Revision: 20329
http://sourceforge.net/p/jmol/code/20329
Author: hansonr
Date: 2015-02-25 12:33:41 +0000 (Wed, 25 Feb 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.3.12_2015.02.25"
new feature: show chemical drawing
new feature: show drawing
-- pops up window with drawing of model
-- service is from NCI
-- uses SMILES if structure was not loaded using $... (NCI) or :... (PubChem)
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
trunk/Jmol/src/org/jmol/console/ImageDialog.java
trunk/Jmol/src/org/jmol/modelset/ModelSet.java
trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
trunk/Jmol/src/org/jmol/viewer/FileManager.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
2015-02-25 04:41:22 UTC (rev 20328)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
2015-02-25 12:33:41 UTC (rev 20329)
@@ -256,7 +256,7 @@
binaryDoc.setOutputChannel(out);
processBinaryDocument();
}
- finalizeSubclassReader(); // upstairs
+ finalizeSubclassReader(); // upstairs
if (!isFinalized)
finalizeReaderASCR();
} catch (Throwable e) {
@@ -375,6 +375,8 @@
protected void finalizeReaderASCR() throws Exception {
isFinalized = true;
if (asc.atomSetCount > 0) {
+ if (asc.atomSetCount == 1)
+ asc.setCurrentModelInfo("dbName", htParams.get("dbName"));
applySymmetryAndSetTrajectory();
asc.finalizeStructures();
if (doCentralize)
Modified: trunk/Jmol/src/org/jmol/console/ImageDialog.java
===================================================================
--- trunk/Jmol/src/org/jmol/console/ImageDialog.java 2015-02-25 04:41:22 UTC
(rev 20328)
+++ trunk/Jmol/src/org/jmol/console/ImageDialog.java 2015-02-25 12:33:41 UTC
(rev 20329)
@@ -69,6 +69,7 @@
public ImageDialog(Viewer vwr, String title, Map<String, GenericImageDialog>
imageMap){
super(Platform.getWindow((Container) vwr.display) instanceof JFrame ?
(JFrame) Platform.getWindow((Container) vwr.display) : null, title, false);
this.vwr = vwr;
+ this.setResizable(false);
console = vwr.getConsole();
addWindowListener(this);
this.title = title;
Modified: trunk/Jmol/src/org/jmol/modelset/ModelSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2015-02-25 04:41:22 UTC
(rev 20328)
+++ trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2015-02-25 12:33:41 UTC
(rev 20329)
@@ -300,6 +300,15 @@
return -1;
}
+ public String getModelDataBaseName(BS bsAtoms) {
+ for (int i = 0; i < mc; i++) {
+ if (bsAtoms.equals(am[i].bsAtoms))
+ return (String) getInfo(i, "dbName");
+ }
+ return null;
+ }
+
+
public void setTrajectory(int modelIndex) {
if (modelIndex >= 0 && isTrajectory(modelIndex) &&
at[am[modelIndex].firstAtomIndex].mi != modelIndex)
trajectory.setModel(modelIndex);
@@ -3897,6 +3906,6 @@
Object o = (haveBioModels ? bioModelset.getAllHeteroList(modelIndex) :
null);
return (Map<String, String>) (o == null ? getInfoM("hetNames") : o);
}
-
+
}
Modified: trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-02-25 04:41:22 UTC
(rev 20328)
+++ trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-02-25 12:33:41 UTC
(rev 20329)
@@ -3706,18 +3706,28 @@
if (!chk)
vwr.getNMRPredict(true);
return;
- case T.smiles:
case T.drawing:
case T.chemical:
+ case T.smiles:
checkLength(tok == T.chemical ? 3 : 2);
if (chk)
return;
try {
- msg = vwr.getSmiles(null);
+ if (tok != T.smiles)
+ msg = vwr.getDataBaseName(null);
+ if (msg != null && (msg.startsWith("$") || msg.startsWith(":"))) {
+ msg = msg.substring(1);
+ } else {
+ msg = null;
+ }
+ if (msg == null)
+ msg = vwr.getSmiles(null);
} catch (Exception ex) {
msg = ex.getMessage();
}
switch (tok) {
+ case T.smiles:
+ break;
case T.drawing:
if (msg.length() > 0) {
vwr.fm.loadImage(vwr.setLoadFormat("_" + msg, '2', false), "\1" +
msg);
Modified: trunk/Jmol/src/org/jmol/viewer/FileManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/FileManager.java 2015-02-25 04:41:22 UTC
(rev 20328)
+++ trunk/Jmol/src/org/jmol/viewer/FileManager.java 2015-02-25 12:33:41 UTC
(rev 20329)
@@ -192,7 +192,10 @@
boolean isAppend) {
if (htParams.get("atomDataOnly") == null)
setLoadState(htParams);
+ String name0 = name;
name = vwr.resolveDatabaseFormat(name);
+ if (!name0.equals(name) && (name0.startsWith("$") || name0.startsWith(":")
|| name0.startsWith("==")))
+ htParams.put("dbName", name0);
int pt = name.indexOf("::");
String nameAsGiven = (pt >= 0 ? name.substring(pt + 2) : name);
String fileType = (pt >= 0 ? name.substring(0, pt) : null);
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-02-25 04:41:22 UTC
(rev 20328)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-02-25 12:33:41 UTC
(rev 20329)
@@ -19,9 +19,9 @@
new feature: show chemical drawing
new feature: show drawing
-- pops up window with drawing of model
- -- somewhat limited in scope and size, as it uses SMILES
+ -- service is from NCI
+ -- uses SMILES if structure was not loaded using $... (NCI) or :... (PubChem)
-
JmolVersion="14.3.12_2015.02.24"
new feature: show IMAGE
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-02-25 04:41:22 UTC (rev
20328)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-02-25 12:33:41 UTC (rev
20329)
@@ -8508,6 +8508,10 @@
setShapeProperty(JC.SHAPE_MEASURES, "delete", Integer.valueOf(i));
}
+ public String getDataBaseName(BS bs) throws Exception {
+ return ms.getModelDataBaseName(bs == null ? bsA() : bs);
+ }
+
@Override
public String getSmiles(BS bs) throws Exception {
return getSmilesOpt(bs, -1, -1, false, false, false, false, false);
This was sent by the SourceForge.net collaborative development platform, the
world's largest Open Source development site.
------------------------------------------------------------------------------
Dive into the World of Parallel Programming The Go Parallel Website, sponsored
by Intel and developed in partnership with Slashdot Media, is your hub for all
things parallel software development, from weekly thought leadership blogs to
news, videos, case studies, tutorials and more. Take a look and join the
conversation now. http://goparallel.sourceforge.net/
_______________________________________________
Jmol-commits mailing list
Jmol-commits@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-commits
