Revision: 21627
http://sourceforge.net/p/jmol/code/21627
Author: hansonr
Date: 2017-05-31 03:16:55 +0000 (Wed, 31 May 2017)
Log Message:
-----------
Modified Paths:
--------------
trunk/Jmol-datafiles/cip/checkCIP.spt
Modified: trunk/Jmol-datafiles/cip/checkCIP.spt
===================================================================
--- trunk/Jmol-datafiles/cip/checkCIP.spt 2017-05-31 03:15:14 UTC (rev
21626)
+++ trunk/Jmol-datafiles/cip/checkCIP.spt 2017-05-31 03:16:55 UTC (rev
21627)
@@ -5,8 +5,7 @@
// 5/21/2017 4:57:14 PM -- adds AY-236.193,194,195,196 spiro
// 5/27/2017 10:26:49 AM -- finalized - full validation
-sourcedir = "cip" // local version
-
+//sourcedir = "cip" // local version
sourcedir = "https://www.stolaf.edu/people/hansonr/jmol/cip";
@@ -13,13 +12,22 @@
// Check a set of Jmol 3D files -- first line includes "CIP:xxxxx;"
function checkCIP(info, n) {
+ if (0 + info > 0) {
+ n = info
+ info = thisSDF
+ }
thisSDF = info
var first = (n ? n : info.first)
var last = (n ? n : info.last)
for (var i = first; i <= last; i++) {
if (info.skip & i) continue
+// load @{info.sdffile} @i
+// var bb = _M.molData.ref_pname_pin
var f = sourceDir + "/testSuites/"+info.id+"/" + info.id + "_" + (("000" +
i)%-3) + ".mol";
checkrs(f, 1, "*")
+// var rs = {chirality != ""}.label("%i%[chirality]").join(" ")
+// frame title @{"CIP:" + rs + "; BB:" + bb + ";"}
+// write coord @_modelFile
}
}
@@ -73,20 +81,14 @@
n = 1;
var doCheck = !!key
var a = 0;
+ fname = fname.replace("://",":/")
if (fname.find("//")) {
fname = fname.split("//")
- 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;
+ key = fname[2]
+ fname = fname[1]
+ doCheck = key
}
+ fname = fname.replace(":/", "://")
if (thisN && (nOK + 1) != thisN) {
nOK++;
return;
@@ -114,7 +116,7 @@
var rs = {selected}.label("%[chirality]").join("")
var isok = true
- print " " + doCheck + " key=" + key + " found=" + rs
+ var isjmol = false
if (doCheck) {
var ref = ""
if (docheck != key) {
@@ -122,12 +124,15 @@
// accepts data in various forms
ref = _M.molData["chiral_atoms"].replace("\n","").replace(" ","") +
_M.molData["stereounits"] + _M.molData["stereo"]
} else if (_modelTitle.find("CIP:")) {
- ref = _modelTitle.split("CIP:")[2].split(";")[1]
+ ref = _modelTitle.split("CIP:")[2].split(";")[1]
+ isjmol = true
}
}
if (ref) {
rs = ""
- if (ref.find("focus:")) {
+ if (isjmol){
+ rs = {selected}.label("%i%[chirality]").join(" ")
+ } else if (ref.find("focus:")) {
// MY64
var tokens = ref.split("focus:");
ref = ""
@@ -178,6 +183,7 @@
} else {
var s = "" + n + "??\t" + fname + "\t // found " + rs + "; should be "
+ key
print s
+// ans = "yes"
ans = prompt(s.replace("\t"," ") + " \n\n continue?", "yes")
}
if (ans != "yes") quit
@@ -192,35 +198,6 @@
///// older code for extracting from SDF files
-// check selected models in a multi-model 2D- or 3D-SDF file
-
-function checkRSDF(info, n) {
- thisSDF = info
- var first = (n ? n : info.first)
- var last = (n ? n : info.last)
- for (var i = first; i <= last; i++) {
- if (info.skip & i) continue
- var f,pt,issdf,bb
- var fix = (info.override ? info.override["" + i] : "")
- if (fix.find("@3D ") == 1) {
- if (dowrite) {
- load @{info.sdffile} i
- bb = _M.molData.ref_pname_pin
- }
- f = info.prefix3d + i + ".mol"
- fix = fix.split("@3D ")[2]
- pt = 1
- issdf = false
- } else {
- f = info.sdffile
- issdf = true
- pt = i
- }
- var f = f + (fix ? "//" + fix : "")
- checkrs(f, pt, "*")
- }
-}
-
function findSDF(info, what) {
if (!what) {
what = info
@@ -242,6 +219,29 @@
}
print "" + found.length + " found for " + what + ": " + format("json",
ivals)
}
+
+function bhtest(info, n) {
+ // bhtest 3
+ // bhtest MV64 3
+ if (info) {
+ if (!n) {
+ n = info
+ info = ""
+ }
+ }
+ checkCIP((info ? info : thisSDF),n)
+ label %a;background labels yellow
+ refresh
+ select *
+ //set loglevel 6
+ print _M.molData
+ print {*}.chirality.join(",").trim(",")
+ //print {*}.chirality.pivot
+ print {*}.find("SMILES")
+ showRS
+}
+
+
/////////////////////////////////////////////////////////////////////
//
// structures from a multi-model SDF file that may have stereochemistry
annotations
@@ -313,6 +313,7 @@
// full test run
checkCIP(AY236)
+quit
checkCIP(MV116)
checkCIP(MV64)
checkRdir("bytype/centres", "*")
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