Revision: 21571
http://sourceforge.net/p/jmol/code/21571
Author: hansonr
Date: 2017-04-29 18:49:38 +0000 (Sat, 29 Apr 2017)
Log Message:
-----------
CIP test files and scripts
Modified Paths:
--------------
trunk/Jmol-datafiles/cip/RSEZ.txt
trunk/Jmol-datafiles/cip/checkCIP.spt
Added Paths:
-----------
trunk/Jmol-datafiles/cip/MP/
trunk/Jmol-datafiles/cip/MP/(3sa,4S,5R)-1,4-dibromo-3-[bromo(fluoro)methyl]-4-fluorobuta-1,2-diene.mol
trunk/Jmol-datafiles/cip/MP/(Sa)-6,6'-dibromobiphenyl-2,2'-dicarboxylic_acid.mol
trunk/Jmol-datafiles/cip/MP.txt
trunk/Jmol-datafiles/cip/RSEZ/rule_3_with_axial_chirality_8R_3d.mol
Removed Paths:
-------------
trunk/Jmol-datafiles/cip/AX/
Added:
trunk/Jmol-datafiles/cip/MP/(3sa,4S,5R)-1,4-dibromo-3-[bromo(fluoro)methyl]-4-fluorobuta-1,2-diene.mol
===================================================================
---
trunk/Jmol-datafiles/cip/MP/(3sa,4S,5R)-1,4-dibromo-3-[bromo(fluoro)methyl]-4-fluorobuta-1,2-diene.mol
(rev 0)
+++
trunk/Jmol-datafiles/cip/MP/(3sa,4S,5R)-1,4-dibromo-3-[bromo(fluoro)methyl]-4-fluorobuta-1,2-diene.mol
2017-04-29 18:49:38 UTC (rev 21571)
@@ -0,0 +1,30 @@
+(3sa,4S,5R)-1,4-dibromo-3-[bromo(fluoro)methyl]-4-fluorobuta-1,2-diene
+ ACD/Labs09291019313D
+
+ 13 12 0 0 0 0 0 0 0 0 1 V2000
+ 7.6049 -5.2027 -1.8578 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 8.8787 -5.5516 -1.5340 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 10.1523 -5.9043 -1.2117 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 11.0475 -4.9377 -0.4771 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 10.6678 -7.2666 -1.5928 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 6.1985 -5.5621 -0.6621 Br 0 0 0 0 0 0 0 0 0 0 0 0
+ 9.2085 -8.3682 -2.2305 Br 0 0 0 0 0 0 0 0 0 0 0 0
+ 10.1896 -3.2155 -0.2468 Br 0 0 0 0 0 0 0 0 0 0 0 0
+ 11.5950 -7.1381 -2.5814 F 0 0 0 0 0 0 0 0 0 0 0 0
+ 12.1879 -4.7608 -1.1980 F 0 0 0 0 0 0 0 0 0 0 0 0
+ 7.3942 -4.7063 -2.8294 H 0 0 0 0 0 0 0 0 0 0 0 0
+ 11.2913 -5.3697 0.5205 H 0 0 0 0 0 0 0 0 0 0 0 0
+ 11.1323 -7.7453 -0.7000 H 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 2 2 0 0 0 0
+ 2 3 2 0 0 0 0
+ 3 4 1 0 0 0 0
+ 3 5 1 0 0 0 0
+ 1 6 1 0 0 0 0
+ 5 7 1 0 0 0 0
+ 4 8 1 0 0 0 0
+ 5 9 1 0 0 0 0
+ 4 10 1 0 0 0 0
+ 1 11 1 0 0 0 0
+ 4 12 1 0 0 0 0
+ 5 13 1 0 0 0 0
+M END
Added:
trunk/Jmol-datafiles/cip/MP/(Sa)-6,6'-dibromobiphenyl-2,2'-dicarboxylic_acid.mol
===================================================================
---
trunk/Jmol-datafiles/cip/MP/(Sa)-6,6'-dibromobiphenyl-2,2'-dicarboxylic_acid.mol
(rev 0)
+++
trunk/Jmol-datafiles/cip/MP/(Sa)-6,6'-dibromobiphenyl-2,2'-dicarboxylic_acid.mol
2017-04-29 18:49:38 UTC (rev 21571)
@@ -0,0 +1,62 @@
+(Sa)-6,6'-dibromobiphenyl-2,2'-dicarboxylic acid
+ ACD/Labs09291020033D
+
+ 28 29 0 0 0 0 0 0 0 0 1 V2000
+ 5.1564 -7.4478 -1.3180 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 5.9217 -8.5713 -1.0351 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.7797 -7.5413 -1.4379 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 5.2848 -9.7991 -0.8624 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.1535 -8.7638 -1.2723 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.9073 -9.8883 -0.9846 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 9.5089 -7.4866 -1.6315 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 10.1799 -8.2443 -0.6874 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 8.1319 -7.5804 -1.7556 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 9.4705 -9.0979 0.1396 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 7.4111 -8.4392 -0.9254 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 8.0935 -9.1930 0.0210 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 6.0359 -11.0262 -0.5387 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 6.0049 -5.7904 -1.5547 Br 0 0 0 0 0 0 0 0 0 0 0 0
+ 7.1315 -10.3580 1.1418 Br 0 0 0 0 0 0 0 0 0 0 0 0
+ 7.4707 -6.7462 -2.7766 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 6.7618 -7.2522 -3.6163 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 7.6618 -5.4000 -2.7692 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 5.7465 -11.6629 0.4492 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 7.0568 -11.4364 -1.3346 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.1779 -6.6359 -1.6667 H 0 0 0 0 0 0 0 0 0 0 0 0
+ 2.0496 -8.8423 -1.3701 H 0 0 0 0 0 0 0 0 0 0 0 0
+ 3.4031 -10.8692 -0.8508 H 0 0 0 0 0 0 0 0 0 0 0 0
+ 10.0785 -6.7994 -2.2930 H 0 0 0 0 0 0 0 0 0 0 0 0
+ 11.2843 -8.1676 -0.5939 H 0 0 0 0 0 0 0 0 0 0 0 0
+ 10.0065 -9.7068 0.8988 H 0 0 0 0 0 0 0 0 0 0 0 0
+ 7.2111 -4.8211 -3.4661 H 0 0 0 0 0 0 0 0 0 0 0 0
+ 7.5751 -12.2738 -1.1017 H 0 0 0 0 0 0 0 0 0 0 0 0
+ 2 1 1 0 0 0 0
+ 3 1 2 0 0 0 0
+ 4 2 2 0 0 0 0
+ 5 3 1 0 0 0 0
+ 6 4 1 0 0 0 0
+ 6 5 2 0 0 0 0
+ 8 7 1 0 0 0 0
+ 9 7 2 0 0 0 0
+ 10 8 2 0 0 0 0
+ 11 9 1 0 0 0 0
+ 12 10 1 0 0 0 0
+ 12 11 2 0 0 0 0
+ 2 11 1 0 0 0 0
+ 4 13 1 0 0 0 0
+ 1 14 1 0 0 0 0
+ 12 15 1 0 0 0 0
+ 9 16 1 0 0 0 0
+ 16 17 2 0 0 0 0
+ 16 18 1 0 0 0 0
+ 13 19 2 0 0 0 0
+ 13 20 1 0 0 0 0
+ 21 3 1 0 0 0 0
+ 22 5 1 0 0 0 0
+ 23 6 1 0 0 0 0
+ 24 7 1 0 0 0 0
+ 25 8 1 0 0 0 0
+ 26 10 1 0 0 0 0
+ 27 18 1 0 0 0 0
+ 28 20 1 0 0 0 0
+M END
Added: trunk/Jmol-datafiles/cip/MP.txt
===================================================================
--- trunk/Jmol-datafiles/cip/MP.txt (rev 0)
+++ trunk/Jmol-datafiles/cip/MP.txt 2017-04-29 18:49:38 UTC (rev 21571)
@@ -0,0 +1,3 @@
+(Sa)-6,6'-dibromobiphenyl-2,2'-dicarboxylic_acid.mol//PP
+(3sa,4S,5R)-1,4-dibromo-3-[bromo(fluoro)methyl]-4-fluorobuta-1,2-diene.mol//ppSR
+
Property changes on: trunk/Jmol-datafiles/cip/MP.txt
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property
Added: trunk/Jmol-datafiles/cip/RSEZ/rule_3_with_axial_chirality_8R_3d.mol
===================================================================
--- trunk/Jmol-datafiles/cip/RSEZ/rule_3_with_axial_chirality_8R_3d.mol
(rev 0)
+++ trunk/Jmol-datafiles/cip/RSEZ/rule_3_with_axial_chirality_8R_3d.mol
2017-04-29 18:49:38 UTC (rev 21571)
@@ -0,0 +1,77 @@
+rule_3_with_axial_chirality_8R_3d
+ Mrv0541 06141422523D
+
+ 31 30 0 0 0 0 999 V2000
+ -5.2951 4.9092 1.4840 C 0 0 0 0 0 0 0 0 0 0 0 0
+ -4.2293 4.5660 1.0615 C 0 0 0 0 0 0 0 0 0 0 0 0
+ -3.1136 4.2346 0.5594 C 0 0 0 0 0 0 0 0 0 0 0 0
+ -2.2436 3.2152 1.2395 C 0 0 0 0 0 0 0 0 0 0 0 0
+ -2.8319 1.8640 1.2366 C 0 0 0 0 0 0 0 0 0 0 0 0
+ -3.1040 1.2388 -0.0777 C 0 0 0 0 0 0 0 0 0 0 0 0
+ -3.0741 1.2456 2.4198 C 0 0 0 0 0 0 0 0 0 0 0 0
+ -3.7332 -0.0421 2.6351 C 0 0 2 0 0 0 0 0 0 0 0 0
+ -4.8640 0.1330 3.5472 C 0 0 0 0 0 0 0 0 0 0 0 0
+ -4.9367 -0.0124 4.8959 C 0 0 0 0 0 0 0 0 0 0 0 0
+ -3.8217 -0.4446 5.7618 C 0 0 0 0 0 0 0 0 0 0 0 0
+ -6.2291 0.2558 5.5604 C 0 0 0 0 0 0 0 0 0 0 0 0
+ -6.6832 1.6311 5.4194 C 0 0 0 0 0 0 0 0 0 0 0 0
+ -6.1080 2.6072 5.9855 C 0 0 0 0 0 0 0 0 0 0 0 0
+ -3.9527 -1.8172 6.2327 C 0 0 0 0 0 0 0 0 0 0 0 0
+ -4.2704 -2.7700 5.4601 C 0 0 0 0 0 0 0 0 0 0 0 0
+ -4.6028 -3.6240 4.6937 C 0 0 0 0 0 0 0 0 0 0 0 0
+ -2.3117 0.0558 -0.3735 C 0 0 0 0 0 0 0 0 0 0 0 0
+ -1.0627 -0.0034 -0.1736 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 0.1104 -0.0595 0.0439 C 0 0 0 0 0 0 0 0 0 0 0 0
+ -2.7918 -1.0405 3.0176 O 0 0 0 0 0 0 0 0 0 0 0 0
+ -4.1535 -0.4289 1.7070 H 0 0 0 0 0 0 0 0 0 0 0 0
+ 1.3497 -0.1253 0.2914 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 2.0738 0.9856 0.8675 C 0 0 0 0 0 0 0 0 0 0 0 0
+ -6.4263 5.3082 1.8936 C 0 0 0 0 0 0 0 0 0 0 0 0
+ -7.0121 4.8491 3.1319 C 0 0 0 0 0 0 0 0 0 0 0 0
+ -4.9667 -4.4956 3.8516 C 0 0 0 0 0 0 0 0 0 0 0 0
+ -5.1830 -5.8748 4.2166 C 0 0 0 0 0 0 0 0 0 0 0 0
+ -5.5758 3.5410 6.5095 C 0 0 0 0 0 0 0 0 0 0 0 0
+ -5.0285 4.5440 7.0562 C 0 0 0 0 0 0 0 0 0 0 0 0
+ -3.8822 4.4400 7.9339 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 2 2 0 0 0 0
+ 2 3 2 0 0 0 0//2 E
+ 3 4 1 0 0 0 0
+ 4 5 1 0 0 0 0
+ 5 6 1 0 0 0 0
+ 5 7 2 0 0 0 0// 6 Z
+ 7 8 1 0 0 0 0
+ 8 9 1 0 0 0 0
+ 9 10 2 0 0 0 0// 9
+ 10 11 1 0 0 0 0
+ 10 12 1 0 0 0 0
+ 12 13 1 0 0 0 0
+ 13 14 2 0 0 0 0// 13
+ 11 15 1 0 0 0 0
+ 15 16 2 0 0 0 0//15
+ 16 17 2 0 0 0 0
+ 6 18 1 0 0 0 0
+ 18 19 2 0 0 0 0//18 E
+ 19 20 2 0 0 0 0
+ 8 21 1 0 0 0 0
+ 8 22 1 0 0 0 0
+ 20 23 2 0 0 0 0//22
+ 23 24 1 0 0 0 0
+ 1 25 2 0 0 0 0//24
+ 25 26 1 0 0 0 0
+ 17 27 2 0 0 0 0//26
+ 27 28 1 0 0 0 0
+ 29 30 2 0 0 0 0//28
+ 14 29 2 0 0 0 0//29
+ 30 31 1 0 0 0 0
+M END
+> <chiral_atoms>
+8 R
+
+> <stereogenic_bonds>
+6 E
+2 Z
+18 E
+13 Z
+15 Z
+
+$$$$
Modified: trunk/Jmol-datafiles/cip/RSEZ.txt
===================================================================
--- trunk/Jmol-datafiles/cip/RSEZ.txt 2017-04-29 18:15:15 UTC (rev 21570)
+++ trunk/Jmol-datafiles/cip/RSEZ.txt 2017-04-29 18:49:38 UTC (rev 21571)
@@ -1,8 +1,5 @@
-
# test for Rule 4/5 bond E/Z generation
test1.mol//SEER
# next is proposed - stereochemistry uncertain
test2.mol//REEREEREE
test3.mol//SEESEESEE
-
-#stop
Modified: trunk/Jmol-datafiles/cip/checkCIP.spt
===================================================================
--- trunk/Jmol-datafiles/cip/checkCIP.spt 2017-04-29 18:15:15 UTC (rev
21570)
+++ trunk/Jmol-datafiles/cip/checkCIP.spt 2017-04-29 18:49:38 UTC (rev
21571)
@@ -1,6 +1,6 @@
// checkCIP.spt -- test suite for Jmol CIPChirality.java
// Bob Hanson hans...@stolaf.edu 4/18/2017 7:44:43 AM
-// updated 4/27/2017 2:38:10 PM
+// updated 4/29/2017 1:26:31 PM
nOK = 0;
@@ -34,6 +34,7 @@
load @m @n filter "2D"
if (!{_H}) calculate hydrogens
set labelfor {_C} "%[atomname]"
+ rotate best
refresh
background label yellow
color labels black
@@ -59,18 +60,17 @@
var items = focus.split("descriptor:")
var atoms = items[1].split(true)
rs = items[2].trim()
- var n = atoms.length
- for (var j = 1; j <= n; j++) {
- refs[1 + atoms[j]] = rs
- }
+ var na = atoms.length
+ refs[1 + atoms[1]] = rs // first
+ refs[1 + atoms[0]] = rs // last
}
- var n = refs.length
- for (var j = 1; j <= n; j++) {
+ var na = refs.length
+ for (var j = 1; j <= na; j++) {
if (refs[j])
ref += "" + j + refs[j]
}
}
- key = ref;
+ key =
ref.replace("Sa","P").replace("Ra","M").replace("sa","p").replace("ra","m");
rs = {selected}.label("%i%[chirality]").join("")
} else if (key == "*") {
key = ""
@@ -79,7 +79,7 @@
print "OK\t" + m + "\t" + rs
nOK++
} else {
- var s = "??\t" + m + "\t found " + rs + "; should be " + key
+ var s = "" + n + "??\t" + m + "\t found " + rs + "; should be " + key
refresh
print s
var ans = prompt(s.replace("\t"," ") + " \n\n continue?", "yes")
@@ -91,6 +91,8 @@
refresh
}
+// check a set of files in a directory based on a file listing with annotations
+
function checkRdir(name, type) {
x = load(name + ".txt").lines
for (var f in x) {
@@ -107,11 +109,13 @@
}
}
+// check selected models in a multi-model SDF file
-function checkRSDF(reffile, n, skip) {
- for (var i = 1; i <= n; i++) {
+function checkRSDF(reffile, first, last, skip, corrections) {
+ for (var i = first; i <= last; i++) {
if (skip & i) continue;
- checkrs(reffile, i, "*")
+ var fix = corrections["" + i];
+ checkrs(reffile + (fix ? "//" + fix : ""), i, "*")
}
}
@@ -118,30 +122,38 @@
//////////////////////////////////////////////////////////////////////////
-
//
-// structures from a multi-model SDF file that has focus:/descriptor:
annotations
+// reading files from a directory cip/xx based on file list in cip/xx.txt
//
-checkRSDF("cip/stereo_test_cases.sdf",
- ({15 16 17 18 19 20 24}) // allene
- || ({53}) // cumulene
- || ({12}) // extra "11E" in file
- || ({34 35 36 37}) // pentacoordinate P; axial
- || ({}) // failed
-)
+checkRdir("cip/MP", "*");
+checkRdir("cip/RSEZ", "*");
+checkRdir("cip/NN", "*");
+checkRdir("cip/EZ", "*");
+checkRdir("cip/SP", "*");
+checkRdir("cip/RS", "*");
+checkRdir("cip/R", "R");
+checkRdir("cip/S", "S");
+
//
-// reading files from a directory cip/xx based on file list in cip/xx.txt
+// structures from a multi-model SDF file that has focus:/descriptor:
annotations
//
-checkRdir("cip/NN", "?");
-checkRdir("cip/EZ", "?");
-checkRdir("cip/SP", "?");
-checkRdir("cip/RS", "?");
-checkRdir("cip/R", "R");
-checkRdir("cip/S", "S");
+
+corrections = {
+ "12":"SEREEE", // extra "11E" in file
+ "53":"ZREEZZZZZZZ" // cumulene indication is not in order we can handle in
SDF file
+}
+skip =
+ ({34 35 36 37}) || // pentacoordinate P; axial
+ //({15 16 17 18 19 20 24 53}) || // allene, cumulene
+ ({}) // failed or ignore
+
+checkRSDF("cip/testSuites/stereo_test_cases.sdf", 1, 64, skip, corrections)
+
+
print "DONE: " + nOK
@@ -149,6 +161,7 @@
// individual checks made along the way
+checkrs("cip/SREZ/test1.mol", "SEER")
checkrs("cip/RS/Mata_fig7_I_R.mol","?")
checkrs("testn2.mol","?")
checkrs("cip/EZ/deb.mol");
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