Revision: 21553
http://sourceforge.net/p/jmol/code/21553
Author: hansonr
Date: 2017-04-26 04:31:56 +0000 (Wed, 26 Apr 2017)
Log Message:
-----------
CIP Rule 4 work complete
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 2017-04-25 21:39:12 UTC
(rev 21552)
+++ trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-04-26 04:31:56 UTC
(rev 21553)
@@ -1634,23 +1634,27 @@
// We are trying to ascertain that
// R lull R luuu
// S luuu is the same as S lull
- // maybe "min for one is the same as min for the other?"
//
+ // Solution is to SUM all winners.
String[] aList = PT.split(aStr, "|");
String[] bList = PT.split(bStr, "|");
int minScore = Integer.MAX_VALUE;
+ int sumScore = 0;
aStr = aList[0];
bStr = bList[0];
for (int i = 0; i < 2; i++) {
for (int j = 0; j < 2; j++) {
int score = compareRule4PairStr(aList[i], bList[j], true);
- if (score <= minScore) {
- minScore = score;
+ sumScore += score;
+ if (score != TIED && Math.abs(score) <= minScore) {
+ minScore = Math.abs(score);
aStr = aList[i];
bStr = bList[j];
}
}
}
+ if (sumScore == TIED)
+ return TIED;
}
} else {
// trim off priority numbers
@@ -1660,6 +1664,17 @@
return compareRule4PairStr(aStr, bStr, false);
}
+ /**
+ * Comparison of two strings such as RSSR and SRSS for Rule 4b.
+ *
+ * @param aStr
+ * @param bStr
+ * @param isRSTest
+ * return a score qualified by measure of how far into the
comparison
+ * when we find a like/unlike distance
+ *
+ * @return 0 (TIED), -1 (A_WINS), 1 (B_WINS), Integer.MIN_VALUE (IGNORE)
+ */
private int compareRule4PairStr(String aStr, String bStr, boolean
isRSTest) {
System.out.println(this + " Rule 4b comparing " + aStr + " " + bStr);
doCheckPseudo = false;
@@ -1672,7 +1687,7 @@
boolean alike = (aref == aStr.charAt(c));
boolean blike = (bref == bStr.charAt(c));
if (alike != blike)
- return (isRSTest ? c : alike ? A_WINS : B_WINS);
+ return (isRSTest ? c : 1) * (alike ? A_WINS : B_WINS);
}
if (isRSTest)
return TIED;
@@ -1682,6 +1697,13 @@
return aref < bref ? A_WINS : B_WINS;
}
+ /**
+ * Retrieve the Mata Rule 4b list for a given atom.
+ *
+ * @param ia
+ * @return a String representation of the path through the atoms
+ *
+ */
private String getMataList(int ia) {
String[] rule4List = atoms[ia].rule4List;
int n = 0;
@@ -1706,6 +1728,14 @@
}
}
+ /**
+ * This is the key Mata method -- getting the correct sequence of atoms.
+ *
+ * @param lst
+ * @param aref
+ * @return one string, possibly separated by | indicating that the result
+ * has both an R and S side to it
+ */
private String getMataSequence(String[] lst, String aref) {
int n = lst.length;
String[] sorted = new String[n];
@@ -1723,7 +1753,6 @@
if (rs.indexOf(aref) != 1)
sorted[pt++] = rs;
}
-
for (int i = 0; i < n; i++) {
System.out.println("Sorted Mata list " + i + " " + sorted[i]);
}
@@ -1739,6 +1768,12 @@
return mlist;
}
+ /**
+ * Determine the reference configuration.
+ *
+ * @param lst
+ * @return
+ */
private String getMataRef(String[] lst) {
// get highest-ranking chiral unit
int pt = Integer.MAX_VALUE;
This was sent by the SourceForge.net collaborative development platform, the
world's largest Open Source development site.
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Jmol-commits mailing list
Jmol-commits@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-commits
