Revision: 21578
http://sourceforge.net/p/jmol/code/21578
Author: hansonr
Date: 2017-04-29 23:15:49 +0000 (Sat, 29 Apr 2017)
Log Message:
-----------
Jmol.___JmolVersion="14.15.3"
bug fix: CIP chirality may not show M/P for atropisomeric atoms
test: load "$2,2'-dibromobiphenyl"; calculate chirality; print
{*}.chirality.join("")
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/symmetry/CIPChirality.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 2017-04-29 20:03:21 UTC
(rev 21577)
+++ trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-04-29 23:15:49 UTC
(rev 21578)
@@ -160,7 +160,6 @@
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;
static final int RULE_3 = 3;
@@ -204,16 +203,22 @@
Lst<BS> lstSmallRings = new Lst<BS>();
/**
- * Max priorities across an entire molecule, for cyclic loops
+ * max priorities across an entire molecule, for cyclic loops
*/
int nPriorityMax;
/**
- * Max ring size from closures, across a molecule
+ * max ring size from closures, across a molecule
*
*/
int maxRingSize;
+ /**
+ * don't do this atom again (atropisomer)
+ *
+ */
+ BS bsAtropisomeric;
+
V3 vNorm = new V3();
V3 vNorm2 = new V3();
V3 vTemp = new V3();
@@ -243,6 +248,9 @@
public void getChiralityForAtoms(Node[] atoms, BS bsAtoms, BS
bsAtropisomeric) {
if (bsAtoms.isEmpty())
return;
+
+ this.bsAtropisomeric = bsAtropisomeric;
+
init();
BS bsToDo = BSUtil.copy(bsAtoms);
@@ -271,7 +279,7 @@
// 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,
bsAtropisomeric);
+ getAtomBondChirality(atoms[i], false, RULE_3, lstEZ, bsToDo);
}
@@ -286,7 +294,7 @@
if (haveAlkenes) {
for (int i = bsToDo.nextSetBit(0); i >= 0; i = bsToDo.nextSetBit(i + 1))
- getAtomBondChirality(atoms[i], false, RULE_5, lstEZ, bsToDo,
bsAtropisomeric);
+ getAtomBondChirality(atoms[i], false, RULE_5, lstEZ, bsToDo);
}
@@ -456,6 +464,8 @@
* @param lstEZ
*/
private void clearSmallRingEZ(Node[] atoms, Lst<int[]> lstEZ) {
+ for (int j = lstSmallRings.size(); --j >= 0;)
+ lstSmallRings.get(j).andNot(bsAtropisomeric);
for (int i = lstEZ.size(); --i >= 0;) {
int[] ab = lstEZ.get(i);
for (int j = lstSmallRings.size(); --j >= 0;) {
@@ -523,18 +533,17 @@
* @param ruleMax
* @param lstEZ
* @param bsToDo
- * @param bsAtrop
*/
private void getAtomBondChirality(Node atom, boolean allBonds, int ruleMax,
- Lst<int[]> lstEZ, BS bsToDo, BS bsAtrop) {
+ Lst<int[]> lstEZ, BS bsToDo) {
int index = atom.getIndex();
Edge[] bonds = atom.getEdges();
- if (bsAtrop.get(index)) {
+ if (bsAtropisomeric.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))
+ if (!bsAtropisomeric.get(index1))
continue;
getAxialOrEZChirality(atom, atom1, true, ruleMax);
break;
@@ -549,8 +558,6 @@
if ((allBonds || index2 > index)
&& getBondChiralityLimited(bond, atom, ruleMax) != NO_CHIRALITY) {
lstEZ.addLast(new int[] { index, index2 });
- //bsToDo.clear(index);
- //bsToDo.clear(index2);
}
}
}
@@ -728,16 +735,14 @@
int c = NO_CHIRALITY;
if (atop >= 0 && btop >= 0) {
if (isAxial) {
- c = (isPos(b2.atoms[btop], b2, a1, a1.atoms[atop]) ? STEREO_P
- : STEREO_M);
+ c = (isPos(b2.atoms[btop], b2, a1, a1.atoms[atop]) ? STEREO_P :
STEREO_M);
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);
+ c = (isCis(b2.atoms[btop], b2, a1, a1.atoms[atop]) ? STEREO_Z :
STEREO_E);
}
}
- if (c != NO_CHIRALITY) {
+ if (c != NO_CHIRALITY && (isAxial || !isAtropisomeric(a) &&
!isAtropisomeric(b))) {
a.setCIPChirality(c);
b.setCIPChirality(c);
if (Logger.debugging)
@@ -746,6 +751,10 @@
return c;
}
+ private boolean isAtropisomeric(Node a) {
+ return bsAtropisomeric != null && bsAtropisomeric.get(a.getIndex());
+ }
+
/**
* Check cis vs. trans nature of a--b==c--d.
*
@@ -1211,7 +1220,7 @@
Logger.info(" too many bonds on " + atom);
return null;
}
- if (parent == null && currentRule != RULE_0) {
+ if (parent == null) {
// For top level, we do not allow two 1H atoms.
int atomIsotope = other.getAtomicAndIsotopeNumber();
if (atomIsotope == 1) {
@@ -1508,8 +1517,6 @@
public int checkCurrentRule(CIPAtom b) {
switch (currentRule) {
default:
- case RULE_0:
- return b.atom == atom ? TIED : b.atom == null ? A_WINS : atom == null
? B_WINS : TIED;
case RULE_1:
int score = checkRule1a(b);
return (score == TIED ? checkRule1b(b) : score);
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-04-29 20:03:21 UTC
(rev 21577)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-04-29 23:15:49 UTC
(rev 21578)
@@ -49,8 +49,13 @@
# 10. Run jmol/tools build-release.xml
#
-Jmol.___JmolVersion="14.15.2" // 4/29/17
+Jmol.___JmolVersion="14.15.3"
+bug fix: CIP chirality may not show M/P for atropisomeric atoms
+ test: load "$2,2'-dibromobiphenyl"; calculate chirality; print
{*}.chirality.join("")
+
+JmolVersion="14.15.2" // 4/29/17
+
bug fix: CIP chirality adds axial chirality (M/P[Ra/Sa], m/p[ra/sa]) for
cumulenes
bug fix: CIP chirality adds atropisomer chirality (M/P[Ra/Sa], m/p[ra/sa]) for
biaryls
bug fix: CIP chirality adds cumulene E/Z chirality
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