Revision: 21576
http://sourceforge.net/p/jmol/code/21576
Author: hansonr
Date: 2017-04-29 19:22:53 +0000 (Sat, 29 Apr 2017)
Log Message:
-----------
Jmol.___JmolVersion="14.15.2" // 4/29/17
bug fix: CIP chirality adds axial chirality (M/P[Ra/Sa], m/p[ra/sa]) for
cumulenes
bug fix: CIP chirality adds atropisomer chirality (M/P[Ra/Sa], m/p[ra/sa]) for
biaryls
bug fix: CIP chirality adds cumulene E/Z chirality
-- 816 lines
-- validation data are at
https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol-datafiles/cip/
-- validates for 160 structures (some duplicates; both cip_examples.zip and
stereo_test_cases.sdf)
-- validates for all cases considered:
-- simple R/S and E/Z
-- small-ring removal of E/Z
-- parallel-strand Rule 4b and Rule 5 (Mata)
-- pseudochiral r/s and m/p
-- odd and even cumulenes
-- atropisomers
-- P, S, As, Se, Sb, Te, Bi, Po trigonal pyramidal and tetrahedral
-- imine and diazine E/Z chirality
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 2017-04-29 19:09:27 UTC
(rev 21575)
+++ trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java 2017-04-29 19:22:53 UTC
(rev 21576)
@@ -67,8 +67,8 @@
* validated for Rules 1 and 2 in Jmol 14.13.2;
* E/Z added 14.14.1;
* 4/27/17 Ruled 3-5 completed 14.15.1
- * 4/28/17 Validated for 146 compounds, including imines and diazines
- * 4/29/17 validated for , including S, P,
+ * 4/28/17 Validated for 146 compounds, including imines and diazines, sulfur,
phosphorus
+ * 4/29/17 validated for 160 compounds, including M/P, m/p (axial chirality
for biaryls and odd-number cumulenes)
*
*
* validation suite: see
https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol-datafiles/cip/
@@ -131,90 +131,8 @@
//
//
- // Jmol test suite:
- //
-//checkR.spt -- test suite for Jmol CIPChirality.java
-//Bob Hanson hans...@stolaf.edu 4/18/2017 7:44:43 AM
+
- // function checkRS(m, key) {
- // var doCheck = (_argCount == 2)
- // if (m.find("//")) {
- // key = m.split("//")[2]
- // m = m.split("//")[1]
- // doCheck = key;
- // }
- // print "loading " + @m
- // set useMinimizationThread false
- // if (m) load @m filter "2D"
- // if (!{_H}) calculate hydrogens
- // set labelfor {_C} "%[atomname]"
- // refresh
- // background label yellow
- // color labels black
- // refresh
- // calculate chirality
- // set labelfor {_C && chirality != ""} "%[atomname] %[chirality]"
- // var rs = {chirality != ""}.label("%[chirality]").join("")
- // print " " + doCheck + " " + key + " " + rs
- // if (doCheck) {
- // var ref = (docheck == key ? "" :
_M.molData["chiral_atoms"].replace("\n","").replace(" ",""))
- // if (ref) {
- // key = ref;
- // rs = {chirality != ""}.label("%i%[chirality]").join("")
- // }
- // if (key == rs) {
- // print "OK\t" + m + "\t" + rs
- // } else {
- // var s = "??\t" + m + "\t" + rs + "\t" + key
- // refresh
- // print s
- // var ans = prompt(s.replace("\t"," ") + " \n\n continue?", "yes")
- // if (ans != "yes") quit
- // }
- // } else {
- // print m + "\t" + rs
- // }
- // refresh
- // }
- //
- // function checkRdir(name, type) {
- // x = load(name + ".txt").lines
- // for (f in x) {
- // // f = f.trim();
- // if (f == "#QUIT") break
- // if (!f || f.find("#") == 1) continue
- // if (type)
- // checkRS(name + "/" + f, type)
- // else
- // checkRS(name + "/" + f)
- // }
- // }
- //
- // //set debug
- //
- //
//checkrs("cip/RS/(2R,3R,4R,5S,6R)-2,3,4,5,6-pentachloroheptanedioic_acid_2d.mol");
- // //quit
- // checkRdir("cip/RS", "?");
- // checkRdir("cip/R", "R");
- // checkRdir("cip/S", "S");
- // checkRdir("cip/EZ", "?");
- // print "DONE"
- //
- //
- // checkrs("$(R)-3-hydroxy-1,4-heptadiyne", "R")
- // checkRS("$(R)-glycidol", "R")
- // checkRS("$glucose", "RSRR")
- // checkRS("$(2S,3R)-2,3-oxiranediol", "SR")
- // checkRS("$(S)-2-butanol", "S")
- // checkRS("$(R)-2-butanol", "R")
- // checkRS("$(2S,3R)-2,3-butanediol", "SR")
- // checkRS("$(2S,3S)-2,3-butanediol", "SS")
- // checkRS("$(2R,3R)-2,3-butanediol", "RR")
- // checkRS("$(2R,3S)-2,3-butanediol", "RS")
- // checkRS("$1,4-dimethylcyclohexane", "")
- // checkRS("$cholesterol", "RRSSSRSR") // (3S,8S,9S,10R,13R,14S,17R) and
sidechain (R)
- // checkRS("==ta1", "SSRSRSSRSRS") // taxol (1S,2S,3R,4S,7R,9S,10S,12R,15S)
and sidechain (2R,3S)
-
static final int NO_CHIRALITY = 0;
static final int TIED = NO_CHIRALITY;
static final int B_WINS = 1;
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