Revision: 18622
http://sourceforge.net/p/jmol/code/18622
Author: hansonr
Date: 2013-08-23 16:52:44 +0000 (Fri, 23 Aug 2013)
Log Message:
-----------
bug fix for select n;
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
trunk/Jmol/src/org/jmol/script/T.java
trunk/Jmol/src/org/jmol/viewer/JC.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/StateManager.java
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2013-08-22
18:36:16 UTC (rev 18621)
+++ trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2013-08-23
16:52:44 UTC (rev 18622)
@@ -2346,17 +2346,12 @@
bs.and(bsInsert);
if (pt >= len)
return bs;
- //
- // look for a chain spec -- no colon
- //
- char chainID = identifier.charAt(pt++);
- bs.and(getChainBits(chainID));
- if (pt == len)
- return bs;
- //
- // not applicable
- //
- return null;
+ if(pt != len - 1)
+ return null;
+ // ALA32B (no colon; not ALA32:B)
+ // old school; not supported for multi-character chains
+ bs.and(getChainBits(identifier.charAt(pt)));
+ return bs;
}
private BS getSpecName(String name) {
Modified: trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2013-08-22
18:36:16 UTC (rev 18621)
+++ trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2013-08-23
16:52:44 UTC (rev 18622)
@@ -1953,10 +1953,10 @@
info = (int[]) specInfo;
int seqcodeA = info[0];
int seqcodeB = info[1];
- char chainID = (char) info[2];
+ int chainID = info[2];
bs = new BS();
boolean caseSensitive = viewer.getBoolean(T.chaincasesensitive);
- if (!caseSensitive)
+ if (chainID >= 0 && !caseSensitive)
chainID = Character.toUpperCase(chainID);
for (int i = modelCount; --i >= 0;)
if (models[i].isBioModel)
Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2013-08-22 18:36:16 UTC
(rev 18621)
+++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2013-08-23 16:52:44 UTC
(rev 18622)
@@ -14643,6 +14643,12 @@
msg = viewer.getPathForAllFiles();
break;
case T.nmr:
+ if (optParameterAsString(2).equalsIgnoreCase("1H")) {
+ len = 3;
+ if (!chk)
+ msg = viewer.getNMRPredict(viewer.getModelExtract("selected", true,
false, "V2000"));
+ }
+ break;
case T.smiles:
case T.drawing:
case T.chemical:
Modified: trunk/Jmol/src/org/jmol/script/T.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/T.java 2013-08-22 18:36:16 UTC (rev
18621)
+++ trunk/Jmol/src/org/jmol/script/T.java 2013-08-23 16:52:44 UTC (rev
18622)
@@ -827,8 +827,9 @@
public final static int loadligandformat = strparam | 46;
public final static int logfile = strparam | 47;
public final static int measurementunits = strparam | 48;
- public final static int nmrurlformat = strparam | 49;
- public final static int pathforallfiles = strparam | 50;
+ public final static int nmrpredictformat = strparam | 49;
+ public final static int nmrurlformat = strparam | 50;
+ public final static int pathforallfiles = strparam | 51;
public final static int picking = strparam | 52;
public final static int pickingstyle = strparam | 54;
public final static int picklabel = strparam | 56;
@@ -2221,6 +2222,7 @@
"loadLigandFormat", T.t(loadligandformat),
"logFile", T.t(logfile),
"measurementUnits", T.t(measurementunits),
+ "nmrPredictFormat", T.t(nmrpredictformat),
"nmrUrlFormat", T.t(nmrurlformat),
"pathForAllFiles", T.t(pathforallfiles),
"picking", T.t(picking),
Modified: trunk/Jmol/src/org/jmol/viewer/JC.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/JC.java 2013-08-22 18:36:16 UTC (rev
18621)
+++ trunk/Jmol/src/org/jmol/viewer/JC.java 2013-08-23 16:52:44 UTC (rev
18622)
@@ -1293,6 +1293,7 @@
"mp", "http://www.materialsproject.org/materials/%FILE/cif";,
"nci", "http://cactus.nci.nih.gov/chemical/structure/%FILE";,
"nmr", "http://www.nmrdb.org/predictor?smiles=";,
+ "nmrdb", "http://www.nmrdb.org/service/predictor?POST?molfile=";,
"pdb", "http://www.rcsb.org/pdb/files/%FILE.pdb.gz";,
"pubchem",
"http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/%FILE/SDF?record_type=3d";
};
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-08-22 18:36:16 UTC
(rev 18621)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-08-23 16:52:44 UTC
(rev 18622)
@@ -13,6 +13,8 @@
___JmolVersion="13.3.4"
+bug fix: select 1-5 broken
+
JmolVersion="13.3.4_dev_2013.08.21"
bug fix: JANA2006 reader not processing occupancies
Modified: trunk/Jmol/src/org/jmol/viewer/StateManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/StateManager.java 2013-08-22 18:36:16 UTC
(rev 18621)
+++ trunk/Jmol/src/org/jmol/viewer/StateManager.java 2013-08-23 16:52:44 UTC
(rev 18622)
@@ -694,6 +694,7 @@
loadFormat = databases.get("pdb");
loadLigandFormat = databases.get("ligand");
nmrUrlFormat = databases.get("nmr");
+ nmrPredictFormat = databases.get("nmrdb");
smilesUrlFormat = databases.get("nci") + "/file?format=sdf&get3d=True";
nihResolverFormat = databases.get("nci");
pubChemFormat = databases.get("pubchem");
@@ -918,6 +919,7 @@
//setParamB("navigateSurface", navigateSurface);
setB("navigationPeriodic", navigationPeriodic);
setF("navigationSpeed", navigationSpeed);
+ setS("nmrPredictFormat", nmrPredictFormat);
setS("nmrUrlFormat", nmrUrlFormat);
setB("partialDots", partialDots);
setB("pdbAddHydrogens", pdbAddHydrogens); // new 12.1.51
@@ -1041,7 +1043,7 @@
boolean forceAutoBond = false;
boolean fractionalRelative = false; // true: UNITCELL offset will change
meaning of {1/2 1/2 1/2}
char inlineNewlineChar = '|'; //pseudo static
- String loadFormat, loadLigandFormat, nmrUrlFormat, smilesUrlFormat,
nihResolverFormat, pubChemFormat;
+ String loadFormat, loadLigandFormat, nmrUrlFormat, nmrPredictFormat,
smilesUrlFormat, nihResolverFormat, pubChemFormat;
String edsUrlFormat =
"http://eds.bmc.uu.se/eds/dfs/%LC13/%LCFILE/%LCFILE.omap";;
String edsUrlCutoff =
"load('http://eds.bmc.uu.se/eds/dfs/%LC13/%LCFILE/%LCFILE.sfdat').lines.find('MAP_SIGMA').split('
')[2]";
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2013-08-22 18:36:16 UTC (rev
18621)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2013-08-23 16:52:44 UTC (rev
18622)
@@ -6038,8 +6038,12 @@
private void setStringPropertyTok(String key, int tok, String value) {
switch (tok) {
- // 13.1.2
+ case T.nmrpredictformat:
+ // 13.3.4
+ global.nmrPredictFormat = value;
+ break;
case T.defaultdropscript:
+ // 13.1.2
// for File|Open and Drag/drop
global.defaultDropScript = value;
break;
@@ -8570,6 +8574,14 @@
return xyzdata;
}
+ public String getNMRPredict(String molFile) {
+ // nmrdb cannot handle "." separator and cannot handle c=c
+ int pt = molFile.indexOf("\n");
+ molFile = "Jmol " + version_date + molFile.substring(pt);
+ String url = global.nmrPredictFormat + molFile;
+ return getFileAsString(url);
+ }
+
public void showNMR(String smiles) {
// nmrdb cannot handle "." separator and cannot handle c=c
showUrl(global.nmrUrlFormat
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