Revision: 21650
http://sourceforge.net/p/jmol/code/21650
Author: hansonr
Date: 2017-07-06 00:13:14 +0000 (Thu, 06 Jul 2017)
Log Message:
-----------
* 7/4/17 Jmol 14.20.1 major rewrite to correct and simplify logic; full
validation
* for 433 structures (many duplicates) in AY236, BH64, MV64, MV116, JM, and L
(840 lines)
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 2017-07-05 17:43:33 UTC
(rev 21649)
+++ trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-07-06 00:13:14 UTC
(rev 21650)
@@ -250,6 +250,12 @@
public class CIPChirality {
+
+ public void xxx() {
+
+ }
+
+
//The rules:
//
// P-92.1.3.1 Sequence Rule 1 has two parts:
@@ -2531,9 +2537,8 @@
}
- Logger.info(a
- + (score == A_WINS ? " > " : score == B_WINS ? " < " : " = ") //
Logger
- + b + " by " + reason + "\n"); // Logger
+ if (score == A_WINS || score == B_WINS) // Logger
+ Logger.info((score == A_WINS ? a : b) + " > " + (score == A_WINS ? b :
a) + " by " + reason + "\n"); // Logger
// no tie-breaking for Rules 4b or 5
@@ -2565,10 +2570,11 @@
}
/**
- * Recursively build paths to stereocenters to estabish the path priority
lexicographically.
- *
+ * Recursively build priority paths to stereocenters as a string.
+ *
* @param path
- * @param ignore atom to ignore (parent)
+ * @param ignore
+ * atom to ignore (parent)
*/
private void getRule4PriorityPaths(String path, SimpleNode ignore) {
priorityPath = path + (priority + 1);
@@ -2577,6 +2583,11 @@
atoms[i].getRule4PriorityPaths(priorityPath, null);
}
+ /**
+ * Track the number of R and S in th.e highest-ranking ligand position.
+ *
+ * @param counts ["011020...", nR, nS, sphere]
+ */
private void getRule4Counts(Object[] counts) {
if (sphere > ((Integer) counts[3]).intValue())
return;
@@ -2606,6 +2617,12 @@
atoms[i].getRule4Counts(counts);
}
+ /**
+ * Generate the list of all possible paths to stereocenters that Mata
analysis needs.
+ *
+ * @param rootsub
+ * @param pathInfo
+ */
private void appendRule4Paths(CIPAtom rootsub, String[] pathInfo) {
String s0 = (pathInfo[0] == null ? auxChirality : pathInfo[0]);
if (pathInfo[2] == null)
@@ -2722,10 +2739,9 @@
}
/**
- * This critical method creates a list of downstream (higher-sphere)
- * auxiliary chirality designators (R or S) in the correct order specified
- * by Mata that are passed upstream ultimately to the Sphere-1 root
- * substituent.
+ * Creates a list of downstream (higher-sphere)
+ * auxiliary chirality designators, starting with
+ * those furthest from the root.
*
* @param node1
* first node; sphere 1
@@ -2738,15 +2754,18 @@
String subRS = "", s = (node1 == null ? "" : "~");
if (atom == null)
return s;
+ rule4List = new String[4]; // full list based on atoms[]
+ if (nPriorities == 0 && !isSet) {
+ setNode();
+ if (!isAlkene && !isDuplicate && !isTerminal)
+ sortToRule(RULE_3);
+ }
int rs = -1, nRS = 0;
- rule4List = new String[4]; // full list based on atoms[]
CIPAtom[] ret1 = new CIPAtom[1];
int ruleMax = RULE_5;
- boolean prevIsChiral = false;
+ boolean prevIsChiral = true;
for (int i = 0; i < 4; i++) {
CIPAtom a = atoms[i];
- if (a != null)
- a.setNode();
if (a != null && !a.isDuplicate && !a.isTerminal) {
a.priority = priorities[i];
ret1[0] = null;
@@ -2764,10 +2783,9 @@
nRS++;
subRS = ssub;
prevIsChiral = true;
- } else if (i > 0 && priorities[i] == priorities[i - 1]
- && !prevIsChiral) {
- // two groups have the same priority, and both have no chirality
- ruleMax = 3;
+ } else if (!prevIsChiral && priorities[i] == priorities[i - 1]) {
+ // two groups have the same priority, and neither has a
stereocenter
+ return "~";
} else {
prevIsChiral = false;
}
@@ -2787,11 +2805,9 @@
s = "~";
subRS = "";
isBranch = true;
- break;
- }
- if (isBranch) {
if (ret != null)
ret[0] = this;
+ break;
}
if (isAlkene) {
if (!isBranch && alkeneChild != null) {
@@ -2851,18 +2867,16 @@
atom1.rule4List = new String[4];
for (int i = 0; i < 4; i++) {
for (int j = 0; j < 4; j++) {
- if (atom1.atoms[i] == atoms[j]) {
+ if (atom1.atoms[i] == atoms[j]) {
atom1.rule4List[i] = rule4List[j];
break;
}
}
}
- //rule4List; //227 needs this commented out; 66 needs this in!
int rule = atom1.sortToRule(ruleMax);
- if (rule == TIED)
+ if (rule == TIED) {
s = "~";
- else
- if (rule != TIED) {
+ } else {
rs = atom1.checkHandedness();
s = (rs == STEREO_R ? "R" : rs == STEREO_S ? "S" : "~");
if (rule == RULE_5) {
@@ -2871,7 +2885,6 @@
rule4Type = rs;
}
}
-
}
auxChirality = s;
}
@@ -2897,11 +2910,7 @@
if (isTerminal || isDuplicate)
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);
}
/**
@@ -2908,7 +2917,8 @@
* Determine the ordered CIP winding of this atom. For this, we just take
* the directed normal through the plane containing the top three
* substituent atoms and dot that with the vector from any one of them to
- * the fourth ligand (or the root atom if trigonal pyramidal). If this is
positive, we have R.
+ * the fourth ligand (or the root atom if trigonal pyramidal). If this is
+ * positive, we have R.
*
* @return 1 for "R", 2 for "S"
*/
@@ -2946,9 +2956,6 @@
a.rule4List = null;
a.rootRule4Paths = null;
a.priority = 0;
- //a.rule4Type = 0;
- //a.auxChirality = "~";
- //a.auxEZ = STEREO_UNDETERMINED;
for (int i = 0; i < 4; i++)
if (atoms[i] != null)
a.atoms[i] = atoms[i];
@@ -2963,7 +2970,6 @@
+ (auxChirality == null ? "" : auxChirality)
+ "]");
}
-
}
}
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