Revision: 21551
http://sourceforge.net/p/jmol/code/21551
Author: hansonr
Date: 2017-04-25 15:57:35 +0000 (Tue, 25 Apr 2017)
Log Message:
-----------
Basic Mata handling; still needs work - 2/70 structures not validating
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 14:13:03 UTC
(rev 21550)
+++ trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-04-25 15:57:35 UTC
(rev 21551)
@@ -1600,8 +1600,7 @@
// but generally we will want to process this as "R" and "S"
// note that this analysis cannot be done ahead of time.
return (rule4List[i] == null && rule4List[j] == null ? TIED
- : rule4List[i] != null && rule4List[j] != null ? compareRule4Pair(
- rule4List[i], rule4List[j]) : rule4List[i] == null ? B_WINS
+ : rule4List[i] != null && rule4List[j] != null ? compareRule4Pair(i,
j) : rule4List[i] == null ? B_WINS
: A_WINS);
}
@@ -1608,26 +1607,34 @@
/**
* Chapter 9 Rules 4 and 5: like vs. unlike
*
- * Compare two strings such as RSSSR and SRSRR for like and unlike
- * and find a winner. Return IGNORE if they are identical; return A_WINS or
- * B_WINS if there is a winner, and set this.doCheckPseudo if they are
- * opposites with reference atom R or S (but not r or s).
+ * Compare two strings such as RSSSR and SRSRR for like and unlike and find
+ * a winner. Return IGNORE if they are identical; return A_WINS or B_WINS
if
+ * there is a winner, and set this.doCheckPseudo if they are opposites with
+ * reference atom R or S (but not r or s).
*
- * @param aStr
- * @param bStr
+ * @param ia
+ * @param ib
* @return 0 (TIED), -1 (A_WINS), or 1 (B_WINS), or Integer.MIN_VALUE
* (IGNORE)
*/
- private int compareRule4Pair(String aStr, String bStr) {
-
+ private int compareRule4Pair(int ia, int ib) {
+ String aStr = rule4List[ia];
+ String bStr = rule4List[ib];
+
if (aStr != null && aStr.indexOf("?") == 0) {
- System.out.println(this + " " + aStr + " " + bStr);
- System.out.println("???????????");
+ aStr = getMataList(atoms[ia].rule4List);
+ bStr = getMataList(atoms[ib].rule4List);
+ if (aStr.length() != bStr.length()) {
+ // bStr must have R and S options, but aStr does not
+ return (aStr.length() < bStr.length() ? A_WINS : B_WINS);
+ }
+ if (aStr.indexOf("|") >= 0 || bStr.indexOf("|") >= 0)
+ return TIED; // TODO!
}
// TODO: preliminary only. The challenge is to get these strings lined
up right.
- aStr = PT.rep(aStr, "~", "");
- bStr = PT.rep(bStr, "~", "");
+ aStr = PT.rep(aStr, "~", "");
+ bStr = PT.rep(bStr, "~", "");
System.out.println("Rule 4b comparing " + aStr + " " + bStr);
doCheckPseudo = false;
int n = aStr.length();
@@ -1635,9 +1642,9 @@
return TIED;
char aref = aStr.charAt(0);
char bref = bStr.charAt(0);
- for (int j = 1; j < n; j++) {
- boolean alike = (aref == aStr.charAt(j));
- boolean blike = (bref == bStr.charAt(j));
+ for (int c = 1; c < n; c++) {
+ boolean alike = (aref == aStr.charAt(c));
+ boolean blike = (bref == bStr.charAt(c));
if (alike != blike)
return (alike ? A_WINS : B_WINS);
}
@@ -1647,7 +1654,85 @@
return aref < bref ? A_WINS : B_WINS;
}
+ private String getMataList(String[] rule4List) {
+ String[] listA = condenseList(rule4List);
+ Arrays.sort(listA);
+ String aref = getMataRef(listA);
+ switch (aref.length()) {
+ default:
+ case 0:
+ System.out.println("???");
+ return "???";
+ case 1:
+ return getMataSequence(listA, aref);
+ case 2:
+ return getMataSequence(listA, "R") + "|" + getMataSequence(listA,
"S");
+ }
+ }
+
+ private String getMataSequence(String[] lst, String aref) {
+ int n = lst.length;
+ String[] sorted = new String[n];
+ int pt = 0;
+ int len = 0;
+ for (int i = 0; i < n; i++) {
+ String rs = lst[i];
+ if (rs.length() > len)
+ len = rs.length();
+ if (rs.startsWith(aref))
+ sorted[pt++] = rs;
+ }
+ for (int i = 0; i < n; i++) {
+ String rs = lst[i];
+ if (!rs.startsWith(aref))
+ sorted[pt++] = rs;
+ }
+ String mlist = "";
+ char ch;
+ for (int i = 0; i < len; i++) {
+ for (int j = 0; j < n; j++) {
+ String rs = sorted[j];
+ if (i < rs.length() && (ch = rs.charAt(i)) != '~' && ch != ';')
+ mlist += ch;
+ }
+ }
+ return mlist;
+ }
+
+ private String getMataRef(String[] lst) {
+ // TODO: does not take into consideration initial ~~
+ switch (lst.length) {
+ case 1:
+ // R or S
+ return lst[0].substring(0, 1);
+ case 2:
+ // RR RS SR SS
+ return (lst[0].charAt(0) == lst[1].charAt(0) ?
+ lst[0].substring(0, 1) : "RS");
+ case 3:
+ return lst[1].substring(0, 1);
+ }
+ return "";
+ }
+
/**
+ * remove unnecessary nulls
+ * @param a
+ * @return trimmed array
+ */
+ private String[] condenseList(String[] a) {
+ int n = 0;
+ for (int i = a.length; --i >= 0;)
+ if (a[i] != null)
+ n++;
+ String[] b = new String[n];
+ for (int i = a.length; --i >= 0;)
+ if (a[i] != null)
+ b[--n] = a[i];
+ return b;
+ }
+
+ /**
* Reverse the path to the parent and check r/s chirality
*
* @param ties
@@ -1738,8 +1823,8 @@
auxPseudo.createAuxiliaryRSCenters(true);
int rs = -1;
String subRS = "";
- String s = "~";
- boolean done = false;
+ String s = (isRoot ? "" : "~");
+ boolean done = true;
if (atom != null) {
rule4List = new String[4]; // full list based on atoms[]
int[] mataList = new int[4]; //sequential pointers into rule4List
@@ -1760,30 +1845,42 @@
}
}
int adj = TIED;
- if (nRS == 0) {
+ switch (nRS) {
+ case 0:
subRS = "";
- } else if (nRS == 2 && !isRoot) {
- // we want to now if these two are enantiomorphic, identical, or
diastereomorphic.
- switch (adj = (compareRule4aEnantiomers(rule4List[mataList[0]],
rule4List[mataList[1]]))) {
- case DIASTEREOMERIC:
- case NOT_RELEVANT:
- // create a ?<sphere>[....] object
- adj = TIED;
- break;
- case TIED:
- // identical -- nothing we can do about this -- two identical
ligands
- adj = IGNORE;
- subRS = "";
- break;
- case A_WINS:
- case B_WINS:
- // enantiomers -- we have an r/s situation
- subRS = "";
- break;
+ break;
+ case 1:
+ break;
+ case 2:
+ if (!isRoot) {
+ // we want to now if these two are enantiomorphic, identical, or
diastereomorphic.
+ switch (adj = (compareRule4aEnantiomers(rule4List[mataList[0]],
rule4List[mataList[1]]))) {
+ case DIASTEREOMERIC:
+ done = false;
+ break;
+ case NOT_RELEVANT:
+ // create a ?<sphere>[....] object ?
+ adj = TIED;
+ break;
+ case TIED:
+ // identical -- nothing we can do about this -- two identical
ligands
+ subRS = "";
+ break;
+ case A_WINS:
+ case B_WINS:
+ // enantiomers -- we have an r/s situation
+ subRS = "";
+ break;
+ }
}
+ break;
+ case 3:
+ case 4:
+ done = false;
}
- if (adj == IGNORE) {
- // same chirality -- leave this as ~
+ if (!done) {
+ s = "?" + sphere;
+ subRS = "[" + subRS + "]";
} else if (!isRoot && (bondCount == 4 && nPriorities >= 3 -
Math.abs(adj)
|| bondCount == 3 && elemNo > 10 && nPriorities >= 2 -
Math.abs(adj))) {
// if here, adj is TIED (0), A_WINS (-1), or B_WINS (1)
@@ -1799,13 +1896,11 @@
if (adj != TIED)
s = s.toLowerCase();
}
- } else if (nRS > 1) {
- s = "?" + sphere;
- subRS = "[" + subRS + "]";
}
}
s += subRS;
- System.out.println(this + " creating aux " + s);
+ if (sphere < 2 && !done)
+ System.out.println(this + " creating aux " + s);
return s;
}
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