Revision: 21488
http://sourceforge.net/p/jmol/code/21488
Author: hansonr
Date: 2017-04-06 23:19:22 +0000 (Thu, 06 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
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 2017-04-06 23:03:23 UTC
(rev 21487)
+++ trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-04-06 23:19:22 UTC
(rev 21488)
@@ -20,6 +20,50 @@
*/
public class CIPChirality {
+ // 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("$1,4-dimethylcyclohexane") // no chirality
+ // delay 1
+ // checkchiral("$cholesterol") // (3S,8S,9S,10R,13R,14S,17R) and sidechain R
+
Viewer vwr;
public CIPChirality() {
@@ -44,11 +88,12 @@
public String getRorS(CIPAtom a) {
try {
- if (!a.sortFourAtoms())
+ CIPAtom[] atoms = a.sortFourAtoms();
+ if (atoms == null)
return "";
SmilesMatcherInterface sm = vwr.getSmilesMatcher();
- switch (sm.getChirality(a.atoms[3].atom, a.atoms[2].atom,
- a.atoms[1].atom, a.atoms[0].atom)) {
+ switch (sm.getChirality(atoms[3].atom, atoms[2].atom,
+ atoms[1].atom, atoms[0].atom)) {
case 1:
return "R";
case 2:
@@ -231,7 +276,7 @@
*
* @return true if we have four distinct atoms in the end
*/
- boolean sortFourAtoms() {
+ CIPAtom[] sortFourAtoms() {
for (int i = 0; i < 4; i++) {
CIPAtom a = atoms[i];
for (int j = i + 1; j < 4; j++) {
@@ -255,19 +300,18 @@
b.isAbove++;
break;
case 0:
- return false;
+ return null;
}
}
}
}
- CIPAtom[] atemp = new CIPAtom[4];
+ CIPAtom[] ret = new CIPAtom[4];
for (int i = 0; i < 4; i++)
- atemp[atoms[i].isAbove] = atoms[i];
- atoms = atemp;
+ ret[atoms[i].isAbove] = atoms[i];
if (Logger.debugging)
for (int i = 0; i < 4; i++)
- Logger.info("" + atoms[i]);
- return true;
+ Logger.info("" + ret[i]);
+ return ret;
}
/**
@@ -299,6 +343,7 @@
}
}
// all are the same -- check to break tie next level
+ // now isDummy counts
for (int i = 0; i < a.nAtoms; i++) {
CIPAtom ai = a.atoms[i];
CIPAtom bi = b.atoms[i];
@@ -315,12 +360,10 @@
}
/**
- * used in Array.sort and sortFourAtoms
+ * used in Array.sort and sortFourAtoms; includes isDummy check
*/
@Override
public int compareTo(CIPAtom a) {
-
- // check to see that atoms are non-null and are different
return a.atom == atom ? 0 : a.atom == null ? -1 : atom == null ? 1
: a.elemNo != elemNo ? (a.elemNo < elemNo ? -1 : 1)
: a.massNo != massNo ? (a.massNo < massNo ? -1 : 1)
@@ -337,7 +380,6 @@
* @return 1 if b is higher; -1 if a is higher; otherwise 0
*/
static public int compareAB(CIPAtom a, CIPAtom b) {
- // check to see that atoms are non-null and are different
return b.atom == a.atom ? 0 : b.atom == null ? -1 : a.atom == null ? 1
: b.elemNo != a.elemNo ? (b.elemNo < a.elemNo ? -1 : 1)
: b.massNo != a.massNo ? (b.massNo < a.massNo ? -1 : 1) : 0;
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-04-06 23:03:23 UTC
(rev 21487)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-04-06 23:19:22 UTC
(rev 21488)
@@ -49,7 +49,7 @@
# 10. Run jmol/tools build-release.xml
#
-Jmol.___JmolVersion="14.12.0-beta" // 2017-04-06
+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
@@ -56,7 +56,51 @@
-- 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
+
+
JmolVersion="14.11.3" // 2017-04-06
bug fix: partial bond order for orders > 3 not working
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