Revision: 21570
http://sourceforge.net/p/jmol/code/21570
Author: hansonr
Date: 2017-04-29 18:15:15 +0000 (Sat, 29 Apr 2017)
Log Message:
-----------
Jmol.___JmolVersion="14.15.2" // 4/29/17
bug fix: CIP chirality adds axial chirality (Ra/Sa, ra/sa) for cumulenes
bug fix: CIP chirality adds atropisomer chirality (Ra/Sa, ra/sa) for biaryls
bug fix: CIP chirality adds cumulene E/Z chirality
-- validates for 160 structures (some duplicates; both cip_examples.zip and
stereo_test_cases.sdf)
-- 817 lines
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java
trunk/Jmol/src/org/jmol/symmetry/Symmetry.java
trunk/Jmol/src/org/jmol/viewer/JC.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-04-28 18:59:41 UTC
(rev 21569)
+++ trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-04-29 18:15:15 UTC
(rev 21570)
@@ -16,7 +16,6 @@
import org.jmol.util.Logger;
import org.jmol.util.Node;
import org.jmol.viewer.JC;
-import org.jmol.viewer.Viewer;
/**
* A relatively efficient implementation of Cahn-Ingold-Prelog rules for
assigning
@@ -68,7 +67,8 @@
* 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
- * 4/28/17 Validated for 146 compounds, including imines and diazines
+ * 4/28/17 Validated for 146 compounds, including imines and diazines
+ * 4/29/17 validated for , including S, P,
*
*
* validation suite: see
https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol-datafiles/cip/
@@ -87,6 +87,7 @@
// for(all atoms) getChirality(applyRules1-3)
// for(all double bonds) checkEZ()
// for(all atoms still without designations) getChirality(applyRules1-5)
+ // for(all double bonds) checkEZ()
// if (haveAlkenes) removeUnnecessaryEZDesignations()
// }
//
@@ -224,17 +225,20 @@
static final int STEREO_SAME = Integer.MAX_VALUE;
static final int STEREO_UNDETERMINED = -1;
- static final int STEREO_BOTH = 3;
static final int STEREO_RS = -1;
static final int STEREO_EZ = -2;
+ static final int STEREO_ALLENE = -3;
- static final int STEREO_R = 1;
- static final int STEREO_S = 2;
+ static final int STEREO_R = JC.CIP_CHIRALITY_R_FLAG;
+ static final int STEREO_S = JC.CIP_CHIRALITY_S_FLAG;
- static final int STEREO_Z = 1;
- static final int STEREO_E = 2;
+ static final int STEREO_Z = JC.CIP_CHIRALITY_Z_FLAG;
+ static final int STEREO_E = JC.CIP_CHIRALITY_E_FLAG;
+ static final int STEREO_BOTH_RS = STEREO_R | STEREO_S;
+ static final int STEREO_BOTH_EZ = STEREO_Z | STEREO_E;
+
static final int RULE_0 = 0;
static final int RULE_1 = 1;
static final int RULE_2 = 2;
@@ -247,11 +251,6 @@
public String getRuleName() {
return "" + currentRule;
}
- /**
- * Jmol viewer that created this CIPChirality object
- *
- */
- private Viewer vwr;
/**
* incremental pointer providing a unique ID to every CIPAtom for debugging
@@ -302,11 +301,6 @@
// for reflection
}
- public CIPChirality setViewer(Viewer vwr) {
- this.vwr = vwr;
- return this;
- }
-
/**
* Initialize for a new molecular determination.
*
@@ -321,11 +315,11 @@
* A more general determination of chirality that involves ultimately all
* Rules 1-5.
*
- * @param atoms
- *
- * @param bsAtoms
+ * @param atoms atoms to process
+ * @param bsAtoms bit set of all atoms to process
+ * @param bsAtropisomeric bit set of all biphenyl-like connections
*/
- public void getChiralityForAtoms(Node[] atoms, BS bsAtoms) {
+ public void getChiralityForAtoms(Node[] atoms, BS bsAtoms, BS
bsAtropisomeric) {
if (bsAtoms.isEmpty())
return;
init();
@@ -356,7 +350,7 @@
// using BSAtoms here because we need the entire graph, even starting
with an H atom.
getSmallRings(atoms[bsAtoms.nextSetBit(0)]);
for (int i = bsToDo.nextSetBit(0); i >= 0; i = bsToDo.nextSetBit(i + 1))
- getAtomBondChirality(atoms[i], false, RULE_3, lstEZ, bsToDo);
+ getAtomBondChirality(atoms[i], false, RULE_3, lstEZ, bsToDo,
bsAtropisomeric);
}
@@ -371,7 +365,7 @@
if (haveAlkenes) {
for (int i = bsToDo.nextSetBit(0); i >= 0; i = bsToDo.nextSetBit(i + 1))
- getAtomBondChirality(atoms[i], false, RULE_5, lstEZ, bsToDo);
+ getAtomBondChirality(atoms[i], false, RULE_5, lstEZ, bsToDo,
bsAtropisomeric);
}
@@ -395,7 +389,7 @@
bsToDo.clear(i);
continue;
}
- if (!haveAlkenes && couldBeEZ(atoms[i], null))
+ if (!haveAlkenes && couldBeChiralAlkene(atoms[i], null) !=
STEREO_UNDETERMINED)
// do Rule 3, and check for rings that in the end should force removal
of E/Z designations
haveAlkenes = true;
}
@@ -461,19 +455,19 @@
* @param b optional other atom
* @return if the atom could be an EZ node
*/
- private boolean couldBeEZ(Node a, Node b) {
+ private int couldBeChiralAlkene(Node a, Node b) {
switch (a.getCovalentBondCount()) {
default:
- return false;
+ return STEREO_UNDETERMINED;
case 2:
// imines and diazines
if (a.getElementNumber () != 7) // nitrogen
- return false;
+ return STEREO_UNDETERMINED;
break;
case 3:
// first-row only (IUPAC 2013.P-93.2.4)
if (!isFirstRow(a))
- return false;
+ return STEREO_UNDETERMINED;
break;
}
Edge[] bonds = a.getEdges();
@@ -481,16 +475,16 @@
for (int i = bonds.length; --i >= 0;)
if (bonds[i].getCovalentOrder() == 2) {
if (++n > 1)
- return false; // no central allenes
+ return STEREO_ALLENE; //central allenes
Node other = bonds[i].getOtherAtomNode(a);
if (!isFirstRow(other))
- return false;
+ return STEREO_UNDETERMINED;
if (b != null && (other != b || b.getCovalentBondCount() == 1)) {
// could be allene central, but I think this is not necessary
- return false;
+ return STEREO_UNDETERMINED;
}
}
- return true;
+ return STEREO_EZ;
}
/**
@@ -595,7 +589,7 @@
public int getBondChirality(Edge bond) {
init();
getSmallRings(bond.getOtherAtomNode(null));
- return getBondChiralityLimited(bond, RULE_3);
+ return (bond.getCovalentOrder() == 2 ? getBondChiralityLimited(bond, null,
RULE_3) : NO_CHIRALITY);
}
/**
@@ -602,22 +596,38 @@
* Get E/Z characteristics for specific atoms
*
* @param atom
- * @param allBonds true to do all bonds to these atoms from other atoms, not
just among them
- * @param ruleMax
+ * @param allBonds
+ * true to do all bonds to these atoms from other atoms, not just
among
+ * them
+ * @param ruleMax
* @param lstEZ
- * @param bsToDo
+ * @param bsToDo
+ * @param bsAtrop
*/
- private void getAtomBondChirality(Node atom, boolean allBonds, int ruleMax,
Lst<int[]>lstEZ, BS bsToDo) {
+ private void getAtomBondChirality(Node atom, boolean allBonds, int ruleMax,
+ Lst<int[]> lstEZ, BS bsToDo, BS bsAtrop) {
+ int index = atom.getIndex();
Edge[] bonds = atom.getEdges();
- int index = atom.getIndex();
+ if (bsAtrop.get(index)) {
+ for (int j = bonds.length; --j >= 0;) {
+ Node atom1 = bonds[j].getOtherAtomNode(atom);
+ int index1 = atom1.getIndex();
+ if (!allBonds && index1 < index || !bsAtrop.get(index1))
+ continue;
+ getAxialOrEZChirality(atom, atom1, true, ruleMax);
+ break;
+ }
+ return;
+ }
for (int j = bonds.length; --j >= 0;) {
Edge bond = bonds[j];
if (bond.getCovalentOrder() == 2) {
- int index2 = bond.getOtherAtomNode(atom).getIndex();
+ Node atom2 = getLastCumuleneAtom(bond, atom, null);
+ int index2 = atom2.getIndex();
if ((allBonds || index2 > index)
- && getBondChiralityLimited(bond, ruleMax) != NO_CHIRALITY) {
- lstEZ.addLast(new int[] {index, index2});
+ && getBondChiralityLimited(bond, atom, ruleMax) != NO_CHIRALITY) {
+ lstEZ.addLast(new int[] { index, index2 });
//bsToDo.clear(index);
//bsToDo.clear(index2);
}
@@ -626,6 +636,41 @@
}
/**
+ *
+ * @param bond
+ * @param atom
+ * @param nSP2 return of number of sp2 carbons in this alkene or cumulene
+ * @return the terminal atom of this alkene or cumulene
+ */
+ private Node getLastCumuleneAtom(Edge bond, Node atom, int[] nSP2) {
+ // we know this is a double bond
+ Node atom2 = bond.getOtherAtomNode(atom);
+ // connected atom must have only two covalent bonds
+ if (nSP2 != null)
+ nSP2[0] = 2;
+ while (true) {
+ if (atom2.getCovalentBondCount() != 2)
+ return atom2;
+ Edge[] edges = atom2.getEdges();
+ for (int i = edges.length; --i >= 0;) {
+ Node atom3 = (bond = edges[i]).getOtherAtomNode(atom2);
+ if (atom3 == atom)
+ continue;
+ // connected atom must only have one other bond, and it must be double
to continue
+ if (bond.getCovalentOrder() != 2)
+ return atom2; // was atom3
+ // a=2=3
+ if (nSP2 != null)
+ nSP2[0]++;
+ atom = atom2;
+ atom2 = atom3;
+ // we know we only have two covalent bonds
+ break;
+ }
+ }
+ }
+
+ /**
* Determine R/S or one half of E/Z determination
*
* @param atom
@@ -663,8 +708,7 @@
if (cipAtom.set()) {
for (currentRule = RULE_1; currentRule <= ruleMax && !isChiral;
currentRule++) {
if (Logger.debugging)
- Logger.info("-Rule " + getRuleName() + " CIPChirality for "
- + cipAtom + "-----");
+ Logger.info("-Rule " + getRuleName() + " CIPChirality for " +
cipAtom + "-----");
if (currentRule == RULE_4) {
cipAtom.resetAuxiliaryChirality();
@@ -675,10 +719,9 @@
isChiral = true;
if (Logger.debugging) {
Logger.info(currentRule + ">>>>" + cipAtom);
- for (int i = 0; i < cipAtom.bondCount; i++) {
- if (cipAtom.atoms[i] == null)
- Logger.info(cipAtom.atoms[i] + " "
- + Integer.toHexString(cipAtom.prevPriorities[i]));
+ for (int i = 0; i < cipAtom.bondCount; i++) { // Logger
+ if (cipAtom.atoms[i] == null) // Logger
+ Logger.info(cipAtom.atoms[i] + " " +
Integer.toHexString(cipAtom.prevPriorities[i]));
}
}
if (cipAtom.achiral) {
@@ -701,59 +744,88 @@
rs = rs | JC.CIP_CHIRALITY_PSEUDO_FLAG;
}
if (Logger.debugging)
- Logger.info(atom + " " + rs);
- if (Logger.debugging)
- Logger.info("----------------------------------");
+ Logger.info(atom + " " + rs +
"\n----------------------------------");
}
} catch (Throwable e) {
System.out.println(e + " in CIPChirality");
- if (!vwr.isJS)
- e.printStackTrace();
- return STEREO_BOTH;
+ /**
+ * @j2sNative
+ * alert(e);
+ */
+ {
+ e.printStackTrace();
+ }
+ return STEREO_BOTH_RS;
}
return rs;
}
/**
- * Determine E or Z for a bond.
+ * Determine the axial or E/Z chirality for this bond, with the given
starting atom a
+ *
* @param bond
+ * @param a first atom to consider, or null
* @param ruleMax
- * @return [0:none, 1:Z, 2:E]
+ * @return one of: {NO_CHIRALITY | STEREO_Z | STEREO_E | STEREO_Ra |
STEREO_Sa | STEREO_ra | STEREO_sa}
*/
- private int getBondChiralityLimited(Edge bond, int ruleMax) {
- // TODO: need to make sure that R/S chirality is taken into account here.
- // or perhaps in Rule 4?
-
+ private int getBondChiralityLimited(Edge bond, Node a, int ruleMax) {
if (Logger.debugging)
Logger.info("get Bond Chirality " + bond);
- int ez = NO_CHIRALITY;
- Node[] atoms = vwr.ms.at;
- if (bond.getCovalentOrder() == 2) {
- Node a = atoms[bond.getAtomIndex1()];
- Node b = atoms[bond.getAtomIndex2()];
- if (!couldBeEZ(a,b))
- return NO_CHIRALITY;
- htPathPoints = new Hashtable<String, Integer>();
- CIPAtom a1 = new CIPAtom().create(a, null, false, true);
- CIPAtom b1 = new CIPAtom().create(b, null, false, true);
- int atop = getAtomChiralityLimited(a, a1, b1, ruleMax) - 1;
- htPathPoints = new Hashtable<String, Integer>();
- CIPAtom a2 = new CIPAtom().create(a, null, false, true);
- CIPAtom b2 = new CIPAtom().create(b, null, false, true);
- int btop = getAtomChiralityLimited(b, b2, a2, ruleMax) - 1;
- if (atop >= 0 && btop >= 0) {
- ez = (isCIS(b2.atoms[btop], b2, a1, a1.atoms[atop]) ? STEREO_Z
+ if (a == null)
+ a = bond.getOtherAtomNode(null);
+ Node b = bond.getOtherAtomNode(a);
+ if (couldBeChiralAlkene(a, b) == STEREO_UNDETERMINED)
+ return NO_CHIRALITY;
+ int[] nSP2 = new int[1];
+ b = getLastCumuleneAtom(bond, a, nSP2);
+ boolean isCumulene = (nSP2[0] > 2);
+ boolean isAxial = isCumulene && (nSP2[0] % 2 == 1);
+ return getAxialOrEZChirality(a, b, isAxial, ruleMax);
+ }
+
+ /**
+ * Determine the axial or E/Z chirality for the a-b bond.
+ *
+ * @param a
+ * @param b
+ * @param isAxial
+ * @param ruleMax
+ * @return one of: {NO_CHIRALITY | STEREO_Z | STEREO_E | STEREO_Ra |
STEREO_Sa
+ * | STEREO_ra | STEREO_sa}
+ */
+ private int getAxialOrEZChirality(Node a, Node b, boolean isAxial, int
ruleMax) {
+ htPathPoints = new Hashtable<String, Integer>();
+ CIPAtom a1 = new CIPAtom().create(a, null, false, true);
+ CIPAtom b1 = new CIPAtom().create(b, null, false, true);
+ a1.canBePseudo = a1.isOddCumulene = isAxial;
+ int atop = getAtomChiralityLimited(a, a1, b1, ruleMax) - 1;
+ htPathPoints = new Hashtable<String, Integer>();
+ CIPAtom a2 = new CIPAtom().create(a, null, false, true);
+ CIPAtom b2 = new CIPAtom().create(b, null, false, true);
+ b2.canBePseudo = b2.isOddCumulene = isAxial;
+ int btop = getAtomChiralityLimited(b, b2, a2, ruleMax) - 1;
+ int c = NO_CHIRALITY;
+ if (atop >= 0 && btop >= 0) {
+ if (isAxial) {
+ c = (isRa(b2.atoms[btop], b2, a1, a1.atoms[atop]) ? STEREO_R
+ : STEREO_S);
+ if (c != NO_CHIRALITY) {
+ c |= JC.CIP_CHIRALITY_AXIAL_FLAG;
+ if ((a2.ties == null) != (b2.ties == null))
+ c |= JC.CIP_CHIRALITY_PSEUDO_FLAG;
+ }
+ } else {
+ c = (isCis(b2.atoms[btop], b2, a1, a1.atoms[atop]) ? STEREO_Z
: STEREO_E);
}
- if (ez != 0) {
- a.setCIPChirality(ez << 3);
- b.setCIPChirality(ez << 3);
- }
+ }
+ if (c != NO_CHIRALITY) {
+ a.setCIPChirality(c);
+ b.setCIPChirality(c);
if (Logger.debugging)
- Logger.info(bond + " "
- + (ez == STEREO_Z ? "Z" : ez == STEREO_E ? "E" : "_"));
+ Logger.info(a + "-" + b + " " + JC.getCIPChiralityName(c));
}
- return ez;
+ return c;
}
/**
@@ -765,7 +837,7 @@
* @param d
* @return true if this is a cis relationship
*/
- boolean isCIS(CIPAtom a, CIPAtom b, CIPAtom c, CIPAtom d) {
+ boolean isCis(CIPAtom a, CIPAtom b, CIPAtom c, CIPAtom d) {
Measure.getNormalThroughPoints(a.atom.getXYZ(), b.atom.getXYZ(),
c.atom.getXYZ(), vNorm, vTemp);
V3 vNorm2 = new V3();
@@ -774,6 +846,20 @@
return (vNorm.dot(vNorm2) > 0);
}
+ /**
+ *
+ * @param a
+ * @param b
+ * @param c
+ * @param d
+ * @return true if torsion angle is
+ */
+ boolean isRa(CIPAtom a, CIPAtom b, CIPAtom c, CIPAtom d) {
+ float angle = Measure.computeTorsion(a.atom.getXYZ(), b.atom.getXYZ(),
c.atom.getXYZ(),
+ d.atom.getXYZ(), true);
+ return angle < 0;
+ }
+
final static int[] PRIORITY_SHIFT = new int[] { 24, 20, 12, 8, 4, 0 };
private class CIPAtom implements Comparable<CIPAtom>, Cloneable {
@@ -982,6 +1068,22 @@
boolean canBePseudo = true;
+ /**
+ * used to determine pseudochirality
+ */
+ Lst<int[]> ties;
+
+ /**
+ * used to defer pseudochirality check
+ */
+ boolean isOddCumulene;
+
+ /**
+ * first =X= atom in a string of =X=X=X=...
+ */
+ private CIPAtom nextSP2;
+
+
CIPAtom() {
// had a problem in JavaScript that the constructor of an inner function
cannot
// access this.b$ yet. That assignment is made after construction.
@@ -1120,15 +1222,14 @@
isAlkene = true;
if (isParentBond) {
knownAtomChirality = bond.getCIPChirality(false);
- if (elemNo == 6 && atom.getCovalentBondCount() == 2) {
- // allene presumed; could be C=C=O or C=C=N
- if (isAlkene && parent != null && parent.isAlkene)
- alkeneParent = (parent.alkeneParent == null ? parent :
parent.alkeneParent);
+ if (atom.getCovalentBondCount() == 2 && atom.getValence() == 4) {
parent.isAlkeneAtom2 = false;
} else {
- alkeneParent = parent;
+ isAlkeneAtom2 = true;
}
- isAlkeneAtom2 = true;
+ alkeneParent = (parent.alkeneParent == null ? parent :
parent.alkeneParent);
+ if (parent.alkeneParent == null)
+ parent.nextSP2 = this;
}
}
}
@@ -1206,8 +1307,6 @@
atoms[i] = new CIPAtom().create(other, this, isDuplicate, isAlkene);
if (currentRule > RULE_2)
prevPriorities[i] = getBasePriority(atoms[i]);
- // if (Logger.debugging)
- // Logger.info(this + " adding " + i + " " + atoms[i]);
return atoms[i];
}
@@ -1217,18 +1316,17 @@
*
*/
void sortSubstituents() {
-
if (Logger.debugging) {
Logger.info(root + "---sortSubstituents---" + this);
- for (int i = 0; i < 4; i++) {
- Logger.info(getRuleName() + ": " + this + "[" + i + "]="
- + atoms[i].myPath + " " +
Integer.toHexString(prevPriorities[i]));
+ for (int i = 0; i < 4; i++) { // Logger
+ Logger.info(getRuleName() + ": " + this + "[" + i + "]=" +
atoms[i].myPath + " " + Integer.toHexString(prevPriorities[i]));
}
+ Logger.info("---");
}
int[] indices = new int[4];
- Lst<int[]>ties = null;
+ ties = null;
for (int i = 0; i < 4; i++) {
priorities[i] = 1;
@@ -1247,8 +1345,7 @@
if (score == TIED)
score = (checkRule4List ? checkRule4And5(i, j) : a.compareTo(b));
if (Logger.debuggingHigh)
- Logger.info("ordering " + this.id + "." + i + "." + j + " " + this
- + "-" + a + " vs " + b + " = " + score);
+ Logger.info("ordering " + this.id + "." + i + "." + j + " " + this
+ "-" + a + " vs " + b + " = " + score);
switch (score) {
case IGNORE:
// just increment the index and go on to the next rule -- no
breaking of the tie
@@ -1328,7 +1425,7 @@
if (nPriorities > nPriorityMax)
nPriorityMax = nPriorities;
- if (ties != null) {
+ if (ties != null && !isOddCumulene) {
switch (ties.size()) {
case 1:
checkPseudoHandedness(ties.get(0), indices);
@@ -1340,9 +1437,8 @@
}
if (Logger.debugging) {
Logger.info(atom + " nPriorities = " + nPriorities);
- for (int i = 0; i < 4; i++)
- Logger.info(this.myPath + "[" + i + "]=" + atoms[i] + " "
- + priorities[i] + " new");
+ for (int i = 0; i < 4; i++) // Logger
+ Logger.info(this.myPath + "[" + i + "]=" + atoms[i] + " " +
priorities[i] + " new");
Logger.info("-------");
}
}
@@ -1596,15 +1692,16 @@
CIPAtom winner1 = null;
CIPAtom winner2 = null;
CIPAtom atom1 = null;
- auxEZ = STEREO_BOTH;
+ auxEZ = STEREO_BOTH_EZ;
sortSubstituents();
+ //System.out.println("checking EZ for " + this);
winner2 = getTopAtom();
if (winner2 != null) {
if (auxParentReversed == null) {
if (Logger.debugging)
- Logger.info("reversing path for " + parent);
+ Logger.info("reversing path for " + alkeneParent);
atom1 = (CIPAtom) alkeneParent.clone();
- atom1.addReturnPath(this, alkeneParent);
+ atom1.addReturnPath(alkeneParent.nextSP2, alkeneParent);
} else {
atom1 = auxParentReversed;
}
@@ -1611,16 +1708,14 @@
atom1.sortSubstituents();
winner1 = atom1.getTopAtom();
if (winner1 != null) {
- auxEZ = (isCIS(winner2, this, atom1, winner1) ? STEREO_Z
+ auxEZ = (isCis(winner2, this, atom1, winner1) ? STEREO_Z
: STEREO_E);
- if (Logger.debugging)
- Logger.info("getZaux " + (auxEZ == STEREO_Z ? "Z" : "E")
- + " for " + atom + "=" + alkeneParent.atom + " : "
- + winner1 + " " + winner2);
}
}
}
alkeneParent.auxEZ = auxEZ;
+ if (Logger.debugging)
+ Logger.info("getZaux " + alkeneParent + " " + auxEZ);
return auxEZ;
}
@@ -2054,7 +2149,7 @@
}
}
s += subRS;
- System.out.println(this + " creating aux " + s);
+// System.out.println(this + " creating aux " + s);
return s;
}
@@ -2083,7 +2178,7 @@
for (int i = 1; i < n; i++) {
int i1 = " RS".indexOf(rs1.charAt(i));
int score = i1 + " RS".indexOf(rs2.charAt(i));
- if (score != 0 && score != STEREO_BOTH)
+ if (score != 0 && score != STEREO_BOTH_RS)
return DIASTEREOMERIC;
if (finalScore == TIED)
finalScore = (i1 == STEREO_R ? A_WINS : B_WINS);
@@ -2121,9 +2216,8 @@
atom1.atoms[bondCount - 1] = atoms[Math.max(indices[ia], indices[ib])];
int rs = atom1.checkHandedness();
if (Logger.debugging) {
- for (int i = 0; i < 4; i++)
- Logger.info("pseudo " + rs + " " + priorities[i] + " "
- + atoms[i].myPath);
+ for (int i = 0; i < 4; i++) // Logger
+ Logger.info("pseudo " + rs + " " + priorities[i] + " " +
atoms[i].myPath);
}
if (rs == STEREO_R || rs == STEREO_S) {
isPseudo = true;
@@ -2181,7 +2275,7 @@
Logger.info("replace " + this + "[" + i + "]=" + newSub);
prevPriorities[i] = getBasePriority(atoms[i]);
parent = newParent;
- break;
+ return;
}
}
Modified: trunk/Jmol/src/org/jmol/symmetry/Symmetry.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/Symmetry.java 2017-04-28 18:59:41 UTC
(rev 21569)
+++ trunk/Jmol/src/org/jmol/symmetry/Symmetry.java 2017-04-29 18:15:15 UTC
(rev 21570)
@@ -795,13 +795,14 @@
@Override
public void calculateCIPChiralityForAtoms(Viewer vwr, BS bsAtoms) {
CIPChirality cip = getCIPChirality(vwr);
- cip.getChiralityForAtoms(vwr.ms.at, bsAtoms);
+ BS bsAtropisomer = vwr.getAtomBitSet("smarts('a-a')");
+ cip.getChiralityForAtoms(vwr.ms.at, bsAtoms, bsAtropisomer);
}
CIPChirality cip;
private CIPChirality getCIPChirality(Viewer vwr) {
- return (cip == null ? (cip = ((CIPChirality)
Interface.getInterface("org.jmol.symmetry.CIPChirality", vwr,
"script"))).setViewer(vwr) : cip);
+ return (cip == null ? (cip = ((CIPChirality)
Interface.getInterface("org.jmol.symmetry.CIPChirality", vwr, "script"))) :
cip);
}
}
Modified: trunk/Jmol/src/org/jmol/viewer/JC.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/JC.java 2017-04-28 18:59:41 UTC (rev
21569)
+++ trunk/Jmol/src/org/jmol/viewer/JC.java 2017-04-29 18:15:15 UTC (rev
21570)
@@ -49,11 +49,16 @@
public final static int CIP_CHIRALITY_S_FLAG = 2;
public final static int CIP_CHIRALITY_NONE = 3;
public final static int CIP_CHIRALITY_PSEUDO_FLAG = 4;
- public final static int CIP_CHIRALITY_r_FLAG = 5;
- public final static int CIP_CHIRALITY_s_FLAG = 6;
+ public final static int CIP_CHIRALITY_r_FLAG = CIP_CHIRALITY_R_FLAG |
CIP_CHIRALITY_PSEUDO_FLAG;
+ public final static int CIP_CHIRALITY_s_FLAG = CIP_CHIRALITY_S_FLAG |
CIP_CHIRALITY_PSEUDO_FLAG;
public final static int CIP_CHIRALITY_CANTDETERMINE = 7;
- public final static int CIP_CHIRALITY_Z_FLAG = 1 << 3;
- public final static int CIP_CHIRALITY_E_FLAG = 2 << 3; // Z|E is "no
chirality"
+ public final static int CIP_CHIRALITY_Z_FLAG = 1 << 3; // 0x08
+ public final static int CIP_CHIRALITY_E_FLAG = 2 << 3; // 0x10 Z|E is "no
chirality"
+ public final static int CIP_CHIRALITY_AXIAL_FLAG = 4 << 3;
+ public final static int CIP_CHIRALITY_Ra_FLAG = CIP_CHIRALITY_R_FLAG |
CIP_CHIRALITY_AXIAL_FLAG;
+ public final static int CIP_CHIRALITY_Sa_FLAG = CIP_CHIRALITY_S_FLAG |
CIP_CHIRALITY_AXIAL_FLAG;
+ public final static int CIP_CHIRALITY_ra_FLAG = CIP_CHIRALITY_Ra_FLAG |
CIP_CHIRALITY_PSEUDO_FLAG;
+ public final static int CIP_CHIRALITY_sa_FLAG = CIP_CHIRALITY_Sa_FLAG |
CIP_CHIRALITY_PSEUDO_FLAG;
public static String getCIPChiralityName(int flags) {
switch (flags) {
@@ -61,6 +66,10 @@
return "Z";
case CIP_CHIRALITY_E_FLAG:
return "E";
+ case CIP_CHIRALITY_Ra_FLAG:
+ return "Ra";
+ case CIP_CHIRALITY_Sa_FLAG:
+ return "Sa";
case CIP_CHIRALITY_R_FLAG:
return "R";
case CIP_CHIRALITY_S_FLAG:
@@ -69,6 +78,10 @@
return "r";
case CIP_CHIRALITY_s_FLAG:
return "s";
+ case CIP_CHIRALITY_ra_FLAG:
+ return "ra";
+ case CIP_CHIRALITY_sa_FLAG:
+ return "sa";
case CIP_CHIRALITY_CANTDETERMINE:
return "?";
case CIP_CHIRALITY_NONE:
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-04-28 18:59:41 UTC
(rev 21569)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-04-29 18:15:15 UTC
(rev 21570)
@@ -49,15 +49,24 @@
# 10. Run jmol/tools build-release.xml
#
-Jmol.___JmolVersion="14.15.1" // 4/28/17
+Jmol.___JmolVersion="14.15.2" // 4/29/17
+bug fix: CIP chirality adds axial chirality (Ra/Sa, ra/sa) for cumulenes
+bug fix: CIP chirality adds atropisomer chirality (Ra/Sa, ra/sa) for biaryls
+bug fix: CIP chirality adds cumulene E/Z chirality
+ -- validates for 160 structures (some duplicates; both cip_examples.zip and
stereo_test_cases.sdf)
+ -- 817 lines
+
+
+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 adds P, S, As, Se, Sb, Te, Bi, Po trigonal pyramidal
and tetrahedral
+bug fix: 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
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