Revision: 21563
http://sourceforge.net/p/jmol/code/21563
Author: hansonr
Date: 2017-04-27 19:00:54 +0000 (Thu, 27 Apr 2017)
Log Message:
-----------
Jmol.___JmolVersion="14.15.1" // 4/28/17
new feature: x.split(true)
-- does a white-space token split of the string value of x
new feature: MOL/SDF reader reads M ISO lines for isotopes
new feature: CIP chirality adds P, S, As, Se, Sb, Te, Bi, Po trigonal pyramidal
and tetrahedral
new feature: CIP chirality adds imine and diazine E/Z chirality
bug fix: CIP chirality broken for carbonyl groups
bug fix: CIP chirality E/Z should not be indicated for rings of size < 8
code: CIPChirality.java 779 lines Rules 1-5 validated on 145 compounds
- see https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol-datafiles/cip/
code: CIP optimizations
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/molxyz/MolReader.java
trunk/Jmol/src/org/jmol/modelset/Atom.java
trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java
trunk/Jmol/src/org/jmol/util/Elements.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/adapter/readers/molxyz/MolReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/molxyz/MolReader.java
2017-04-27 17:06:47 UTC (rev 21562)
+++ trunk/Jmol/src/org/jmol/adapter/readers/molxyz/MolReader.java
2017-04-27 19:00:54 UTC (rev 21563)
@@ -32,6 +32,7 @@
import org.jmol.adapter.smarter.AtomSetCollectionReader;
import org.jmol.adapter.smarter.Atom;
import org.jmol.api.JmolAdapter;
+import org.jmol.util.Elements;
import org.jmol.util.Logger;
/**
@@ -278,46 +279,69 @@
Atom[] atoms = asc.atoms;
Map<String, String> molData = new Hashtable<String, String>();
- boolean haveData = false;
-
rd();
while (line != null && line.indexOf("$$$$") != 0) {
- if (line.indexOf(">") != 0) {
- rd();
+ if (line.indexOf(">") == 0) {
+ readMolData(molData);
continue;
}
- String dataName = PT.trim(line, "> <").toLowerCase();
- String data = "";
- float[] fdata = null;
- while (rd() != null && line.indexOf("$$$$") != 0
- && line.indexOf(">") != 0) {
- data += line + "\n";
+ if (line.startsWith("M ISO")) {
+ readIsotopes();
continue;
}
- data = PT.trim(data, "\n");
- Logger.info(dataName + ":" + data.replace('\n', '|'));
- haveData = true;
- molData.put(dataName, data);
- if (dataName.toUpperCase().contains("_PARTIAL_CHARGES")) {
- try {
- fdata = PT.parseFloatArray(data);
- for (int i = asc.getLastAtomSetAtomIndex(), n = asc.ac; i < n; i++)
- atoms[i].partialCharge = 0;
- int pt = 0;
- for (int i = (int) fdata[pt++]; --i >= 0;) {
- int atomIndex = (int) fdata[pt++] + iatom0 - 1;
- float partialCharge = fdata[pt++];
- atoms[atomIndex].partialCharge = partialCharge;
- }
- } catch (Exception e) {
- for (int i = asc.getLastAtomSetAtomIndex(), n = asc.ac; i < n; i++)
- atoms[i].partialCharge = 0;
- return;
+ rd();
+ }
+ if (!molData.isEmpty())
+ asc.setModelInfoForSet("molData", molData, asc.iSet);
+ }
+
+ private void readIsotopes() throws Exception {
+ int n = parseIntAt(line, 6);
+ try {
+ for (int i = 0, pt = 9; i < n; i++) {
+ int ipt = parseIntAt(line, pt) - 1;
+ Atom atom = asc.atoms[ipt];
+ String ss = atom.getElementSymbol();
+ int iso = parseIntAt(line, pt + 4) +
Elements.getNaturalIsotope(JmolAdapter.getElementNumber(ss));
+ pt += 8;
+ String s = atom.elementSymbol = "" + iso + atom.elementSymbol;
+ System.out.println(s);
+ atom.elementSymbol = s;
+ }
+ } catch (Throwable e) {}
+ rd();
+ }
+
+ private void readMolData(Map<String, String> molData) throws Exception {
+ Atom[] atoms = asc.atoms;
+ String dataName = PT.trim(line, "> <").toLowerCase();
+ String data = "";
+ float[] fdata = null;
+ while (rd() != null && line.indexOf("$$$$") != 0
+ && line.indexOf(">") != 0) {
+ data += line + "\n";
+ continue;
+ }
+ data = PT.trim(data, "\n");
+ Logger.info(dataName + ":" + data.replace('\n', '|'));
+ molData.put(dataName, data);
+ if (dataName.toUpperCase().contains("_PARTIAL_CHARGES")) {
+ try {
+ fdata = PT.parseFloatArray(data);
+ for (int i = asc.getLastAtomSetAtomIndex(), n = asc.ac; i < n; i++)
+ atoms[i].partialCharge = 0;
+ int pt = 0;
+ for (int i = (int) fdata[pt++]; --i >= 0;) {
+ int atomIndex = (int) fdata[pt++] + iatom0 - 1;
+ float partialCharge = fdata[pt++];
+ atoms[atomIndex].partialCharge = partialCharge;
}
+ } catch (Exception e) {
+ for (int i = asc.getLastAtomSetAtomIndex(), n = asc.ac; i < n; i++)
+ atoms[i].partialCharge = 0;
+ return;
}
}
- if (haveData)
- asc.setModelInfoForSet("molData", molData, asc.iSet);
}
public void addMolAtom(int iAtom, int isotope, String elementSymbol,
Modified: trunk/Jmol/src/org/jmol/modelset/Atom.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/Atom.java 2017-04-27 17:06:47 UTC (rev
21562)
+++ trunk/Jmol/src/org/jmol/modelset/Atom.java 2017-04-27 19:00:54 UTC (rev
21563)
@@ -1334,7 +1334,8 @@
@Override
public int getNominalMass() {
- return Math.round(getMass());
+ int mass = getIsotopeNumber();
+ return (mass > 0 ? mass : Elements.getNaturalIsotope(getElementNumber()));
}
private float getMass() {
Modified: trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-04-27 17:06:47 UTC
(rev 21562)
+++ trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-04-27 19:00:54 UTC
(rev 21563)
@@ -67,7 +67,8 @@
* 4/6/17 Introduced in Jmol 14.12.0;
* validated for Rules 1 and 2 in Jmol 14.13.2;
* E/Z added 14.14.1;
- * 4/27/17 Ruled 3-5 completed 14.15.1
+ * 4/27/17 Ruled 3-5 completed 14.15.1
+ * 4/28/17 Validated for 146 compounds, including imines and diazines
*
*
* validation suite: see
https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol-datafiles/cip/
@@ -401,8 +402,10 @@
private boolean couldBeChiralAtom(Node a) {
boolean mustBePlanar = false;
switch (a.getCovalentBondCount()) {
- case 4:
- break;
+ default:
+ return false;
+ case 2:
+ return a.getElementNumber() == 7; // could be diazine or imine
case 3:
switch (a.getElementNumber()) {
case 6: // C
@@ -417,13 +420,14 @@
case 83: // Bi
case 84: // Po
break;
+ case 4:
+ break;
default:
return false;
}
break;
- // could add case 2 for imines here
- default:
- return false;
+ case 4:
+ break;
}
// check that the atom has at most one 1H atom
Edge[] edges = a.getEdges();
@@ -453,7 +457,7 @@
return false;
case 2:
// imines and diazines
- if (a.getElementNumber() != 7) // nitrogen
+ if (a.getElementNumber () != 7) // nitrogen
return false;
break;
case 3:
@@ -1228,6 +1232,7 @@
priorities[i]++;
if (Logger.debuggingHigh)
Logger.info(this + "." + b + " B-beats " + a);
+
break;
case A_WINS:
indices[j]++;
Modified: trunk/Jmol/src/org/jmol/util/Elements.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Elements.java 2017-04-27 17:06:47 UTC (rev
21562)
+++ trunk/Jmol/src/org/jmol/util/Elements.java 2017-04-27 19:00:54 UTC (rev
21563)
@@ -176,6 +176,27 @@
/* 7 Rf - Mt */ 261f, 262f, 263f, 262f, 265f, 268f
};
+ public final static int[] isotopeMass = {
+ 0,
+ /* 1 H */ 1, 4,
+ /* 2 Li */ 7, 9, 11, 12, 14, 16, 19, 20,
+ /* 3 Na */ 23,24, 27, 28, 31, 32, 35, 40,
+ /* 4 K */ 39, 40, 45, 48, 51, 52, 55, 56, 59, 59, 64,
65, 70, 73, 75, 79, 80, 84,
+
+ /* 5 Rb */ 85, 88, 89, 91, 93, 96, 98, 101, 103, 106, 108, 112,
115, 119, 122, 128, 127, 131,
+
+ /* 6 Cs, Ba, actinides */ 133, 137, 139, 140, 141, 144, 145, 150,
152, 157, 159, 163, 165, 167, 169, 173, 175,
+ 179, 181, 184, 186, 190, 192, 195, 197, 201, 204, 207, 209,
209, 210, 222,
+
+ /* 7 Fr, Ra, lanthanides */
+ 223, 226, 227, 232, 231, 238, 237, 244, 243, 247, 247, 251, 252,
257, 258, 259, 260,
+ /* 7 Rf - Mt */ 261, 262, 263, 262, 265, 268
+ };
+
+ public static int getNaturalIsotope(int elementNumber) {
+ return isotopeMass[elementNumber];
+ }
+
public static float getAtomicMass(int i) {
return (i < 1 || i >= atomicMass.length ? 0 : atomicMass[i]);
}
@@ -459,21 +480,7 @@
return 0;
}
- private static int[] naturalIsotopeMasses = {
- 1, 1, // H
- 6, 12,// C
- 7, 14,// N
- 8, 16,// O -- can add any number more if desired
- };
- public static int getNaturalIsotope(int elementNumber) {
- for (int i = 0; i < naturalIsotopeMasses.length; i += 2)
- if (naturalIsotopeMasses[i] == elementNumber)
- return naturalIsotopeMasses[++i];
- return 0;
- }
-
-
// add as we go
private final static String naturalIsotopes = "1H,12C,14N";
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-04-27 17:06:47 UTC
(rev 21562)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-04-27 19:00:54 UTC
(rev 21563)
@@ -49,17 +49,19 @@
# 10. Run jmol/tools build-release.xml
#
-Jmol.___JmolVersion="14.15.1" // 4/26/17
+Jmol.___JmolVersion="14.15.1" // 4/28/17
new feature: x.split(true)
-- does a white-space token split of the string value of x
+new feature: MOL/SDF reader reads M ISO lines for isotopes
new feature: CIP chirality adds P, S, As, Se, Sb, Te, Bi, Po trigonal
pyramidal and tetrahedral
+new feature: CIP chirality adds imine and diazine E/Z chirality
bug fix: CIP chirality broken for carbonyl groups
bug fix: CIP chirality E/Z should not be indicated for rings of size < 8
-code: CIPChirality.java 763 lines Rules 1-5 validated on 86 compounds
+code: CIPChirality.java 779 lines Rules 1-5 validated on 145 compounds
- see https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol-datafiles/cip/
code: CIP optimizations
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