Revision: 21675
http://sourceforge.net/p/jmol/code/21675
Author: hansonr
Date: 2017-07-23 20:07:02 +0000 (Sun, 23 Jul 2017)
Log Message:
-----------
adds Rule 6
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java
trunk/Jmol/src/org/jmol/viewer/JC.java
Modified: trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-07-21 22:33:07 UTC
(rev 21674)
+++ trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-07-23 20:07:02 UTC
(rev 21675)
@@ -55,8 +55,10 @@
*
* - deeply validated
*
- * - included revised Rules 1b, and 2.
+ * - includes revised Rules 1b, and 2.
*
+ * - includes a proposed Rule 6.
+ *
* - implemented in Java (Jmol) and JavaScript (JSmol)
*
* - only two Java classes; roughly 1000 lines
@@ -64,7 +66,7 @@
* - efficient, one-pass process for each center using a single finite digraph
* for all auxiliary descriptors
*
- * - exhaustive processing of all 8 sequence rules (1a, 1b, 2, 3, 4a, 4b, 4c,
5)
+ * - exhaustive processing of all 9 sequence rules (1a, 1b, 2, 3, 4a, 4b, 4c,
5, 6)
*
* - includes R/S, r/s, M/P (axial, not planar), E/Z
*
@@ -143,6 +145,7 @@
*
* code history:
*
+ * 7/23/17 Jmol 14.20.4 adds Rule 6; rewrite/consolidation of spiro, C3,
double spiran code (846 lines)
* 7/19/17 Jmol 14.20.3 fixing Rule 2 (880 lines)
* 7/13/17 Jmol 14.20.3 more thorough spiro testing (858 lines)
* 7/10/17 Jmol 14.20.2 adding check for C3 and double
@@ -233,6 +236,14 @@
*
* See CIPAtom.getMass();
*
+ * PROPOSED Rule 6:
+ *
+ * Rule 6: In the case of a digraph with more than two root-duplicate nodes,
any one of
+ * the still-indistinguishable ligands is given higher priority than the
others.
+ *
+ * Rationale: This rule is stated in CIP(1966) p. 357.
+ *
+ *
* @author Bob Hanson hans...@stolaf.edu
*/
public class CIPChirality {
@@ -539,10 +550,12 @@
static final int STEREO_BOTH_RS = STEREO_R | STEREO_S; // must be the number
3
static final int STEREO_BOTH_EZ = STEREO_E | STEREO_Z;
- static final int RULE_1a = 1, RULE_1b = 2, RULE_2 = 3, RULE_3 = 4,
- RULE_4a = 5, RULE_4bTEST = 6, RULE_4b = 7, RULE_4c = 8,
- RULE_5 = 9,
- RULE_6 = 10;
+ static final int RULE_1a = 1, RULE_1b = 2,
+ RULE_2 = 3,
+ RULE_3 = 4,
+ RULE_4a = 5, RULE_4b = 6, RULE_4c = 7,
+ RULE_5 = 8,
+ RULE_6 = 9;
boolean isRule4TEST = false;
@@ -656,13 +669,10 @@
*
*/
boolean setAuxiliary;
- public boolean haveIsotopes;
public CIPChirality() {
// for reflection
System.out.println("TESTING Rule 1b option " + rule1bOption);
- isRule4TEST = false;
- System.out.println("TESTING Rule 4b option " + isRule4TEST);
}
/**
@@ -1182,25 +1192,19 @@
parentAtom, null, true, false, false)).htPathPoints;
} else {
if (!(root = cipAtom = new CIPAtom().create(atom, null, false, false,
- false)).canBePseudo) {
+ false)).isSP3) {
// This is a root-atom call.
// Just checking here that center has 4 covalent bonds or is
trigonal pyramidal.
return NO_CHIRALITY;
}
- haveIsotopes = false;
}
if (cipAtom.setNode()) {
- for (currentRule = RULE_1a; currentRule <= RULE_5; currentRule++) {
-
+ for (currentRule = RULE_1a; currentRule <= RULE_6; currentRule++) {
+
if (Logger.debugging)
Logger.info("-Rule " + getRuleName() + " CIPChirality for "
+ cipAtom + "-----"); // Logger
switch (currentRule) {
- case RULE_4bTEST:
- case RULE_4b:
- if (isRule4TEST != (currentRule == RULE_4bTEST))
- continue;
- break;
case RULE_4a:
case RULE_4c:
if (currentRule == RULE_4a) {
@@ -1210,11 +1214,20 @@
break;
}
}
+ // we need to presort with no tie-breaking for Rules 4
cipAtom.sortSubstituents(Integer.MIN_VALUE);
+ break;
+ case RULE_5:
+ break;
+ case RULE_6:
+ if (!cipAtom.setupRule6(false))
+ continue;
+ break;
}
// initial call to sortSubstituents does all, recursively
+ int nPrioritiesPrev = cipAtom.nPriorities;
if (cipAtom.sortSubstituents(0)) {
if (Logger.debugging) {
Logger.info(currentRule + ">>>>" + cipAtom);
@@ -1229,13 +1242,45 @@
if (isAlkeneEndCheck)
return (cipAtom.atoms[0].isDuplicate ? 2 : 1);
- rs = cipAtom.checkHandedness()
- | (currentRule == RULE_5 && cipAtom.canBePseudo ?
JC.CIP_CHIRALITY_PSEUDO_FLAG
- : 0);
+ rs = cipAtom.checkHandedness();
+ if (currentRule == RULE_5 && (cipAtom.nPriorities != 4 ||
nPrioritiesPrev != 2)) {
+
+ rs |= JC.CIP_CHIRALITY_PSEUDO_FLAG;
+
+ // Exclude special case:
+
+ // P-92.2.1.1(c) pseudoasymmetric centers must have
+ // two and only two enantiomorphic ligands
+ //
+
+ // Rule 5 has decided the issue, but how many decisions did we
make?
+ // If priorities [0 0 2 2] went to [0 1 2 3] then
+ // we have two Rule-5 decisions -- R,S,R',S'.
+ // In that case, Rule 5 results in R/S, not r/s.
+ //
+ // S
+ // -
+ // -
+ // R---C---R' despite this being Rule 5, the results is R,
not r.
+ // -
+ // -
+ // S'
+ //
+ // --------- mirror plane
+ //
+ // R'
+ // -
+ // -
+ // S---C---S' not superimposible
+ // -
+ // -
+ // R
+ //
+ }
if (Logger.debugging)
Logger.info(atom + " " + JC.getCIPChiralityName(rs) + " by Rule "
+ getRuleName() + "\n----------------------------------");
// Logger
- break;
+ return rs;
}
}
}
@@ -1290,10 +1335,10 @@
private int setBondChirality(SimpleNode a, SimpleNode pa, SimpleNode pb,
SimpleNode b, boolean isAxial) {
CIPAtom a1 = new CIPAtom().create(a, null, true, false, false);
- int atop = getAlkeneEndTopPriority(a1, pa, isAxial);
+ int atop = getAtomChiralityLimited(null, a1, pa) - 1;
int ruleA = currentRule;
CIPAtom b2 = new CIPAtom().create(b, null, true, false, false);
- int btop = getAlkeneEndTopPriority(b2, pb, isAxial);
+ int btop = getAtomChiralityLimited(null, b2, pb) - 1;
int ruleB = currentRule;
int c = (atop >= 0 && btop >= 0 ? getEneChirality(b2.atoms[btop], b2, a1,
a1.atoms[atop], isAxial, true) : NO_CHIRALITY);
@@ -1357,19 +1402,6 @@
}
/**
- * Alkene end check for final bond chirality, not auxiliary.
- *
- * @param a
- * @param pa
- * @param isAxial
- * @return -1, 0, or 1
- */
- private int getAlkeneEndTopPriority(CIPAtom a, SimpleNode pa, boolean
isAxial) {
- a.canBePseudo = isAxial;
- return getAtomChiralityLimited(null, a, pa) - 1;
- }
-
- /**
* Check cis vs. trans nature of a--b==c--d.
*
* @param a
@@ -1473,7 +1505,7 @@
* updating lstSmallRings
*
*/
- private int atomIndex;
+ int atomIndex;
/**
* true atom covalent bond count; cached for better performance
@@ -1551,16 +1583,14 @@
* the number of distinct priorities determined for this atom for the
* current rule; 0-4 for the root atom; 0-3 for all others
*/
- private int nPriorities;
+ int nPriorities;
/**
- * pointer to this branch's spiro end atom if it is found to be spiro
+ * number of root-duplicate atoms (root atom only
*/
- private CIPAtom spiroEnd;
+ int nRootDuplicates;
- private int nSpiro;
-
/**
* Rule 1b hash table that maintains distance of the associated
* nonduplicated atom node
@@ -1622,7 +1652,7 @@
* than one R/S decision made, so this center cannot be r/s; initially just
* indicates that the atom has 4 covalent bonds or is trigonal pyriamidal
*/
- boolean canBePseudo = true;
+ boolean isSP3 = true;
/**
* auxiliary chirality as determined in createAuxiliaryRule4Data;
@@ -1675,10 +1705,6 @@
*/
int rule4Type;
- private boolean rule4checkIdentical = true;
-
- private char rule4Ref = 'R';
-
private BS bsTemp = new BS();
// flag to reverse the Rule 2 result for a few isotope types
@@ -1685,10 +1711,9 @@
private boolean reverseRule2;
- // flag for C3-symmetry checking reference atom index
+ // reference index for Rule 6
- private int c3RefIndex = -1;
- private int c4RefIndex = -1;
+ int rule6refIndex = -1;
CIPAtom() {
// had a problem in JavaScript that the constructor of an inner function
cannot
@@ -1695,6 +1720,36 @@
// access this.b$ yet. That assignment is made after construction.
}
+ public boolean setupRule6(boolean isAux) {
+ if (nPriorities > 2 || (isAux ? countDuplicates(atomIndex) :
nRootDuplicates) <= 2)
+ return false;
+ // we have more than two root-duplicates and priorities array is one of:
+ // [0 0 0 0] CIP Helv Chim. Acta 1966 #33 -- double spiran
+ // [0 0 2 2] P-93.5.3.2 spiro
+ // [0 1 1 1] or [0 0 0 3] CIP Helv. Chim. Acta 1966 #32 -- C3-symmetric
+ root.rule6refIndex = atoms[priorities[2]].atomIndex;
+ // could be priorities[1] as well; just so it is not 0 or 3,
+ // as that could be the singlet in the C3-symmetric case.
+ // we need to presort again
+ sortSubstituents(Integer.MIN_VALUE);
+ return true;
+ }
+
+ private int countDuplicates(int index) {
+ int n = 0;
+ for (int i = 0; i < 4; i++) {
+ if (atoms[i] == null)
+ continue;
+ if (atoms[i].isDuplicate) {
+ if (atoms[i].atomIndex == index)
+ n++;
+ } else {
+ n += atoms[i].countDuplicates(index);
+ }
+ }
+ return n;
+ }
+
/**
*
* @param atom
@@ -1720,7 +1775,7 @@
elemNo = (isDuplicate && isKekuleAmbiguous ? parent
.getKekuleElementNumber() : atom.getElementNumber());
bondCount = atom.getCovalentBondCount();
- canBePseudo = (bondCount == 4 || bondCount == 3 && !isAlkene
+ isSP3 = (bondCount == 4 || bondCount == 3 && !isAlkene
&& (elemNo > 10 || bsAzacyclic != null &&
bsAzacyclic.get(atomIndex)));
if (parent != null)
sphere = parent.sphere + 1;
@@ -1757,9 +1812,7 @@
// pointing to original atom
isDuplicate = true;
rootDistance = 0;
- root.nSpiro++;
- if (rootSubstituent.spiroEnd == null)
- rootSubstituent.spiroEnd = parent;
+ root.nRootDuplicates++;
} else if (bsPath.get(atomIndex)) {
isDuplicate = true;
rootDistance = (isParentBond ? parent.sphere : htPathPoints.get(
@@ -1791,8 +1844,6 @@
*/
private float getMass() {
if (mass == UNDETERMINED && (mass = atom.getMass()) == (int) mass) {
- // this is an isotope
- haveIsotopes = true;
if (isType(RULE_2_nXX_REV_XX))
reverseRule2 = true;
else if (elemNo > 92 || isType(RULE_2_nXX_EQ_XX))
@@ -1832,31 +1883,6 @@
return ave / n;
}
- // /**
- // * Calculate the average element numbers of associated double-bond
atoms
- // * weighted by their most significant Kekule resonance
contributor(s). We
- // * only consider simple benzenoid systems -- 6-membered rings and
their
- // * 6-memebered rings fused to them. Calculated for the parent of an
- // * sp2-duplicate atom.
- // *
- // * @return an averaged element number
- // */
- // private float getKekuleMass() {
- // SimpleEdge[] edges = atom.getEdges();
- // SimpleEdge bond;
- // float ave = 0;
- // int n = 0;
- // for (int i = edges.length; --i >= 0;)
- // if ((bond = edges[i]).isCovalent()) {
- // SimpleNode other = bond.getOtherNode(atom);
- // if (bsKekuleAmbiguous.get(other.getIndex())) {
- // n++;
- // ave += other.getMass();
- // }
- // }
- // return ave / n;
- // }
-
/**
* Create a bit set that gives all the atoms in this ring if it is smaller
* than 8.
@@ -2024,7 +2050,7 @@
if (rule4List[i] != null && atoms[i].atom != null
&& !atoms[i].isTerminal)
atoms[i].sortSubstituents(Integer.MIN_VALUE);
- if (!canBePseudo)
+ if (!isSP3)
return false;
}
}
@@ -2032,7 +2058,6 @@
ignoreTies |= (currentRule == RULE_4b || currentRule == RULE_5);
int[] indices = new int[4], prevPrior = new int[4];
- int nPrioritiesPrev = nPriorities;
for (int i = 0; i < 4; i++) {
prevPrior[i] = priorities[i];
priorities[i] = 0;
@@ -2099,49 +2124,7 @@
priorities = newPriorities;
rule4List = newRule4List;
nPriorities = bsTemp.cardinality();
-
- if (parent == null) {
-
- // Check for special root-only cases:
-
- // P-92.2.1.1(c) pseudoasymmetric centers must have
- // two and only two enantiomorphic ligands
- //
- // P-33.5.3.1 spiro compounds have increased constraints
-
- if (currentRule == RULE_5) {
- if (nSpiro > 0)
- checkSpiro();
- if (nPriorities == 4 && nPrioritiesPrev == 2) {
-
- // Rule 5 has decided the issue, but how many decisions did we make?
- // If priorities [0 0 2 2] went to [0 1 2 3] then
- // we have two Rule-5 decisions -- R,S,R',S'.
- // In that case, Rule 5 results in R/S, not r/s.
- //
- // S
- // -
- // -
- // R---C---R' despite this being Rule 5, the results is R, not
r.
- // -
- // -
- // S'
- //
- // --------- mirror plane
- //
- // R'
- // -
- // -
- // S---C---S' not superimposible
- // -
- // -
- // R
- //
- canBePseudo = false;
- }
- }
- }
- if ((Logger.debuggingHigh) && atoms[2].atom != null
+ if (Logger.debuggingHigh && atoms[2].atom != null
&& atoms[2].elemNo != 1) { // Logger
Logger.info(dots() + atom + " nPriorities = " + nPriorities);
for (int i = 0; i < 4; i++) { // Logger
@@ -2157,71 +2140,6 @@
}
/**
- * CheckSpiro uses the concept that Andrey Yerin suggested that
- * covers all spiro, double spiro, C3-, C3-symmetric cases from CIP(1966).
- * Incredibly simple!
- *
- */
- private void checkSpiro() {
- boolean swap23 = false;
- int a = 0, b = -1;
- switch (nPriorities * 10 + priorities[3]) {
- case 10:
- // // CIP Helv Chim. Acta 1966 #33 -- double spiran
- // // 0-1,2-3 or 0-1,3-2
- // // 0-2,1-3 or
- // // 0-3,1-2
- b = 1;
- swap23 = true; // just the way it has to be
- break;
- case 21:
- case 23:
- // CIP Helv. Chim. Acta 1966 #32
- // [0 1 1 1] or [0 0 0 3]
- a = priorities[1];
- break;
- case 22:
- //
- // We have priorities [0 0 2 2], possibly being spiro
- //
- b = getSpiroEnd(0);
- break;
- default:
- return;
- }
- if (atoms[a].spiroEnd == null)
- return;
- c3RefIndex = atoms[a].atomIndex;
- if (b >= 0)
- c4RefIndex = atoms[b].atomIndex;
- if (sortByRule(RULE_6)) {
- currentRule = RULE_6;
- if (swap23) {
- CIPAtom atom = atoms[2];
- atoms[2] = atoms[3];
- atoms[3] = atom;
- }
- }
- }
-
- /**
- * Find the other end of a loop to root.
- *
- * @param i0
- * index of the spiro starting atom
- * @return pointer to spiro end of atoms[0] -- either -1 (not spiro), 0,
1, 2,
- * or 3
- */
- private int getSpiroEnd(int i0) {
- CIPAtom a = atoms[i0].spiroEnd;
- if (a != null)
- for (int i = 0; i < 4; i++)
- if (i != i0 && a.atom == atoms[i].atom)
- return i;
- return -1;
- }
-
- /**
* Provide an indent for clarity in debugging messages
*
* @return a string of dots based on the value of atom.sphere.
@@ -2391,28 +2309,27 @@
* @param maxRule
* @return TIED or deciding rule RULE_1a - RULE_5
*/
- private int sortToRule(int maxRule) {
+ private int sortToRule(int maxRule, boolean skipRules4And5) {
for (int i = RULE_1a; i <= maxRule; i++)
- if (sortByRule(i))
+ if ((!skipRules4And5 || i < RULE_4a || i > RULE_5) &&sortByRule(i))
return i;
- return TIED;
+ return 0;
}
/**
- * Sort by a given rule, preserving currentRule.
+ * Sort by a given rule, preserving currentRule, which could be 4 or 5
*
* @param rule
* @return true if a decision has been made
*/
private boolean sortByRule(int rule) {
- if ((rule == RULE_4b || rule == RULE_4bTEST)
- && (rule == RULE_4bTEST) != isRule4TEST)
- return false;
int current = currentRule;
currentRule = rule;
+ int rule6ref = root.rule6refIndex;
if (rule == RULE_6)
- sortSubstituents(Integer.MIN_VALUE);
+ setupRule6(true);
boolean isChiral = sortSubstituents(0);
+ root.rule6refIndex = rule6ref;
currentRule = current;
return isChiral;
}
@@ -2428,7 +2345,7 @@
* @return 0 (TIED), -1 (A_WINS), or 1 (B_WINS), or Intege.MIN_VALUE
* (IGNORE)
*/
- public int checkCurrentRule(CIPAtom b) {
+ private int checkCurrentRule(CIPAtom b) {
switch (currentRule) {
default:
case RULE_1a:
@@ -2443,38 +2360,19 @@
return checkRules4ac(b, " sr SR PM");
case RULE_4c:
return checkRules4ac(b, " s r p m");
- case RULE_4bTEST:
- return checkRule4Test(b);
case RULE_4b:
case RULE_5:
return TIED; // not carried out here because these need access to a
full list of ligands
case RULE_6:
- int score;
- return ((score = checkRule6(b, root.c3RefIndex)) != TIED ? score :
root.c4RefIndex >= 0 ? checkRule6(b, root.c4RefIndex) : score);
+ return checkRule6(b);
}
}
- private int checkRule6(CIPAtom b, int refIndex) {
- return ((atomIndex == refIndex) == (b.atomIndex == refIndex) ? TIED :
- atomIndex == refIndex ? A_WINS : B_WINS);
+ private int checkRule6(CIPAtom b) {
+ return ((atomIndex == root.rule6refIndex) == (b.atomIndex ==
root.rule6refIndex) ? TIED :
+ atomIndex == root.rule6refIndex ? A_WINS : B_WINS);
}
- private int checkRule4Test(CIPAtom b) {
- // TODO
- boolean isNS = (auxChirality == '~');
- if (rootSubstituent.atomIndex == b.rootSubstituent.atomIndex) {
- // sortSubstituent checking priority within a ligand
- if (isNS || b.auxChirality == '~')
- return (!isNS ? A_WINS : b.auxChirality != '~' ? B_WINS : TIED);
- return (auxChirality == b.auxChirality ? TIED
- : auxChirality == rootSubstituent.rule4Ref ? A_WINS : B_WINS);
- }
- //
- return (isNS ? TIED
- : (auxChirality == b.auxChirality) ==
rootSubstituent.rule4checkIdentical ? TIED
- : auxChirality == rootSubstituent.rule4Ref ? A_WINS : B_WINS);
- }
-
/**
* Looking for same atom or ghost atom or element number
*
@@ -3003,16 +2901,19 @@
char c = '~';
if (atom == null)
return "" + c;
+
rule4List = new String[4]; // full list based on atoms[]
if (nPriorities == 0 && !isSet) {
setNode();
if (!isAlkene && !isDuplicate && !isTerminal)
- sortToRule(RULE_3);
+ sortToRule(RULE_3, false);
}
int rs = -1, nRS = 0;
CIPAtom[] ret1 = new CIPAtom[1];
- int ruleMax = RULE_5;
+ boolean skipRules4And5 = false;
boolean prevIsChiral = true;
+ // have to allow two same f because could be a C3-symmetric subunit
+ boolean allowTwoSame = (node1 != null && !isAlkene && nPriorities == 1);
for (int i = 0; i < 4; i++) {
CIPAtom a = atoms[i];
if (a != null && !a.isDuplicate && !a.isTerminal) {
@@ -3033,11 +2934,13 @@
retThread = rsPath;
prevIsChiral = true;
} else {
- if (!prevIsChiral && priorities[i] == priorities[i - 1]) {
- if (node1 == null)
+ if (!allowTwoSame && !prevIsChiral && priorities[i] ==
priorities[i - 1]) {
+ // actually, I don't think priorities are set yet.
+ if (node1 == null) {
for (; i >= 0; --i)
rule4List[i] = null;
// two groups have the same priority, and neither has a
stereocenter
+ }
return "~";
}
prevIsChiral = false;
@@ -3050,7 +2953,7 @@
retThread = "";
//$FALL-THROUGH$
case 1:
- ruleMax = RULE_3;
+ skipRules4And5 = true;
break;
case 2:
case 3:
@@ -3110,7 +3013,7 @@
}
}
}
- } else if (canBePseudo) {
+ } else if (isSP3) {
// if here, adj is TIED (0) or NOT_RELEVANT
CIPAtom atom1 = (CIPAtom) clone();
if (atom1.setNode()) {
@@ -3124,8 +3027,8 @@
}
}
}
- int rule = atom1.sortToRule(ruleMax);
- if (rule == TIED) {
+ int rule = atom1.sortToRule(RULE_6, skipRules4And5);
+ if (rule < RULE_1a) {
c = '~';
} else {
rs = atom1.checkHandedness();
Modified: trunk/Jmol/src/org/jmol/viewer/JC.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/JC.java 2017-07-21 22:33:07 UTC (rev
21674)
+++ trunk/Jmol/src/org/jmol/viewer/JC.java 2017-07-23 20:07:02 UTC (rev
21675)
@@ -99,7 +99,7 @@
}
}
- private static final String[] ruleNames = {"", "1a", "1b", "2", "3", "4a",
"4b", "4b", "4c", "5", "6"};
+ private static final String[] ruleNames = {"", "1a", "1b", "2", "3", "4a",
"4b", "4c", "5", "6"};
public static String getCIPRuleName(int i) {
return ruleNames[i];
}
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