Revision: 21624
http://sourceforge.net/p/jmol/code/21624
Author: hansonr
Date: 2017-05-29 17:13:02 +0000 (Mon, 29 May 2017)
Log Message:
-----------
Modified Paths:
--------------
trunk/Jmol-datafiles/cip/bytype/more.txt
trunk/Jmol-datafiles/cip/checkCIP.spt
Added Paths:
-----------
trunk/Jmol-datafiles/cip/bytype/more/testJM1.mol
trunk/Jmol-datafiles/cip/bytype/more/testJM2.mol
Added: trunk/Jmol-datafiles/cip/bytype/more/testJM1.mol
===================================================================
--- trunk/Jmol-datafiles/cip/bytype/more/testJM1.mol
(rev 0)
+++ trunk/Jmol-datafiles/cip/bytype/more/testJM1.mol 2017-05-29 17:13:02 UTC
(rev 21624)
@@ -0,0 +1,101 @@
+c:/jmol-dev/bobtest/testjm1.mol
+__Jmol-14_05171710413D 1 1.00000 0.00000 0
+Jmol version 14.15.5 2017-05-14 14:04 EXTRACT: ({0:47})
+ 48 48 0 0 0 0 1 V2000
+ 0.39535 -2.95996 -0.67803 C 0 0 0 0 0 0
+ -0.23850 -1.78040 0.07932 C 0 0 0 0 0 0
+ -0.96024 -2.27200 0.77115 H 0 0 0 0 0 0
+ 0.78491 -1.07216 0.93421 C 0 0 0 0 0 0
+ 0.24537 -0.55234 1.75359 H 0 0 0 0 0 0
+ 1.65585 -2.13922 1.63428 C 0 0 0 0 0 0
+ 1.69841 -0.06967 0.27383 C 0 0 0 0 0 0
+ 2.64654 -0.08910 0.88815 H 0 0 0 0 0 0
+ 2.14812 -0.39726 -1.13639 C 0 0 0 0 0 0
+ 1.19563 1.36343 0.40389 C 0 0 0 0 0 0
+ 0.99046 1.56646 1.45578 H 0 0 0 0 0 0
+ 2.35932 2.30312 0.01189 C 0 0 0 0 0 0
+ 0.01613 1.68278 -0.49397 C 0 0 0 0 0 0
+ 0.10700 1.16076 -1.45145 H 0 0 0 0 0 0
+ 0.10010 3.18852 -0.85184 C 0 0 0 0 0 0
+ -1.34777 1.43201 0.10888 C 0 0 0 0 0 0
+ -2.03217 2.19387 -0.35031 H 0 0 0 0 0 0
+ -1.40976 1.69146 1.61126 C 0 0 0 0 0 0
+ -1.95599 0.08145 -0.22356 C 0 0 0 0 0 0
+ -2.77592 0.27675 -0.95662 H 0 0 0 0 0 0
+ -2.63669 -0.50201 1.01549 C 0 0 0 0 0 0
+ -1.01161 -0.90244 -0.88332 C 0 0 0 0 0 0
+ -0.33461 -0.38539 -1.56367 H 0 0 0 0 0 0
+ -1.86093 -1.83290 -1.78507 C 0 0 0 0 0 0
+ 0.90530 -3.61388 0.02940 H 0 0 0 0 0 0
+ -0.38358 -3.52068 -1.19464 H 0 0 0 0 0 0
+ 1.11330 -2.58102 -1.40525 H 0 0 0 0 0 0
+ 2.15575 -2.75039 0.88292 H 0 0 0 0 0 0
+ 2.40250 -1.64691 2.25758 H 0 0 0 0 0 0
+ 1.02390 -2.77292 2.25649 H 0 0 0 0 0 0
+ 1.29008 -0.36620 -1.80783 H 0 0 0 0 0 0
+ 2.88956 0.33323 -1.46022 H 0 0 0 0 0 0
+ 2.58820 -1.39432 -1.15493 H 0 0 0 0 0 0
+ 2.66182 2.09795 -1.01499 H 0 0 0 0 0 0
+ 2.03270 3.33976 0.09420 H 0 0 0 0 0 0
+ 3.20371 2.13412 0.68019 H 0 0 0 0 0 0
+ 1.03860 3.38710 -1.36950 H 0 0 0 0 0 0
+ -0.73537 3.45524 -1.49903 H 0 0 0 0 0 0
+ 0.05632 3.78199 0.06135 H 0 0 0 0 0 0
+ -1.15225 2.73152 1.81131 H 0 0 0 0 0 0
+ -2.41812 1.49071 1.97329 H 0 0 0 0 0 0
+ -0.70328 1.03742 2.12240 H 0 0 0 0 0 0
+ -3.42346 0.17399 1.35015 H 0 0 0 0 0 0
+ -3.07072 -1.47104 0.76923 H 0 0 0 0 0 0
+ -1.90087 -0.62498 1.81033 H 0 0 0 0 0 0
+ -2.47962 -1.22958 -2.44928 H 0 0 0 0 0 0
+ -1.20069 -2.46547 -2.37837 H 0 0 0 0 0 0
+ -2.49993 -2.45851 -1.16180 H 0 0 0 0 0 0
+ 1 2 1 0 0 0
+ 2 3 1 0 0 0
+ 2 4 1 0 0 0
+ 4 5 1 0 0 0
+ 4 6 1 0 0 0
+ 4 7 1 0 0 0
+ 7 8 1 0 0 0
+ 7 9 1 0 0 0
+ 7 10 1 0 0 0
+ 10 11 1 0 0 0
+ 10 12 1 0 0 0
+ 10 13 1 0 0 0
+ 13 14 1 0 0 0
+ 13 15 1 0 0 0
+ 13 16 1 0 0 0
+ 16 17 1 0 0 0
+ 16 18 1 0 0 0
+ 16 19 1 0 0 0
+ 19 20 1 0 0 0
+ 19 21 1 0 0 0
+ 19 22 1 0 0 0
+ 22 23 1 0 0 0
+ 2 22 1 0 0 0
+ 22 24 1 0 0 0
+ 1 25 1 0 0 0
+ 1 26 1 0 0 0
+ 1 27 1 0 0 0
+ 6 28 1 0 0 0
+ 6 29 1 0 0 0
+ 6 30 1 0 0 0
+ 9 31 1 0 0 0
+ 9 32 1 0 0 0
+ 9 33 1 0 0 0
+ 12 34 1 0 0 0
+ 12 35 1 0 0 0
+ 12 36 1 0 0 0
+ 15 37 1 0 0 0
+ 15 38 1 0 0 0
+ 15 39 1 0 0 0
+ 18 40 1 0 0 0
+ 18 41 1 0 0 0
+ 18 42 1 0 0 0
+ 21 43 1 0 0 0
+ 21 44 1 0 0 0
+ 21 45 1 0 0 0
+ 24 46 1 0 0 0
+ 24 47 1 0 0 0
+ 24 48 1 0 0 0
+M END
Added: trunk/Jmol-datafiles/cip/bytype/more/testJM2.mol
===================================================================
--- trunk/Jmol-datafiles/cip/bytype/more/testJM2.mol
(rev 0)
+++ trunk/Jmol-datafiles/cip/bytype/more/testJM2.mol 2017-05-29 17:13:02 UTC
(rev 21624)
@@ -0,0 +1,101 @@
+c:/jmol-dev/bobtest/testjm2.mol
+__Jmol-14_05171710413D 1 1.00000 0.00000 0
+Jmol version 14.15.5 2017-05-14 14:04 EXTRACT: ({0:47})
+ 48 48 0 0 0 0 1 V2000
+ 3.41751 -0.30239 0.11322 C 0 0 0 0 0 0
+ 1.95921 -0.14682 0.55873 C 0 0 0 0 0 0
+ 1.94191 0.11007 1.62117 H 0 0 0 0 0 0
+ 1.30578 0.97956 -0.24129 C 0 0 0 0 0 0
+ 1.00026 0.63012 -1.21858 H 0 0 0 0 0 0
+ 2.33872 2.10256 -0.43530 C 0 0 0 0 0 0
+ 0.12072 1.53848 0.54130 C 0 0 0 0 0 0
+ 0.08237 1.07984 1.53139 H 0 0 0 0 0 0
+ 0.34609 3.04765 0.74755 C 0 0 0 0 0 0
+ -1.19695 1.33937 -0.18782 C 0 0 0 0 0 0
+ -1.32300 2.23629 -0.84673 H 0 0 0 0 0 0
+ -2.36045 1.39851 0.80386 C 0 0 0 0 0 0
+ -1.26399 0.13170 -1.09173 C 0 0 0 0 0 0
+ -0.46046 0.19674 -1.84718 H 0 0 0 0 0 0
+ -2.58030 0.21095 -1.90136 C 0 0 0 0 0 0
+ -1.20071 -1.23440 -0.44114 C 0 0 0 0 0 0
+ -0.94033 -1.97084 -1.22594 H 0 0 0 0 0 0
+ -2.60774 -1.67101 0.01364 C 0 0 0 0 0 0
+ -0.24273 -1.35450 0.72400 C 0 0 0 0 0 0
+ -0.37790 -0.50570 1.40499 H 0 0 0 0 0 0
+ -0.62625 -2.61143 1.53708 C 0 0 0 0 0 0
+ 1.22363 -1.46823 0.34894 C 0 0 0 0 0 0
+ 1.68276 -2.20145 1.04827 H 0 0 0 0 0 0
+ 1.46351 -1.99347 -1.05932 C 0 0 0 0 0 0
+ 3.94903 0.63524 0.27557 H 0 0 0 0 0 0
+ 3.89204 -1.09414 0.69291 H 0 0 0 0 0 0
+ 3.44843 -0.55894 -0.94575 H 0 0 0 0 0 0
+ 3.20114 1.71345 -0.97657 H 0 0 0 0 0 0
+ 1.88874 2.91561 -1.00500 H 0 0 0 0 0 0
+ 2.65835 2.47442 0.53827 H 0 0 0 0 0 0
+ 0.41929 3.53997 -0.22221 H 0 0 0 0 0 0
+ -0.49099 3.46707 1.30570 H 0 0 0 0 0 0
+ 1.26945 3.20426 1.30516 H 0 0 0 0 0 0
+ -2.36799 2.37025 1.29757 H 0 0 0 0 0 0
+ -3.30007 1.25458 0.27045 H 0 0 0 0 0 0
+ -2.24216 0.61277 1.55000 H 0 0 0 0 0 0
+ -2.58759 1.12539 -2.49464 H 0 0 0 0 0 0
+ -2.65228 -0.65210 -2.56323 H 0 0 0 0 0 0
+ -3.42834 0.21544 -1.21659 H 0 0 0 0 0 0
+ -3.27097 -1.71684 -0.85015 H 0 0 0 0 0 0
+ -2.54991 -2.65457 0.47995 H 0 0 0 0 0 0
+ -2.99701 -0.95032 0.73287 H 0 0 0 0 0 0
+ -0.55303 -3.49261 0.89972 H 0 0 0 0 0 0
+ 0.05238 -2.71774 2.38341 H 0 0 0 0 0 0
+ -1.64853 -2.51048 1.90157 H 0 0 0 0 0 0
+ 0.99798 -1.32278 -1.78143 H 0 0 0 0 0 0
+ 2.53546 -2.04523 -1.25004 H 0 0 0 0 0 0
+ 1.02906 -2.98851 -1.15484 H 0 0 0 0 0 0
+ 1 2 1 0 0 0
+ 2 3 1 0 0 0
+ 2 4 1 0 0 0
+ 4 5 1 0 0 0
+ 4 6 1 0 0 0
+ 4 7 1 0 0 0
+ 7 8 1 0 0 0
+ 7 9 1 0 0 0
+ 7 10 1 0 0 0
+ 10 11 1 0 0 0
+ 10 12 1 0 0 0
+ 10 13 1 0 0 0
+ 13 14 1 0 0 0
+ 13 15 1 0 0 0
+ 13 16 1 0 0 0
+ 16 17 1 0 0 0
+ 16 18 1 0 0 0
+ 16 19 1 0 0 0
+ 19 20 1 0 0 0
+ 19 21 1 0 0 0
+ 19 22 1 0 0 0
+ 22 23 1 0 0 0
+ 2 22 1 0 0 0
+ 22 24 1 0 0 0
+ 1 25 1 0 0 0
+ 1 26 1 0 0 0
+ 1 27 1 0 0 0
+ 6 28 1 0 0 0
+ 6 29 1 0 0 0
+ 6 30 1 0 0 0
+ 9 31 1 0 0 0
+ 9 32 1 0 0 0
+ 9 33 1 0 0 0
+ 12 34 1 0 0 0
+ 12 35 1 0 0 0
+ 12 36 1 0 0 0
+ 15 37 1 0 0 0
+ 15 38 1 0 0 0
+ 15 39 1 0 0 0
+ 18 40 1 0 0 0
+ 18 41 1 0 0 0
+ 18 42 1 0 0 0
+ 21 43 1 0 0 0
+ 21 44 1 0 0 0
+ 21 45 1 0 0 0
+ 24 46 1 0 0 0
+ 24 47 1 0 0 0
+ 24 48 1 0 0 0
+M END
Modified: trunk/Jmol-datafiles/cip/bytype/more.txt
===================================================================
--- trunk/Jmol-datafiles/cip/bytype/more.txt 2017-05-29 16:46:46 UTC (rev
21623)
+++ trunk/Jmol-datafiles/cip/bytype/more.txt 2017-05-29 17:13:02 UTC (rev
21624)
@@ -1,4 +1,10 @@
-# Rule 4b R/S + E/Z ?
-#dimethylcyclodecadiene.mol
+# distinguishing simple E/Z from auxiliary seqCis/seqTrans
+dimethylcyclodecadiene.mol//EEsEEs
+# these next two are NOT the same, but they have the same RS descriptors
+# probably needs to be an adjustment to the LOCANT rules, not the SEQUENCE
rules
+testJM1.mol//SRSRRSRS
+testJM2.mol//SRRSRSSR
+# just a good case
+testJM3.mol//Rssrrr
# impossibly deep
#chebi51439.mol
Modified: trunk/Jmol-datafiles/cip/checkCIP.spt
===================================================================
--- trunk/Jmol-datafiles/cip/checkCIP.spt 2017-05-29 16:46:46 UTC (rev
21623)
+++ trunk/Jmol-datafiles/cip/checkCIP.spt 2017-05-29 17:13:02 UTC (rev
21624)
@@ -7,7 +7,7 @@
sourcedir = "cip" // local version
-sourcedir = "https://chemapps.stolaf.edu/jmol/cip";
+sourcedir = "https://www.stolaf.edu/people/hansonr/jmol/cip";
// Check a set of Jmol 3D files -- first line includes "CIP:xxxxx;"
@@ -26,7 +26,7 @@
// check a set of files in a directory based on a file listing with annotations
function checkRdir(name, type) {
- var x = load(name + ".txt").lines
+ var x = load(sourceDir + "/" + name + ".txt").lines
for (var f in x) {
f = f.trim();
if (f == "#QUIT") break
@@ -33,7 +33,7 @@
if (f == "#stop") exit
if (!f || f.find("#") == 1) continue
if (f.find("$") != 1)
- f = sourceDir + "/bytype/" + name + "/" + f
+ f = sourceDir + "/" + name + "/" + f
if (type)
checkRS(f, type)
else
@@ -64,7 +64,7 @@
thisN = 0;
stopped = false;
- function checkRS(fname, n, key, isQuiet) {
+function checkRS(fname, n, key, isQuiet) {
if (_argCount == 2 && 0 + n != n) {
key = n;
n = 0;
@@ -75,8 +75,16 @@
var a = 0;
if (fname.find("//")) {
fname = fname.split("//")
- key = fname[2]
- fname = fname[1]
+ switch (fname.length) {
+ case 2:
+ key = fname[2]
+ fname = fname[1]
+ break;
+ case 3:
+ // http://
+ key = fname[3]
+ fname = fname[1] + "//" + fname[2]
+ }
doCheck = key;
}
if (thisN && (nOK + 1) != thisN) {
@@ -256,7 +264,7 @@
]
//
-// Test Suite MV-64 (Mikko Vainio, \x8Fbo Akademi University, Turku, Finland)
+// Test Suite MV-64 (Mikko Vainio, \xAEbo Akademi University, Turku, Finland)
//
MV64 = [
@@ -268,7 +276,7 @@
]
//
-// Test Suite MV-116 (Mikko Vainio, \x8Fbo Akademi University, Turku, Finland)
+// Test Suite MV-116 (Mikko Vainio, \xAEbo Akademi University, Turku, Finland)
//
// ZIP file cleaned of redundant 2D files, hypervalent models, and undefined
stereochemistry, planar chirality
@@ -293,7 +301,7 @@
/////////////////////////////////////////////////////////////////////
-var ans = prompt("Do single test?", "yes")
+var ans = prompt("Do a special test?", "no")
if (ans == "null") quit
if (ans == "yes") {
set debughigh
@@ -307,8 +315,8 @@
checkCIP(AY236)
checkCIP(MV116)
checkCIP(MV64)
-checkRdir("bytypes/centres", "*");
-checkRdir("bytypes/more", "*");
+checkRdir("bytype/centres", "*")
+checkRdir("bytype/more", "*")
print "DONE: " + nOK
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