Revision: 20887
http://sourceforge.net/p/jmol/code/20887
Author: hansonr
Date: 2015-12-13 16:26:55 +0000 (Sun, 13 Dec 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.4.0_2015.12.13"
bug fix: zoomTo not setting time to 0 in the case of scriptWait
bug fix: set selectAllModels should restrict action of display/hide as well
bug fix: set selectAllModels not working appropriately
bug fix: set selectAllModels should not be saved in state
bug fix: JmolData.jar does not update atom screen positions upon REFRESH or
select {visible}
bug fix: JmolData.jar -p flag does not work properly
bug fix: model 0 issued when more than one PDB file is open does not execute
model *
Modified Paths:
--------------
branches/v14_4/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java
branches/v14_4/Jmol/src/org/jmol/io/FileReader.java
branches/v14_4/Jmol/src/org/jmol/io/FilesReader.java
branches/v14_4/Jmol/src/org/jmol/script/ScriptEval.java
branches/v14_4/Jmol/src/org/jmol/viewer/FileManager.java
branches/v14_4/Jmol/src/org/jmol/viewer/JC.java
branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: branches/v14_4/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java
2015-12-13 16:03:49 UTC (rev 20886)
+++ branches/v14_4/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java
2015-12-13 16:26:55 UTC (rev 20887)
@@ -121,6 +121,7 @@
protected Map<String, String> htGroup1;
private int nAtoms0;
+ private int titleAtomSet = 1;
@Override
public void initializeReader() throws Exception {
@@ -182,6 +183,8 @@
isLigand = false;
if (iHaveDesiredModel)
return false;
+ if (desiredModelNumber != Integer.MIN_VALUE)
+ appendLoadNote(null);
newModel(++modelNumber);
haveCellWaveVector = false;
if (auditBlockCode == null)
@@ -266,8 +269,10 @@
processSymmetrySpaceGroupName();
} else if (key.startsWith("_space_group_transform")) {
processUnitCellTransform();
+ } else if (key.contains("_database_code")) {
+ addModelTitle("ID");
} else if (titleRecords.contains("_" + key + "__")) {
- appendLoadNote("TITLE: " + parser.fullTrim(data) + "\n");
+ addModelTitle("TITLE");
} else {
processSubclassEntry();
}
@@ -275,6 +280,12 @@
return true;
}
+ private void addModelTitle(String key) {
+ if (asc.atomSetCount > titleAtomSet)
+ appendLoadNote("\nMODEL: " + (titleAtomSet = asc.atomSetCount));
+ appendLoadNote(key + ": " + parser.fullTrim(data));
+ }
+
protected void processSubclassEntry() throws Exception {
if (modDim > 0)
getModulationReader().processEntry();
@@ -698,6 +709,8 @@
|| (isLigand = key.equals("_chem_comp_atom_comp_id"))) {
if (!processAtomSiteLoopBlock(isLigand))
return;
+ if (thisDataSetName.equals("global"))
+ asc.setCollectionName(thisDataSetName = chemicalName);
asc.setAtomSetName(thisDataSetName);
asc.setCurrentModelInfo("chemicalName", chemicalName);
asc.setCurrentModelInfo("structuralFormula", thisStructuralFormula);
Modified: branches/v14_4/Jmol/src/org/jmol/io/FileReader.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/io/FileReader.java 2015-12-13 16:03:49 UTC
(rev 20886)
+++ branches/v14_4/Jmol/src/org/jmol/io/FileReader.java 2015-12-13 16:26:55 UTC
(rev 20887)
@@ -79,7 +79,7 @@
vwr.zap(false, true, false);
String errorMessage = null;
Object t = null;
- if (fullPathNameIn.contains("_CHANGEABLE_"))
+ if (fullPathNameIn.contains("#_DOCACHE_"))
reader = getChangeableReader(vwr, nameAsGivenIn, fullPathNameIn);
if (reader == null) {
t = fm.getUnzippedReaderOrStreamFromName(fullPathNameIn,
Modified: branches/v14_4/Jmol/src/org/jmol/io/FilesReader.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/io/FilesReader.java 2015-12-13
16:03:49 UTC (rev 20886)
+++ branches/v14_4/Jmol/src/org/jmol/io/FilesReader.java 2015-12-13
16:26:55 UTC (rev 20887)
@@ -95,7 +95,7 @@
subFileList = PT.split(name, "|");
name = subFileList[0];
}
- if (name.contains("_CHANGEABLE_"))
+ if (name.contains("#_DOCACHE_"))
return FileReader.getChangeableReader(vwr, namesAsGivenIn[i], name);
Object t = fm.getUnzippedReaderOrStreamFromName(name, null,
true, forceBinary, false, true, htParams);
Modified: branches/v14_4/Jmol/src/org/jmol/script/ScriptEval.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/script/ScriptEval.java 2015-12-13
16:03:49 UTC (rev 20886)
+++ branches/v14_4/Jmol/src/org/jmol/script/ScriptEval.java 2015-12-13
16:26:55 UTC (rev 20887)
@@ -8049,7 +8049,7 @@
xTrans = 0;
if (Float.isNaN(yTrans))
yTrans = 0;
- if (isSameAtom && Math.abs(zoom - newZoom) < 1)
+ if (isSameAtom && Math.abs(zoom - newZoom) < 1 || !useThreads())
floatSecondsTotal = 0;
vwr.moveTo(this, floatSecondsTotal, center, JC.center, Float.NaN, null,
newZoom, xTrans, yTrans, Float.NaN, null, Float.NaN, Float.NaN,
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/FileManager.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/FileManager.java 2015-12-13
16:03:49 UTC (rev 20886)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/FileManager.java 2015-12-13
16:26:55 UTC (rev 20887)
@@ -595,7 +595,7 @@
}
if (bytes == null && (bytes = getCachedPngjBytes(name)) != null &&
htParams != null)
htParams.put("sourcePNGJ", Boolean.TRUE);
- name = name.replace("_CHANGEABLE_", "");
+ name = name.replace("#_DOCACHE_", "");
String fullName = name;
String[] subFileList = null;
if (name.indexOf("|") >= 0) {
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/JC.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/JC.java 2015-12-13 16:03:49 UTC
(rev 20886)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/JC.java 2015-12-13 16:26:55 UTC
(rev 20887)
@@ -61,15 +61,17 @@
"nmr", "http://www.nmrdb.org/new_predictor?POST?molfile=";,
"nmrdb", "http://www.nmrdb.org/service/predictor?POST?molfile=";,
"pdb", "http://www.rcsb.org/pdb/files/%FILE.pdb.gz";,
+ // in Jmol 14.5, we changed "pdb", but here we want the cif
+ "pdb0", "http://www.rcsb.org/pdb/files/%FILE.pdb.gz";,
"pdbe", "http://www.ebi.ac.uk/pdbe/entry-files/download/%FILE.cif";,
"pdbe2", "http://www.ebi.ac.uk/pdbe/static/entry/%FILE_updated.cif";,
"pubchem",
"http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/%FILE/SDF?record_type=3d";,
"map",
"http://www.ebi.ac.uk/pdbe/api/%TYPE/%FILE?pretty=false&metadata=true";,
"rna3d", "http://rna.bgsu.edu/rna3dhub/%TYPE/download/%FILE";,
"aflow",
"http://aflowlib.mems.duke.edu/users/jmolers/binary_new/%FILE.aflow_binary";,
- // _CHANGEABLE_ flag indicates that the loaded file should be saved in any
state in full
- "ams",
"http://rruff.geo.arizona.edu/AMS/viewJmol.php?_CHANGEABLE_&mineral=%file&action=showcif";,
- "am",
"'http://rruff.geo.arizona.edu/AMS/CIF_text_files/'+load('http://rruff.geo.arizona.edu/AMS/minerals/%FILE').split(\"viewJmol('\")[(%n
== 0 ? 0 : %n + 1)].split(\"'\")[1]+'_cif.txt'"
+ // _#CHANGEABLE_ flag indicates that the loaded file should be saved in
any state in full
+ // ' at start indicates a Jmol script evaluation
+ "ams", "'http://rruff.geo.arizona.edu/AMS/viewJmol.php?'+(0+'%file'==0?
'mineral':('%file'.length==7? 'amcsd':'id'))+'=%file&action=showcif#_DOCACHE_'"
};
public static String[] macros = {
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2015-12-13
16:03:49 UTC (rev 20886)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2015-12-13
16:26:55 UTC (rev 20887)
@@ -7,8 +7,9 @@
# see also http://chemapps.stolaf.edu/jmol/zip for daily updates
-Jmol.___JmolVersion="14.4.0_2015.12.10"
+Jmol.___JmolVersion="14.4.0_2015.12.13"
+bug fix: zoomTo not setting time to 0 in the case of scriptWait
bug fix: set selectAllModels should restrict action of display/hide as well
bug fix: set selectAllModels not working appropriately
bug fix: set selectAllModels should not be saved in state
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