Revision: 21499
http://sourceforge.net/p/jmol/code/21499
Author: hansonr
Date: 2017-04-08 20:20:20 +0000 (Sat, 08 Apr 2017)
Log Message:
-----------
Jmol.___JmolVersion="14.13.1"
new feature: set labelfor {atomset} "value"
-- allows setting of label with out changing current selection
-- uses same syntax as LABEL command after {atomset}
-- for example:
set labelfor @atoms @myLabel
set labelfor {atomno <= 3} @{["a","b","c"]}
set labelfor {_C && chirality != ""} "%[atomname] %[chirality]"
bug fix: {*}.chirality with triple bonds fails
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/AtomCollection.java
trunk/Jmol/src/org/jmol/modelset/BondCollection.java
trunk/Jmol/src/org/jmol/modelset/ModelSet.java
trunk/Jmol/src/org/jmol/script/ScriptEval.java
trunk/Jmol/src/org/jmol/script/ScriptExpr.java
trunk/Jmol/src/org/jmol/smiles/SmilesAromatic.java
trunk/Jmol/src/org/jmol/smiles/SmilesMatcher.java
trunk/Jmol/src/org/jmol/smiles/SmilesSearch.java
trunk/Jmol/src/org/jmol/smiles/SmilesStereo.java
trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java
trunk/Jmol/src/org/jmol/symmetry/Symmetry.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/api/SmilesMatcherInterface.java
===================================================================
--- trunk/Jmol/src/org/jmol/api/SmilesMatcherInterface.java 2017-04-07
23:40:05 UTC (rev 21498)
+++ trunk/Jmol/src/org/jmol/api/SmilesMatcherInterface.java 2017-04-08
20:20:20 UTC (rev 21499)
@@ -56,6 +56,4 @@
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 2017-04-07 23:40:05 UTC
(rev 21498)
+++ trunk/Jmol/src/org/jmol/api/SymmetryInterface.java 2017-04-08 20:20:20 UTC
(rev 21499)
@@ -218,6 +218,6 @@
void toFractionalM(M4 m);
- public String getChirality(Viewer vwr, Atom atom);
+ public int getChirality(Viewer vwr, Atom atom);
}
Modified: trunk/Jmol/src/org/jmol/modelset/Atom.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/Atom.java 2017-04-07 23:40:05 UTC (rev
21498)
+++ trunk/Jmol/src/org/jmol/modelset/Atom.java 2017-04-08 20:20:20 UTC (rev
21499)
@@ -25,13 +25,11 @@
package org.jmol.modelset;
-import javax.annotation.processing.RoundEnvironment;
-
import javajs.util.CU;
import javajs.util.Lst;
+import javajs.util.P3;
import javajs.util.PT;
import javajs.util.SB;
-import javajs.util.P3;
import javajs.util.T3;
import javajs.util.V3;
@@ -46,11 +44,11 @@
import org.jmol.modelsetbio.BioModel;
import org.jmol.script.T;
import org.jmol.util.C;
+import org.jmol.util.Edge;
import org.jmol.util.Elements;
import org.jmol.util.Node;
import org.jmol.util.Point3fi;
import org.jmol.util.Tensor;
-import org.jmol.util.Edge;
import org.jmol.util.Vibration;
import org.jmol.viewer.JC;
import org.jmol.viewer.Viewer;
@@ -72,9 +70,6 @@
public final static int ATOM_INFRAME_NOTHIDDEN = ATOM_INFRAME |
ATOM_NOTHIDDEN;
public final static int ATOM_SHAPE_VIS_MASK = ~ATOM_INFRAME_NOTHIDDEN;
- private final static byte VIBRATION_VECTOR_FLAG = 1;
- private final static byte IS_HETERO_FLAG = 2;
- private final static byte FLAG_MASK = 3;
public static final int RADIUS_MAX = 16;
public static final float RADIUS_GLOBAL = 16.1f;
@@ -86,11 +81,20 @@
public Group group;
private float userDefinedVanDerWaalRadius;
byte valence;
-
private short atomicAndIsotopeNumber;
public BS atomSymmetry;
- private byte formalChargeAndFlags;
+ private byte formalChargeAndFlags; // cccc RSvh
+
+ private final static int CHARGE_OFFSET = 4;
+ private final static int VIBRATION_VECTOR_FLAG = 1;
+ private final static int IS_HETERO_FLAG = 2;
+ private final static int CHIRALITY_OFFSET = 2;
+ private final static int CHIRALITY_R_FLAG = 1;
+ private final static int CHIRALITY_S_FLAG = 2; // 3 is "no chirality"
+ private final static int CHIRALITY_MASK = 12;
+ private final static int FLAG_MASK = 0xF;
+
public short madAtom;
public short colixAtom;
@@ -193,6 +197,7 @@
}
private void deleteBondAt(int i) {
+ setChirality(0);
int newLength = bonds.length - 1;
if (newLength == 0) {
bonds = null;
@@ -352,9 +357,13 @@
return (formalChargeAndFlags & VIBRATION_VECTOR_FLAG) != 0;
}
+ /**
+ *
+ * @param charge from -3 to 7
+ */
public void setFormalCharge(int charge) {
formalChargeAndFlags = (byte)((formalChargeAndFlags & FLAG_MASK)
- | ((charge == Integer.MIN_VALUE ? 0 : charge > 7 ? 7 : charge < -3 ?
-3 : charge) << 2));
+ | ((charge == Integer.MIN_VALUE ? 0 : charge > 7 ? 7 : charge < -3 ?
-3 : charge) << CHARGE_OFFSET));
}
void setVibrationVector() {
@@ -363,7 +372,7 @@
@Override
public int getFormalCharge() {
- return formalChargeAndFlags >> 2;
+ return formalChargeAndFlags >> CHARGE_OFFSET;
}
// a percentage value in the range 0-100
@@ -1384,12 +1393,27 @@
}
/**
- * Determine R/S chirality at this position
+ * Determine R/S chirality at this position; non-H atoms only; cached in
formalChargeAndFlags
+ *
* @return "" or "R" or "S"
*/
private String getChirality() {
- return group.chain.model.ms.getChirality(this);
+ int flags = (formalChargeAndFlags & CHIRALITY_MASK) >> CHIRALITY_OFFSET;
+ if (flags == 0 && atomicAndIsotopeNumber > 1) {
+ flags = group.chain.model.ms.getChirality(this);
+ formalChargeAndFlags |= ((flags == 0 ? 3 : flags) << CHIRALITY_OFFSET);
+ }
+ return (flags == CHIRALITY_R_FLAG ? "R" : flags == CHIRALITY_S_FLAG ? "S"
: "");
}
+
+ /**
+ *
+ * @param c [0:unknown; 1: R; 2: S; 3: none]
+ */
+ void setChirality(int c) {
+ formalChargeAndFlags = (byte)((formalChargeAndFlags & ~CHIRALITY_MASK)
+ | (c << CHIRALITY_OFFSET));
+ }
@Override
public char getInsertionCode() {
Modified: trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2017-04-07
23:40:05 UTC (rev 21498)
+++ trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2017-04-08
20:20:20 UTC (rev 21499)
@@ -113,6 +113,8 @@
protected P3 averageAtomPoint;
+ protected boolean haveChirality;
+
/**
* Binary Space Partitioning Forest
*/
Modified: trunk/Jmol/src/org/jmol/modelset/BondCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/BondCollection.java 2017-04-07
23:40:05 UTC (rev 21498)
+++ trunk/Jmol/src/org/jmol/modelset/BondCollection.java 2017-04-08
20:20:20 UTC (rev 21499)
@@ -83,6 +83,9 @@
public void resetMolecules() {
molecules = null;
moleculeCount = 0;
+ if (haveChirality)
+ for (int i = ac; --i >= 0;)
+ at[i].setChirality(0);
}
public BondIterator getBondIteratorForType(int bondType, BS bsAtoms) {
Modified: trunk/Jmol/src/org/jmol/modelset/ModelSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2017-04-07 23:40:05 UTC
(rev 21498)
+++ trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2017-04-08 20:20:20 UTC
(rev 21499)
@@ -940,6 +940,7 @@
modelNames = mergeModelSet.modelNames;
modelNumbers = mergeModelSet.modelNumbers;
frameTitles = mergeModelSet.frameTitles;
+ haveChirality = mergeModelSet.haveChirality;
if (msInfo != null)
msInfo.remove("models");
mergeAtomArrays(mergeModelSet);
@@ -4068,7 +4069,14 @@
return (dssrData == null || dssrData.length <= i ? Float.NaN :
dssrData[i]);
}
- public String getChirality(Atom atom) {
+ /**
+ * Determine the Cahn-Ingold-Prelog R/S chirality of an atom
+ *
+ * @param atom
+ * @return [0:none, 1:R, 2:S]
+ */
+ public int getChirality(Atom atom) {
+ haveChirality = true;
return Interface.getSymmetry(vwr, "ms").getChirality(vwr, atom);
}
Modified: trunk/Jmol/src/org/jmol/script/ScriptEval.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEval.java 2017-04-07 23:40:05 UTC
(rev 21498)
+++ trunk/Jmol/src/org/jmol/script/ScriptEval.java 2017-04-08 20:20:20 UTC
(rev 21499)
@@ -2686,7 +2686,7 @@
setSize(iShape, (tok == T.halo ? -1000f : 1f));
return;
case T.label:
- cmdLabel(1);
+ cmdLabel(1, null);
return;
case T.vector:
cmdVector();
@@ -4134,7 +4134,7 @@
vwr.invertSelected(pt, plane, iAtom, bs);
}
- private void cmdLabel(int index) throws ScriptException {
+ private void cmdLabel(int index, BS bs) throws ScriptException {
if (chk)
return;
sm.loadShape(JC.SHAPE_LABELS);
@@ -4156,7 +4156,7 @@
default:
strLabel = paramAsStr(index);
}
- sm.setLabel(strLabel, vwr.bsA());
+ sm.setLabel(strLabel, bs == null ? vwr.bsA() : bs);
}
public void cmdLoad() throws ScriptException {
@@ -6718,7 +6718,7 @@
cmdHistory(2);
return;
case T.label:
- cmdLabel(2);
+ cmdLabel(2, null);
return;
case T.unitcell:
cmdUnitcell(2);
@@ -7100,7 +7100,7 @@
if (lckey.indexOf("label") == 0
&& PT
.isOneOf(lckey.substring(5),
-
";front;group;atom;offset;offsetexact;offsetabsolute;pointer;alignment;toggle;scalereference;"))
{
+
";front;group;atom;offset;offsetexact;offsetabsolute;pointer;alignment;toggle;scalereference;for;"))
{
if (cmdSetLabel(lckey.substring(5)))
return;
}
@@ -7342,6 +7342,11 @@
Object propertyValue = null;
setShapeProperty(JC.SHAPE_LABELS, "setDefaults", vwr.slm.noneSelected);
while (true) {
+ if (str.equals("for")) {
+ BS bs = atomExpressionAt(2);
+ cmdLabel(iToken + 1, bs);
+ return true;
+ }
if (str.equals("scalereference")) {
float scaleAngstromsPerPixel = floatParameter(2);
if (scaleAngstromsPerPixel >= 5) // actually a zoom value
Modified: trunk/Jmol/src/org/jmol/script/ScriptExpr.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptExpr.java 2017-04-07 23:40:05 UTC
(rev 21498)
+++ trunk/Jmol/src/org/jmol/script/ScriptExpr.java 2017-04-08 20:20:20 UTC
(rev 21499)
@@ -2502,7 +2502,7 @@
fixed[j] = T.tv(T.decimal, getFloatEncodedInt("" + v), v);
} else if (v instanceof String) {
if (!forceString && !isExpression) {
- if ((tok != T.set || j > 1 && st[1].tok != T.echo)
+ if ((tok != T.set || j > 1 && st[1].tok != T.echo &&
!"labelfor".equalsIgnoreCase(st[1].value.toString()))
&& T.tokAttr(tok, T.mathExpressionCommand)) {
v = getParameter((String) v, T.variable, true);
}
Modified: trunk/Jmol/src/org/jmol/smiles/SmilesAromatic.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesAromatic.java 2017-04-07 23:40:05 UTC
(rev 21498)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesAromatic.java 2017-04-08 20:20:20 UTC
(rev 21499)
@@ -27,6 +27,8 @@
import java.util.Hashtable;
import javajs.util.Lst;
+import javajs.util.Measure;
+import javajs.util.P3;
import javajs.util.V3;
import org.jmol.java.BS;
@@ -250,9 +252,8 @@
if (cutoff <= 0)
cutoff = 0.01f;
- V3 vTemp = new V3();
- V3 vA = new V3();
- V3 vB = new V3();
+ V3 vNorm = null;
+ V3 vTemp = null;
V3 vMean = null;
int nPoints = bs.cardinality();
V3[] vNorms = new V3[nPoints * 2];
@@ -285,18 +286,21 @@
}
}
- if (vMean == null)
+ if (vMean == null) {
vMean = new V3();
+ vNorm = new V3();
+ vTemp = new V3();
+ }
// check the normal for r1 - i - r2 plane
// check the normal for r1 - iSub - r2 plane
for (int k = 0, j = i; k < 2; k++) {
- SmilesSearch.getNormalThroughPoints(atoms[r1], atoms[j], atoms[r2],
- vTemp, vA, vB);
- if (!addNormal(vTemp, vMean, maxDev))
+ Measure.getNormalThroughPoints((P3) atoms[r1], (P3) atoms[j], (P3)
atoms[r2],
+ vNorm, vTemp);
+ if (!addNormal(vNorm, vMean, maxDev))
return false;
- vNorms[nNorms++] = V3.newV(vTemp);
+ vNorms[nNorms++] = V3.newV(vNorm);
if ((j = iSub) < 0)
break;
}
Modified: trunk/Jmol/src/org/jmol/smiles/SmilesMatcher.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesMatcher.java 2017-04-07 23:40:05 UTC
(rev 21498)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesMatcher.java 2017-04-08 20:20:20 UTC
(rev 21499)
@@ -581,9 +581,4 @@
return null;
}
- @Override
- public int getChirality(Node atom4, Node atom3, Node atom2, Node atom1) {
- return SmilesStereo.getHandedness(atom4, atom3, atom2, atom1, new VTemp());
- }
-
}
Modified: trunk/Jmol/src/org/jmol/smiles/SmilesSearch.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesSearch.java 2017-04-07 23:40:05 UTC
(rev 21498)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesSearch.java 2017-04-08 20:20:20 UTC
(rev 21499)
@@ -32,7 +32,6 @@
import javajs.util.P3;
import javajs.util.SB;
import javajs.util.T3;
-import javajs.util.V3;
import org.jmol.java.BS;
import org.jmol.util.BSUtil;
@@ -1864,31 +1863,7 @@
}
}
}
-
- /**
- * calculates a normal to a plane for three points and returns a signed
- * distance
- *
- * @param pointA
- * @param pointB
- * @param pointC
- * @param vNorm
- * @param vAB
- * @param vAC
- * @return a signed distance
- */
- static float getNormalThroughPoints(Node pointA, Node pointB, Node pointC,
- V3 vNorm, V3 vAB, V3 vAC) {
- vAB.sub2((P3) pointB, (P3) pointA);
- vAC.sub2((P3) pointC, (P3) pointA);
- vNorm.cross(vAB, vAC);
- vNorm.normalize();
- // ax + by + cz + d = 0
- // so if a point is in the plane, then N dot X = -d
- vAB.setT((P3) pointA);
- return -vAB.dot(vNorm);
- }
-
+
Node findImplicitHydrogen(Node atom) {
// if (haveTopo) {
// SmilesAtom sAtom = (SmilesAtom) atom;
Modified: trunk/Jmol/src/org/jmol/smiles/SmilesStereo.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesStereo.java 2017-04-07 23:40:05 UTC
(rev 21498)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesStereo.java 2017-04-08 20:20:20 UTC
(rev 21499)
@@ -829,9 +829,9 @@
case 4: // tetrahedral, square planar
if (atom3 == null || atom4 == null)
return "";
- float d = SmilesSearch.getNormalThroughPoints(atom1, atom2, atom3,
- v.vTemp, v.vA, v.vB);
- if (Math.abs(distanceToPlane(v.vTemp, d, (P3) atom4)) < 0.2f) {
+ float d = Measure.getNormalThroughPoints((P3) atom1, (P3) atom2, (P3)
atom3,
+ v.vTemp, v.vA);
+ if (Math.abs(Measure.distanceToPlaneV(v.vTemp, d, (P3) atom4)) < 0.2f) {
chiralClass = SQUARE_PLANAR;
if (checkStereochemistryAll(false, atom0, chiralClass, 1, atom1, atom2,
atom3, atom4, atom5, atom6, v))
@@ -863,7 +863,7 @@
case TETRAHEDRAL:
return (isNot == (getHandedness(atom2, atom3, atom4, atom1, v) !=
order));
case SQUARE_PLANAR:
- getPlaneNormals(atom1, atom2, atom3, atom4, v);
+ getPlaneNormals((P3) atom1, (P3) atom2, (P3) atom3, (P3) atom4, v);
// vNorm1 vNorm2 vNorm3 are right-hand normals for the given
// triangles
// 1-2-3, 2-3-4, 3-4-1
@@ -914,7 +914,7 @@
|| !isDiaxial(atom0, atom0, atom2, atom4, v, -0.95f)
|| !isDiaxial(atom0, atom0, atom3, atom5, v, -0.95f))
return false;
- getPlaneNormals(atom2, atom3, atom4, atom5, v);
+ getPlaneNormals((P3) atom2, (P3) atom3, (P3) atom4, (P3) atom5, v);
// check for proper order 2-3-4-5
// n1n2n3
if (v.vNorm2.dot(v.vNorm3) < 0 || v.vNorm3.dot(v.vNorm4) < 0)
@@ -948,8 +948,7 @@
* @return 1 for "@", 2 for "@@"
*/
static int getHandedness(Node a, Node b, Node c, Node pt, VTemp v) {
- float d = SmilesSearch.getNormalThroughPoints(a, b, c, v.vTemp, v.vA,
- v.vB);
+ float d = Measure.getNormalThroughPoints((P3) a, (P3) b, (P3) c, v.vTemp,
v.vA);
// int atat = (distanceToPlane(v.vTemp, d, (P3) pt) > 0 ? 1 : 2);
// System.out.println("$ draw p1 " + P3.newP((P3)a) +" color red '"+a+"
[2]'");
// System.out.println("$ draw p2 " + P3.newP((P3)b) +" color green '"+b+"
[3]'");
@@ -956,26 +955,19 @@
// System.out.println("$ draw p3 " + P3.newP((P3)c) +" color blue '"+c+"
[4]'");
// System.out.println("$ draw p " + P3.newP((P3)a) +" " + P3.newP((P3)b) +"
" + P3.newP((P3)c) +"" );
// System.out.println("$ draw v vector {" + P3.newP((P3)pt) +"} " +
v.vTemp+" '"+ (atat==2 ? "@@" : "@")+ pt + " [1]' color " + (atat == 2 ?
"white" : "yellow"));
- return (distanceToPlane(v.vTemp, d, (P3) pt) > 0 ? 1 : 2);
+ return (Measure.distanceToPlaneV(v.vTemp, d, (P3) pt) > 0 ? 1 : 2);
}
- private static void getPlaneNormals(Node atom1, Node atom2, Node atom3,
- Node atom4, VTemp v) {
- SmilesSearch.getNormalThroughPoints(atom1, atom2, atom3, v.vNorm2,
- v.vTemp1, v.vTemp2);
- SmilesSearch.getNormalThroughPoints(atom2, atom3, atom4, v.vNorm3,
- v.vTemp1, v.vTemp2);
- SmilesSearch.getNormalThroughPoints(atom3, atom4, atom1, v.vNorm4,
- v.vTemp1, v.vTemp2);
+ private static void getPlaneNormals(P3 atom1, P3 atom2, P3 atom3,
+ P3 atom4, VTemp v) {
+ Measure.getNormalThroughPoints(atom1, atom2, atom3, v.vNorm2,
+ v.vTemp1);
+ Measure.getNormalThroughPoints(atom2, atom3, atom4, v.vNorm3,
+ v.vTemp1);
+ Measure.getNormalThroughPoints(atom3, atom4, atom1, v.vNorm4,
+ v.vTemp1);
}
- static float distanceToPlane(V3 norm, float w, P3 pt) {
- return (norm == null ? Float.NaN : (norm.x * pt.x + norm.y * pt.y + norm.z
- * pt.z + w)
- / (float) Math
- .sqrt(norm.x * norm.x + norm.y * norm.y + norm.z * norm.z));
- }
-
static int checkChirality(String pattern, int index, SmilesAtom newAtom)
throws InvalidSmilesException {
int stereoClass = 0;
Modified: trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-04-07 23:40:05 UTC
(rev 21498)
+++ trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-04-08 20:20:20 UTC
(rev 21499)
@@ -2,9 +2,12 @@
import java.util.Arrays;
+import javajs.util.Measure;
+import javajs.util.P3;
+import javajs.util.V3;
+
import org.jmol.java.BS;
-import org.jmol.api.SmilesMatcherInterface;
import org.jmol.util.BSUtil;
import org.jmol.util.Edge;
import org.jmol.util.Logger;
@@ -12,82 +15,45 @@
import org.jmol.viewer.Viewer;
/**
- * A relatively simple implementation of Cahn-Ingold-Prelog rules for
assigning R/S chirality
+ * A relatively simple implementation of Cahn-Ingold-Prelog rules for assigning
+ * R/S chirality. Based on private knowledge of rules.
*
- * [1] getChirality(Node)
- * new CIPAtom(Node)
- * set()
- * return getRorS();
- *
- * [2] CIPAtom.getRorS()
- * sortSubstituents()
- * return f(SmilesMatcher().getChirality())
- *
- *
- * [3] sortSubstituents()
- * if (necessary)
- * breakTie(a,b)
- *
- * [4] breakTie(a,b)
- * a.set(), b.set()
- * for each substituent...
- * compareAB(a.atoms[i], b.atoms[i])
- * if (all are tied) ...
- * sortSubstituents(a.atoms)
- * sortSubstituents(b.atoms)
- * for each substituent...
- * breakTie(a.atoms[i], b.atoms[i])
- *
*
* Introduced in Jmol 14.12.0
*
- * @author Bob Hanson hans...@stolaf.edu
+ * @author Bob Hanson hans...@stolaf.edu
*/
public class CIPChirality {
- // Checked using:
-
- // function checkchiral(m) {
- // if (m) load @m
- // background label yellow
- // color labels black
- // select _C
- // label %[atomname]
- // refresh
- // var b = {_C}
- // for (var a in b) {
- // var c = a.chirality;
- // print _smilesString + " " + a + c
- // if (c) {
- // select a
- // c = a.atomname + " " + c
- // label @c
- // }
- // }
- // select *
- // }
+ // Pseudocode:
//
- // checkchiral("$(R)-glycidol")
- // delay 1
- // checkchiral("$glucose")
- // delay 1
- // checkchiral("$(2S,3R)-2,3-oxiranediol")
- // delay 1
- // checkchiral("$(S)-2-butanol")
- // delay 1
- // checkchiral("$(R)-2-butanol")
- // delay 1
- // checkchiral("$(2S,3R)-2,3-butanediol")
- // delay 1
- // checkchiral("$(2S,3S)-2,3-butanediol")
- // delay 1
- // checkchiral("$(2R,3R)-2,3-butanediol")
- // delay 1
- // checkchiral("$(2R,3S)-2,3-butanediol")
- // delay 1
- // checkchiral("$1,4-dimethylcyclohexane") // no chirality
- // delay 1
- // checkchiral("$cholesterol") // (3S,8S,9S,10R,13R,14S,17R) and sidechain R
+ // [1] if !(sortSubstituents()) return NO_CHIRALITY
+ // return getChirality(firstAtom = true)
+ //
+ //
+ // [3] sortSubstituents()
+ // for all pairs of substituents i,j...
+ // compare(i,j)
+ // if (TIED and firstAtom)
+ // breakTie(i,j) or return NO_CHIRALITY
+ //
+ // [4] breakTie(a,b)
+ // for each substituent i of a and b...
+ // compareIgnoreDummy(a.sub_i, b.sub_i)
+ // if (a winner) return A_WINS or B_WINS
+ // a.sortSubstituents(firstAtom = false)
+ // b.sortSubstituents(firstAtom = false)
+ // for each substituent...
+ // breakTie(a.sub_i, b.sub_i) or return TIED
+ // return TIED
+ //
+ // [5] return checkWinding()
+ // return
+
+ static final int NO_CHIRALITY = 0;
+ static final int TIED = NO_CHIRALITY;
+ static final int A_WINS = 1;
+ static final int B_WINS = -1;
Viewer vwr;
@@ -100,146 +66,124 @@
return this;
}
- public String getChirality(Node atom) {
- if (atom.getCovalentBondCount() != 4)
- return "";
- CIPAtom a = new CIPAtom(atom, null, false);
- if (!a.set())
- return "";
- String rs = getRorS(a);
- if (Logger.debugging)
- Logger.info(atom + " " + rs);
- return rs;
- }
+ /**
+ * Determine the Cahn-Ingold-Prelog R/S chirality of an atom
+ *
+ * @param atom
+ * @return [0:none, 1:R, 2:S]
+ */
+ public int getChirality(Node atom) {
+ int rs = NO_CHIRALITY;
+ CIPAtom a;
+ if (atom.getCovalentBondCount() != 4
+ || !(a = new CIPAtom(atom, null, false)).set())
+ return rs;
- private String getRorS(CIPAtom a) {
try {
- CIPAtom[] atoms = sortSubstituents(a.atoms, false);
- if (atoms == null)
- return "";
- SmilesMatcherInterface sm = vwr.getSmilesMatcher();
- switch (sm.getChirality(atoms[3].atom, atoms[2].atom,
- atoms[1].atom, atoms[0].atom)) {
- case 1:
- return "R";
- case 2:
- return "S";
- default:
- return "";
- }
+ if (a.sortSubstituents())
+ rs = getHandedness(a);
} catch (Throwable e) {
- e.printStackTrace();
- return "";
+ System.out.println(e + " in CIPChirality");
+ if (!vwr.isJS)
+ e.printStackTrace();
}
+ if (Logger.debugging)
+ Logger.info(atom + " " + (rs == 1 ? "R" : rs == 2 ? "S" : ""));
+ return rs;
}
/**
- * Sort the substituents of an atom in preparation for comparing the set
with other atoms
+ * determine the winding of the circuit p1--p2--p3 relative to point p4
*
- * @param atoms may be 3 or 4 atoms here
- * @param allowTie
- *
- * @return true if we have four distinct atoms in the end
+ * @param a
+ * @return 1 for "R", 2 for "S"
*/
- private static CIPAtom[] sortSubstituents(CIPAtom[] atoms, boolean allowTie)
{
- int n = atoms.length;
- for (int i = 0; i < n; i++)
- atoms[i].isAbove = 0;
- for (int i = 0; i < n; i++) {
- CIPAtom a = atoms[i];
- for (int j = i + 1; j < n; 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:
- if (allowTie)
- a.isAbove++;
- else
- return null;
- }
- }
- }
- }
- CIPAtom[] ret = new CIPAtom[n];
- for (int i = 0; i < n; i++)
- ret[atoms[i].isAbove] = atoms[i];
- if (Logger.debugging)
- for (int i = 0; i < n; i++)
- Logger.info("" + ret[i]);
- return ret;
+ static int getHandedness(CIPAtom a) {
+ P3 p1 = (P3) a.atoms[0].atom; // highest priority
+ P3 p2 = (P3) a.atoms[1].atom;
+ P3 p3 = (P3) a.atoms[2].atom;
+ P3 p4 = (P3) a.atoms[3].atom; // lowest priority
+ V3 vNorm = new V3();
+ float d = Measure.getNormalThroughPoints(p1, p2, p3, vNorm, new V3());
+ return (Measure.distanceToPlaneV(vNorm, d, p4) > 0 ? 1 : 2);
}
/**
- * Break a tie at any level in the iteration between to atoms that
- * otherwise are the same by sorting heir
+ * Break a tie at any level in the iteration between to atoms that otherwise
+ * are the same by sorting their substituents.
*
* @param a
* @param b
- * @return -1
+ * @return 1 to indicate a is the winner, -1 to indicate b is the winner; 0
+ * for a tie
*/
- private static int breakTie(CIPAtom a, CIPAtom b) {
- if (!a.set() || !b.set() || a.isTerminal || a.atom == b.atom)
- return 0;
+ static int breakTie(CIPAtom a, CIPAtom b) {
+
+ // If one of them is a dummy atom (from an alkene, alkyne, or ring) and
the other isn't,
+ // then the dummy is the loser.
+ if (a.isDummy != b.isDummy)
+ return (a.isDummy ? -1 : 1);
+
+ // If both are dummies, it's a tie.
+ if (a.isDummy && b.isDummy)
+ return TIED;
+
+ // return NO_CHIRALITY/TIED if:
+ // a) one or the other can't be set (because it has too many connections)
+ // b) or one or the other is terminal (has no substituents)
+ // c) or they are the same atom
+
+ if (!a.set() || !b.set()
+ || a.isTerminal || b.isTerminal
+ || a.atom == b.atom)
+ return NO_CHIRALITY;
if (Logger.debugging)
Logger.info("tie for " + a + " and " + b);
- // check to see if any of the three connections to a and b are different.
+
+ // Phase I -- shallow check using compareIgnoreDummy
+ //
+ // Check to see if any of the three connections to a and b are different.
+ // Note that we do not consider dummy atom different from a regular atom
here
+ // because we are just looking for atom differences, not substituent
differences.
+ //
+ // Say we have {O (O) C} and {O O H}
+ //
+ // The rules require that we first only look at just the atoms, so OOC
beats OOH.
+
+ int score = compareAB(a, b, true);
+ if (score != TIED)
+ return score;
+
+ // Phase I -- deep check using breakTie
+ //
+ // OK, so all three are nominally the same.
+ // Now seriously deep-sort each list based on substituents
+ // and then check them one by one to see if the tie can be broken.
+
+ a.sortSubstituents();
+ b.sortSubstituents();
+ return compareAB(a, b, false);
+ }
+
+ private static int compareAB(CIPAtom a, CIPAtom b, boolean ignoreDummy) {
for (int i = 0; i < a.nAtoms; i++) {
CIPAtom ai = a.atoms[i];
CIPAtom bi = b.atoms[i];
- int score = (int) Math.signum(compareAB(ai, bi));
- switch (score) {
- case -1:
- case 1:
+ int score = (ignoreDummy ? compareIgnoreDummy(ai, bi) : breakTie(ai,
bi));
+ if (score != TIED)
return score;
- case 0:
- break;
- }
}
- // all are the same -- check to break tie next level
- // now isDummy counts
-
- a.atoms = sortSubstituents(a.atoms, true);
- b.atoms = sortSubstituents(b.atoms, true);
-
- for (int i = 0; i < a.nAtoms; i++) {
- CIPAtom ai = a.atoms[i];
- CIPAtom bi = b.atoms[i];
- int score = (ai.isDummy == bi.isDummy ? breakTie(ai, bi) : ai.isDummy ?
-1 : 1);
- switch (score) {
- case -1:
- case 1:
- return score;
- case 0:
- }
- }
- // all are the same and no tie breakers
- return 0;
+ return TIED;
}
private class CIPAtom implements Comparable<CIPAtom> {
/**
- * Use of Node allows us to implement this in SMILES or Jmol.
+ * Use of Node allows us to implement this in SMILES or Jmol.
*
*/
Node atom;
-
+
/**
* One of the two key characteristics for assigning R and S
*/
@@ -253,24 +197,24 @@
CIPAtom parent;
/**
- * Dummy atoms have massNo and elemNo but no substituents.
- * They are slightly lower in priority than standard atoms.
+ * Dummy atoms have massNo and elemNo but no substituents. They are
slightly
+ * lower in priority than standard atoms.
*
*/
boolean isDummy = true;
-
+
/**
* Terminal (single-valence) atoms need not be followed further.
*
*/
boolean isTerminal;
-
+
/**
* We only set an atom once.
*
*/
boolean isSet;
-
+
/**
* For the main four atoms, isAbove will increment each time they "win" in
a
* priority contest, thus leading to our desired ordering.
@@ -277,21 +221,21 @@
*
*/
int isAbove;
-
+
/**
- * It is important to keep track of the path to this atom in order
- * to prevent infinite cycling. This is taken care of by bsPath.
- * The last atom in the path when cyclic is a dummy atom.
+ * It is important to keep track of the path to this atom in order to
+ * prevent infinite cycling. This is taken care of by bsPath. The last atom
+ * in the path when cyclic is a dummy atom.
*
*/
BS bsPath;
-
+
/**
* The substituents -- 4 for the base carbon; 3 or fewer for other atoms.
*
*/
CIPAtom[] atoms;
-
+
/**
* Number of substituent atoms.
*/
@@ -299,18 +243,20 @@
@Override
public String toString() {
- return atom.toString() + (isDummy ? " *" : "" + " " + (isAbove + 1));
+ return (atom == null ? "<null>" : atom.toString())
+ + (isDummy ? " *" : "" + " " + (isAbove + 1));
}
/**
*
- * @param atom or null to indicate a null placeholder
+ * @param atom
+ * or null to indicate a null placeholder
* @param parent
* @param isDummy
*/
- public CIPAtom(Node atom, CIPAtom parent, boolean isDummy) {
+ CIPAtom(Node atom, CIPAtom parent, boolean isDummy) {
if (atom == null)
- return;
+ return;
this.atom = atom;
this.parent = parent;
this.isTerminal = atom.getCovalentBondCount() == 1;
@@ -334,13 +280,9 @@
*
*/
boolean set() {
- if (isTerminal)
+ if (isTerminal || isSet)
return true;
- if (isSet)
- return true;
isSet = true;
- if (isDummy)
- return false;
atoms = new CIPAtom[parent == null ? 4 : 3];
int nBonds = atom.getBondCount();
Edge[] bonds = atom.getEdges();
@@ -355,19 +297,19 @@
int order = bond.getCovalentOrder();
switch (order) {
case 3:
- if (!addAtom(pt++, other, true)) {
+ if (!addAtom(pt++, other, false)) {
isTerminal = true;
return false;
}
//$FALL-THROUGH$
case 2:
- if (!addAtom(pt++, other, true)) {
+ if (!addAtom(pt++, other, order != 2)) {
isTerminal = true;
return false;
}
//$FALL-THROUGH$
case 1:
- if (!addAtom(pt++, other, false)) {
+ if (!addAtom(pt++, other, order != 1)) {
isTerminal = true;
return false;
}
@@ -381,6 +323,9 @@
nAtoms = pt;
for (; pt < atoms.length; pt++)
atoms[pt] = new CIPAtom(null, null, true);
+
+ // Do an initial atom-only shallow sort using a.compareTo(b)
+
Arrays.sort(atoms);
return !isTerminal;
}
@@ -401,29 +346,82 @@
}
/**
- * used in Array.sort and sortFourAtoms; includes isDummy check
+ * Deep-Sort the substituents of an atom.
+ * Don't allow ties if this is the first atom (parent == null).
+ *
+ * @return true if this is not the first atom or if all four substituents
are unique
*/
+ boolean sortSubstituents() {
+ boolean allowTie = (parent != null);
+ int n = atoms.length;
+ for (int i = 0; i < n; i++)
+ atoms[i].isAbove = 0;
+ for (int i = 0; i < n; i++) {
+ CIPAtom a = atoms[i];
+ for (int j = i + 1; j < n; j++) {
+ CIPAtom b = atoms[j];
+ int score = a.compareTo(b);
+ if (Logger.debugging)
+ Logger.info("comparing " + n + " " + i + " " + j + " " + a + " and
" + b + " = " + score);
+ switch (score) {
+ case A_WINS:
+ a.isAbove++;
+ break;
+ case B_WINS:
+ b.isAbove++;
+ break;
+ case TIED:
+ switch (breakTie(a, b)) {
+ case TIED:
+ if (!allowTie)
+ return false;
+ //$FALL-THROUGH$
+ case A_WINS:
+ a.isAbove++;
+ break;
+ case B_WINS:
+ b.isAbove++;
+ break;
+ }
+ break;
+ }
+ }
+ }
+ CIPAtom[] ret = new CIPAtom[n];
+ for (int i = 0; i < n; i++)
+ ret[atoms[i].isAbove] = atoms[i];
+ if (Logger.debugging)
+ for (int i = 0; i < n; i++)
+ Logger.info("" + ret[i]);
+ atoms = ret;
+ return true;
+ }
+
+ /**
+ * Used in Array.sort and sortSubstituents; includes check for dummy.
+ */
@Override
public int compareTo(CIPAtom a) {
return a.atom == atom ? 0 : a.atom == null ? -1 : atom == null ? 1
: a.elemNo != elemNo ? (a.elemNo < elemNo ? -1 : 1)
- : a.massNo != massNo ? (a.massNo < massNo ? -1 : 1)
- : a.isDummy != isDummy ? (a.isDummy ? -1 : 1) : 0;
+ : a.massNo != massNo ? (a.massNo < massNo ? -1 : 1)
+ : a.isDummy != isDummy ? (a.isDummy ? -1 : 1) : 0;
}
}
/**
- * Used only in breakTie; do not check dummy
+ * Used only in breakTie; do not check dummy, because this is only a shallow
+ * sort.
*
* @param a
* @param b
* @return 1 if b is higher; -1 if a is higher; otherwise 0
*/
- static public int compareAB(CIPAtom a, CIPAtom b) {
+ static int compareIgnoreDummy(CIPAtom a, CIPAtom b) {
return b.atom == a.atom ? 0 : b.atom == null ? -1 : a.atom == null ? 1
: b.elemNo != a.elemNo ? (b.elemNo < a.elemNo ? -1 : 1)
- : b.massNo != a.massNo ? (b.massNo < a.massNo ? -1 : 1) : 0;
+ : b.massNo != a.massNo ? (b.massNo < a.massNo ? -1 : 1) : 0;
}
}
Modified: trunk/Jmol/src/org/jmol/symmetry/Symmetry.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/Symmetry.java 2017-04-07 23:40:05 UTC
(rev 21498)
+++ trunk/Jmol/src/org/jmol/symmetry/Symmetry.java 2017-04-08 20:20:20 UTC
(rev 21499)
@@ -765,8 +765,14 @@
return lst;
}
+ /**
+ * Determine the Cahn-Ingold-Prelog R/S chirality of an atom
+ *
+ * @param atom
+ * @return [0:none, 1:R, 2:S]
+ */
@Override
- public String getChirality(Viewer vwr, Atom atom) {
+ public int getChirality(Viewer vwr, Atom atom) {
CIPChirality cip = getCIPChirality(vwr);
return cip.getChirality(atom);
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-04-07 23:40:05 UTC
(rev 21498)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-04-08 20:20:20 UTC
(rev 21499)
@@ -49,8 +49,21 @@
# 10. Run jmol/tools build-release.xml
#
-Jmol.___JmolVersion="14.12.1"
+Jmol.___JmolVersion="14.13.1"
+new feature: set labelfor {atomset} "value"
+ -- allows setting of label with out changing current selection
+ -- uses same syntax as LABEL command after {atomset}
+ -- for example:
+
+ set labelfor @atoms @myLabel
+ set labelfor {atomno <= 3} @{["a","b","c"]}
+ set labelfor {_C && chirality != ""} "%[atomname] %[chirality]"
+
+bug fix: {*}.chirality with triple bonds fails
+
+JmolVersion="14.12.1"
+
bug fix: NBO update
bug fix: JavaScript bug - missing Math.signum(f) - causes {atom}.chirality to
not work in JSmol
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