From: <ha...@us...> - 2016-02-05 03:46:49
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Revision: 20945 http://sourceforge.net/p/jmol/code/20945 Author: hansonr Date: 2016-02-05 03:46:46 +0000 (Fri, 05 Feb 2016) Log Message: ----------- Jmol.___JmolVersion="14.4.2_2016.02.05" bug fix: LOAD $benzene; SHOW smiles should give c1ccccc1 not c1=cc=cc=c1 bug fix: LOAD FILES "$caffeine" ":caffeine";print {1.1}.find("SMARTS",{2.1}) should give atoms, but it does not. Problem is with aromatic structure to SMILES shows c=c instead of just cc. (SMARTS searching with c=c does not match Modified Paths: -------------- branches/v14_4/Jmol/src/org/jmol/smiles/SmilesBond.java branches/v14_4/Jmol/src/org/jmol/smiles/SmilesGenerator.java branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties trunk/Jmol/src/org/jmol/smiles/SmilesBond.java trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v14_4/Jmol/src/org/jmol/smiles/SmilesBond.java =================================================================== --- branches/v14_4/Jmol/src/org/jmol/smiles/SmilesBond.java 2016-02-04 15:01:39 UTC (rev 20944) +++ branches/v14_4/Jmol/src/org/jmol/smiles/SmilesBond.java 2016-02-05 03:46:46 UTC (rev 20945) @@ -52,8 +52,6 @@ static String getBondOrderString(int order) { switch (order) { - case 1: - return ""; case 2: return "="; case 3: Modified: branches/v14_4/Jmol/src/org/jmol/smiles/SmilesGenerator.java =================================================================== --- branches/v14_4/Jmol/src/org/jmol/smiles/SmilesGenerator.java 2016-02-04 15:01:39 UTC (rev 20944) +++ branches/v14_4/Jmol/src/org/jmol/smiles/SmilesGenerator.java 2016-02-05 03:46:46 UTC (rev 20945) @@ -567,7 +567,7 @@ if (sp2Atoms == null) sp2Atoms = new Node[5]; if (bondPrev != null) { - strBond = SmilesBond.getBondOrderString(bondPrev.getCovalentOrder()); + strBond = (isAromatic && bsAromatic.get(prevIndex) ? "" : SmilesBond.getBondOrderString(bondPrev.getCovalentOrder())); if (prevSp2Atoms == null) sp2Atoms[nSp2Atoms++] = prevAtom; else Modified: branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2016-02-04 15:01:39 UTC (rev 20944) +++ branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2016-02-05 03:46:46 UTC (rev 20945) @@ -7,8 +7,16 @@ # see also http://chemapps.stolaf.edu/jmol/zip for daily updates -Jmol.___JmolVersion="14.4.2_2016.02.04" +Jmol.___JmolVersion="14.4.2_2016.02.05" +bug fix: LOAD $benzene; SHOW smiles should give c1ccccc1 not c1=cc=cc=c1 +bug fix: LOAD FILES "$caffeine" ":caffeine";print {1.1}.find("SMARTS",{2.1}) + should give atoms, but it does not. Problem is with aromatic structure + to SMILES shows c=c instead of just cc. (SMARTS searching with c=c does + not match + +JmolVersion="14.4.2_2016.02.04" + FEATURE NOTE: Prior to this version if the MO command was issued after use of rotateSelected, the orbitals were calculated improperly, because the basis functions always must be applied for the original file coordinate Modified: trunk/Jmol/src/org/jmol/smiles/SmilesBond.java =================================================================== --- trunk/Jmol/src/org/jmol/smiles/SmilesBond.java 2016-02-04 15:01:39 UTC (rev 20944) +++ trunk/Jmol/src/org/jmol/smiles/SmilesBond.java 2016-02-05 03:46:46 UTC (rev 20945) @@ -52,8 +52,6 @@ static String getBondOrderString(int order) { switch (order) { - case 1: - return ""; case 2: return "="; case 3: Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2016-02-04 15:01:39 UTC (rev 20944) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2016-02-05 03:46:46 UTC (rev 20945) @@ -64,8 +64,12 @@ TODO: isosurface molecular has an issue with 2gb1 -Jmol.___JmolVersion="14.5.2_2016.02.04" +Jmol.___JmolVersion="14.5.2_2016.02.05" +bug fix: LOAD $benzene; SHOW smiles should give c1ccccc1 not c1=cc=cc=c1 + +JmolVersion="14.5.2_2016.02.04" + FEATURE NOTE: Prior to this version if the MO command was issued after use of rotateSelected, the orbitals were calculated improperly, because the basis functions always must be applied for the original file coordinate This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |