Revision: 20767
http://sourceforge.net/p/jmol/code/20767
Author: hansonr
Date: 2015-09-09 12:52:37 +0000 (Wed, 09 Sep 2015)
Log Message:
-----------
TODO: Although isolated polyhedra are working in SMARTS searching,
for a SMILES representation, it will be important to allow a given atom
to be in more than one polyhedron (edge- or face-connected polyhedra).
But then that will require to references to the same atom. The solution
is probabably something like [(3)], indicating that this atom is equated
with
another in the SMILES string:
[Fe][O(1)].[Fe][O(1)]
then bond references to that oxygen from some other source would be to
both?
....C(2) ....C(4) ???
Jmol.___JmolVersion="14.3.16_2015.09.09"
code: javajs.util reconciled with swingjs project
bug fix: polyhedra.stereoSmiles --> polyhedra.polySmiles; central atom added in
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/shapespecial/Polyhedron.java
trunk/Jmol/src/org/jmol/smiles/SmilesMatcher.java
trunk/Jmol/src/org/jmol/smiles/SmilesParser.java
trunk/Jmol/src/org/jmol/smiles/SmilesStereo.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/shapespecial/Polyhedron.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapespecial/Polyhedron.java 2015-09-09
11:50:30 UTC (rev 20766)
+++ trunk/Jmol/src/org/jmol/shapespecial/Polyhedron.java 2015-09-09
12:52:37 UTC (rev 20767)
@@ -36,7 +36,7 @@
private V3[] normals;
private short[] normixes;
- public String smiles, smarts, stereoSmiles;
+ public String smiles, smarts, polySmiles;
private SymmetryInterface pointGroup;
private Float volume;
@@ -89,8 +89,8 @@
info.put("smarts", smarts);
if (smiles != null)
info.put("smiles", smiles);
- if (stereoSmiles != null)
- info.put("stereoSmiles", stereoSmiles);
+ if (polySmiles != null)
+ info.put("polySmiles", polySmiles);
if (pointGroup != null)
info.put("pointGroup", pointGroup.getPointGroupName());
Object energy = vwr.ms.getInfo(centralAtom.mi, "Energy");
@@ -181,7 +181,7 @@
if (smarts == null) {
smarts = sm.polyhedronToSmiles(centralAtom, faces, nVertices, null,
JC.SMILES_TOPOLOGY | JC.SMILES_NOSTEREO, null);
smiles = sm.polyhedronToSmiles(centralAtom, faces, nVertices,
vertices, JC.SMILES_TYPE_SMILES | JC.SMILES_NOSTEREO, null);
- stereoSmiles = sm.polyhedronToSmiles(centralAtom, faces, nVertices,
vertices, JC.SMILES_TYPE_SMILES | JC.SMILES_ATOM_COMMENT, details);
+ polySmiles = sm.polyhedronToSmiles(centralAtom, faces, nVertices,
vertices, JC.SMILES_TYPE_SMILES | JC.SMILES_ATOM_COMMENT, details);
}
} catch (Exception e) {
}
Modified: trunk/Jmol/src/org/jmol/smiles/SmilesMatcher.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesMatcher.java 2015-09-09 11:50:30 UTC
(rev 20766)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesMatcher.java 2015-09-09 12:52:37 UTC
(rev 20767)
@@ -412,9 +412,9 @@
null, flags | JC.SMILES_EXPLICIT_H | JC.SMILES_NOAROMATIC
| JC.SMILES_NOSTEREO);
if (!JC.checkFlag(flags, JC.SMILES_NOSTEREO)) {
- s = "//* " + center + " ["
+ s = "//* " + center + " *//\t["
+ Elements.elementSymbolFromNumber(center.getElementNumber()) + "@PH"
- + atomCount + (details == null ? "" : "/" + details + "/") + "] *//"
+ s;
+ + atomCount + (details == null ? "" : "/" + details + "/") + "]" + s;
}
return s;
}
Modified: trunk/Jmol/src/org/jmol/smiles/SmilesParser.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesParser.java 2015-09-09 11:50:30 UTC
(rev 20766)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesParser.java 2015-09-09 12:52:37 UTC
(rev 20767)
@@ -1305,6 +1305,7 @@
break;
case '"':
case '%':
+ case '/':
ch2 = ch;
break;
case '(':
Modified: trunk/Jmol/src/org/jmol/smiles/SmilesStereo.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesStereo.java 2015-09-09 11:50:30 UTC
(rev 20766)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesStereo.java 2015-09-09 12:52:37 UTC
(rev 20767)
@@ -205,7 +205,9 @@
sAtom.stereo = null;
break;
case STEREOCHEMISTRY_POLYHEDRAL:
- if (nBonds != atomCount)
+ // we allow no bonds here, indicating that the next N atoms are
associated (but not connected)
+ // with this atom
+ if (nBonds != 0 && nBonds != atomCount)
sAtom.stereo = null;
break;
case STEREOCHEMISTRY_ALLENE:
@@ -473,8 +475,8 @@
case STEREOCHEMISTRY_POLYHEDRAL:
if (sAtom.stereo.isNot)
isNot = !isNot;
- if (nH > 1)
- continue; // no chirality for [CH2@]
+ if (nH > 1 || sAtom.bondCount == 0)
+ continue; // no chirality for [CH2@]; skip if just an indicator
if (isSmilesFind) {
// TODO
continue;
@@ -842,11 +844,14 @@
int n = Integer.parseInt(pattern.substring(index, pt));
if (isPoly) {
atomCount = n;
- // we may have more to get? Distance?
if (pt < len && pattern.charAt(pt) == '(') {
details = SmilesParser.getSubPattern(pattern, pt, '(');
pt += details.length() + 2;
}
+ if (pt < len && pattern.charAt(pt) == '/') {
+ directives = SmilesParser.getSubPattern(pattern, pt, '/');
+ pt += directives.length() + 2;
+ }
} else {
order = n;
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-09-09 11:50:30 UTC
(rev 20766)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-09-09 12:52:37 UTC
(rev 20767)
@@ -58,8 +58,28 @@
TODO: image off stops JSmol
-Jmol.___JmolVersion="14.3.16_2015.09.08"
+TODO: Although isolated polyhedra are working in SMARTS searching,
+ for a SMILES representation, it will be important to allow a given atom
+ to be in more than one polyhedron (edge- or face-connected polyhedra).
+ But then that will require to references to the same atom. The solution
+ is probabably something like [(3)], indicating that this atom is equated
with
+ another in the SMILES string:
+
+ [Fe][O(1)].[Fe][O(1)]
+
+ then bond references to that oxygen from some other source would be to
both?
+
+ ....C(2) ....C(4) ???
+
+Jmol.___JmolVersion="14.3.16_2015.09.09"
+code: javajs.util reconciled with swingjs project
+
+bug fix: polyhedra.stereoSmiles --> polyhedra.polySmiles; central atom added in
+
+
+JmolVersion="14.3.16_2015.09.08"
+
code: Efficient JSON parser javajs.util.JSONParser
JmolVersion="14.3.16_2015.09.06"
@@ -190,7 +210,7 @@
bug fix: plot property with nothing more throws Exception
bug fix: Gaussian Dialog does not add final line ending when saving
-new feature: Jmol SMILES/SMARTS generic stereoSMILES polyhedron option
@PHn(....)
+new feature: Jmol SMILES/SMARTS generic polySMILES polyhedron option @PHn(....)
-- totally generic; will work with any number of connected atoms
-- suitable replacement for all TP, OH, etc.
-- standard equivalence to [C@] is [C@PH4(234)]
@@ -244,7 +264,7 @@
$ calculate symmetry polyhedra
C1 #1 Td
- $ print @1.polyhedra.stereoSmiles
+ $ print @1.polyhedra.polySmiles
//* C1 #1 *// [C@PH4].
//* H5 #5 *// [H]123.
//* H2 #2 *// [H]245.
@@ -262,7 +282,7 @@
color chlorine blue
polyhedra 4 bonds distancefactor 3.0
calculate symmetry polyhedra
- print @1.polyhedra.stereoSmiles
+ print @1.polyhedra.polySmiles
C1 #1 C1
@@ -274,7 +294,7 @@
$ invertselected
$ polyhedra 4 bonds distancefactor 3.0
calculate symmetry polyhedra
- print @1.polyhedra.stereoSmiles
+ print @1.polyhedra.polySmiles
C1 #1 C1
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