Revision: 20346
http://sourceforge.net/p/jmol/code/20346
Author: hansonr
Date: 2015-02-28 19:58:56 +0000 (Sat, 28 Feb 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.3.12_2015.02.28"
bug fix: late discovery of mmCIF format does not load secondary structure
bug fix: reading PNGJ file saved after load with /dssr or /rna3d annotations
ignores annotations
bug fix: {*}.find("~d~G:C") broken (find with bioSMARTS)
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java
trunk/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java 2015-02-28
19:29:35 UTC (rev 20345)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java 2015-02-28
19:58:56 UTC (rev 20346)
@@ -353,9 +353,7 @@
@Override
protected void finalizeSubclassReader() throws Exception {
- if (isMMCIF)
- finalizeSubclass();
- else
+ if (!isMMCIF || !finalizeSubclass())
applySymmetryAndSetTrajectory();
int n = asc.atomSetCount;
if (n > 1)
@@ -374,8 +372,9 @@
addJmolScript("calculate aromatic");
}
- protected void finalizeSubclass() throws Exception {
+ protected boolean finalizeSubclass() throws Exception {
// MMCifReader only
+ return false;
}
@Override
@@ -1021,7 +1020,6 @@
int modelField = fieldOf[MODEL_NO];
int siteMult = 0;
while (parser.getData()) {
- if (isMMCIF) {
if (modelField >= 0) {
fieldProperty(modelField);
int modelNo = parseIntStr(field);
@@ -1047,7 +1045,6 @@
if (skipping)
continue;
}
- }
Atom atom = null;
if (haveCoord) {
atom = new Atom();
@@ -1184,6 +1181,10 @@
}
break;
case GROUP_PDB:
+ if (!isMMCIF) {
+ setIsPDB();
+ isMMCIF = true;
+ }
if ("HETATM".equals(field))
atom.isHetero = true;
break;
@@ -1315,9 +1316,8 @@
return true;
}
-// private Lst<Map<String, String>> vCompnds;
-// private Map<String, Map<String, String>> htModels;
-
+ protected Map<String, String> htHetero;
+
/**
* @param atom
* @param assemblyId
@@ -1325,7 +1325,12 @@
* @return true if valid atom
*/
protected boolean processSubclassAtom(Atom atom, String assemblyId, String
strChain) {
- return false; // MMCifReader only
+ if (atom.isHetero && htHetero != null) {
+ asc.setCurrentModelInfo("hetNames", htHetero);
+ asc.setInfo("hetNames", htHetero);
+ htHetero = null;
+ }
+ return true;
}
protected boolean filterCIFAtom(Atom atom, String assemblyId) {
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
2015-02-28 19:29:35 UTC (rev 20345)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
2015-02-28 19:58:56 UTC (rev 20346)
@@ -94,7 +94,7 @@
}
@Override
- protected void finalizeSubclass() throws Exception {
+ protected boolean finalizeSubclass() throws Exception {
if (byChain && !isBiomolecule)
for (String id : chainAtomMap.keySet())
createParticle(id);
@@ -133,7 +133,7 @@
asc.xtalSymmetry = null;
}
}
-
+ return true;
}
////////////////////////////////////////////////////////////////
@@ -511,8 +511,6 @@
return true;
}
- private Map<String, String> htHetero;
-
private void addHetero(String groupName, String hetName) {
if (!vwr.getJBR().isHetero(groupName))
return;
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-02-28 19:29:35 UTC
(rev 20345)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-02-28 19:58:56 UTC
(rev 20346)
@@ -16,6 +16,7 @@
Jmol.___JmolVersion="14.3.12_2015.02.28"
+bug fix: late discovery of mmCIF format does not load secondary structure
bug fix: reading PNGJ file saved after load with /dssr or /rna3d annotations
ignores annotations
bug fix: {*}.find("~d~G:C") broken (find with bioSMARTS)
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