Revision: 21608
http://sourceforge.net/p/jmol/code/21608
Author: hansonr
Date: 2017-05-18 04:50:52 +0000 (Thu, 18 May 2017)
Log Message:
-----------
Jmol.___JmolVersion="14.15.5"
bug fix: CML reader does not read 2D wedge/hash information
bug fix: CIP fix for missing branch descriptors; 984 lines
bug fix: CIP adds helicene M/P chirality
- validated using CCDC structures HEXHEL02 HEXHEL03 HEXHEL04 ODAGOS ODAHAF
- http://pubs.rsc.org/en/content/articlehtml/2017/CP/C6CP07552E
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/symmetry/CIPChirality.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 2017-05-17 22:09:46 UTC
(rev 21607)
+++ trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-05-18 04:50:52 UTC
(rev 21608)
@@ -278,7 +278,9 @@
static final int TIED = NO_CHIRALITY;
static final int B_WINS = 1;
static final int A_WINS = -1;
- static final int DIASTEREOMERIC = Integer.MAX_VALUE;
+ static final int DIASTEREOMERIC = -3;
+ static final int DIASTEREOMERIC_A_WINS = -2;
+ static final int DIASTEREOMERIC_B_WINS = 2;
static final int IGNORE = Integer.MIN_VALUE;
static final int NOT_RELEVANT = Integer.MIN_VALUE;
@@ -2198,7 +2200,7 @@
private int checkRule4And5(int i, int j) {
return (rule4List[i] == null && rule4List[j] == null ? TIED
: rule4List[j] == null ? A_WINS : rule4List[i] == null ? B_WINS
- : compareRootMataPair(i, j));
+ : compareMataPair(i, j));
}
/**
@@ -2214,7 +2216,7 @@
* @return 0 (TIED), -1 (A_WINS), or 1 (B_WINS), or Integer.MIN_VALUE
* (IGNORE)
*/
- private int compareRootMataPair(int ia, int ib) {
+ private int compareMataPair(int ia, int ib) {
boolean isRule5 = (currentRule == RULE_5);
// note that opposites will need to generate "R" or "S" keys, which will
be
// resolved as "r" or "s"
@@ -2473,7 +2475,7 @@
String subRS = "";
String s = (node1 == null ? "" : "~");
boolean isBranch = false;
- boolean isrs = false;
+ boolean noPseudo = false;
if (atom != null) {
rule4List = new String[4]; // full list based on atoms[]
int[] mataList = new int[4]; //sequential pointers into rule4List
@@ -2513,12 +2515,13 @@
case 2:
if (node1 != null) {
// we want to now if these two are enantiomorphic, identical, or
diastereomorphic.
- adj = (compareRule4aEnantiomers(rule4List[mataList[0]],
- rule4List[mataList[1]]));
+ adj = (compareRule4aIsomers(mataList[0],mataList[1]));
switch (adj) {
- case DIASTEREOMERIC:
+ case TIED:
+ // identical
isBranch = true;
- s = "";
+ s = "~";
+ subRS = "";
break;
case NOT_RELEVANT:
s = "";
@@ -2525,16 +2528,15 @@
isBranch = true;
adj = TIED;
break;
- case TIED:
- // identical
- isBranch = true;
- s = "~"; // was "u"
- subRS = "";
- break;
+ case DIASTEREOMERIC_A_WINS:
+ case DIASTEREOMERIC_B_WINS:
+ adj -= sign(adj);
+ subRS = "r";
+ //$FALL-THROUGH$
case A_WINS:
case B_WINS:
isBranch = true;
- isrs = subRS.indexOf("r") >= 0;
+ noPseudo = subRS.indexOf("r") >= 0;
// enantiomers -- we have an r/s situation
// process to determine chirality, but then set ret[0] to be null
subRS = "";
@@ -2543,9 +2545,44 @@
}
break;
case 3:
+ //
+ // check for exactly one enantiomeric pair among the three groups
+ //
+ // {RRS} e d
+ // {SSR} d
+ // {SRS} two enantiomers and a diastereomer (r/s)
+ //
+ //
+ int irs = 0, jrs = 0, adj0 = TIED;
+ for (int i = 0; i < 2; i++) {
+ for (int j = i + 1; j < 3; j++) {
+ adj0 = (compareRule4aIsomers(mataList[i],mataList[j]));
+ switch (adj0) {
+ case A_WINS:
+ case B_WINS:
+ if (adj == TIED) {
+ adj = adj0;
+ irs = i;
+ jrs = j;
+ continue;
+ }
+ i = j = 3;
+ adj = TIED;
+ break;
+ default:
+ break;
+ }
+ }
+ }
+ if (adj != TIED) {
+ mataList[0] = mataList[irs];
+ mataList[1] = mataList[jrs];
+ }
+ //$FALL-THROUGH$
case 4:
s = "";
isBranch = true;
+ break;
}
if (isBranch) {
subRS = "";
@@ -2552,7 +2589,6 @@
if (ret != null)
ret[0] = this;
}
-
if (!isBranch || adj == A_WINS || adj == B_WINS) {
if (isAlkene) {
if (!isBranch && alkeneChild != null) {
@@ -2601,6 +2637,9 @@
} else if (node1 != null
&& (bondCount == 4 && nPriorities >= 3 - Math.abs(adj) ||
isTrigonalPyramidal
&& nPriorities >= 2 - Math.abs(adj))) {
+ // if adj is 1 or -1, then we check for one fewer priorities
because
+ // it means we had two groups that were either enantiomers or
diasteriomers
+
if (isBranch) {
// if here, adj is A_WINS (-1), or B_WINS (1)
// we check based on A winning, but then reverse it if B
actually won
@@ -2612,8 +2651,8 @@
s = (adj == A_WINS ? "s" : "r");
break;
}
- if (isrs)
- s = s.toUpperCase(); // Rule 4c // AY-236.148
+ if (noPseudo)
+ s = s.toUpperCase(); // Rule 4c or diasteriomers // AY-236.148
auxChirality = s;
subRS = "";
if (ret != null)
@@ -2626,10 +2665,7 @@
atom1.sortByRule(RULE_1a);
rs = atom1.checkHandedness();
s = (rs == STEREO_R ? "R" : rs == STEREO_S ? "S" : "~");
-// if (root.atomIndex == 12) {
-// System.out.println("determining " + s + " for " + root +
"->" + atom1);
-// rs = atom1.checkHandedness();
-// }
+ System.out.println("determining " + s + " for " + root + "->"
+ atom1);
node1.addMataRef(sphere, priority, rs);
}
}
@@ -2687,13 +2723,15 @@
/**
* Check for enantiomeric strings such as S;R; or SR
*
- * @param rs1
- * @param rs2
+ * @param i1
+ * @param i2
* @return NOT_RELEVANT if there is no stereochemistry, TIED if they are
equal,
- * A_WINS for enantiomer Rxxx, B_WINS for Sxxxx, or DIASTEREOMERIC
- * if diastereomeric
+ * A_WINS for enantiomer Rxxx, B_WINS for Sxxxx, or
DIASTERIOMERIC_A_WINS
+ * or DIASTERIOMERIC_B_WINS
*/
- private int compareRule4aEnantiomers(String rs1, String rs2) {
+ private int compareRule4aIsomers(int i1, int i2) {
+ String rs1 = rule4List[i1];
+ String rs2 = rule4List[i2];
if (rs1.charAt(0) != rs2.charAt(0))
return NOT_RELEVANT;
int n = rs1.length();
@@ -2702,7 +2740,16 @@
if (rs1.equals(rs2))
return TIED;
String rs = (rs1.indexOf("R") < 0 && rs1.indexOf("S") < 0 ? "~rs" :
"~RS");
- return checkEnantiomer(rs1, rs2, 1, n, rs);
+ int score = checkEnantiomer(rs1, rs2, 1, n, rs);
+ if (score == DIASTEREOMERIC) {
+ switch (compareMataPair(i1, i2)) {
+ case A_WINS:
+ return DIASTEREOMERIC_A_WINS;
+ case B_WINS:
+ return DIASTEREOMERIC_B_WINS;
+ }
+ }
+ return score;
}
/**
@@ -2728,8 +2775,9 @@
int score = i1 + rs.indexOf(rs2.charAt(i));
if (score == 0)
continue;
- if (score != STEREO_BOTH_RS)
+ if (score != STEREO_BOTH_RS) {
return DIASTEREOMERIC;
+ }
if (finalScore == TIED)
finalScore = (i1 == STEREO_R ? A_WINS : B_WINS);
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-05-17 22:09:46 UTC
(rev 21607)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-05-18 04:50:52 UTC
(rev 21608)
@@ -57,18 +57,42 @@
Jmol.___JmolVersion="14.15.5"
+bug fix: CML reader does not read 2D wedge/hash information
+bug fix: CIP fix for missing branch descriptors; 984 lines
+
+bug fix: CIP adds helicene M/P chirality
+ - validated using CCDC structures HEXHEL02 HEXHEL03 HEXHEL04 ODAGOS ODAHAF
+ - http://pubs.rsc.org/en/content/articlehtml/2017/CP/C6CP07552E
+
code: CIP: additional simplification;
code: CIP status: implementation complete, including:
All subrules implemented fully: 1a, 1b, 2, 3, 4a, 4b, 4c, 5
- R/S, E/Z, M/P, r/s, seqCis/seqTrans (as Z/E)
+ R/S, E/Z, M/P (odd-cumulene and helicene), r/s, seqCis/seqTrans (as
Z/E)
benzenoid (including fused benzenoid heteroaromatic) Mancude ring
"Kekule weighted" atom number adjustments
- proposed Rule 1b amendment:
- A duplicate atom in a Kekule-weighted system is given a root
distance equal to
- its sphere, not the sphere of its duplicated atom.
-IUPAC Blue Book 2103 errors:
+ * Added logic to Rule 1b: The root distance for a Kekule-ambiguous duplicate
+ * atom is its own sphere, not the sphere of its duplicated atom.
+ *
+ * Stated more precisely:
+ *
+ * Proposed amended Sequence Rule 1:
+ *
+ * (1a) higher atomic number precedes lower;
+ *
+ * (1b) in comparing two duplicate nodes, lower root distance precedes higher
+ * root distance, where "root distance" is defined:
+ *
+ * (i) in the case of a duplicate atom for which the atomic number is averaged
+ * over two or more atoms in applying Rule 1a, the distance from the duplicate
+ * node itself to the root node; and
+ *
+ * (ii) in all other cases, the distance of its corresponding nonduplicated
atom
+ * node to the root node.
+ *
+IUPAC Blue Book 2013 errors of note:
+
,"147":"r,,,R,,,,r,,,S" // chiral phosphine -- disagrees with BB P-93.5.1.1.2
for S vs R
{
"id" : "148"
@@ -151,11 +175,11 @@
var skip = ({27 229}) || // E/Z only; missing chirality
({95 96 98 99 100 101 102 103 104 108 109 110 111 112 200}) || //
trigonal planar, square planar, or hypervalent
- ({32 33}) || // helicene
+ ({32 33}) || // helicene // added in Jmol 14.15.5
({201 202})|| // spirocyclic central (redundant) atom designation
missing (axial designation option)
({212 213})|| // chiral conformation 1,4-benzene in a ring
({38 84}) || // ignore -- 38: Mancude for cyclopentadienyl; 84:
unknown error with P compound
- ({203}) || // // chiral bridgehead amine
+ ({203}) || // // chiral bridgehead amine // fixed in Jmol
14.15.5
Issue: Full implementation of the rules requires a slight modification of Rule
1b.
Specifically, aromatic duplicate atoms must reference the sphere of their own
parent, not their
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