Revision: 21555
http://sourceforge.net/p/jmol/code/21555
Author: hansonr
Date: 2017-04-26 05:19:28 +0000 (Wed, 26 Apr 2017)
Log Message:
-----------
CIP validation
Modified Paths:
--------------
trunk/Jmol-datafiles/cip/checkCIP.spt
Added Paths:
-----------
trunk/Jmol-datafiles/cip/RS/mata2005Fig8VIb.mol
Removed Paths:
-------------
trunk/Jmol-datafiles/cip/CompleteDraft(1).pdf
Deleted: trunk/Jmol-datafiles/cip/CompleteDraft(1).pdf
===================================================================
(Binary files differ)
Added: trunk/Jmol-datafiles/cip/RS/mata2005Fig8VIb.mol
===================================================================
--- trunk/Jmol-datafiles/cip/RS/mata2005Fig8VIb.mol
(rev 0)
+++ trunk/Jmol-datafiles/cip/RS/mata2005Fig8VIb.mol 2017-04-26 05:19:28 UTC
(rev 21555)
@@ -0,0 +1,172 @@
+c:/jmol-dev/bobtest/mata2005Fig8VIb.mol
+__Jmol-14_04251712353D 1 1.00000 0.00000 0
+Jmol version 14.15.1 2017-04-25 07:17 EXTRACT: ({0:83})
+ 84 83 0 0 0 0 1 V2000
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+M END
Modified: trunk/Jmol-datafiles/cip/checkCIP.spt
===================================================================
--- trunk/Jmol-datafiles/cip/checkCIP.spt 2017-04-26 05:00:18 UTC (rev
21554)
+++ trunk/Jmol-datafiles/cip/checkCIP.spt 2017-04-26 05:19:28 UTC (rev
21555)
@@ -4,16 +4,15 @@
// sample execution requires that cip/ directory be in the current Jmol
directory
// as indicated with the CD command.
+// checkR.spt -- test suite for Jmol CIPChirality.java
+// Bob Hanson hans...@stolaf.edu 4/18/2017 7:44:43 AM
+
nOK = 0;
+thisN = 0;
- function checkRS(m, n, key) {
- if (_argCount < 3) {
- key = n
- n = 1
- }
- if (!n) n = 1
- var doCheck = (!!key)
+ function checkRS(m, key) {
+ var doCheck = (_argCount == 2)
var a = 0;
if (m.find("//")) {
key = m.split("//")[2]
@@ -24,9 +23,13 @@
}
doCheck = key;
}
- print "loading " + m + " " + n
+ if (thisN && (nOK + 1) != thisN) {
+ nOK++;
+ return;
+ }
+ print "loading " + (nOK + 1) + ": " + m
set useMinimizationThread false
- load @m @n filter "2D"
+ load @m filter "2D"
if (!{_H}) calculate hydrogens
set labelfor {_C} "%[atomname]"
refresh
@@ -43,10 +46,7 @@
var rs = {selected}.label("%[chirality]").join("")
print " " + doCheck + " key=" + key + " found=" + rs
if (doCheck) {
- var ref = (docheck == key ? "" :
_M.molData.chiral_atoms.replace("\n","").replace(" ",""))
- if (!ref && docheck != key) {
- ref = checkSDF()
- }
+ var ref = (docheck == key ? "" :
_M.molData["chiral_atoms"].replace("\n","").replace(" ",""))
if (ref) {
key = ref;
rs = {selected}.label("%i%[chirality]").join("")
@@ -70,7 +70,7 @@
function checkRdir(name, type) {
x = load(name + ".txt").lines
for (var f in x) {
- f = f.trim()
+ f = f.trim();
if (f == "#QUIT") break
if (!f || f.find("#") == 1) continue
if (f.find("$") != 1)
@@ -82,47 +82,20 @@
}
}
-//set debug
+//checkrs("cip/RS/Mata_fig7_I_R.mol","?")
+//checkrs("testn2.mol","?")
-function checksdf(){
- ref = _M.molData.stereounits
- if (ref) {
- var tokens = ("end " + ref).split(true)
- ref = ""
- var atlist = []
- var s = ""
- for (var i = tokens.length; i > 0; i--) {
- var token = tokens[i]
- if (token.find(":")) continue
- var itoken = 0 + token
- if (token == "0" || itoken) {
- atlist.push(itoken + 1)
- } else {
- for (var j = 1; j <= atlist.length; j++) {
- ref = "" + atlist[j] + s + ref
- }
- atlist = []
- if (token == "end") break
- s = token
- }
- }
- }
- print ref
- return ref
-}
-
-/**
- *
-//checkrs("cip/EZ/deb.mol");
+checkRdir("cip/RS", "?");
checkRdir("cip/SP", "?");
-checkRdir("cip/RS", "?");
checkRdir("cip/EZ", "?");
checkRdir("cip/R", "R");
checkRdir("cip/S", "S");
print "DONE: " + nOK
- /**
+/**
+
+checkrs("cip/EZ/deb.mol");
checkrs("$(R)-3-hydroxy-1,4-heptadiyne", "R")
checkRS("$(R)-glycidol", "R")
checkRS("$glucose", "RSRR")
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