Revision: 21670
http://sourceforge.net/p/jmol/code/21670
Author: hansonr
Date: 2017-07-21 22:22:08 +0000 (Fri, 21 Jul 2017)
Log Message:
-----------
Jmol.___JmolVersion="14.20.4"
bug fix: CIPChirality covers all special spiro cases and C3-symmetry
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/symmetry/CIPChirality.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 2017-07-20 14:37:14 UTC
(rev 21669)
+++ trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-07-21 22:22:08 UTC
(rev 21670)
@@ -540,10 +540,10 @@
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_4a = 5, RULE_4bTEST = 6, RULE_4b = 7, RULE_4c = 8,
+ RULE_5 = 9,
+ RULE_6 = 10;
- RULE_4bTEST = 6, RULE_4b = 7, RULE_4c = 8, RULE_5 = 9;
-
boolean isRule4TEST = false;
static String prefixString = ".........."; // Logger only
@@ -1557,7 +1557,7 @@
* pointer to this branch's spiro end atom if it is found to be spiro
*/
- private CIPAtom spiroEnd, spiroEnd1;
+ private CIPAtom spiroEnd;
private int nSpiro;
@@ -1681,10 +1681,15 @@
private BS bsTemp = new BS();
- // flag to reverse the ruling for a few isotope types
+ // flag to reverse the Rule 2 result for a few isotope types
private boolean reverseRule2;
+ // flag for C3-symmetry checking reference atom index
+
+ private int c3RefIndex = -1;
+ private int c4RefIndex = -1;
+
CIPAtom() {
// had a problem in JavaScript that the constructor of an inner function
cannot
// access this.b$ yet. That assignment is made after construction.
@@ -1753,15 +1758,8 @@
isDuplicate = true;
rootDistance = 0;
root.nSpiro++;
- if (rootSubstituent.spiroEnd == null) {
+ if (rootSubstituent.spiroEnd == null)
rootSubstituent.spiroEnd = parent;
- } else if (rootSubstituent.spiroEnd.sphere > parent.sphere) {
- rootSubstituent.spiroEnd1 = rootSubstituent.spiroEnd;
- rootSubstituent.spiroEnd = parent;
- } else if (rootSubstituent.spiroEnd1 == null
- || rootSubstituent.spiroEnd1.sphere > parent.sphere) {
- rootSubstituent.spiroEnd1 = parent;
- }
} else if (bsPath.get(atomIndex)) {
isDuplicate = true;
rootDistance = (isParentBond ? parent.sphere : htPathPoints.get(
@@ -1998,7 +1996,7 @@
* pseudochirality is also done here.
*
* @param sphere
- * current working sphere
+ * current working sphere; Integer.MIN_VALUE to not break ties
* @return all priorities assigned
*
*/
@@ -2016,13 +2014,22 @@
// Just before Rule4a we must sort all substituents without breaking
ties
if (isTerminal)
return false;
- for (int i = 0; i < 4; i++)
- if (rule4List[i] != null && atoms[i].atom != null
- && !atoms[i].isTerminal)
- atoms[i].sortSubstituents(Integer.MIN_VALUE);
- if (!canBePseudo)
- return false;
+ if (currentRule == RULE_6) {
+ for (int i = 0; i < 4; i++)
+ if (atoms[i] != null && !atoms[i].isDuplicate && atoms[i].atom !=
null
+ && atoms[i].setNode())
+ atoms[i].sortSubstituents(Integer.MIN_VALUE);
+ } else {
+ for (int i = 0; i < 4; i++)
+ if (rule4List[i] != null && atoms[i].atom != null
+ && !atoms[i].isTerminal)
+ atoms[i].sortSubstituents(Integer.MIN_VALUE);
+ if (!canBePseudo)
+ return false;
+ }
}
+
+ ignoreTies |= (currentRule == RULE_4b || currentRule == RULE_5);
int[] indices = new int[4], prevPrior = new int[4];
int nPrioritiesPrev = nPriorities;
@@ -2037,7 +2044,7 @@
Logger.info(getRuleName() + ": " + this + "[" + i + "]="
+ atoms[i].myPath + " " + Integer.toHexString(prevPrior[i])); //
Logger
}
- Logger.info("---");
+ Logger.info("---" + nPriorities);
}
int loser, score;
@@ -2059,7 +2066,7 @@
: (score = checkPriority(a, b, i, j)) != TIED ? score
: ignoreTies ? IGNORE : sign(a
.breakTie(b, sphere + 1))) {
- case B_WINS:
+ case B_WINS:
loser = i;
//$FALL-THROUGH$
case A_WINS:
@@ -2102,15 +2109,11 @@
//
// P-33.5.3.1 spiro compounds have increased constraints
- // We do the spiro test first, as it may inform the pseudoasymmetric
test.
+ if (currentRule == RULE_5) {
+ if (nSpiro > 0)
+ checkSpiro();
+ if (nPriorities == 4 && nPrioritiesPrev == 2) {
- if (nSpiro > 0) {
- int nprev = checkSpiro();
- if (nprev == 2)
- nPrioritiesPrev = 2;
- }
- if (currentRule == RULE_5 && 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'.
@@ -2136,7 +2139,7 @@
//
canBePseudo = false;
}
-
+ }
}
if ((Logger.debuggingHigh) && atoms[2].atom != null
&& atoms[2].elemNo != 1) { // Logger
@@ -2145,7 +2148,7 @@
Logger.info(dots() + myPath + "[" + i + "]=" + atoms[i] + " "
+ priorities[i] + " " + Integer.toHexString(priorities[i])); //
Logger
}
- Logger.info(dots() + "-------");
+ Logger.info(dots() + "-------" + nPriorities);
}
// We are done if the number of priorities equals the bond count.
@@ -2153,94 +2156,53 @@
return (nPriorities == bondCount);
}
- private int checkSpiro() {
- if (nSpiro >= 42)
- return -1; // disallow O_h-cubane, which has 42 root termination
pathways
+ /**
+ * CheckSpiro uses the concept that Mikko Vainio discovered that
+ * covers all spiro, double spiro, C3-, C3-symmetric cases from CIP(1966).
+ * Incredibly simple!
+ *
+ */
+ private void checkSpiro() {
boolean swap23 = false;
- int nPrev = 0;
- if (nPriorities == 1) {
- // 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
- int a2, a3;
- if ((getSpiroType(0, false)) >= 0 && (a2 = getSpiroType(0, true)) >= 0
- && (getSpiroType(1, false)) >= 0
- && (a3 = getSpiroType(1, true)) >= 0
- && (getSpiroType(2, false)) >= 0 && (getSpiroType(2, true)) >= 0
- && (getSpiroType(3, false)) >= 0 && (getSpiroType(3, true)) >= 0) {
- nPriorities = 4;
- swap23 = (a2 < a3);
- }
- } else if (nPriorities == 2) {
- swap23 = false;
- switch (priorities[3]) {
- case 1:
- case 3:
- // CIP Helv. Chim. Acta 1966 #32
- // [0 1 1 1] or [0 0 0 3]
- int first = (priorities[3] == 1 ? 1 : 0);
- int a1 = getSpiroType(first, false);
- if (a1 >= 0) {
- // BH64_069, BH64_070
- int a2 = getSpiroType(a1, false);
- int a3 = getSpiroType(a2, false);
- if (a1 != a2 && a2 != a3 && a3 != a1) {
- nPriorities = 4;
- swap23 = (a2 > a1);
- }
- }
- break;
- case 2:
- //
- // We have priorities [0 0 2 2], possibly being spiro
- //
- int end0,
- end1;
- if ((end0 = getSpiroType(0, false)) >= 2
- && (end1 = getSpiroType(1, false)) >= 2 && end0 != end1) {
- //
- // We are done, because the two spiro ends set both of these ties.
- // a a'b b' (order is already OK)
- // a a'b'b (needs switching)
- //
- // P-93.2.3.2
- //
- // We have priorities [0 0 2 2], possibly being spiro
- //
- // b b
- // /- -\
- // / - - \
- // a--C--a' R a--C--a' S
- // - / \ -
- // -/ \-
- // b' b'
- //
- // a==a' and b==b'; order of precedence is set to a > a' > b > b'
- //
- // Note that this is really a case of axial chirality. It is the
same as:
- //
- // b' a'
- // - -
- // - -
- // a--C--b M a--C--b P
- // - -
- // - -
- // a' b'
+ 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
- nPrev = 2;
- nPriorities = 4;
- swap23 = (end1 == 2);
- }
- break;
+ if (atoms[a].spiroEnd == null)
+ return;
+ 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;
+ }
+ 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;
}
}
- if (swap23) {
- CIPAtom a = atoms[2];
- atoms[2] = atoms[3];
- atoms[3] = a;
- }
- return nPrev;
}
/**
@@ -2248,12 +2210,11 @@
*
* @param i0
* index of the spiro starting atom
- * @return pointer to spiro end of atoms[0] -- either 0 (not spiro), 1, 2,
+ * @return pointer to spiro end of atoms[0] -- either -1 (not spiro), 0,
1, 2,
* or 3
*/
- private int getSpiroType(int i0, boolean checkEnd1) {
- CIPAtom a = (i0 < 0 ? null : checkEnd1 ? atoms[i0].spiroEnd1
- : atoms[i0].spiroEnd);
+ 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)
@@ -2284,7 +2245,6 @@
// Two duplicates of the same atom are always tied
// if they have the same root distance.
- // System.out.println("breaking tie for \n" + this.myPath + "\n" +
b.myPath);
if (isDuplicate && b.isDuplicate && atom == b.atom
&& rootDistance == b.rootDistance)
return TIED;
@@ -2392,10 +2352,12 @@
/**
* Used in sortSubstituents
- *
+ * @param a
* @param b
+ * @param i
+ * @param j
*
- * @return 0 (TIED), -1 (A_WINS), or 1 (B_WINS)
+ * @return 0 (TIED), -1 (A_WINS), 1 (B_WINS), or Integer.MIN_VALUE (IGNORE)
*/
private int checkPriority(CIPAtom a, CIPAtom b, int i, int j) {
switch (currentRule) {
@@ -2449,6 +2411,8 @@
return false;
int current = currentRule;
currentRule = rule;
+ if (rule == RULE_6)
+ sortSubstituents(Integer.MIN_VALUE);
boolean isChiral = sortSubstituents(0);
currentRule = current;
return isChiral;
@@ -2481,13 +2445,21 @@
case RULE_4c:
return checkRules4ac(b, " s r p m");
case RULE_4bTEST:
- return (checkRule4Test(b));
+ 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
+ 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);
}
}
-
+
+ private int checkRule6(CIPAtom b, int refIndex) {
+ return ((atomIndex == refIndex) == (b.atomIndex == refIndex) ? TIED :
+ atomIndex == refIndex ? A_WINS : B_WINS);
+ }
+
private int checkRule4Test(CIPAtom b) {
// TODO
boolean isNS = (auxChirality == '~');
@@ -2540,9 +2512,6 @@
* @return 0 (TIED), -1 (A_WINS), or 1 (B_WINS)
*/
private int checkRule2(CIPAtom b) {
- System.out.println(getMass() + " vs " + b.getMass() + " " + (b.getMass()
== getMass() ? TIED :
- (reverseRule2 || b.reverseRule2) == (b.mass > mass) ? A_WINS :
B_WINS));
-
return (b.getMass() == getMass() ? TIED :
(reverseRule2 || b.reverseRule2) == (b.mass > mass) ? A_WINS : B_WINS);
}
@@ -2756,6 +2725,9 @@
String reason = "Rule 4b"; // Logger
while (true) {
+
+ if (aref == '-' && bref == '-')
+ return IGNORE;
// check for RS on only one side
if ((aref == '?') != (bref == '?')) {
@@ -2924,7 +2896,7 @@
return auxChirality;
int nR = ((Integer) rule4Count[1]).intValue(), nS = ((Integer)
rule4Count[2])
.intValue();
- return (nR > nS ? 'R' : nR < nS ? 'S' : '?');
+ return (nR > nS ? 'R' : nR < nS ? 'S' : nR == 0 ? '-' : '?');
}
/**
@@ -3000,12 +2972,12 @@
* @return 0 (TIED), -1 (A_WINS), 1 (B_WINS), Integer.MIN_VALUE (IGNORE)
*/
private int compareRule4PairStr(String aStr, String bStr, boolean
isRSTest) {
+ int n = aStr.length();
+ if (n == 0 || n != bStr.length())
+ return TIED;
if (Logger.debugging)
Logger.info(dots() + this.myPath + " Rule 4b comparing " + aStr + " "
+ bStr);
- int n = aStr.length();
- if (n == 0 || n != bStr.length())
- return TIED;
char aref = aStr.charAt(0), bref = bStr.charAt(0);
for (int c = 1; c < n; c++) {
boolean alike = (aref == aStr.charAt(c));
@@ -3062,9 +3034,13 @@
retThread = rsPath;
prevIsChiral = true;
} else {
- if (!prevIsChiral && priorities[i] == priorities[i - 1])
+ if (!prevIsChiral && priorities[i] == priorities[i - 1]) {
+ if (node1 == null)
+ for (; i >= 0; --i)
+ rule4List[i] = null;
// two groups have the same priority, and neither has a
stereocenter
return "~";
+ }
prevIsChiral = false;
}
}
@@ -3096,8 +3072,7 @@
// case we have a simple E/Z (c/t), and there is no need to check AND
// it does not contribute to the Mata sequence (similar to r/s or
m/p).
//
- if (!isEvenEne
- || (auxEZ == STEREO_BOTH_EZ || auxEZ == UNDETERMINED)
+ if (!isEvenEne || (auxEZ == STEREO_BOTH_EZ || auxEZ == UNDETERMINED)
&& alkeneChild.bondCount >= 2 && !isKekuleAmbiguous) {
rs = getAuxEneWinnerChirality(this, alkeneChild, !isEvenEne,
RULE_5);
//
@@ -3191,7 +3166,11 @@
return TIED;
int isRa = test.indexOf(auxChirality), isRb = test
.indexOf(b.auxChirality);
- return (isRa > isRb + 1 ? A_WINS : isRb > isRa + 1 ? B_WINS : TIED);
+ return (isRa > isRb + 1 ?
+ A_WINS :
+ isRb > isRa + 1 ?
+ B_WINS
+ : TIED);
}
/**
Modified: trunk/Jmol/src/org/jmol/viewer/JC.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/JC.java 2017-07-20 14:37:14 UTC (rev
21669)
+++ trunk/Jmol/src/org/jmol/viewer/JC.java 2017-07-21 22:22:08 UTC (rev
21670)
@@ -99,7 +99,7 @@
}
}
- private static final String[] ruleNames = {"", "1a", "1b", "2", "3", "4a",
"4b", "4b", "4c", "5"};
+ private static final String[] ruleNames = {"", "1a", "1b", "2", "3", "4a",
"4b", "4b", "4c", "5", "6"};
public static String getCIPRuleName(int i) {
return ruleNames[i];
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-07-20 14:37:14 UTC
(rev 21669)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-07-21 22:22:08 UTC
(rev 21670)
@@ -56,8 +56,12 @@
# TODO: fix UNDO
-Jmol.___JmolVersion="14.20.3" // 2017.07.20
+Jmol.___JmolVersion="14.20.4"
+bug fix: CIPChirality covers all special spiro cases and C3-symmetry
+
+JmolVersion="14.20.3" // 2017.07.20
+
bug fix: ROTATE should not stop spin if it does not initiate a spin
bug fix: CIPChirality tests for CIP1966#31,#32 douple spirans and C3 compounds
bug fix: CIPChirality for Rule 2 using atomic masses and not for duplicate
atoms
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