Revision: 21531
http://sourceforge.net/p/jmol/code/21531
Author: hansonr
Date: 2017-04-21 11:39:24 +0000 (Fri, 21 Apr 2017)
Log Message:
-----------
CIP all except parallel Rule 4 (Mata) and inositols
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 2017-04-21 04:17:07 UTC
(rev 21530)
+++ trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-04-21 11:39:24 UTC
(rev 21531)
@@ -200,6 +200,23 @@
static final int STEREO_Z = 1;
static final int STEREO_E = 2;
+ static final int RULE_1A = 0;
+ static final int RULE_1B = 1;
+ static final int RULE_2 = 2;
+ static final int RULE_3 = 3;
+ static final int RULE_4 = 4;
+ static final int RULE_5 = 5;
+
+ public String getRuleName() {
+ switch (currentRule) {
+ case RULE_1A:
+ return "1a";
+ case RULE_1B:
+ return "1b";
+ default:
+ return "" + currentRule;
+ }
+ }
/**
* Jmol viewer that created this CIPChirality object
*
@@ -222,7 +239,7 @@
* The current rule being applied exhaustively.
*
*/
- int currentRule = 0;
+ int currentRule = RULE_1A;
/**
* Rule 1b hash table that maintains distance of the associated nonduplicated
@@ -378,18 +395,18 @@
}
root = cipAtom;
cipAtom.parent = parent;
- currentRule = 0;
+ currentRule = RULE_1A;
if (cipAtom.set()) {
try {
if (iref >= 0)
cipAtom.bsPath.set(iref);
boolean doResetAux = false;
- for (currentRule = 0; currentRule <= ruleMax && !isChiral;
currentRule++) {
+ for (currentRule = RULE_1A; currentRule <= ruleMax && !isChiral;
currentRule++) {
if (Logger.debugging)
- Logger.info("-Rule " + currentRule + " CIPChirality for "
+ Logger.info("-Rule " + getRuleName() + " CIPChirality for "
+ cipAtom + "-----");
- if (currentRule == 4 && useAuxiliaries) {
+ if (currentRule == RULE_4 && useAuxiliaries) {
cipAtom.createAuxiliaryRSCenters(true);
doResetAux = true;
}
@@ -811,7 +828,7 @@
// Do an initial atom-only shallow sort using a.compareTo(b)
int ruleNow = currentRule;
- currentRule = 0;
+ currentRule = RULE_1A;
Arrays.sort(atoms);
currentRule = ruleNow;
@@ -849,7 +866,7 @@
}
}
atoms[i] = new CIPAtom(other, this, isDuplicate);
- if (currentRule > 2)
+ if (currentRule > RULE_2)
prevPriorities[i] = getBasePriority(atoms[i]);
// if (Logger.debugging)
// Logger.info(this + " adding " + i + " " + atoms[i]);
@@ -871,7 +888,7 @@
if (Logger.debugging) {
Logger.info("---sortSubstituents---" + atom);
for (int i = 0; i < n; i++)
- Logger.info(currentRule + ": " + this + "[" + i + "]=" +
atoms[i].myPath
+ Logger.info(getRuleName() + ": " + this + "[" + i + "]=" +
atoms[i].myPath
+ " " + Integer.toHexString(prevPriorities[i]));
}
@@ -884,7 +901,7 @@
// if (prevPriorities[i] != 0 &&
// (prevPriorities[i]&0xFF000000) !=
(getBasePriority(atoms[i]) & 0xFF000000))
// System.out.println("???????");
- if (prevPriorities[i] == 0 && currentRule > 1)
+ if (prevPriorities[i] == 0 && currentRule > RULE_1B)
prevPriorities[i] = getBasePriority(atoms[i]);
}
for (int i = 0; i < n; i++) {
@@ -893,13 +910,13 @@
CIPAtom b = atoms[j];
if (Logger.debuggingHigh)
Logger.info("ordering " + this.id + "." + i + "." + j + " " + this
- + "-" + a + " vs " + b + " "
+ + "-" + a + " vs " + b + " " + " Rule " + getRuleName()
+ Integer.toHexString(prevPriorities[i]) + " "
+ Integer.toHexString(prevPriorities[j]));
int score = compareSubs(a, b, i, j);
if (Logger.debuggingHigh)
Logger.info("ordering " + this.id + "." + i + "." + j + " " + this
- + "-" + a + " vs " + b + " = " + score);
+ + "-" + a + " vs " + b + " = " + score + " Rule " +
getRuleName());
switch (score) {
case NA:
System.out.println("OHNO");
@@ -908,7 +925,7 @@
indices[i]++;
priorities[i]++;
if (Logger.debuggingHigh)
- Logger.info(atom + "." + b + " B-beats " + a + " ind="
+ Logger.info(atom + "." + b + " B-beats " + a + " Rule " +
getRuleName()+ " ind="
+ indices[i]);
break;
case A_WINS:
@@ -915,7 +932,7 @@
indices[j]++;
priorities[j]++;
if (Logger.debuggingHigh)
- Logger.info(atom + "." + a + " A-beats " + b + " ind="
+ Logger.info(atom + "." + a + " A-beats " + b + " Rule " +
getRuleName()+ " ind="
+ indices[j]);
break;
case TIED:
@@ -926,7 +943,7 @@
case TIED:
indices[i]++;
if (Logger.debuggingHigh)
- Logger.info(atom + "." + b + " ends up with tie with " + a
+ Logger.info(atom + "." + b + " ends up with tie with " + a + "
Rule " + getRuleName()
+ " ind=" + indices[i]);
break;
case B_WINS:
@@ -933,7 +950,7 @@
indices[i]++;
priorities[i]++;
if (Logger.debuggingHigh)
- Logger.info(atom + "." + b + " wins in tie with " + a + " ind="
+ Logger.info(atom + "." + b + " wins in tie with " + a + " Rule
" + getRuleName() + " ind="
+ indices[i] + "\n");
break;
case A_WINS:
@@ -940,7 +957,7 @@
indices[j]++;
priorities[j]++;
if (Logger.debuggingHigh)
- Logger.info(atom + "." + a + " wins in tie with " + b + " ind="
+ Logger.info(atom + "." + a + " wins in tie with " + " Rule " +
getRuleName() + b + " ind="
+ indices[j] + "\n");
break;
}
@@ -1001,7 +1018,7 @@
if (Logger.debugging) {
Logger.info(atom + " nPriorities = " + nPriorities);
for (int i = 0; i < n; i++)
- Logger.info(atom + "[" + i + "]=" + atoms[i] + " " + priorities[i]);
+ Logger.info(this.myPath + "[" + i + "]=" + atoms[i] + " " +
priorities[i] + " new");
Logger.info("-------");
}
}
@@ -1096,12 +1113,12 @@
if (Logger.debugging)
Logger.info("compareAB "
+ (score == B_WINS ? bi + " beats " + ai : ai + " beats " + bi)
- + " by Rule " + currentRule);
+ + " by Rule " + getRuleName());
return score;
}
}
if (Logger.debugging)
- Logger.info("compareAB ends in tie for " + this + " vs. " + b);
+ Logger.info("compareAB ends in tie for " + this + " vs. " + b + " Rule
" + getRuleName());
return TIED;
}
@@ -1135,17 +1152,17 @@
public int checkCurrentRule(CIPAtom b) {
switch (currentRule) {
default:
- case 0:
+ case RULE_1A:
return checkRule1a(b);
- case 1:
+ case RULE_1B:
return checkRule1b(b);
- case 2:
+ case RULE_2:
return checkRule2(b);
- case 3:
+ case RULE_3:
return checkRule3(b);
- case 4:
+ case RULE_4:
return checkRule4(b);
- case 5:
+ case RULE_5:
return checkRule5(b);// handled at the end of Rule 4 checkRule5(b);
}
}
@@ -1301,7 +1318,7 @@
atom1.atoms[indices[ib]] = new CIPAtom(null, atom1, false);
atom1.addReturnPath(null, path);
int thisRule = currentRule;
- currentRule = 1;
+ currentRule = RULE_1A;
atom1.sortSubstituents();
// Now add the tied branches at the end; it doesn't matter where they
// go as long as they are together and in order.
@@ -1338,8 +1355,9 @@
if (atom == null)
return;
for (int i = 0; i < 4; i++) {
- if (atoms[i] != null)
- atoms[i].createAuxiliaryRSCenters(false);
+ CIPAtom a = atoms[i];
+ if (a != null && !a.isDuplicate && !a.isTerminal)
+ a.createAuxiliaryRSCenters(false);
}
System.out.println("createAux " + this + " " + nPriorities + " " +
isRoot);
if (isRoot || bondCount != 4 || nPriorities > 0 && nPriorities < 3)
@@ -1352,8 +1370,8 @@
Lst<CIPAtom> path = getReturnPath(this);
atom1.addReturnPath(null, path);
int thisRule = currentRule;
- currentRule = 1;
- atom1.sortSubstituents();
+ currentRule = RULE_1A;
+ atom1.sortSubstituents(); //this sort is not going right
currentRule = thisRule;
int rs = checkHandedness(atom1);
System.out.println(rs + " " + myPath + JC.getCIPChiralityName(rs));
@@ -1514,6 +1532,7 @@
a.priorities = new int[4];
a.prevPriorities = new int[4];
for (int i = 0; i < 4; i++) {
+ a.priorities[i] = priorities[i];
if (atoms[i] != null) {
a.atoms[i] = atoms[i];
a.prevPriorities[i] = getBasePriority(atoms[i]);
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