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[Jmol-commits] SF.net SVN: jmol:[10953] trunk/Jmol/src/org/jmol/viewer
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From: <ha...@us...> - 2009-06-04 02:26:08
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Revision: 10953
http://jmol.svn.sourceforge.net/jmol/?rev=10953&view=rev
Author: hansonr
Date: 2009-06-04 02:26:06 +0000 (Thu, 04 Jun 2009)
Log Message:
-----------
version=11.7.40 # new feature: load "@x" -- inline load of data contained in variable x.
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Eval.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java 2009-06-04 01:56:47 UTC (rev 10952)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2009-06-04 02:26:06 UTC (rev 10953)
@@ -4291,10 +4291,12 @@
Hashtable htParams = new Hashtable();
int i = 1;
// ignore optional file format
- // String filename = "";
+ // String filename = "";
String modelName = null;
String filename;
int tokType = 0;
+ boolean needToLoad = true;
+ String sOptions = "";
if (statementLength == 1) {
i = 0;
} else {
@@ -4310,16 +4312,18 @@
i = 2;
loadScript.append(" " + modelName);
isAppend = (modelName.equalsIgnoreCase("append"));
- atomDataOnly = Parser.isOneOf(modelName.toLowerCase(), JmolConstants.LOAD_ATOM_DATA_TYPES);
+ atomDataOnly = Parser.isOneOf(modelName.toLowerCase(),
+ JmolConstants.LOAD_ATOM_DATA_TYPES);
if (atomDataOnly) {
- htParams.put("atomDataOnly",Boolean.TRUE);
- htParams.put("modelNumber", new Integer(1));
- isAppend = true;
- tokType = Token.getTokenFromName(modelName.toLowerCase()).tok;
- if (tokType == Token.vibration)
- tokType = Token.vibXyz;
+ htParams.put("atomDataOnly", Boolean.TRUE);
+ htParams.put("modelNumber", new Integer(1));
+ isAppend = true;
+ tokType = Token.getTokenFromName(modelName.toLowerCase()).tok;
+ if (tokType == Token.vibration)
+ tokType = Token.vibXyz;
}
- if (isAppend && ((filename = optParameterAsString(2))
+ if (isAppend
+ && ((filename = optParameterAsString(2))
.equalsIgnoreCase("trajectory") || filename
.equalsIgnoreCase("models"))) {
modelName = filename;
@@ -4333,7 +4337,7 @@
if (isPoint3f(i)) {
Point3f pt = getPoint3f(i, false);
i = iToken + 1;
- //first last stride
+ // first last stride
htParams.put("firstLastStep", new int[] { (int) pt.x, (int) pt.y,
(int) pt.z });
loadScript.append(" " + Escape.escape(pt));
@@ -4359,19 +4363,13 @@
}
if (filename.equals("string[]"))
return;
- if (!isSyntaxCheck || isScriptCheck && fileOpenCheck) {
- if (filename.startsWith("@") && filename.length() > 1) {
- htParams.put("fileData", getStringParameter(filename.substring(1), false));
- filename = "string";
- }
- viewer.openFile(filename, htParams, null, isAppend);
- loadScript.append(" ");
- if (!filename.equals("string")
- && !filename.equals("string[]"))
- loadScript.append("/*file*/");
- loadScript.append(Escape.escape(modelName = (String) htParams
- .get("fullPathName")));
- }
+
+ viewer.openFile(filename, htParams, null, isAppend);
+ loadScript.append(" ");
+ if (!filename.equals("string") && !filename.equals("string[]"))
+ loadScript.append("/*file*/");
+ loadScript.append(Escape.escape(modelName = (String) htParams
+ .get("fullPathName")));
} else if (getToken(i + 1).tok == Token.leftbrace
|| theTok == Token.point3f || theTok == Token.integer
|| theTok == Token.identifier && tokAt(i + 3) != Token.coord) {
@@ -4384,7 +4382,6 @@
if (filename.equals("string[]"))
return;
int tok;
- String sOptions = "";
if ((tok = tokAt(i)) == Token.identifier
&& parameterAsString(i).equalsIgnoreCase("manifest")) {
String manifest = stringParameter(++i);
@@ -4405,10 +4402,10 @@
tok = tokAt(i);
sOptions += " " + Escape.escape(lattice);
}
- if (tok == Token.identifier
+ if (tok == Token.identifier
&& parameterAsString(i).equalsIgnoreCase("packed")) {
if (lattice == null)
- lattice = new Point3f(555,555,-1);
+ lattice = new Point3f(555, 555, -1);
htParams.put("packed", Boolean.TRUE);
sOptions += " PACKED";
}
@@ -4420,20 +4417,21 @@
int iGroup = -1;
float distance = 0;
/*
- * # Jmol 11.3.9 introduces the capability of visualizing the close contacts
- * around a crystalline protein (or any other cyrstal structure) that are to
- * atoms that are in proteins in adjacent unit cells or adjacent to the
- * protein itself. The option RANGE x, where x is a distance in angstroms,
- * placed right after the braces containing the set of unit cells to load
- * does this. The distance, if a positive number, is the maximum distance
- * away from the closest atom in the {1 1 1} set. If the distance x is a
- * negative number, then -x is the maximum distance from the {not symmetry} set.
- * The difference is that in the first case the primary unit cell (555) is
- * first filled as usual, using symmetry operators, and close contacts to
- * this set are found. In the second case, only the file-based atoms (
- * Jones-Faithful operator x,y,z) are initially included, then close
- * contacts to that set are found. Depending upon the application, one or the
- * other of these options may be desirable.
+ * # Jmol 11.3.9 introduces the capability of visualizing the close
+ * contacts around a crystalline protein (or any other cyrstal
+ * structure) that are to atoms that are in proteins in adjacent unit
+ * cells or adjacent to the protein itself. The option RANGE x, where x
+ * is a distance in angstroms, placed right after the braces containing
+ * the set of unit cells to load does this. The distance, if a positive
+ * number, is the maximum distance away from the closest atom in the {1
+ * 1 1} set. If the distance x is a negative number, then -x is the
+ * maximum distance from the {not symmetry} set. The difference is that
+ * in the first case the primary unit cell (555) is first filled as
+ * usual, using symmetry operators, and close contacts to this set are
+ * found. In the second case, only the file-based atoms ( Jones-Faithful
+ * operator x,y,z) are initially included, then close contacts to that
+ * set are found. Depending upon the application, one or the other of
+ * these options may be desirable.
*/
if (tokAt(i) == Token.range) {
i++;
@@ -4443,13 +4441,13 @@
htParams.put("symmetryRange", new Float(distance));
if (tokAt(i) == Token.spacegroup) {
++i;
- String spacegroup = TextFormat.simpleReplace(parameterAsString(i++),
+ String spacegroup = TextFormat.simpleReplace(parameterAsString(i++),
"''", "\"");
sOptions += " spacegroup " + Escape.escape(spacegroup);
if (spacegroup.equalsIgnoreCase("ignoreOperators")) {
iGroup = -999;
} else {
- if (spacegroup.indexOf(",") >= 0) //Jones Faithful
+ if (spacegroup.indexOf(",") >= 0) // Jones Faithful
if ((lattice.x < 9 && lattice.y < 9 && lattice.z == 0))
spacegroup += "#doNormalize=0";
iGroup = viewer.getSymmetry().determineSpaceGroupIndex(spacegroup);
@@ -4477,16 +4475,6 @@
htParams.put("filter", filter);
sOptions += " FILTER " + Escape.escape(filter);
}
-
- if (!isSyntaxCheck || isScriptCheck && fileOpenCheck) {
- viewer.openFile(filename, htParams, null, isAppend);
- loadScript.append(" ");
- if (!filename.equals("string") && !filename.equals("string[]"))
- loadScript.append("/*file*/");
- loadScript.append(Escape.escape(modelName = (String) htParams
- .get("fullPathName")));
- loadScript.append(sOptions);
- }
} else {
if (i != 2) {
modelName = parameterAsString(i++);
@@ -4545,7 +4533,22 @@
if (!isSyntaxCheck || isScriptCheck && fileOpenCheck) {
viewer.openFiles(modelName, filenames, null, isAppend, htParams);
}
+ needToLoad = false;
}
+ if (needToLoad && (!isSyntaxCheck || isScriptCheck && fileOpenCheck)) {
+ if (filename.startsWith("@") && filename.length() > 1) {
+ htParams.put("fileData", getStringParameter(filename.substring(1),
+ false));
+ filename = "string";
+ }
+ viewer.openFile(filename, htParams, null, isAppend);
+ loadScript.append(" ");
+ if (!filename.equals("string") && !filename.equals("string[]"))
+ loadScript.append("/*file*/");
+ loadScript.append(Escape.escape(modelName = (String) htParams
+ .get("fullPathName")));
+ loadScript.append(sOptions);
+ }
if (isSyntaxCheck && !(isScriptCheck && fileOpenCheck)) {
viewer.deallocateReaderThreads();
return;
@@ -4587,7 +4590,8 @@
}
if (msg.length() > 0)
Logger.info(msg);
- if (defaultScript.length() > 0 && !isScriptCheck) //NOT checking embedded scripts here
+ if (defaultScript.length() > 0 && !isScriptCheck) // NOT checking embedded
+ // scripts here
runScript(defaultScript);
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2009-06-04 01:56:47 UTC (rev 10952)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2009-06-04 02:26:06 UTC (rev 10953)
@@ -3,6 +3,8 @@
version=11.7.40
+# new feature: load "@x" -- inline load of data contained in variable x.
+#
# new feature: {*}.label = xxx and {*}.label("%[label]") and select label="xxx"
#
# new feature: An XML reader for Materials Studio .xsd files http://accelrys.com/products/materials-studio/
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