Revision: 21677
http://sourceforge.net/p/jmol/code/21677
Author: hansonr
Date: 2017-07-24 02:43:49 +0000 (Mon, 24 Jul 2017)
Log Message:
-----------
Jmol.___JmolVersion="14.20.4"
bug fix: CIPChirality new Rule 6 covers all special spiro cases and C3-symmetry
bug fix: SMILES generator fails for [2H]/C=C/[1H]
bug fix: write SDF fails for 1H. (Must use M ISO.)
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/smiles/SmilesGenerator.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/PropertyManager.java
Modified: trunk/Jmol/src/org/jmol/smiles/SmilesGenerator.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesGenerator.java 2017-07-23 20:07:50 UTC
(rev 21676)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesGenerator.java 2017-07-24 02:43:49 UTC
(rev 21677)
@@ -290,7 +290,7 @@
boolean forceBrackets)
throws InvalidSmilesException {
- if (!explicitH && atom.getElementNumber() == 1
+ if (!explicitH && atom.getAtomicAndIsotopeNumber() == 1
&& atom.getEdges().length > 0)
atom = atoms[atom.getBondedAtomIndex(0)]; // don't start with H
@@ -309,7 +309,7 @@
for (int j = bsSelected.nextSetBit(0); j >= 0; j = bsSelected
.nextSetBit(j + 1)) {
Node a = atoms[j];
- if (a.getElementNumber() == 1 && a.getIsotopeNumber() == 0
+ if (a.getAtomicAndIsotopeNumber() == 1
&& a.getBondCount() > 0 && a.getBondedAtomIndex(0) != iHypervalent)
bsSelected.clear(j);
}
@@ -469,7 +469,7 @@
for (int b = 0; b < bb.length; b++) {
SimpleNode other;
if (bb[b].getCovalentOrder() != 1 || (other =
bb[b].getOtherNode(atomA)).getElementNumber() == 1
- && other.getIsotopeNumber() == 1)
+ && other.getIsotopeNumber() == 0)
continue;
edges[j][edgeCount++] = bb[b];
if (getBondStereochemistry(bb[b], atomA) != '\0') {
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-07-23 20:07:50 UTC
(rev 21676)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-07-24 02:43:49 UTC
(rev 21677)
@@ -58,7 +58,9 @@
Jmol.___JmolVersion="14.20.4"
-bug fix: CIPChirality covers all special spiro cases and C3-symmetry
+bug fix: CIPChirality new Rule 6 covers all special spiro cases and C3-symmetry
+bug fix: SMILES generator fails for [2H]/C=C/[1H]
+bug fix: write SDF fails for 1H. (Must use M ISO.)
JmolVersion="14.20.3" // 2017.07.20
Modified: trunk/Jmol/src/org/jmol/viewer/PropertyManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/PropertyManager.java 2017-07-23 20:07:50 UTC
(rev 21676)
+++ trunk/Jmol/src/org/jmol/viewer/PropertyManager.java 2017-07-24 02:43:49 UTC
(rev 21677)
@@ -1346,11 +1346,12 @@
if (o instanceof SV)
o = ((SV) o).asString();
int valueType = (o == null ? T.nada : T.getTokFromName("" + o));
- SB atomValues = (valueType == T.nada ? null : new SB());
+ SB atomValues = (valueType == T.nada && !asSDF ? null : new SB());
for (int i = bsAtoms.nextSetBit(0), n = 0; i >= 0; i = bsAtoms
- .nextSetBit(i + 1))
+ .nextSetBit(i + 1)) {
getAtomRecordMOL(iModel, ms, mol, atomMap[i] = ++n, ms.at[i], q, pTemp,
- asV3000, asJSON, atomValues, valueType);
+ asV3000, asJSON, atomValues, valueType, asSDF);
+ }
if (asV3000) {
mol.append("M V30 END ATOM\nM V30 BEGIN BOND\n");
} else if (asJSON) {
@@ -1474,7 +1475,8 @@
*/
private void getAtomRecordMOL(int iModel, ModelSet ms, SB mol, int n, Atom
a, Quat q,
- P3 pTemp, boolean asV3000, boolean asJSON, SB
atomValues, int tokValue) {
+ P3 pTemp, boolean asV3000, boolean asJSON, SB
atomValues,
+ int tokValue, boolean asSDF) {
//https://cactus.nci.nih.gov/chemical/structure/caffeine/file?format=sdf&get3d=true
//__Jmol-14_06161707413D 1 1.00000 0.00000 0
//Jmol version 14.19.1 2017-06-12 00:33 EXTRACT: ({0:23})
@@ -1488,7 +1490,7 @@
int elemNo = a.getElementNumber();
String sym = (a.isDeleted() ? "Xx" : Elements
.elementSymbolFromNumber(elemNo));
- int iso = a.getIsotopeNumber();
+ int isotope = a.getIsotopeNumber();
int charge = a.getFormalCharge();
Object [] o = new Object[] { pTemp };
if (asV3000) {
@@ -1496,8 +1498,8 @@
.append(PT.sprintf(" %12.5p %12.5p %12.5p 0", "p", o));
if (charge != 0)
mol.append(" CHG=").appendI(charge);
- if (iso != 0)
- mol.append(" MASS=").appendI(iso);
+ if (isotope != 0)
+ mol.append(" MASS=").appendI(isotope);
mol.append("\n");
} else if (asJSON) {
if (n != 1)
@@ -1507,8 +1509,8 @@
mol.append("\"l\":\"").append(a.getElementSymbol()).append("\",");
if (charge != 0)
mol.append("\"c\":").appendI(charge).append(",");
- if (iso != 0 && iso != Elements.getNaturalIsotope(elemNo))
- mol.append("\"m\":").appendI(iso).append(",");
+ if (isotope != 0)
+ mol.append("\"m\":").appendI(isotope).append(",");
mol.append("\"x\":").appendF(a.x).append(",\"y\":").appendF(a.y)
.append(",\"z\":").appendF(a.z).append("}");
} else {
@@ -1516,13 +1518,18 @@
mol.append(" ").append(sym);
if (sym.length() == 1)
mol.append(" ");
- if (iso > 0)
- iso -= Elements.getNaturalIsotope(a.getElementNumber());
- PT.rightJustify(mol, " ", "" + iso);
+ PT.rightJustify(mol, " ", "" + (isotope > 0 ? isotope -
Elements.getNaturalIsotope(a.getElementNumber()) : 0));
+ if (asSDF && isotope > 0) {
+ atomValues.append("M ISO 1");
+ PT.rightJustify(atomValues, " ", "" + n);
+ PT.rightJustify(atomValues, " ", "" + isotope);
+ atomValues.append("\n");
+ }
+
PT.rightJustify(mol, " ", "" + (charge == 0 ? 0 : 4 - charge));
mol.append(" ").append(getAtomParity(a));
mol.append(" 0 0 0\n");
- String label = (atomValues == null || asV3000 ? null :
+ String label = (tokValue == T.nada || asV3000 ? null :
getAtomPropertyAsString(a, tokValue));
if (label != null && (label = label.trim()).length() > 0) {
String sn = " " + n + " ";
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