Revision: 21490
http://sourceforge.net/p/jmol/code/21490
Author: hansonr
Date: 2017-04-07 00:38:50 +0000 (Fri, 07 Apr 2017)
Log Message:
-----------
Jmol.___JmolVersion="14.12.0" // 2017-04-06
new feature: {atom}.chirality
-- uses Cohen-Ingold-Prelog rules to assign R or S to a carbon center
-- ignores sulfur chirality
-- may not fully implement high symmetry cases
-- not fully tested
-- Checked using:
function checkchiral(m) {
if (m) load @m
background label yellow
color labels black
select _C
label %[atomname]
refresh
var b = {_C}
for (var a in b) {
var c = a.chirality;
print _smilesString + " " + a + c
if (c) {
select a
c = a.atomname + " " + c
label @c
}
}
select *
}
checkchiral("$(R)-glycidol")
delay 1
checkchiral("$glucose")
delay 1
checkchiral("$(2S,3R)-2,3-oxiranediol")
delay 1
checkchiral("$(S)-2-butanol")
delay 1
checkchiral("$(R)-2-butanol")
delay 1
checkchiral("$(2S,3R)-2,3-butanediol")
delay 1
checkchiral("$(2S,3S)-2,3-butanediol")
delay 1
checkchiral("$(2R,3R)-2,3-butanediol")
delay 1
checkchiral("$(2R,3S)-2,3-butanediol")
delay 1
checkchiral("$1,4-dimethylcyclohexane")
delay 1
checkchiral("$cholesterol") // (3S,8S,9S,10R,13R,14S,17R) and sidechain R
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 2017-04-07 00:35:17 UTC
(rev 21489)
+++ trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-04-07 00:38:50 UTC
(rev 21490)
@@ -88,7 +88,7 @@
public String getRorS(CIPAtom a) {
try {
- CIPAtom[] atoms = sortFourAtoms(a.atoms, false);
+ CIPAtom[] atoms = sortSubstituents(a.atoms, false);
if (atoms == null)
return "";
SmilesMatcherInterface sm = vwr.getSmilesMatcher();
@@ -108,13 +108,14 @@
}
/**
- * The main loop that starts all the iteration of breakTie.
+ * Sort the substituents of an atom in preparation for comparing the set
with other atoms
*
- * @param atoms
+ * @param atoms may be 3 or 4 atoms here
+ * @param allowTie
*
* @return true if we have four distinct atoms in the end
*/
- private static CIPAtom[] sortFourAtoms(CIPAtom[] atoms, boolean allowTie) {
+ private static CIPAtom[] sortSubstituents(CIPAtom[] atoms, boolean allowTie)
{
int n = atoms.length;
for (int i = 0; i < n; i++)
atoms[i].isAbove = 0;
@@ -187,8 +188,8 @@
// all are the same -- check to break tie next level
// now isDummy counts
- a.atoms = sortFourAtoms(a.atoms, true);
- b.atoms = sortFourAtoms(b.atoms, true);
+ a.atoms = sortSubstituents(a.atoms, true);
+ b.atoms = sortSubstituents(b.atoms, true);
for (int i = 0; i < a.nAtoms; i++) {
CIPAtom ai = a.atoms[i];
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