Revision: 21486
http://sourceforge.net/p/jmol/code/21486
Author: hansonr
Date: 2017-04-06 20:58:28 +0000 (Thu, 06 Apr 2017)
Log Message:
-----------
Jmol.___JmolVersion="14.12.0-beta" // 2017-04-06
new feature: {atom}.chirality
-- uses Cohen-Ingold-Prelog rules to assign R or S to a carbon center
-- ignores sulfur chirality
-- not fully tested
-- does not fully implement high symmetry cases
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/api/SmilesMatcherInterface.java
trunk/Jmol/src/org/jmol/api/SymmetryInterface.java
trunk/Jmol/src/org/jmol/modelset/Atom.java
trunk/Jmol/src/org/jmol/modelset/LabelToken.java
trunk/Jmol/src/org/jmol/modelset/ModelSet.java
trunk/Jmol/src/org/jmol/script/T.java
trunk/Jmol/src/org/jmol/smiles/SmilesAtom.java
trunk/Jmol/src/org/jmol/smiles/SmilesMatcher.java
trunk/Jmol/src/org/jmol/symmetry/Symmetry.java
trunk/Jmol/src/org/jmol/util/Elements.java
trunk/Jmol/src/org/jmol/util/Node.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Added Paths:
-----------
trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java
Modified: trunk/Jmol/src/org/jmol/api/SmilesMatcherInterface.java
===================================================================
--- trunk/Jmol/src/org/jmol/api/SmilesMatcherInterface.java 2017-04-06
12:09:34 UTC (rev 21485)
+++ trunk/Jmol/src/org/jmol/api/SmilesMatcherInterface.java 2017-04-06
20:58:28 UTC (rev 21486)
@@ -56,4 +56,6 @@
public int[][] getMapForJME(String jme, Atom[] at, BS bsAtoms);
+ public int getChirality(Node atom4, Node atom3, Node atom2, Node atom1);
+
}
Modified: trunk/Jmol/src/org/jmol/api/SymmetryInterface.java
===================================================================
--- trunk/Jmol/src/org/jmol/api/SymmetryInterface.java 2017-04-06 12:09:34 UTC
(rev 21485)
+++ trunk/Jmol/src/org/jmol/api/SymmetryInterface.java 2017-04-06 20:58:28 UTC
(rev 21486)
@@ -218,4 +218,6 @@
void toFractionalM(M4 m);
+ public String getChirality(Viewer vwr, Atom atom);
+
}
Modified: trunk/Jmol/src/org/jmol/modelset/Atom.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/Atom.java 2017-04-06 12:09:34 UTC (rev
21485)
+++ trunk/Jmol/src/org/jmol/modelset/Atom.java 2017-04-06 20:58:28 UTC (rev
21486)
@@ -25,6 +25,8 @@
package org.jmol.modelset;
+import javax.annotation.processing.RoundEnvironment;
+
import javajs.util.CU;
import javajs.util.Lst;
import javajs.util.PT;
@@ -1317,6 +1319,12 @@
return group.chain.model.ms.getVibCoord(i, ch);
}
+ @Override
+
+ public int getNominalMass() {
+ return Math.round(getMass());
+ }
+
private float getMass() {
float mass = getIsotopeNumber();
return (mass > 0 ? mass : Elements.getAtomicMass(getElementNumber()));
@@ -1335,6 +1343,8 @@
return getAtomType();
case T.chain:
return getChainIDStr();
+ case T.chirality:
+ return getChirality();
case T.sequence:
return getGroup1('?');
case T.seqcode:
@@ -1373,6 +1383,14 @@
return "";
}
+ /**
+ * Determine R/S chirality at this position
+ * @return "" or "R" or "S"
+ */
+ private String getChirality() {
+ return group.chain.model.ms.getChirality(this);
+ }
+
@Override
public char getInsertionCode() {
return group.getInsertionCode();
Modified: trunk/Jmol/src/org/jmol/modelset/LabelToken.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/LabelToken.java 2017-04-06 12:09:34 UTC
(rev 21485)
+++ trunk/Jmol/src/org/jmol/modelset/LabelToken.java 2017-04-06 20:58:28 UTC
(rev 21486)
@@ -168,7 +168,8 @@
T.screeny, T.screenz, T.screenxyz, // added in 12.3.30
T.magneticshielding, T.chemicalshift, T.chainno, T.seqid,
T.modx, T.mody, T.modz, T.modo, T.modxyz, T.symop,
- T.nbo // added in 14.8.2
+ T.nbo, // added in 14.8.2
+ T.chirality // added in 14.11.4
};
public LabelToken() {
Modified: trunk/Jmol/src/org/jmol/modelset/ModelSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2017-04-06 12:09:34 UTC
(rev 21485)
+++ trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2017-04-06 20:58:28 UTC
(rev 21486)
@@ -4068,7 +4068,11 @@
return (dssrData == null || dssrData.length <= i ? Float.NaN :
dssrData[i]);
}
+ public String getChirality(Atom atom) {
+ return Interface.getSymmetry(vwr, "ms").getChirality(vwr, atom);
+ }
+
}
Modified: trunk/Jmol/src/org/jmol/script/T.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/T.java 2017-04-06 12:09:34 UTC (rev
21485)
+++ trunk/Jmol/src/org/jmol/script/T.java 2017-04-06 20:58:28 UTC (rev
21486)
@@ -555,6 +555,7 @@
public final static int strucid = strproperty |13;
public final static int symbol = strproperty |14 | settable;
public final static int symmetry = strproperty |15 | predefinedset;
+ public final static int chirality = strproperty |16;
public final static int atomno = intproperty | 1 | settable;
public final static int atomid = intproperty | 2;
@@ -2361,6 +2362,7 @@
"bondmode",
"boundBoxColor",
"boundingBoxColor",
+ "chirality",
"currentLocalPath",
"dataSeparator",
"defaultAngleLabel",
@@ -3407,6 +3409,7 @@
bondmode, // "bondmode"
boundboxcolor, // "boundBoxColor"
-1, // "boundingBoxColor"
+ chirality,
currentlocalpath, // "currentLocalPath"
dataseparator, // "dataSeparator"
defaultanglelabel, // "defaultAngleLabel"
Modified: trunk/Jmol/src/org/jmol/smiles/SmilesAtom.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesAtom.java 2017-04-06 12:09:34 UTC
(rev 21485)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesAtom.java 2017-04-06 20:58:28 UTC
(rev 21486)
@@ -851,5 +851,11 @@
return Float.NaN;
}
+ @Override
+ public int getNominalMass() {
+ // TODO
+ return getAtomicMass();
+ }
+
}
Modified: trunk/Jmol/src/org/jmol/smiles/SmilesMatcher.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesMatcher.java 2017-04-06 12:09:34 UTC
(rev 21485)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesMatcher.java 2017-04-06 20:58:28 UTC
(rev 21486)
@@ -581,4 +581,9 @@
return null;
}
+ @Override
+ public int getChirality(Node atom4, Node atom3, Node atom2, Node atom1) {
+ return SmilesStereo.getHandedness(atom4, atom3, atom2, atom1, new VTemp());
+ }
+
}
Added: trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java
(rev 0)
+++ trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-04-06 20:58:28 UTC
(rev 21486)
@@ -0,0 +1,233 @@
+package org.jmol.symmetry;
+
+import java.util.Arrays;
+
+import javajs.util.BS;
+
+import org.jmol.api.SmilesMatcherInterface;
+import org.jmol.util.Edge;
+import org.jmol.util.Logger;
+import org.jmol.util.Node;
+import org.jmol.viewer.Viewer;
+
+public class CIPChirality {
+
+ Viewer vwr;
+ BS bsFound;
+
+ public CIPChirality() {
+ // for reflection
+ }
+
+ public CIPChirality setViewer(Viewer vwr) {
+ this.vwr = vwr;
+ return this;
+ }
+
+ public String getChirality(Node atom) {
+ if (atom.getCovalentBondCount() != 4)
+ return "";
+ bsFound = new BS();
+ CIPAtom a = new CIPAtom(atom, null, false);
+
+ String rs = (a.set() ? getRorS(a) : "");
+ if (Logger.debugging)
+ Logger.info(atom + " " + rs);
+
+ return rs;
+ }
+
+ public String getRorS(CIPAtom a) {
+ try {
+ if (!a.sortAtoms())
+ return "";
+ SmilesMatcherInterface sm = vwr.getSmilesMatcher();
+ switch (sm.getChirality(a.atoms[3].atom, a.atoms[2].atom,
+ a.atoms[1].atom, a.atoms[0].atom)) {
+ case 1:
+ return "R";
+ case 2:
+ return "S";
+ default:
+ return "";
+ }
+ } catch (Throwable e) {
+ e.printStackTrace();
+ return "";
+ }
+ }
+
+ private class CIPAtom implements Comparable<CIPAtom> {
+ String path = ";";
+ Node atom;
+ boolean isDummy = true;
+ boolean isTerminal;
+ boolean isSet;
+ int isAbove;
+ CIPAtom parent;
+ CIPAtom[] atoms;
+ private int nAtoms;
+
+ @Override
+ public String toString() {
+ return path + " " + atom + (isDummy ? " *" : "");
+ }
+
+ public CIPAtom(Node atom, CIPAtom parent, boolean isDummy) {
+ if (atom == null)
+ return;
+ this.atom = atom;
+ this.isTerminal = atom.getCovalentBondCount() == 1;
+ int iatom = atom.getIndex();
+ if (bsFound.get(iatom)) {
+ isDummy = true;
+ } else {
+ bsFound.set(iatom);
+ this.isDummy = isDummy;
+ }
+ this.parent = parent;
+ if (parent != null)
+ path = parent.path;
+ path += getPathString();
+ }
+
+ private String getPathString() {
+ String elemno = "000" + atom.getElementNumber();
+ String mass = "00" + (isDummy ? 0 : atom.getNominalMass());
+ return elemno.substring(elemno.length() - 3) + "_"
+ + mass.substring(mass.length() - 3) + ";";
+ }
+
+ boolean set() {
+ if (isTerminal)
+ return true;
+ if (isSet)
+ return true;
+ atoms = new CIPAtom[parent == null ? 4 : 3];
+ int nBonds = atom.getBondCount();
+ Edge[] bonds = atom.getEdges();
+ int pt = 0;
+ for (int i = 0; i < nBonds; i++) {
+ Edge bond = bonds[i];
+ if (!bond.isCovalent())
+ continue;
+ Node other = bond.getOtherAtomNode(atom);
+ if (parent != null && parent.atom == other)
+ continue;
+ int order = bond.getCovalentOrder();
+ switch (order) {
+ case 3:
+ if (!addAtom(pt++, other, true)) {
+ isTerminal = true;
+ return false;
+ }
+ //$FALL-THROUGH$
+ case 2:
+ if (!addAtom(pt++, other, true)) {
+ isTerminal = true;
+ return false;
+ }
+ //$FALL-THROUGH$
+ case 1:
+ if (!addAtom(pt++, other, false)) {
+ isTerminal = true;
+ return false;
+ }
+ break;
+ default:
+ isTerminal = true;
+ return false;
+ }
+ }
+ isTerminal = (pt == 0);
+ nAtoms = pt;
+ for (; pt < atoms.length; pt++)
+ atoms[pt] = new CIPAtom(null, null, true);
+ return !isTerminal;
+ }
+
+ private boolean addAtom(int i, Node other, boolean isDummy) {
+ if (i >= atoms.length)
+ return false;
+ atoms[i] = new CIPAtom(other, this, isDummy);
+ return true;
+ }
+
+ boolean sortAtoms() {
+
+ for (int i = 0; i < nAtoms; i++) {
+ CIPAtom a = atoms[i];
+ for (int j = i + 1; j < nAtoms; j++) {
+ CIPAtom b = atoms[j];
+ int score = (int) Math.signum(a.compareTo(b));
+ if (Logger.debugging)
+ Logger.info("comparing " + a + " and " + b + " = " + score);
+ switch (score) {
+ case 1:
+ a.isAbove++;
+ break;
+ case -1:
+ b.isAbove++;
+ break;
+ case 0:
+ switch (breakTie(a, b)) {
+ case 1:
+ a.isAbove++;
+ break;
+ case -1:
+ b.isAbove++;
+ break;
+ case 0:
+ return false;
+ }
+ }
+ }
+ }
+ for (int i = 0; i < nAtoms; i++)
+ atoms[i].path += ";" + atoms[i].isAbove;
+ Arrays.sort(atoms);
+ if (Logger.debugging)
+ for (int i = 0; i < nAtoms; i++)
+ Logger.info("" + atoms[i]);
+ return true;
+ }
+
+ private int breakTie(CIPAtom a, CIPAtom b) {
+ if (a.isDummy || !a.set() || !b.set() || a.isTerminal || a.atom ==
b.atom)
+ return 0;
+ if (Logger.debugging)
+ Logger.info("tie for " + a + " and " + b);
+ Arrays.sort(a.atoms);
+ Arrays.sort(b.atoms);
+ // check to see if any of the three connections to a and b are different.
+ for (int i = 0; i < a.nAtoms; i++) {
+ int score = (int) Math.signum(a.atoms[i].compareTo(b.atoms[i]));
+ switch (score) {
+ case -1:
+ case 1:
+ return score;
+ }
+ }
+ // all are the same -- check to break tie next level
+ for (int i = 0; i < a.nAtoms; i++) {
+ int score = breakTie(a.atoms[i], b.atoms[i]);
+ switch (score) {
+ case -1:
+ case 1:
+ return score;
+ }
+ }
+ // all are the same and no tie breakers
+ return 0;
+ }
+
+ @Override
+ public int compareTo(CIPAtom a) {
+ // check to see that atoms are non-null and are different, and path is
different
+ return a.atom == null && atom == null ? 0 : a.atom == null ? -1
+ : atom == null ? 1 : a.atom == atom ? 0 : -a.path.compareTo(path);
+ }
+
+ }
+
+}
Property changes on: trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property
Modified: trunk/Jmol/src/org/jmol/symmetry/Symmetry.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/Symmetry.java 2017-04-06 12:09:34 UTC
(rev 21485)
+++ trunk/Jmol/src/org/jmol/symmetry/Symmetry.java 2017-04-06 20:58:28 UTC
(rev 21486)
@@ -765,4 +765,16 @@
return lst;
}
+ @Override
+ public String getChirality(Viewer vwr, Atom atom) {
+ CIPChirality cip = getCIPChirality(vwr);
+ return cip.getChirality(atom);
+ }
+
+ CIPChirality cip;
+
+ private CIPChirality getCIPChirality(Viewer vwr) {
+ return (cip == null ? (cip = ((CIPChirality)
Interface.getInterface("org.jmol.symmetry.CIPChirality", vwr,
"script"))).setViewer(vwr) : cip);
+ }
+
}
Modified: trunk/Jmol/src/org/jmol/util/Elements.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Elements.java 2017-04-06 12:09:34 UTC (rev
21485)
+++ trunk/Jmol/src/org/jmol/util/Elements.java 2017-04-06 20:58:28 UTC (rev
21486)
@@ -475,7 +475,7 @@
// add as we go
- private final static String naturalIsotopes = "1H,12C,14N,";
+ private final static String naturalIsotopes = "1H,12C,14N";
public final static boolean isNaturalIsotope(String isotopeSymbol) {
return (naturalIsotopes.indexOf(isotopeSymbol + ",") >= 0);
Modified: trunk/Jmol/src/org/jmol/util/Node.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Node.java 2017-04-06 12:09:34 UTC (rev
21485)
+++ trunk/Jmol/src/org/jmol/util/Node.java 2017-04-06 20:58:28 UTC (rev
21486)
@@ -46,6 +46,7 @@
public int getValence();
public void set(float x, float y, float z);
public int getMoleculeNumber(boolean inModel);
+ public int getNominalMass();
/**
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-04-06 12:09:34 UTC
(rev 21485)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-04-06 20:58:28 UTC
(rev 21486)
@@ -49,8 +49,16 @@
# 10. Run jmol/tools build-release.xml
#
-Jmol.___JmolVersion="14.11.3" // 2017-04-06
+Jmol.___JmolVersion="14.12.0-beta" // 2017-04-06
+new feature: {atom}.chirality
+ -- uses Cohen-Ingold-Prelog rules to assign R or S to a carbon center
+ -- ignores sulfur chirality
+ -- not fully tested
+ -- does not fully implement high symmetry cases
+
+JmolVersion="14.11.3" // 2017-04-06
+
bug fix: partial bond order for orders > 3 not working
-- for example: connect {_C} {_C} partial 5.3
bug fix: NBO MODEL loading with no file name goes to wrong directory
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