Revision: 21634
http://sourceforge.net/p/jmol/code/21634
Author: hansonr
Date: 2017-06-12 05:33:38 +0000 (Mon, 12 Jun 2017)
Log Message:
-----------
Jmol.___JmolVersion="14.18.2"
bug fix: CIP gives wrong alkene root distance for cyclopropene
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 2017-06-08 12:51:21 UTC
(rev 21633)
+++ trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-06-12 05:33:38 UTC
(rev 21634)
@@ -425,8 +425,8 @@
public CIPChirality() {
// for reflection
- System.out.println("TESTING ALLOWRULE1B");
- allowRule1bAlkenes = false;
+ //System.out.println("TESTING ALLOWRULE1B");
+ //allowRule1bAlkenes = false;
}
/**
@@ -773,7 +773,7 @@
* tracks all atoms in this molecular unit
*/
private void getSmallRings(SimpleNode atom, BS bs) {
- root = new CIPAtom().create(atom, null, false, false);
+ root = new CIPAtom().create(atom, null, false, false, false);
addSmallRings(root, bs);
}
@@ -800,7 +800,7 @@
|| (atom2 = bond.getOtherNode(a.atom)).getCovalentBondCount() == 1
|| a.parent != null && atom2 == a.parent.atom)
continue;
- CIPAtom r = a.addAtom(pt++, atom2, false, false);
+ CIPAtom r = a.addAtom(pt++, atom2, false, false, false);
if (r.isDuplicate)
r.updateRingList();
}
@@ -968,7 +968,7 @@
boolean isChiral = false, isAlkene = false;
try {
if (cipAtom == null) {
- cipAtom = new CIPAtom().create(atom, null, false, isAlkene);
+ cipAtom = new CIPAtom().create(atom, null, false, isAlkene, false);
int nSubs = atom.getCovalentBondCount(), elemNo =
atom.getElementNumber();
isAlkene = (nSubs == 3 && elemNo <= 10 &&
!cipAtom.isTrigonalPyramidal); // (IUPAC 2013.P-93.2.4)
if (nSubs != (parent == null ? 4 : 3)
@@ -1071,10 +1071,10 @@
*/
private int setBondChirality(SimpleNode a, SimpleNode pa, SimpleNode pb,
SimpleNode b,
boolean isAxial, int ruleMax) {
- CIPAtom a1 = new CIPAtom().create(a, null, false, true);
+ CIPAtom a1 = new CIPAtom().create(a, null, false, true, false);
int atop = getAlkeneEndTopPriority(a1, pa, isAxial, ruleMax);
int ruleA = currentRule;
- CIPAtom b2 = new CIPAtom().create(b, null, false, true);
+ CIPAtom b2 = new CIPAtom().create(b, null, false, true, false);
int btop = getAlkeneEndTopPriority(b2, pb, isAxial, ruleMax);
int ruleB = currentRule;
int c = (atop >= 0 && btop >= 0 ? getEneChirality(b2.atoms[btop], b2, a1,
@@ -1127,7 +1127,7 @@
int ruleMax) {
a.canBePseudo = a.isAxialRoot = isAxial;
return getAtomChiralityLimited(a.atom, a,
- new CIPAtom().create(pa, null, false, true), ruleMax) - 1;
+ new CIPAtom().create(pa, null, false, true, false), ruleMax) - 1;
}
/**
@@ -1429,10 +1429,11 @@
* @param parent
* @param isDuplicate
* @param isAlkene
+ * @param isParentBond TODO
* @return this
*/
CIPAtom create(SimpleNode atom, CIPAtom parent, boolean isDuplicate,
- boolean isAlkene) {
+ boolean isAlkene, boolean isParentBond) {
this.id = ++ptID;
this.parent = parent;
if (atom == null)
@@ -1481,8 +1482,8 @@
rootSubstituent.spiroEnd = parent;
} else if (bsPath.get(atomIndex)) {
isDuplicate = true;
- rootDistance = rootSubstituent.htPathPoints.get(
- Integer.valueOf(atomIndex)).intValue();
+ rootDistance = (isParentBond ? parent.sphere :
rootSubstituent.htPathPoints.get(
+ Integer.valueOf(atomIndex)).intValue());
} else {
bsPath.set(atomIndex);
rootSubstituent.htPathPoints.put(Integer.valueOf(atomIndex),
@@ -1492,8 +1493,7 @@
if (Logger.debugging) {
if (sphere < MAX_PATH) // Logger
myPath = (parent != null ? parent.myPath + "-" : "") + this; //
Logger
- if (Logger.debuggingHigh)
- Logger.info("new CIPAtom " + myPath);
+ Logger.info("new CIPAtom " + myPath);
}
return this;
}
@@ -1583,13 +1583,13 @@
// from here on, isTerminal indicates an error condition
switch (order) {
case 3:
- if (addAtom(pt++, other, isParentBond, false) == null) {
+ if (addAtom(pt++, other, isParentBond, false, isParentBond) == null)
{
isTerminal = true;
return false;
}
//$FALL-THROUGH$
case 2:
- if (addAtom(pt++, other, order != 2 || isParentBond, order == 2) ==
null) {
+ if (addAtom(pt++, other, order != 2 || isParentBond, order == 2,
isParentBond) == null) {
isTerminal = true;
return false;
}
@@ -1596,7 +1596,7 @@
//$FALL-THROUGH$
case 1:
if (!isParentBond
- && addAtom(pt++, other, order != 1 && elemNo <= 10, false) ==
null) {
+ && addAtom(pt++, other, order != 1 && elemNo <= 10, false,
false) == null) {
isTerminal = true;
return false;
}
@@ -1610,7 +1610,7 @@
isTerminal = (pt == 0);
nAtoms = pt;
for (; pt < atoms.length; pt++)
- atoms[pt] = new CIPAtom().create(null, this, true, false);
+ atoms[pt] = new CIPAtom().create(null, this, true, false, false);
// Do an initial very shallow atom-only Rule 1 sort using a.compareTo(b)
@@ -1646,7 +1646,7 @@
* @param isAlkene
* @return new atom or null
*/
- CIPAtom addAtom(int i, SimpleNode other, boolean isDuplicate, boolean
isAlkene) {
+ CIPAtom addAtom(int i, SimpleNode other, boolean isDuplicate, boolean
isAlkene, boolean isParentBond) {
if (i >= atoms.length) {
if (Logger.debugging)
Logger.info(" too many bonds on " + atom);
@@ -1664,7 +1664,7 @@
}
}
return atoms[i] = new CIPAtom()
- .create(other, this, isDuplicate, isAlkene);
+ .create(other, this, isDuplicate, isAlkene, isParentBond);
}
/**
@@ -1887,14 +1887,24 @@
if (isTerminal != b.isTerminal)
return (isTerminal ? B_WINS : A_WINS) * (sphere + 1);
-// not necessary after all // Rule 1b requires a special presort to ensure
that all duplicate atoms
-// // are in the right order -- first by element number and then by root
distance.
-//
-// if (currentRule == RULE_1b && false) {
-// preSortRule1b();
-// b.preSortRule1b();
-// }
+ // Rule 1b requires a special presort to ensure that all duplicate atoms
+ // are in the right order -- first by element number and then by root
distance.
+ // Otherwise we are liable to have an a-b alignment such as the following
+ // when we have SMARTS C1...C=C1
+ //
+ // a b
+ // C C
+ // (C-alk) (C-ring)
+ // (C-ring) (C-alk)
+ // H H
+ //
+ // see bh64.65
+ if (currentRule == RULE_1b) {
+ preSortRule1b();
+ b.preSortRule1b();
+ }
+
// Phase I -- shallow check only
//
// Check to see if any of the three connections to a and b are different.
@@ -1920,27 +1930,29 @@
return compareDeeply(b, sphere);
}
-// /**
-// * Sort duplicate nodes of the same element by root distance, from
closest
-// * to root to furthest.
-// *
-// */
-// private void preSortRule1b() {
-// CIPAtom a1, a2;
-// for (int i = 0; i < 3; i++) {
-// if (!(a1 = atoms[i]).isDuplicate)
-// continue;
-// for (int j = i + 1; j < 4; j++) {
-// if (!(a2 = atoms[j]).isDuplicate || a1.elemNo != a2.elemNo
-// || a1.rootDistance <= a2.rootDistance)
-// continue;
-// atoms[i] = a2;
-// atoms[j] = a1;
-// j = 4;
-// i = -1;
-// }
-// }
-// }
+ /**
+ * Sort duplicate nodes of the same element by root distance, from closest
+ * to root to furthest.
+ *
+ */
+ private void preSortRule1b() {
+ CIPAtom a1, a2;
+ for (int i = 0; i < 3; i++) {
+ if (!(a1 = atoms[i]).isDuplicate)
+ continue;
+ if (Logger.debuggingHigh)
+ Logger.info("presort1b: " + i + " " + a1.myPath);
+ for (int j = i + 1; j < 4; j++) {
+ if (!(a2 = atoms[j]).isDuplicate || a1.elemNo != a2.elemNo
+ || a1.rootDistance <= a2.rootDistance)
+ continue;
+ atoms[i] = a2;
+ atoms[j] = a1;
+ j = 4;
+ i = -1;
+ }
+ }
+ }
/**
* Just checking for hydrogen.
@@ -2243,7 +2255,7 @@
for (int i = 0, n = path.size(); i < n; i++) {
oldParent = path.get(i);
newSub = (oldParent == null ? new CIPAtom().create(null, this, true,
- isAlkene) : (CIPAtom) oldParent.clone());
+ isAlkene, false) : (CIPAtom) oldParent.clone());
newSub.sphere = thisAtom.sphere + 1;
thisAtom.replaceParentSubstituent(oldSub, newParent, newSub);
if (i > 0 && thisAtom.isAlkene && !thisAtom.isAlkeneAtom2) {
@@ -2914,8 +2926,8 @@
CIPAtom atom1;
// critical here that we do NOT include the tied branches
atom1 = (CIPAtom) clone();
- atom1.atoms[ia] = new CIPAtom().create(null, atom1, false, false);
- atom1.atoms[ib] = new CIPAtom().create(null, atom1, false, false);
+ atom1.atoms[ia] = new CIPAtom().create(null, atom1, false, false, false);
+ atom1.atoms[ib] = new CIPAtom().create(null, atom1, false, false, false);
atom1.addReturnPath(null, this);
// We are guaranteed that only RULE_1a is necessary, because one of our
// paths goes all the way back to the root, without a duplicate atom,
and any
@@ -3024,8 +3036,8 @@
@Override
public String toString() {
return (atom == null ? "<null>" : "[" + currentRule + "." + sphere + ","
- + rootDistance + "." + id + "." + atom.getAtomName()
- + (isDuplicate ? "*" : "") + "]");
+ + id + "." + atom.getAtomName()
+ + (isDuplicate ? "*(" + rootDistance + ")": "") + "]");
}
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-06-08 12:51:21 UTC
(rev 21633)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-06-12 05:33:38 UTC
(rev 21634)
@@ -56,8 +56,12 @@
# TODO: fix UNDO
-Jmol.___JmolVersion="14.18.1" // 2017.06.06
+Jmol.___JmolVersion="14.18.2"
+bug fix: CIP gives wrong alkene root distance for cyclopropene
+
+JmolVersion="14.18.1" // 2017.06.06
+
bug fix: CIP misses Rule 4b cases where a branching atom has R or S chirality.
-- see test_bt_P4.mol and test_bt_O3.mol (BH64.65 and BH64.66)
-- see AY236.179 (3D structure was diasteriomer, so I missed that)
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