Revision: 20985
http://sourceforge.net/p/jmol/code/20985
Author: hansonr
Date: 2016-03-09 02:01:42 +0000 (Wed, 09 Mar 2016)
Log Message:
-----------
JmolVersion="14.4.3_2016.03.08"
new feature: WRITE MOL0 xxx.mol
-- MOL format with no bonds of type 6 or 7 (aromatic single/double)
-- needed for http://metamolecular.com/inchi-js
bug fix: OpenSMILES even-atom cumulene stereochemistry not implemented
-- examples (reporting "DIASTEREOMERS")
print compare("F/C=C=C=C/F","F/C=C=C=C\\F","isomer")
load $F-C=C=C=C-F;print compare("F/C=C=C=C\\F",{1.1},"isomer")
bug fix: SMILES generator unnecessarily over-expressing double-bond / and \.
bug fix: SMILES generator aromaticity should not make ring atoms of quinone
aromatic
bug fix: SMILES generator aromaticity not recognizing issue with exocyclic
double bonds
bug fix: SMILES generator aromaticity is too broadly defined
-- updated aromatic for generation purposes only:
(a) the atom is in a 6-membered ring containing only C, N, or O and
matching SMARTS [#6X3+0,#6X2+1,#6X2-1,#7X2+0,#7X3+1,#8X2+1]
(b) the atom is not doubly bonded to any nonaromatic atom (prevents case of
exocyclic double bonds)
(c) the atom connects with at least two other aromatic atoms
new feature: (JSmol) standard InChI generator (see inchi.htm, inchi/*)
-- JavaScript library for generation of InChIs
-- runs completely in JavaScript
-- equivalent to SHOW CHEMICAL stdinchi
-- about 900 KB
new feature: optional processing of OpenSMILES [CH2:002] ":<n>" atom class.
-- positive integer value only
-- checks the atom property property_osclass
-- for SMARTS, [:0] means "without an osclass"
-- for SMARTS, [!:0] means "any non-zero osclass"
-- for SMARTS, same as [$(select property_osclass=n)]
-- only enabled with Jmol SMILES directive "/opensmiles/"; otherwise ignored
-- for example:
$ load $2-butanol
$ show smiles
C[C@H](O)CC
$ @2.property_osclass=2
$ @3.property_osclass=3
$ @5.property_osclass=5
$ select *
15 atoms selected
$ select on search("/opensmiles/[:3]")
1 atoms selected
$ select on search("/opensmiles/[!:3]")
14 atoms selected
$ select on search("/opensmiles/[:0]")
12 atoms selected
$ select on search("/opensmiles/[!:0]")
3 atoms selected
$ select on search("/opensmiles/[!:3 & !:0]")
2 atoms selected
new feature: {*}.find("OPENSMILES")
-- adds atom class if property_osclass is nonzero
-- for example:
$ load $2-butanol
$ @2.property_osclass=2
$ @3.property_osclass=3
$ @5.property_osclass=5
$ print {*}.find("opensmiles")
C[C@H:2]([OH:5])[CH2:3]C
Modified Paths:
--------------
branches/v14_4/Jmol/src/org/jmol/scriptext/CmdExt.java
branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
branches/v14_4/Jmol/src/org/jmol/viewer/PropertyManager.java
trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/PropertyManager.java
Modified: branches/v14_4/Jmol/src/org/jmol/scriptext/CmdExt.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/scriptext/CmdExt.java 2016-03-08
20:49:29 UTC (rev 20984)
+++ branches/v14_4/Jmol/src/org/jmol/scriptext/CmdExt.java 2016-03-09
02:01:42 UTC (rev 20985)
@@ -3777,7 +3777,7 @@
&& !PT
.isOneOf(
type,
-
";SCENE;JMOL;ZIP;ZIPALL;SPT;HISTORY;MO;NBO;ISOSURFACE;MESH;PMESH;VAR;FILE;FUNCTION;CML;JSON;XYZ;XYZRN;XYZVIB;MENU;MOL;PDB;PGRP;PQR;QUAT;RAMA;SDF;V2000;V3000;INLINE;"))
+
";SCENE;JMOL;ZIP;ZIPALL;SPT;HISTORY;MO;NBO;ISOSURFACE;MESH;PMESH;VAR;FILE;FUNCTION;CML;JSON;XYZ;XYZRN;XYZVIB;MENU;MOL;MOL0;PDB;PGRP;PQR;QUAT;RAMA;SDF;V2000;V3000;INLINE;"))
eval.errorStr2(
ScriptError.ERROR_writeWhat,
"COORDS|FILE|FUNCTIONS|HISTORY|IMAGE|INLINE|ISOSURFACE|JMOL|MENU|MO|NBO|POINTGROUP|QUATERNION
[w,x,y,z] [derivative]"
@@ -3861,7 +3861,7 @@
data = vwr.getCurrentFileAsString("script");
else
writeFileData = true;
- } else if (data == "SDF" || data == "MOL" || data == "V2000"
+ } else if (data == "SDF" || data == "MOL" || data == "MOL0" || data ==
"V2000"
|| data == "V3000" || data == "CD" || data == "JSON" || data == "XYZ"
|| data == "XYZRN" || data == "XYZVIB" || data == "CML") {
data = vwr.getModelExtract("selected", isCoord, false, data);
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2016-03-08
20:49:29 UTC (rev 20984)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2016-03-09
02:01:42 UTC (rev 20985)
@@ -10,6 +10,10 @@
JmolVersion="14.4.3_2016.03.08"
+new feature: WRITE MOL0 xxx.mol
+ -- MOL format with no bonds of type 6 or 7 (aromatic single/double)
+ -- needed for http://metamolecular.com/inchi-js
+
bug fix: OpenSMILES even-atom cumulene stereochemistry not implemented
-- examples (reporting "DIASTEREOMERS")
print compare("F/C=C=C=C/F","F/C=C=C=C\\F","isomer")
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/PropertyManager.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/PropertyManager.java
2016-03-08 20:49:29 UTC (rev 20984)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/PropertyManager.java
2016-03-09 02:01:42 UTC (rev 20985)
@@ -1125,8 +1125,10 @@
/**
*
- * V3000, SDF, JSON, CD, XYZ, XYZVIB, XYZRN, CML, PDB, PQR
+ * V3000, SDF, MOL, JSON, CD, XYZ, XYZVIB, XYZRN, CML, PDB, PQR,
*
+ * MOL0 is MOL with no bonds of type 6 or 7 (aromatic single/double)
+ *
*/
@Override
public String getModelExtract(BS bs, boolean doTransform, boolean isModelKit,
@@ -1140,6 +1142,7 @@
boolean asV3000 = type.equalsIgnoreCase("V3000");
boolean asSDF = type.equalsIgnoreCase("SDF");
+ boolean noAromatic = type.equalsIgnoreCase("MOL0");
boolean asXYZVIB = (!doTransform && type.equalsIgnoreCase("XYZVIB"));
boolean asXYZRN = type.equalsIgnoreCase("XYZRN");
boolean isXYZ = type.toUpperCase().startsWith("XYZ");
@@ -1200,7 +1203,7 @@
BS bsTemp = BSUtil.copy(bsAtoms);
bsTemp.and(ms.getModelAtomBitSetIncludingDeleted(i, false));
bsBonds = getCovalentBondsForAtoms(ms.bo, ms.bondCount, bsTemp);
- if (!(isOK = addMolFile(i, mol, bsTemp, bsBonds, false, false, q)))
+ if (!(isOK = addMolFile(i, mol, bsTemp, bsBonds, false, false,
noAromatic, q)))
break;
mol.append("$$$$\n");
}
@@ -1253,14 +1256,14 @@
}
}
} else {
- isOK = addMolFile(-1, mol, bsAtoms, bsBonds, asV3000, asJSON, q);
+ isOK = addMolFile(-1, mol, bsAtoms, bsBonds, asV3000, asJSON,
noAromatic, q);
}
return (isOK ? mol.toString()
: "ERROR: Too many atoms or bonds -- use V3000 format.");
}
private boolean addMolFile(int iModel, SB mol, BS bsAtoms, BS bsBonds,
- boolean asV3000, boolean asJSON, Quat q) {
+ boolean asV3000, boolean asJSON, boolean
noAromatic, Quat q) {
int nAtoms = bsAtoms.cardinality();
int nBonds = bsBonds.cardinality();
if (!asV3000 && !asJSON && (nAtoms > 999 || nBonds > 999))
@@ -1295,7 +1298,7 @@
}
for (int i = bsBonds.nextSetBit(0), n = 0; i >= 0; i = bsBonds
.nextSetBit(i + 1))
- getBondRecordMOL(mol, ++n, ms.bo[i], atomMap, asV3000, asJSON);
+ getBondRecordMOL(mol, ++n, ms.bo[i], atomMap, asV3000, asJSON,
noAromatic);
// 21 21 0 0 0
if (asV3000) {
mol.append("M V30 END BOND\nM V30 END CTAB\n");
@@ -1420,7 +1423,7 @@
}
private void getBondRecordMOL(SB mol, int n, Bond b, int[] atomMap,
- boolean asV3000, boolean asJSON) {
+ boolean asV3000, boolean asJSON, boolean
noAromatic) {
// 1 2 1 0
int a1 = atomMap[b.atom1.i];
int a2 = atomMap[b.atom2.i];
@@ -1435,10 +1438,10 @@
order = (asJSON ? -3 : 5);
break;
case Edge.BOND_AROMATIC_SINGLE:
- order = (asJSON ? 1: 6);
+ order = (asJSON || noAromatic ? 1: 6);
break;
case Edge.BOND_AROMATIC_DOUBLE:
- order = (asJSON ? 2: 7);
+ order = (asJSON || noAromatic ? 2: 7);
break;
case Edge.BOND_PARTIAL01:
order = (asJSON ? -1: 8);
@@ -2292,7 +2295,8 @@
if (nAtoms == 0)
return "";
// creating an instance prevents pre-loading by JavaScript
- Interface.getInterface("javajs.util.XmlUtil", vwr, "file");
+ if (vwr.isJS)
+ Interface.getInterface("javajs.util.XmlUtil", vwr, "file");
XmlUtil.openTag(sb, "molecule");
XmlUtil.openTag(sb, "atomArray");
BS bsAtoms = new BS();
Modified: trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2016-03-08 20:49:29 UTC
(rev 20984)
+++ trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2016-03-09 02:01:42 UTC
(rev 20985)
@@ -3777,7 +3777,7 @@
&& !PT
.isOneOf(
type,
-
";SCENE;JMOL;ZIP;ZIPALL;SPT;HISTORY;MO;NBO;ISOSURFACE;MESH;PMESH;VAR;FILE;FUNCTION;CML;JSON;XYZ;XYZRN;XYZVIB;MENU;MOL;PDB;PGRP;PQR;QUAT;RAMA;SDF;V2000;V3000;INLINE;"))
+
";SCENE;JMOL;ZIP;ZIPALL;SPT;HISTORY;MO;NBO;ISOSURFACE;MESH;PMESH;VAR;FILE;FUNCTION;CML;JSON;XYZ;XYZRN;XYZVIB;MENU;MOL;MOL0;PDB;PGRP;PQR;QUAT;RAMA;SDF;V2000;V3000;INLINE;"))
eval.errorStr2(
ScriptError.ERROR_writeWhat,
"COORDS|FILE|FUNCTIONS|HISTORY|IMAGE|INLINE|ISOSURFACE|JMOL|MENU|MO|NBO|POINTGROUP|QUATERNION
[w,x,y,z] [derivative]"
@@ -3861,7 +3861,7 @@
data = vwr.getCurrentFileAsString("script");
else
writeFileData = true;
- } else if (data == "SDF" || data == "MOL" || data == "V2000"
+ } else if (data == "SDF" || data == "MOL" || data == "MOL0" || data ==
"V2000"
|| data == "V3000" || data == "CD" || data == "JSON" || data == "XYZ"
|| data == "XYZRN" || data == "XYZVIB" || data == "CML") {
data = vwr.getModelExtract("selected", isCoord, false, data);
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2016-03-08 20:49:29 UTC
(rev 20984)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2016-03-09 02:01:42 UTC
(rev 20985)
@@ -68,6 +68,10 @@
JmolVersion="14.5.3_2016.03.08"
+new feature: WRITE MOL0 xxx.mol
+ -- MOL format with no bonds of type 6 or 7 (aromatic single/double)
+ -- needed for http://metamolecular.com/inchi-js
+
bug fix: OpenSMILES even-atom cumulene stereochemistry not implemented
-- examples (reporting "DIASTEREOMERS")
print compare("F/C=C=C=C/F","F/C=C=C=C\\F","isomer")
Modified: trunk/Jmol/src/org/jmol/viewer/PropertyManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/PropertyManager.java 2016-03-08 20:49:29 UTC
(rev 20984)
+++ trunk/Jmol/src/org/jmol/viewer/PropertyManager.java 2016-03-09 02:01:42 UTC
(rev 20985)
@@ -1125,8 +1125,10 @@
/**
*
- * V3000, SDF, JSON, CD, XYZ, XYZVIB, XYZRN, CML, PDB, PQR
+ * V3000, SDF, MOL, JSON, CD, XYZ, XYZVIB, XYZRN, CML, PDB, PQR,
*
+ * MOL0 is MOL with no bonds of type 6 or 7 (aromatic single/double)
+ *
*/
@Override
public String getModelExtract(BS bs, boolean doTransform, boolean isModelKit,
@@ -1140,6 +1142,7 @@
boolean asV3000 = type.equalsIgnoreCase("V3000");
boolean asSDF = type.equalsIgnoreCase("SDF");
+ boolean noAromatic = type.equalsIgnoreCase("MOL0");
boolean asXYZVIB = (!doTransform && type.equalsIgnoreCase("XYZVIB"));
boolean asXYZRN = type.equalsIgnoreCase("XYZRN");
boolean isXYZ = type.toUpperCase().startsWith("XYZ");
@@ -1200,7 +1203,7 @@
BS bsTemp = BSUtil.copy(bsAtoms);
bsTemp.and(ms.getModelAtomBitSetIncludingDeleted(i, false));
bsBonds = getCovalentBondsForAtoms(ms.bo, ms.bondCount, bsTemp);
- if (!(isOK = addMolFile(i, mol, bsTemp, bsBonds, false, false, q)))
+ if (!(isOK = addMolFile(i, mol, bsTemp, bsBonds, false, false,
noAromatic, q)))
break;
mol.append("$$$$\n");
}
@@ -1253,14 +1256,14 @@
}
}
} else {
- isOK = addMolFile(-1, mol, bsAtoms, bsBonds, asV3000, asJSON, q);
+ isOK = addMolFile(-1, mol, bsAtoms, bsBonds, asV3000, asJSON,
noAromatic, q);
}
return (isOK ? mol.toString()
: "ERROR: Too many atoms or bonds -- use V3000 format.");
}
private boolean addMolFile(int iModel, SB mol, BS bsAtoms, BS bsBonds,
- boolean asV3000, boolean asJSON, Quat q) {
+ boolean asV3000, boolean asJSON, boolean
noAromatic, Quat q) {
int nAtoms = bsAtoms.cardinality();
int nBonds = bsBonds.cardinality();
if (!asV3000 && !asJSON && (nAtoms > 999 || nBonds > 999))
@@ -1295,7 +1298,7 @@
}
for (int i = bsBonds.nextSetBit(0), n = 0; i >= 0; i = bsBonds
.nextSetBit(i + 1))
- getBondRecordMOL(mol, ++n, ms.bo[i], atomMap, asV3000, asJSON);
+ getBondRecordMOL(mol, ++n, ms.bo[i], atomMap, asV3000, asJSON,
noAromatic);
// 21 21 0 0 0
if (asV3000) {
mol.append("M V30 END BOND\nM V30 END CTAB\n");
@@ -1420,7 +1423,7 @@
}
private void getBondRecordMOL(SB mol, int n, Bond b, int[] atomMap,
- boolean asV3000, boolean asJSON) {
+ boolean asV3000, boolean asJSON, boolean
noAromatic) {
// 1 2 1 0
int a1 = atomMap[b.atom1.i];
int a2 = atomMap[b.atom2.i];
@@ -1435,10 +1438,10 @@
order = (asJSON ? -3 : 5);
break;
case Edge.BOND_AROMATIC_SINGLE:
- order = (asJSON ? 1: 6);
+ order = (asJSON || noAromatic ? 1: 6);
break;
case Edge.BOND_AROMATIC_DOUBLE:
- order = (asJSON ? 2: 7);
+ order = (asJSON || noAromatic ? 2: 7);
break;
case Edge.BOND_PARTIAL01:
order = (asJSON ? -1: 8);
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