Revision: 18637
http://sourceforge.net/p/jmol/code/18637
Author: hansonr
Date: 2013-09-02 05:40:40 +0000 (Mon, 02 Sep 2013)
Log Message:
-----------
___JmolVersion="13.3.5_dev_2013.09.01"
new feature: strutureModifiedCallback
bug fix: ID @id vector fails
new feature: show NMR taps into NMRDB directly
-- for now, application only
Modified Paths:
--------------
trunk/Jmol/examples/basic/org/jmol/Export.java
trunk/Jmol/jars/JSpecView.jar
trunk/Jmol/src/org/jmol/adapter/readers/quantum/MoldenReader.java
trunk/Jmol/src/org/jmol/api/JmolAdapter.java
trunk/Jmol/src/org/jmol/script/ScriptCompiler.java
trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
trunk/Jmol/src/org/jmol/util/Escape.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/examples/basic/org/jmol/Export.java
===================================================================
--- trunk/Jmol/examples/basic/org/jmol/Export.java 2013-09-02 00:07:26 UTC
(rev 18636)
+++ trunk/Jmol/examples/basic/org/jmol/Export.java 2013-09-02 05:40:40 UTC
(rev 18637)
@@ -86,6 +86,7 @@
case MINIMIZATION:
case RESIZE:
case SYNC:
+ case STRUCTUREMODIFIED:
case SCRIPT:
case CLICK:
case EVAL:
Modified: trunk/Jmol/jars/JSpecView.jar
===================================================================
(Binary files differ)
Modified: trunk/Jmol/src/org/jmol/adapter/readers/quantum/MoldenReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/quantum/MoldenReader.java
2013-09-02 00:07:26 UTC (rev 18636)
+++ trunk/Jmol/src/org/jmol/adapter/readers/quantum/MoldenReader.java
2013-09-02 05:40:40 UTC (rev 18637)
@@ -213,7 +213,9 @@
slater[1] = type;
slater[2] = gaussianPtr;
slater[3] = nPrimitives;
- nCoef += getDfCoefMaps()[type].length;
+ int n = getDfCoefMaps()[type].length;
+ System.out.println("adding " + n + " coefficients type " +
JmolAdapter.getQuantumShellTag(type) + " for atom " + atomIndex);
+ nCoef += n;
for (int ip = nPrimitives; --ip >= 0;) {
// Read ip primitives, each containing an exponent and one (s,p,d,f)
// or two (sp) contraction coefficient(s)
@@ -355,7 +357,7 @@
}
private boolean checkOrbitalType(String line) {
- if (line.length() > 3 && "5D 6D 7F 10 9G 15".indexOf(line.substring(1,3))
>= 0) {
+ if (line.length() > 3 && "5D 6D 7F 10 9G 15 11
21".indexOf(line.substring(1,3)) >= 0) {
if (orbitalType.indexOf(line) >= 0)
return true;
orbitalType += line;
@@ -371,13 +373,16 @@
fixSlaterTypes(JmolAdapter.SHELL_D_CARTESIAN,
JmolAdapter.SHELL_D_SPHERICAL);
fixSlaterTypes(JmolAdapter.SHELL_F_CARTESIAN,
JmolAdapter.SHELL_F_SPHERICAL);
fixSlaterTypes(JmolAdapter.SHELL_G_CARTESIAN,
JmolAdapter.SHELL_G_SPHERICAL);
+ fixSlaterTypes(JmolAdapter.SHELL_H_CARTESIAN,
JmolAdapter.SHELL_H_SPHERICAL);
}
if (orbitalType.contains("10F")) {
fixSlaterTypes(JmolAdapter.SHELL_F_SPHERICAL,
JmolAdapter.SHELL_F_CARTESIAN);
fixSlaterTypes(JmolAdapter.SHELL_G_SPHERICAL,
JmolAdapter.SHELL_G_CARTESIAN);
+ fixSlaterTypes(JmolAdapter.SHELL_H_SPHERICAL,
JmolAdapter.SHELL_H_CARTESIAN);
}
if (orbitalType.contains("15G")) {
fixSlaterTypes(JmolAdapter.SHELL_G_SPHERICAL,
JmolAdapter.SHELL_G_CARTESIAN);
+ fixSlaterTypes(JmolAdapter.SHELL_H_SPHERICAL,
JmolAdapter.SHELL_H_CARTESIAN);
}
}
@@ -456,7 +461,7 @@
boolean haveModel = false;
if (desiredModelNumber == 0 || desiredModelNumber == nGeom)
desiredModelNumber = nGeom;
- else
+ else if (atomSetCollection.getAtomSetCount() > 0)
finalizeMOData(null);
for (int i = 0; i < nGeom; i++) {
readLines(2);
Modified: trunk/Jmol/src/org/jmol/api/JmolAdapter.java
===================================================================
--- trunk/Jmol/src/org/jmol/api/JmolAdapter.java 2013-09-02 00:07:26 UTC
(rev 18636)
+++ trunk/Jmol/src/org/jmol/api/JmolAdapter.java 2013-09-02 05:40:40 UTC
(rev 18637)
@@ -85,6 +85,8 @@
public final static int SHELL_F_CARTESIAN =
EnumQuantumShell.F_CARTESIAN.id;
public final static int SHELL_G_SPHERICAL =
EnumQuantumShell.G_SPHERICAL.id;
public final static int SHELL_G_CARTESIAN =
EnumQuantumShell.G_CARTESIAN.id;
+ public final static int SHELL_H_SPHERICAL =
EnumQuantumShell.H_SPHERICAL.id;
+ public final static int SHELL_H_CARTESIAN =
EnumQuantumShell.H_CARTESIAN.id;
public static final String SUPPORTED_BASIS_FUNCTIONS =
EnumQuantumShell.SUPPORTED_BASIS_FUNCTIONS;
public static final String NOTE_SCRIPT_FILE = JC.NOTE_SCRIPT_FILE;
@@ -104,6 +106,10 @@
return JC.isHetero(group3);
}
+ public static String getQuantumShellTag(int id) {
+ return EnumQuantumShell.getQuantumShellTag(id);
+ }
+
public static int getQuantumShellTagID(String tag) {
return EnumQuantumShell.getQuantumShellTagID(tag);
}
Modified: trunk/Jmol/src/org/jmol/script/ScriptCompiler.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptCompiler.java 2013-09-02 00:07:26 UTC
(rev 18636)
+++ trunk/Jmol/src/org/jmol/script/ScriptCompiler.java 2013-09-02 05:40:40 UTC
(rev 18637)
@@ -1209,6 +1209,10 @@
&& flowContext.var != null && theTok != T.casecmd
&& theTok != T.defaultcmd && lastToken.tok != T.switchcmd)
return ERROR(ERROR_badContext, ident);
+ if (lastToken.tok == T.define && theTok != T.leftbrace && nTokens != 1) {
+ addTokenToPrefix(T.o(T.string, ident));
+ return CONTINUE;
+ }
switch (theTok) {
case T.identifier:
if (nTokens == 0 && !checkImpliedScriptCmd) {
@@ -2331,12 +2335,6 @@
}
break;
}
- if (Character.isWhitespace(ch)) {
- if (ptSpace < 0)
- ptSpace = ichT;
- } else {
- ptLastChar = ichT;
- }
++ichT;
}
// message/echo/label @x
Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2013-09-02 00:07:26 UTC
(rev 18636)
+++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2013-09-02 05:40:40 UTC
(rev 18637)
@@ -8878,8 +8878,19 @@
switch (tok) {
case T.file:
+ i++;
+ loadScript.append(" " + modelName);
+ if (tokAt(i) == T.varray) {
+ filenames = stringParameterSet(i);
+ i = iToken;
+ if (i + 1 != slen)
+ invArg();
+ if (filenames != null)
+ nFiles = filenames.length;
+ }
+ break;
case T.inline:
- isInline = (tok == T.inline);
+ isInline = true;
i++;
loadScript.append(" " + modelName);
break;
@@ -8918,7 +8929,7 @@
default:
modelName = "fileset";
}
- if (getToken(i).tok != T.string)
+ if (filenames == null && getToken(i).tok != T.string)
error(ERROR_filenameExpected);
}
// long timeBegin = System.currentTimeMillis();
@@ -8947,31 +8958,33 @@
// end-of-command options:
// LOAD SMILES "xxxx" --> load "$xxxx"
- // LOAD "['xxxxx','yyyyy','zzzzz']"
- if (i == 0 || (filename = parameterAsString(filePt)).length() == 0)
+ if (i == 0 || filenames == null
+ && (filename = parameterAsString(filePt)).length() == 0)
filename = viewer.getFullPathName();
- if (filename == null) {
+ if (filename == null && filenames == null) {
zap(false);
return;
}
- if (isSmiles) {
- filename = "$" + filename;
- } else if (!isInline) {
- if (filename.indexOf("[]") >= 0)
- return;
- if (filename.indexOf("[") == 0) {
- filenames = Escape.unescapeStringArray(filename);
- if (filenames != null) {
- if (i == 1)
- loadScript.append(" files");
- if (loadScript.indexOf(" files") < 0)
- invArg();
- for (int j = 0; j < filenames.length; j++)
- loadScript.append(" /*file*/").append(Escape.eS(filenames[j]));
+ if (filenames == null)
+ if (isSmiles) {
+ filename = "$" + filename;
+ } else if (!isInline) {
+ if (filename.indexOf("[]") >= 0)
+ return;
+ if (filename.indexOf("[") == 0) {
+ filenames = Escape.unescapeStringArray(filename);
+ if (filenames != null) {
+ if (i == 1)
+ loadScript.append(" files");
+ nFiles = filenames.length;
+ }
}
}
- }
+ if (filenames != null)
+ for (int j = 0; j < filenames.length; j++)
+ loadScript.append(" /*file*/").append(Escape.eS(filenames[j]));
+
} else if (getToken(i + 1).tok == T.manifest
// model/vibration index or list of model indices
|| theTok == T.integer || theTok == T.varray || theTok == T.leftsquare
@@ -9316,7 +9329,6 @@
filenames = new String[nFiles];
for (int j = 0; j < nFiles; j++)
filenames[j] = fNames.get(j);
- filename = "fileSet";
}
// end of parsing
@@ -9324,6 +9336,9 @@
if (!doLoadFiles)
return;
+ if (filenames != null)
+ filename = "fileSet";
+
// get default filter if necessary
if (appendedData != null) {
@@ -9338,9 +9353,9 @@
// If this is a state script, it may have been created using
// the DOCACHE flag, but we never want that here, because then
// this is a file being loaded from the state script itself.
-// if (isStateScript)
-// filter = TextFormat
-// .simpleReplace(filter.toUpperCase(), "DOCACHE", "");
+ // if (isStateScript)
+ // filter = TextFormat
+ // .simpleReplace(filter.toUpperCase(), "DOCACHE", "");
if (!isStateScript && !isAppend)
viewer.cacheClear();
}
Modified: trunk/Jmol/src/org/jmol/util/Escape.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Escape.java 2013-09-02 00:07:26 UTC (rev
18636)
+++ trunk/Jmol/src/org/jmol/util/Escape.java 2013-09-02 05:40:40 UTC (rev
18637)
@@ -1025,6 +1025,9 @@
}
public static String[] unescapeStringArray(String data) {
+ // was only used for very strange LOAD "[\"...\",\"....\",...]"
+ // now also used for simulation peaks array from JSpecView,
+ // which double-escapes strings, I guess
//TODO -- should recognize '..' as well as "..." ?
if (data == null || !data.startsWith("[") || !data.endsWith("]"))
return null;
@@ -1035,7 +1038,7 @@
String s = Parser.getQuotedStringNext(data, next);
if (s == null)
return null;
- v.addLast(TextFormat.simpleReplace(s, "\\\"", "\""));
+ v.addLast(s);
while (next[0] < data.length() && data.charAt(next[0]) != '"')
next[0]++;
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-09-02 00:07:26 UTC
(rev 18636)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-09-02 05:40:40 UTC
(rev 18637)
@@ -11,8 +11,12 @@
# The quotes above look odd for a parameter file, but they are
# important for the JavaScript version of Jmol.
-___JmolVersion="13.3.5_dev_2013.08.29"
+___JmolVersion="13.3.5_dev_2013.09.01"
+new feature: strutureModifiedCallback
+
+bug fix: ID @id vector fails
+
new feature: show NMR taps into NMRDB directly
-- for now, application only
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