Revision: 21569
http://sourceforge.net/p/jmol/code/21569
Author: hansonr
Date: 2017-04-28 18:59:41 +0000 (Fri, 28 Apr 2017)
Log Message:
-----------
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java
Modified: trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-04-28 01:11:08 UTC
(rev 21568)
+++ trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-04-28 18:59:41 UTC
(rev 21569)
@@ -226,6 +226,9 @@
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_R = 1;
static final int STEREO_S = 2;
@@ -508,7 +511,7 @@
private void getSmallRings(Node atom) {
lstSmallRings = new Lst<BS>();
htPathPoints = new Hashtable<String, Integer>();
- root = new CIPAtom(atom, null, false, false);
+ root = new CIPAtom().create(atom, null, false, false);
addSmallRings(root);
}
@@ -643,7 +646,7 @@
try {
if (cipAtom == null) {
htPathPoints = new Hashtable<String, Integer>();
- cipAtom = new CIPAtom(atom, null, false, isAlkene);
+ cipAtom = new CIPAtom().create(atom, null, false, isAlkene);
int nSubs = atom.getCovalentBondCount();
int elemNo = atom.getElementNumber();
isAlkene = (nSubs == 3 && elemNo <= 10); // (IUPAC 2013.P-93.2.4)
@@ -731,12 +734,12 @@
if (!couldBeEZ(a,b))
return NO_CHIRALITY;
htPathPoints = new Hashtable<String, Integer>();
- CIPAtom a1 = new CIPAtom(a, null, false, true);
- CIPAtom b1 = new CIPAtom(b, null, false, true);
+ 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(a, null, false, true);
- CIPAtom b2 = new CIPAtom(b, null, false, true);
+ 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
@@ -889,6 +892,12 @@
boolean isAlkene;
/**
+ * parent atom of a second alkene or cumulene atom
+ */
+
+ CIPAtom alkeneParent;
+
+ /**
* a flag used in Rule 3 to indicate the second carbon of a double bond
*/
@@ -973,6 +982,10 @@
boolean canBePseudo = true;
+ CIPAtom() {
+ // had a problem in JavaScript that the constructor of an inner function
cannot
+ // access this.b$ yet. That assignment is made after construction.
+ }
/**
*
* @param atom
@@ -980,12 +993,13 @@
* @param parent
* @param isDuplicate
* @param isAlkene
+ * @return this
*/
- CIPAtom(Node atom, CIPAtom parent, boolean isDuplicate, boolean isAlkene) {
+ CIPAtom create(Node atom, CIPAtom parent, boolean isDuplicate, boolean
isAlkene) {
this.id = ++ptID;
this.parent = parent;
if (atom == null)
- return;
+ return this;
this.isAlkene = isAlkene;
this.atom = atom;
this.elemNo = atom.getElementNumber();
@@ -1042,6 +1056,7 @@
Logger.info("new CIPAtom " + parent + "->" + this);
if (isDuplicate && !wasDuplicate)
updateRingList();
+ return this;
}
private void getLonePair() {
@@ -1096,7 +1111,7 @@
if (!bond.isCovalent())
continue;
Node other = bond.getOtherAtomNode(atom);
- boolean isParent = (parent != null && parent.atom == other);
+ boolean isParentBond = (parent != null && parent.atom == other);
int order = bond.getCovalentOrder();
if (order == 2) {
if (elemNo > 10 || !isFirstRow(other))
@@ -1103,19 +1118,27 @@
order = 1;
else {
isAlkene = true;
- if (isParent) {
+ 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);
+ parent.isAlkeneAtom2 = false;
+ } else {
+ alkeneParent = parent;
+ }
isAlkeneAtom2 = true;
- knownAtomChirality = bond.getCIPChirality(false);
}
}
}
- if (nBonds == 1 && order == 1 && isParent) {
+ if (nBonds == 1 && order == 1 && isParentBond) {
isTerminal = true;
return true;
}
switch (order) {
case 3:
- if (addAtom(pt++, other, isParent, false) == null) {
+ if (addAtom(pt++, other, isParentBond, false) == null) {
isTerminal = true;
return false;
}
@@ -1122,13 +1145,13 @@
//$FALL-THROUGH$
case 2:
// look out for S=X, which is not planar
- if (addAtom(pt++, other, order != 2 || isParent, order == 2) ==
null) {
+ if (addAtom(pt++, other, order != 2 || isParentBond, order == 2) ==
null) {
isTerminal = true;
return false;
}
//$FALL-THROUGH$
case 1:
- if (!isParent
+ if (!isParentBond
&& addAtom(pt++, other, order != 1 && elemNo <= 10, false) ==
null) {
isTerminal = true;
return false;
@@ -1142,7 +1165,7 @@
isTerminal = (pt == 0);
nAtoms = pt;
for (; pt < atoms.length; pt++)
- atoms[pt] = new CIPAtom(null, this, true, false);
+ atoms[pt] = new CIPAtom().create(null, this, true, false);
// Do an initial atom-only shallow sort using a.compareTo(b)
@@ -1180,7 +1203,7 @@
}
}
}
- atoms[i] = new CIPAtom(other, this, isDuplicate, isAlkene);
+ atoms[i] = new CIPAtom().create(other, this, isDuplicate, isAlkene);
if (currentRule > RULE_2)
prevPriorities[i] = getBasePriority(atoms[i]);
// if (Logger.debugging)
@@ -1523,11 +1546,14 @@
}
/**
- * Chapter 9 Rule 3. E/Z. If the this atom and the comparison atom b are on
- * the same parent, then this is simply a request to break their tie based
- * on Rule 3; otherwise two paths are being checked for one being seqCis
and
- * one being seqTrans.
+ * Chapter 9 Rule 3. E/Z.
*
+ * We carry out this step only as a tie in the sphere AFTER the second
atom.
+ *
+ * If the this atom and the comparison atom b are on the same parent, then
+ * this is simply a request to break their tie based on Rule 3; otherwise
+ * two paths are being checked for one being seqCis and one being seqTrans.
+ *
* @param b
* @return 0 (TIED), -1 (A_WINS), or 1 (B_WINS)
*/
@@ -1534,7 +1560,9 @@
private int checkRule3(CIPAtom b) {
int za, zb;
return parent == null || !parent.isAlkeneAtom2 || !b.parent.isAlkeneAtom2
- || isDuplicate || b.isDuplicate ? IGNORE
+ || isDuplicate || b.isDuplicate
+ || !isCumulativeType(STEREO_EZ) || !b.isCumulativeType(STEREO_EZ)
+ ? IGNORE
: parent == b.parent
? sign(breakTie(b))
: (za = parent.getEZaux()) < (zb = b.parent.getEZaux()) ? A_WINS
@@ -1541,6 +1569,11 @@
: za > zb ? B_WINS : TIED;
}
+ private boolean isCumulativeType(int type) {
+ return (parent != null && parent.isAlkeneAtom2 &&
+ ((parent.alkeneParent.sphere + parent.sphere) % 2) == (type ==
STEREO_EZ ? 1 : 2));
+ }
+
/**
* Check auxiliary Z by temporarily setting return path.
*
@@ -1559,7 +1592,7 @@
// (because there is no need to do this test until we are on the branch
that includes
// the atom after the alkene).
if (auxEZ == STEREO_UNDETERMINED
- && (auxEZ = parent.auxEZ) == STEREO_UNDETERMINED) {
+ && (auxEZ = alkeneParent.auxEZ) == STEREO_UNDETERMINED) {
CIPAtom winner1 = null;
CIPAtom winner2 = null;
CIPAtom atom1 = null;
@@ -1570,8 +1603,8 @@
if (auxParentReversed == null) {
if (Logger.debugging)
Logger.info("reversing path for " + parent);
- atom1 = (CIPAtom) parent.clone();
- atom1.addReturnPath(this, parent);
+ atom1 = (CIPAtom) alkeneParent.clone();
+ atom1.addReturnPath(this, alkeneParent);
} else {
atom1 = auxParentReversed;
}
@@ -1582,12 +1615,12 @@
: STEREO_E);
if (Logger.debugging)
Logger.info("getZaux " + (auxEZ == STEREO_Z ? "Z" : "E")
- + " for " + this.atom + "=" + this.parent.atom + " : "
+ + " for " + atom + "=" + alkeneParent.atom + " : "
+ winner1 + " " + winner2);
}
}
}
- parent.auxEZ = auxEZ;
+ alkeneParent.auxEZ = auxEZ;
return auxEZ;
}
@@ -1619,7 +1652,7 @@
for (int i = 0, n = path.size(); i < n; i++) {
CIPAtom p = path.get(i);
if (p == null) {
- p = new CIPAtom(null, this, true, isAlkene);
+ p = new CIPAtom().create(null, this, true, isAlkene);
} else {
int s = p.sphere;
p = (CIPAtom) p.clone();
@@ -2072,8 +2105,8 @@
if (auxPseudo == null) {
// critical here that we do NOT include the tied branches
atom1 = (CIPAtom) clone();
- atom1.atoms[indices[ia]] = new CIPAtom(null, atom1, false, isAlkene);
- atom1.atoms[indices[ib]] = new CIPAtom(null, atom1, false, isAlkene);
+ atom1.atoms[indices[ia]] = new CIPAtom().create(null, atom1, false,
isAlkene);
+ atom1.atoms[indices[ib]] = new CIPAtom().create(null, atom1, false,
isAlkene);
atom1.addReturnPath(null, this);
} else {
atom1 = auxPseudo;
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