Menu
▾
▴
[Jmol-commits] SF.net SVN: jmol:[22671] trunk/Jmol/src/org/jmol/view er/Jmol.properties
|
From: <ha...@us...> - 2025-06-10 14:44:14
|
Revision: 22671
http://sourceforge.net/p/jmol/code/22671
Author: hansonr
Date: 2025-06-10 14:44:12 +0000 (Tue, 10 Jun 2025)
Log Message:
-----------
Jmol.___JmolVersion="16.3.27" // (legacy) also 16.3.28 (swingJS)
bug fix: jsmol.js (legacy only) problem with incomplete initialization of applet gives 0-size image error
bug fix: CIF reading and processing of operations can fail with 2/3+x rather than the usual x+2/3
new feature: spinCIF and FINDSPINGROUP output readers
--
note: use of variables starting with $ is not documented.
These are object references
draw ID d... :
$d the center of this drawing
$d[1] the first point
for example:
$ draw id p plane {0 0 0} {1 1 1} {1 0 0}
$ print $p
{0.75 0.25 0.25}
$ print $p[1]
{0.0 0.0 0.0}
$ print $p[2]
{1.0 1.0 1.0}
$ print $p[3]
{1.5 0.5 0.5}
$ draw id p symop 3
print $p
new feature: symop(@2, "basis") or symop(@@2, "basis") {1.1}.symop(@2)
-- returns the single-atom bitset of the basis atom for this atom
(the first atom that is symmetry-equivalent with this atom, as part
of the asymmetric unit)
-- optional choice of specific model (@@2 for current)
-- essentially the same as {this && site=@{@@2.site}}[1] but simpler
-- the {1.1}.symop(@2) form is useful if checking a model that is not the current one
new feature: symop(@@2, "cif2")
-- returns a simple CIF-2 format descriptor of all operations that
transform the basis atom for the site to this atom's position
with the specific translation needed, in the form:
<id> [tx ty tz]
For example,
$ load =ams/quartz 1 packed
$ print symop(@@3, "cif2")
2 [0 0 0]
3 [0 0 0]
new feature: atom.spin
-- for spin space groups only
-- reports the index (1-based) of the spin operation for this atom
new feature: _M.spinList
-- list of spin operations (such as "u,-v,w")
-- _M.spinList[atom.spin] gets the operation string.
-- This list is collected during processing of the spinCIF file.
bug fix: SMARTS searching not distinguishing /open/ from /openstrict/ properly
-- /open/ should not check aromatic ring planarity, while /openstrict/ should.
-- SMARTS options include:
Jmol 0D: (not settable) just check bonding; no planarity issue in 0D (that is, SMARTS against SMILES)
Jmol default 3D: /strict/ check bonding and planarity, using "chemist's" Hueckel rules
OpenSMILES 0D or 3D: /open/, just check bonding using OpenSMILES Hueckel rules;
OpenSMILES 3D: /openstrict/ check bonding and planarity, using OpenSMILES Hueckel rules
turn off aromaticity checks: /noaromatic/ -- just disregard aromatic aspects entirely
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2025-06-02 08:28:34 UTC (rev 22670)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2025-06-10 14:44:12 UTC (rev 22671)
@@ -53,8 +53,120 @@
# FEATURE REQUEST: dock/undock consoles to main window.
# TODO: allow FIXED to work with MODELKIT MINIMIZE
-Jmol.___JmolVersion="16.3.23" // (legacy) also 16.3.24 (swingJS)
+Jmol.___JmolVersion="16.3.27" // (legacy) also 16.3.28 (swingJS)
+bug fix: jsmol.js (legacy only) problem with incomplete initialization of applet gives 0-size image error
+
+bug fix: CIF reading and processing of operations can fail with 2/3+x rather than the usual x+2/3
+
+new feature: spinCIF and FINDSPINGROUP output readers
+ --
+note: use of variables starting with $ is not documented.
+ These are object references
+ draw ID d... :
+ $d the center of this drawing
+ $d[1] the first point
+ for example:
+ $ draw id p plane {0 0 0} {1 1 1} {1 0 0}
+ $ print $p
+ {0.75 0.25 0.25}
+ $ print $p[1]
+ {0.0 0.0 0.0}
+ $ print $p[2]
+ {1.0 1.0 1.0}
+ $ print $p[3]
+ {1.5 0.5 0.5}
+ $ draw id p symop 3
+ print $p
+
+new feature: symop(@2, "basis") or symop(@@2, "basis") {1.1}.symop(@2)
+ -- returns the single-atom bitset of the basis atom for this atom
+ (the first atom that is symmetry-equivalent with this atom, as part
+ of the asymmetric unit)
+ -- optional choice of specific model (@@2 for current)
+ -- essentially the same as {this && site=@{@@2.site}}[1] but simpler
+ -- the {1.1}.symop(@2) form is useful if checking a model that is not the current one
+
+new feature: symop(@@2, "cif2")
+ -- returns a simple CIF-2 format descriptor of all operations that
+ transform the basis atom for the site to this atom's position
+ with the specific translation needed, in the form:
+
+ <id> [tx ty tz]
+
+ For example,
+
+ $ load =ams/quartz 1 packed
+ $ print symop(@@3, "cif2")
+
+ 2 [0 0 0]
+ 3 [0 0 0]
+
+new feature: atom.spin
+ -- for spin space groups only
+ -- reports the index (1-based) of the spin operation for this atom
+
+new feature: _M.spinList
+ -- list of spin operations (such as "u,-v,w")
+ -- _M.spinList[atom.spin] gets the operation string.
+ -- This list is collected during processing of the spinCIF file.
+
+bug fix: SMARTS searching not distinguishing /open/ from /openstrict/ properly
+ -- /open/ should not check aromatic ring planarity, while /openstrict/ should.
+ -- SMARTS options include:
+
+ Jmol 0D: (not settable)\xA0 just check bonding; no planarity issue in 0D (that is, SMARTS against SMILES)
+ Jmol default 3D: /strict/ check bonding and planarity, using "chemist's" Hueckel rules
+ OpenSMILES 0D or 3D: /open/, just check bonding using OpenSMILES Hueckel rules;
+ OpenSMILES 3D: /openstrict/ check bonding and planarity, using OpenSMILES Hueckel rules
+ turn off aromaticity checks: /noaromatic/ -- just disregard aromatic aspects entirely
+
+
+JmolVersion="16.3.25" // (legacy) also 16.3.26 (swingJS)
+
+bug fix: symop(3,"array") should return .draw script with id "sym_", not "array"
+
+bug fix: spin space group loading updated for too many atoms
+
+new feature: PNG, JPG and JPG64 image encoders allow for specified DPI (dots per inch)
+ -- indicated quality > 90 is interpreted as DPI
+ -- PNG values from 1-9 are still (rarely used?) compression options (2 is default for 9 < quality < 90)
+ -- JPG values from 1-90 are still JPG image quality
+ (default 100 - "highest quality" for JPG; 75 for JPG64)
+ -- quality as DPI sets the quality to its default value
+ -- default DPI is now 300 dpi
+ -- quality comes after any image size indication
+ -- for example:
+
+ write PNGJ 600 "xxxx.png"
+
+ OK PNGJ 126817 xxxx.png; quality=2; DPI=600; width=797; height=558
+
+ write IMAGE 300 400 600 "t.jpg"
+
+ OK JPG 65864 t.jpg; quality=100; DPI=600; width=300; height=400
+
+new feature: spinop(3,"uvw")
+ -- generates spin-operator u,v,w string format
+
+new feature: x = matrix(stringMatrix)
+ -- allows stringMatrix to contain functions and math expressions
+ -- used in spinCIF reader:
+
+ mh2c = matrix("[[1,1/sqrt(3),0],[0,2/sqrt(3),0],[0,0,1]]");
+
+new feature: delay (seconds or milliseconds) scriptToRun
+ -- adds optional script to run after this time
+ -- halts currently running script
+
+new feature: x = matrix(axis,angle)
+ -- generates the transformation matrix associated with an axis-angle (angle in degrees)
+
+new feature: VASP POSCAR reader reads # MAGMOM line for magnetic moments
+ -- feature of files created by FINDSYMGROUP
+
+JmolVersion="16.3.23" // (legacy) also 16.3.24 (swingJS)
+
bug fix: load *xxxx should use lower case for retrieving mmCIF files from PDBe.
bug fix: struts do not connect directly to rockets or trace
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
