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[Jmol-commits] SF.net SVN: jmol:[17888] trunk/Jmol/src/org/jmol/viewer
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From: <ha...@us...> - 2013-01-28 08:55:23
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Revision: 17888
http://jmol.svn.sourceforge.net/jmol/?rev=17888&view=rev
Author: hansonr
Date: 2013-01-28 08:55:13 +0000 (Mon, 28 Jan 2013)
Log Message:
-----------
___JmolVersion="13.1.13_dev"
new feature: load =xxx/ where xxx is a database code that can be set up in the future by a user.
-- currently including mp MaterialsProject http://www.materialsproject.org/materials/%FILE/cif
-- along with pdb, smiles, pubchem, ligand, nmr, and cactus
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/JmolConstants.java
trunk/Jmol/src/org/jmol/viewer/StateManager.java
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-01-28 08:35:53 UTC (rev 17887)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-01-28 08:55:13 UTC (rev 17888)
@@ -11,8 +11,9 @@
___JmolVersion="13.1.13_dev"
-new feature: load =xxx= where xxx is a database code that can be set up in the future by a user.
- -- currently including =mp= MaterialsProject http://www.materialsproject.org/materials/%ID/cif
+new feature: load =xxx/ where xxx is a database code that can be set up in the future by a user.
+ -- currently including mp MaterialsProject http://www.materialsproject.org/materials/%FILE/cif
+ -- along with pdb, smiles, pubchem, ligand, nmr, and cactus
bug fix: The "show history" command is supposed to clear out the "show history" command
itself, but only if it is a top-level command (from the console),
Modified: trunk/Jmol/src/org/jmol/viewer/JmolConstants.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/JmolConstants.java 2013-01-28 08:35:53 UTC (rev 17887)
+++ trunk/Jmol/src/org/jmol/viewer/JmolConstants.java 2013-01-28 08:55:13 UTC (rev 17888)
@@ -1293,7 +1293,15 @@
// "@hetero", handled specially
};
- public static String[] databases = { "mp", "http://www.materialsproject.org/materials/%ID/cif" };
+ public static String[] databases = {
+ "cactus", "http://cactus.nci.nih.gov/chemical/structure/%FILE",
+ "ligand", "http://www.rcsb.org/pdb/files/ligand/%FILE.cif",
+ "mp", "http://www.materialsproject.org/materials/%FILE/cif",
+ "pdb", "http://www.rcsb.org/pdb/files/%FILE.pdb.gz",
+ "nmr", "http://www.nmrdb.org/predictor?smiles=",
+ "smiles", "http://cactus.nci.nih.gov/chemical/structure/%FILE/file?format=sdf&get3d=True",
+ "pubchem", "http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/%FILE/SDF?record_type=3d"
+ };
public final static String MODELKIT_ZAP_STRING = "1 0 C 0 0";
public static final String MODELKIT_ZAP_TITLE = "Jmol Model Kit";//do not ever change this -- it is in the state
Modified: trunk/Jmol/src/org/jmol/viewer/StateManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/StateManager.java 2013-01-28 08:35:53 UTC (rev 17887)
+++ trunk/Jmol/src/org/jmol/viewer/StateManager.java 2013-01-28 08:55:13 UTC (rev 17888)
@@ -685,8 +685,22 @@
useScriptQueue = g.useScriptQueue;
useArcBall = g.useArcBall;
databases = g.databases;
+ }
+ if (databases == null) {
+ databases = new Hashtable<String, String>();
+ getDataBaseList(JmolConstants.databases);
+ loadFormat = databases.get("pdb");
+ loadLigandFormat = databases.get("ligand");
+ nmrUrlFormat = databases.get("nmr");
+ smilesUrlFormat = databases.get("smiles");
+ nihResolverFormat = databases.get("cactus");
+ pubChemFormat = databases.get("pubchem");
+
+ // beyond these six, they are just in the form load =xxx/id
+
+ getDataBaseList(userDatabases);
}
-
+
for (EnumCallback item : EnumCallback.values())
resetValue(item.name() + "Callback", g);
@@ -1022,12 +1036,8 @@
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 = "http://www.rcsb.org/pdb/files/%FILE.pdb.gz";
- String loadLigandFormat = "http://www.rcsb.org/pdb/files/ligand/%FILE.cif";
- String nmrUrlFormat = "http://www.nmrdb.org/predictor?smiles=";
- String smilesUrlFormat = "http://cactus.nci.nih.gov/chemical/structure/%FILE/file?format=sdf&get3d=True";
- String nihResolverFormat = "http://cactus.nci.nih.gov/chemical/structure/%FILE";
- String pubChemFormat = "http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/%FILE/SDF?record_type=3d";
+ String loadFormat, loadLigandFormat, nmrUrlFormat, 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]";
String edsUrlOptions = "within 2.0 {*}";
@@ -1738,15 +1748,10 @@
}
public String resolveDataBase(String database, String id) {
- if (databases == null) {
- databases = new Hashtable<String, String>();
- getDataBaseList(JmolConstants.databases);
- getDataBaseList(userDatabases);
- }
String format = databases.get(database.toLowerCase());
if (format == null)
return null;
- return TextFormat.formatStringS(format, "ID", id);
+ return (format.indexOf("%FILE") < 0 ? format + id : TextFormat.formatStringS(format, "FILE", id));
}
private void getDataBaseList(String[] list) {
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2013-01-28 08:35:53 UTC (rev 17887)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2013-01-28 08:55:13 UTC (rev 17888)
@@ -4933,10 +4933,10 @@
f = f.substring(1);
type = '#';
} else
- if (f.indexOf("=") > 0) {
- // =xxxx=....
+ if (f.indexOf("/") > 0) {
+ // =xxxx/....
try {
- int pt = f.indexOf("=");
+ int pt = f.indexOf("/");
String database = f.substring(0, pt);
f = global.resolveDataBase(database, f.substring(pt + 1));
return (f == null ? name : f);
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