields.
syntax: getProperty(propertyType, qualifier, item, item, item,...)
Examples:
print getProperty("boundboxInfo", "center")
print getProperty("boundboxInfo", "vector")
print getProperty("atomInfo",{atomno=3})
print getproperty("bondInfo",{*},2,"atom1")
print getProperty() # displays list of possibilities
x =
getproperty("polymerinfo",{*},"models",2,"polymers",1,"monomers",39,"atomIndex2")
For many property types, the qualifier is an atom set
If the atom set is not given, those properties default to {visible}
For "stateInfo", the qualifier is string: "fileState", "modelState", etc.
Items may be integers or string-based keys
Integer items follow the rules of Jmol math selectors:
1 first item, 0 last item, -1 next to last item, etc.
.type math function
-------------------
You can now test for the type of a Jmol variable.
x = "this".type # sets x to "string"
direct string replacement
-------------------------
Jmol math allows direct string replacement in select atom expressions:
x = "atomno=3"
select @x # or select @{x}
select @{x + 3} # selects atomno=33
x = array("atomno<10","atomno>20")
select @x # OR of the list elements
select @{x[2]} # just element 2 of x (atomno>20)
select @x[2] # same as [EMAIL PROTECTED]
array-based setting of atom properties
--------------------------------------
Set atom properties using an array instead of a DATA statement:
{*}.x = array(2,3,4,5,6);
{atomno<=3}.color = array("red","green","blue")
{*}.property_mydata = array(1.0,5.5,4.4,3.3);
{atomno < 4}.xyz = array({3 4 5},{4 5 6},{5 6 7})
If the array is shorter than the number of atoms selected, then
only that number of atoms are affected
Setting data from a string
--------------------------
Set atom properties from a space-separated string:
{atomno < 5}.property_mydata = "1.0 5.5 4.4 3.3";
Line continuation with "\"
--------------------------
In scripts, "\" at the end of a line marks a continuation of that line
Expanded boundbox command
-------------------------
The boundbox command has been expanded to allow drawing of the bounding
box around a specified set of atoms. Combined with
getProperty("boundboxInfo") this allows calculation of the bounding
rectangle around any set of atoms.
boundbox {atomExpression} [on|off]
sets the bound box around the specified atom expression
default ON/OFF is to NOT change current setting
boundbox {point or expression} {vector to corner} [on|off]
sets the bound box to be centered with a given size based on a vector to
a corner
boundbox CORNERS {point or expression} {point or expression} [on|off]
sets the bound box to encompass the two corner points
show boundbox
now gives valid boundbox commands and volume
isosurface POINTSPERANGSTROM synonym for RESOLUTION
---------------------------------------------------
just symantics here.
isosurface CAP
--------------
isosurface CAP [plane definition]
caps the isosurface at the designated plane.
Specifically for molecular/solvent-type isosurface.
[plane definition] can be {x y z w} or any combination of
three {x y z} points, draw point references, or atom expressions
Set drawPicking TRUE
--------------------
Reports picking of draw objects as a string equivalent of a JavaScript
array:
[ "draw","[drawID]",[modelIndex],[vertexIndex],[x],[y],[z] ]
This goes to the pickCallback function as the second parameter,
with the third parameter (normally the atomIndex), being -2.
connect {...} {...} AROMATIC AUTO
---------------------------------
Similar to calculate aromatic, except it's isolated to this set of
connections; implicit modifyOnly. Can be used in place of
select *; calculate aromatic
POV-Ray shadows
---------------
Shadows can be activated via noShadows parameter in .pov file
set echo MODEL
--------------
You can now set the echos to be model-specific
set echo [echoID] MODEL [model number]
frame title
-----------
The current frame can be titled. This appears in the bottom left-hand
corner.
frame title "this is the title for THIS frame only"
**** Jmol Embedded Script ****
------------------------------
This phrase is recognized in /* ... */ comments and /** ... **/
super-comment blocks.
if found in text read by the SCRIPT command, ONLY this text is processed
and all other text in the file is ignored.
BUG FIXES:
new label fonts not loaded when labels resized
nuisance "render mesh error" console report
bioshapes visible outside of current visible frame set
selecting atoms of atomsets using [-n] or [0] not working
more natural mouse SHIFT-RIGHT behavior (rotate-z)
select statement comparisons of negative decimal properties to "-1" (not
"-1.0") causes none found
Strings too long in state can cause Eclipse "infinite loop" bug
assigning a negative value to a dataAtomNumberField value caused
BitSet.set() exception
Jmol parameter setting syntax too loose. The following statement was
allowed:
pickCallback = myfunction
OK, so that might look good, but it evaluates to
pickCallback = ""
since the VARIABLE myfunction has not been defined. Solution: Don't
allow the syntax
[jmolParameter] = [Token.identifier]
The following is OK:
[jmolParameter] = "some string"
The following is preferred:
SET [jmolParameter] [value]
antialias with translucent but antialiasTranslucent = false; labels,
text, echos, hover, picking, out of alignment
negative formal charges not being accepted
write coord mol not working
connect (..) (..) # with implicit "single" causes state to use "partial 0"
new frame title and state
select by itself not working; oy. Since at least 11.0
ramachandran/quaternion fix for assignment of structure
isosurfaces not taking their default name properly
small fix for povray cap at back side
overly long titles now again substringed in the popup menu.
memory leak in merge -- models[i].modelSet causes modelSet to not finalize.
quaternion
set xxxCallback not allowed
math operations with bond bitsets; % and + operating on arrays
_set variable definition removed
--
Robert M. Hanson
Professor 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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