Revision: 20319
http://sourceforge.net/p/jmol/code/20319
Author: hansonr
Date: 2015-02-22 22:45:34 +0000 (Sun, 22 Feb 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.3.12_2015.02.22d"
bug fix: restriction against getting SMILES string for biomolecule lifted
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/smiles/SmilesGenerator.java
trunk/Jmol/src/org/jmol/smiles/SmilesMatcher.java
trunk/Jmol/src/org/jmol/util/JmolMolecule.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/smiles/SmilesGenerator.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesGenerator.java 2015-02-22 21:54:13 UTC
(rev 20318)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesGenerator.java 2015-02-22 22:45:34 UTC
(rev 20319)
@@ -93,7 +93,7 @@
this.ac = ac;
this.bsSelected = bsSelected = BSUtil.copy(bsSelected);
this.explicitH = explicitH;
- return getSmilesComponent(atoms[i], bsSelected, false);
+ return getSmilesComponent(atoms[i], bsSelected, true, false);
}
String getBioSmiles(BNode[] atoms, int ac, BS bsSelected,
@@ -133,7 +133,7 @@
sb.append("~").appendC(bioStructureName.charAt(0)).append("~");
len++;
} else {
- s = getSmilesComponent(a, bs, true);
+ s = getSmilesComponent(a, bs, false, true);
if (s.equals(lastComponent)) {
end = "";
} else {
@@ -220,18 +220,19 @@
*
* @param atom
* @param bs
+ * @param allowBioResidues
* @param allowConnectionsToOutsideWorld
* @return SMILES
* @throws InvalidSmilesException
*/
- private String getSmilesComponent(Node atom, BS bs,
+ private String getSmilesComponent(Node atom, BS bs, boolean allowBioResidues,
boolean allowConnectionsToOutsideWorld)
throws InvalidSmilesException {
if (!explicitH && atom.getElementNumber() == 1 && atom.getEdges().length >
0)
atom = atoms[atom.getBondedAtomIndex(0)]; // don't start with H
bsSelected = JmolMolecule.getBranchBitSet(atoms, atom.getIndex(),
- BSUtil.copy(bs), null, -1, true, false);
+ BSUtil.copy(bs), null, -1, true, allowBioResidues);
bs.andNot(bsSelected);
bsIncludingH = BSUtil.copy(bsSelected);
if (!explicitH)
Modified: trunk/Jmol/src/org/jmol/smiles/SmilesMatcher.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesMatcher.java 2015-02-22 21:54:13 UTC
(rev 20318)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesMatcher.java 2015-02-22 22:45:34 UTC
(rev 20319)
@@ -138,11 +138,9 @@
boolean bioAddCrossLinks, String bioComment,
boolean explicitH) throws Exception {
InvalidSmilesException.clear();
- if (asBioSmiles)
- return (new SmilesGenerator()).getBioSmiles((BNode[]) atoms, ac,
bsSelected,
- bioAllowUnmatchedRings, bioAddCrossLinks, bioComment);
- return (new SmilesGenerator()).getSmiles(atoms, ac, bsSelected,
- explicitH);
+ return (asBioSmiles ? (new SmilesGenerator()).getBioSmiles((BNode[]) atoms,
+ ac, bsSelected, bioAllowUnmatchedRings, bioAddCrossLinks, bioComment)
+ : (new SmilesGenerator()).getSmiles(atoms, ac, bsSelected, explicitH));
}
@Override
Modified: trunk/Jmol/src/org/jmol/util/JmolMolecule.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/JmolMolecule.java 2015-02-22 21:54:13 UTC
(rev 20318)
+++ trunk/Jmol/src/org/jmol/util/JmolMolecule.java 2015-02-22 22:45:34 UTC
(rev 20319)
@@ -283,7 +283,7 @@
int atomIndex = atom.getIndex();
if (!bsToTest.get(atomIndex))
return allowCyclic;
- if (!allowBioResidue && (atom instanceof BNode)
+ if (!allowBioResidue && atom instanceof BNode
&& ((BNode) atom).getBioStructureTypeName().length() > 0)
return allowCyclic;
bsToTest.clear(atomIndex);
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-02-22 21:54:13 UTC
(rev 20318)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-02-22 22:45:34 UTC
(rev 20319)
@@ -15,8 +15,9 @@
TODO: remove HTML5 dependency on synchronous file loading (check SCRIPT
command for problems)
TODO: implement SHOW IMAGE in JavaScript/Browser
-Jmol.___JmolVersion="14.3.12_2015.02.22b"
+Jmol.___JmolVersion="14.3.12_2015.02.22d"
+bug fix: restriction against getting SMILES string for biomolecule lifted
bug fix: end-on bonds may appear to disappear
bug fix: JavaScript -2.format("%8.3") gives 2.000 not -2.000
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