[Jmol-commits] SF.net SVN: jmol:[22666] trunk/Jmol/src/org/jmol/view er/Jmol.properties

[<ha...@us...>]

Revision: 22666
          http://sourceforge.net/p/jmol/code/22666
Author:   hansonr
Date:     2025-05-19 21:08:52 +0000 (Mon, 19 May 2025)
Log Message:
-----------


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	2025-05-13 05:01:20 UTC (rev 22665)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties	2025-05-19 21:08:52 UTC (rev 22666)
@@ -53,14 +53,78 @@
 # FEATURE REQUEST: dock/undock consoles to main window.
 # TODO: allow FIXED to work with MODELKIT MINIMIZE
 
-Jmol.___JmolVersion="16.3.21" // (legacy) also 16.3.22 (swingJS) 
+Jmol.___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
+
+bug fix: write OBJ does not create rockets or vectors
+
+new feature: BCIF, mmCIF, and MMTF file readers auto-detect carbohydrate residues
+ -- uses _chem_comp.type containing "saccharide" 
+ -- for example:
+  
+      load *3kle
+      select carbohydrate
+      print {selected}.group.pivot.keys.join(",")
+
+        GLC,Z9N
+ 
+new feature: getProperty("cifInfo", fname+ ";keys=tag1,tag2,tag3...")
+ -- retrieve CIF file structure for only specific tags
+ -- now exits parsing once all loop data for the given tags are found
+ -- avoids memory overflow in very large mmcif files
+ -- must be complete tags (partial tags can also be found, but won't close reading) 
+ -- for example:
+    var cifinfo = getProperty("cifInfo", fname+ ";keys=_chem_comp.id,_chem_comp.type,_chem_comp.name" ).models[1];
+
+new feature: array.find("xxxx", "index")
+ -- carries out a string search within an array of strings
+ -- returns an array of indexes (1-based) of elements found with this string
+ -- for example:
+ 
+        var cifinfo = getProperty("cifInfo", fname+ ";keys=_chem_comp.id,_chem_comp.type,_chem_comp.name" ).models[1];
+        var ccids = cifinfo._chem_comp_id; // NAG
+        var cctypes = cifinfo._chem_comp_type; // saccharide
+        var ccnames = cifinfo._chem_comp_name; // N-Acetyl...
+        var list = cctypes.find("saccharide", "index");
+        for (var j in list) {
+            var resid = ccids[j];
+            var name = ccnames[j];
+            ...
+        }
+        
+ new feature array.find("xxxx","i|m|v", "index")
+  -- using "i" (case-insenstive) or "m" (match) or "v" (not-present) or some combination of these
+     carries out a REGEX pattern search
+  -- adding "index" returns the index of element
+  
+
+JmolVersion="16.3.21" // (legacy) also 16.3.22 (swingJS) 
+
+bug fix: PDBe *xxxx should not require lower case entry
+
 bug fix: (Legacy JavaScript only) array sorting may fail in script saving.
 
+new feature: more spin space group support
+ - adds     _space_group_spin.rotation_axis_xyz
+   same as  _space_group_spin.rotation_axis
+ - adds support for spin frame with reciprocal lattice a*, b*, c*
+   limitation: any x* in expression turns all x into x*
+   
+new feature: CIF loader for magnetic structures adds filter "spinonly"
+ - only atoms that have spin are read
+ 
+new feature: matrix.array() same as matrix.array
+
+new feature: point(arrayOfArrays) produces array of points
+
 bug fix: OBJ/MTL exporter has inverted Tr (translucency) setting x; should be 1-x
 
 bug fix: Cartesian exporters (IDTF, Maya, OBJ, VRML) not rendering vector cylinders
 
+
 JmolVersion="16.3.19" // (legacy) also 16.3.20 (swingJS) 
 
 bug fix: (JavaScript legacy only) array sorting fails for arrays of arrays and sort(columnNumber);
@@ -3463,19 +3527,40 @@
 
 bug fix: load "" after load DATA .... fails to load string-based file data
 
+new feature: pat = pattern(<smarts string>) 
+ -- compiles a SMARTS pattern for later use.
+ -- example: 
+     var smarts = pattern('NCN')
+
+new feature: atomset.search(pattern)
+ -- carry out a SMARTS search on set of atoms with a precompiled pattern
+     var smarts = pattern('NCN')
+     load $caffeine
+     var atoms = {*}.search(smarts)
+     print atoms
+
 new feature: target = search(atomset)
- - predefines a target for repetitive SMARTS searching
-new feature: pat = pattern(<smarts string>) 
- - compiles a SMARTS pattern for later use.
-new feature: atomset.search(pat)
- - search a set of atoms with a precompiled pattern
+ -- predefines a target for repetitive SMARTS searching
+ -- example: 
+     load $caffeine
+     var target = search({*})
+     print target.search("NCN")
+
+new feature: target.search(stringPattern)
+ -- search a predefined target with a string pattern
+ -- example: 
+     load $caffeine
+     var target = search({*})
+     print target.search("NCN")
+
 new feature: search(target, pattern)
- - search a predefined target with a precompiled pattern
- - example: 
-     x = search({*})
-     y = pattern('CCCC')
-     atoms = {*}.search(y)
-     print search(x, y)
+ -- search a predefined target with a string or precompiled pattern 
+ -- example: 
+     load $caffeine
+     var target = search({*})
+     print target.search("NCN")
+     var smarts = pattern('NCN')
+     print search(target, smarts)
 
 JmolVersion="16.1.5" // (legacy) also 16.1.6 (SwingJS)
 

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.