Revision: 20378
http://sourceforge.net/p/jmol/code/20378
Author: hansonr
Date: 2015-03-11 23:56:53 +0000 (Wed, 11 Mar 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.2.13_2015.03.11"
bug fix; pdb and mmcif readers not doing biomolecule 2 properly
bug fix: load filter "bychain" broken
Modified Paths:
--------------
branches/v14_2/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
branches/v14_2/Jmol/src/org/jmol/adapter/readers/pdb/PdbReader.java
branches/v14_2/Jmol/src/org/jmol/adapter/smarter/XtalSymmetry.java
branches/v14_2/Jmol/src/org/jmol/modelset/ModelSet.java
branches/v14_2/Jmol/src/org/jmol/modelsetbio/Resolver.java
branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: branches/v14_2/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
2015-03-11 23:56:34 UTC (rev 20377)
+++ branches/v14_2/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
2015-03-11 23:56:53 UTC (rev 20378)
@@ -83,6 +83,8 @@
if (checkFilterKey("BIOMOLECULE")) // PDB format
filter = PT.rep(filter, "BIOMOLECULE", "ASSEMBLY");
isBiomolecule = checkFilterKey("ASSEMBLY");
+ if (isBiomolecule)
+ filter = filter.replace(':', ' '); // no chain selection for biomolecules
// When this reader was split off from CifReader, a bug was introduced
// into the Resolver that made it so that ligand files were read by
@@ -102,13 +104,14 @@
asc.removeCurrentAtomSet();
} else {
if ((validation != null || addedData != null) && !isCourseGrained) {
- MMCifValidationParser vs = ((MMCifValidationParser)
getInterface("org.jmol.adapter.readers.cif.MMCifValidationParser")).set(this);
- String note = null;
+ MMCifValidationParser vs = ((MMCifValidationParser)
getInterface("org.jmol.adapter.readers.cif.MMCifValidationParser"))
+ .set(this);
+ String note = null;
if (addedData == null) {
note = vs.finalizeValidations(modelMap);
} else if (addedDataKey.equals("_rna3d")) {
- note = vs.finalizeRna3d(modelMap);
- } else {
+ note = vs.finalizeRna3d(modelMap);
+ } else {
reader = Rdr.getBR(addedData);
processDSSR(this, htGroup1);
}
@@ -118,18 +121,18 @@
if (!isCourseGrained)
applySymmetryAndSetTrajectory();
}
-
+
if (htSites != null)
addSites(htSites);
- if (vBiomolecules != null && vBiomolecules.size() == 1
+ if (vBiomolecules != null && vBiomolecules.size() > 0
&& (isCourseGrained || asc.ac > 0)) {
asc.setCurrentModelInfo("biomolecules", vBiomolecules);
Map<String, Object> ht = vBiomolecules.get(0);
appendLoadNote("Constructing " + ht.get("name"));
setBiomolecules(ht);
if (thisBiomolecule != null) {
- asc.getXSymmetry().applySymmetryBio(thisBiomolecule,
- unitCellParams, applySymmetryToBonds, filter);
+ asc.getXSymmetry().applySymmetryBio(ht, unitCellParams,
+ applySymmetryToBonds, filter);
asc.xtalSymmetry = null;
}
}
@@ -322,7 +325,8 @@
info.put("assemblies", "$" + list.replace(',', '$'));
info.put("operators", decodeAssemblyOperators(assem[ASSEM_OPERS]));
info.put("biomts", new Lst<M4>());
- thisBiomolecule = info;
+ if (thisBiomolecule == null)
+ thisBiomolecule = info;
Logger.info("assembly " + id + " operators " + assem[ASSEM_OPERS]
+ " ASYM_IDs " + assem[ASSEM_LIST]);
vBiomolecules.addLast(info);
@@ -797,24 +801,37 @@
private void setBiomolecules(Map<String, Object> biomolecule) {
if (!isBiomolecule || assemblyIdAtoms == null && chainAtomCounts == null)
return;
+ Lst<M4> biomts = new Lst<M4>();
+ Lst<String> biomtchains = new Lst<String>();
+ biomolecule.put("biomts", biomts);
+ biomolecule.put("chains", biomtchains);
+ int nBio = vBiomolecules.size();
+ BS bsAll = new BS();
+ int nAtoms = setBiomolecule(biomolecule, biomts, biomtchains, bsAll);
+ for (int i = 1; i < nBio; i++)
+ nAtoms += setBiomolecule(vBiomolecules.get(i), biomts, biomtchains,
bsAll);
+ if (bsAll.cardinality() < asc.ac) {
+ if (asc.bsAtoms == null)
+ asc.bsAtoms = bsAll;
+ else
+ asc.bsAtoms.and(bsAll);
+ }
+ biomolecule.put("atomCount", Integer.valueOf(nAtoms));
+ }
+
+ private int setBiomolecule(Map<String, Object> biomolecule, Lst<M4> biomts,
+ Lst<String> biomtchains, BS bsAll) {
M4 mident = M4.newM4(null);
String[] ops = PT.split((String) biomolecule.get("operators"), ",");
String assemblies = (String) biomolecule.get("assemblies");
- Lst<M4> biomts = new Lst<M4>();
- biomolecule.put("biomts", biomts);
- biomts.addLast(mident);
- for (int j = 0; j < ops.length; j++) {
- M4 m = getOpMatrix(ops[j]);
- if (m != null && !m.equals(mident))
- biomts.addLast(m);
- }
- BS bsAll = new BS();
P3 sum = new P3();
int count = 0;
int nAtoms = 0;
String[] ids = PT.split(assemblies, "$");
+ String chainlist = "";
for (int j = 1; j < ids.length; j++) {
String id = ids[j];
+ chainlist += ":" + id + ";";
if (assemblyIdAtoms != null) {
BS bs = assemblyIdAtoms.get(id);
if (bs != null) {
@@ -835,6 +852,18 @@
}
}
}
+ for (int j = 0; j < ops.length; j++) {
+ M4 m = getOpMatrix(ops[j]);
+ if (m == null)
+ return 0;
+ if (m.equals(mident)) {
+ biomts.add(0, mident);
+ biomtchains.add(0, chainlist);
+ } else {
+ biomts.addLast(m);
+ biomtchains.addLast(chainlist);
+ }
+ }
if (isCourseGrained) {
if (bySymop) {
nAtoms = 1;
@@ -846,10 +875,9 @@
}
} else {
nAtoms = bsAll.cardinality();
- if (nAtoms < asc.ac)
- asc.bsAtoms = bsAll;
}
- biomolecule.put("atomCount", Integer.valueOf(nAtoms * ops.length));
+ return nAtoms * ops.length;
+
}
private void createParticle(String id) {
Modified: branches/v14_2/Jmol/src/org/jmol/adapter/readers/pdb/PdbReader.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/adapter/readers/pdb/PdbReader.java
2015-03-11 23:56:34 UTC (rev 20377)
+++ branches/v14_2/Jmol/src/org/jmol/adapter/readers/pdb/PdbReader.java
2015-03-11 23:56:53 UTC (rev 20378)
@@ -196,6 +196,8 @@
if (checkFilterKey("ASSEMBLY")) // CIF syntax
filter = PT.rep(filter, "ASSEMBLY", "BIOMOLECULE");
isbiomol = checkFilterKey("BIOMOLECULE");
+ if (isbiomol)
+ filter = filter.replace(':', ' '); // no chain choices if biomolecule
boolean byChain = isbiomol && checkFilterKey("BYCHAIN");
boolean bySymop = isbiomol && checkFilterKey("BYSYMOP");
isCourseGrained = byChain || bySymop;
@@ -600,53 +602,58 @@
private void setBiomoleculeAtomCounts() {
for (int i = vBiomolecules.size(); --i >= 0;) {
Map<String, Object> biomolecule = vBiomolecules.get(i);
- String chains = (String) biomolecule.get("chains");
- int nTransforms = ((Lst<M4>) biomolecule.get("biomts")).size();
+ Lst<M4> biomts = (Lst<M4>) biomolecule.get("biomts");
+ Lst<String> biomtchains = (Lst<String>) biomolecule.get("chains");
+ int nTransforms = biomts.size();
int nAtoms = 0;
- for (int j = chains.length() - 1; --j >= 0;)
- if (chains.charAt(j) == ':')
- nAtoms += biomtChainAtomCounts[0 + chains.charAt(j + 1)];
- biomolecule.put("atomCount", Integer.valueOf(nAtoms * nTransforms));
+ for (int k = nTransforms; --k >= 0;) {
+ String chains = biomtchains.get(k);
+ for (int j = chains.length() - 1; --j >= 0;)
+ if (chains.charAt(j) == ':')
+ nAtoms += biomtChainAtomCounts[0 + chains.charAt(j + 1)];
+ }
+ biomolecule.put("atomCount", Integer.valueOf(nAtoms));
}
}
-/*
- REMARK 350 BIOMOLECULE: 1
- REMARK 350 APPLY THE FOLLOWING TO CHAINS: 1, 2, 3, 4, 5, 6,
- REMARK 350 A, B, C
- REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
- REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
- REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
- REMARK 350 BIOMT1 2 0.309017 -0.809017 0.500000 0.00000
- REMARK 350 BIOMT2 2 0.809017 0.500000 0.309017 0.00000
- REMARK 350 BIOMT3 2 -0.500000 0.309017 0.809017 0.00000
-
-
- or, as fount in
http://www.ebi.ac.uk/msd-srv/pqs/pqs-doc/macmol/1k28.mmol
-
-REMARK 350 AN OLIGOMER OF TYPE :HEXAMERIC : CAN BE ASSEMBLED BY
-REMARK 350 APPLYING THE FOLLOWING TO CHAINS:
-REMARK 350 A, D
-REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
-REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
-REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
-REMARK 350 IN ADDITION APPLY THE FOLLOWING TO CHAINS:
-REMARK 350 A, D
-REMARK 350 BIOMT1 2 0.000000 -1.000000 0.000000 0.00000
-REMARK 350 BIOMT2 2 1.000000 -1.000000 0.000000 0.00000
-REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000
-REMARK 350 IN ADDITION APPLY THE FOLLOWING TO CHAINS:
-REMARK 350 A, D
-REMARK 350 BIOMT1 3 -1.000000 1.000000 0.000000 0.00000
-REMARK 350 BIOMT2 3 -1.000000 0.000000 0.000000 0.00000
-REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000
+ /*
+ REMARK 350 BIOMOLECULE: 1
+ REMARK 350 APPLY THE FOLLOWING TO CHAINS: 1, 2, 3, 4, 5, 6,
+ REMARK 350 A, B, C
+ REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
+ REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
+ REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
+ REMARK 350 BIOMT1 2 0.309017 -0.809017 0.500000 0.00000
+ REMARK 350 BIOMT2 2 0.809017 0.500000 0.309017 0.00000
+ REMARK 350 BIOMT3 2 -0.500000 0.309017 0.809017 0.00000
+
+
+ or, as fount in
http://www.ebi.ac.uk/msd-srv/pqs/pqs-doc/macmol/1k28.mmol
+
+ REMARK 350 AN OLIGOMER OF TYPE :HEXAMERIC : CAN BE ASSEMBLED BY
+ REMARK 350 APPLYING THE FOLLOWING TO CHAINS:
+ REMARK 350 A, D
+ REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
+ REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
+ REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
+ REMARK 350 IN ADDITION APPLY THE FOLLOWING TO CHAINS:
+ REMARK 350 A, D
+ REMARK 350 BIOMT1 2 0.000000 -1.000000 0.000000 0.00000
+ REMARK 350 BIOMT2 2 1.000000 -1.000000 0.000000 0.00000
+ REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000
+ REMARK 350 IN ADDITION APPLY THE FOLLOWING TO CHAINS:
+ REMARK 350 A, D
+ REMARK 350 BIOMT1 3 -1.000000 1.000000 0.000000 0.00000
+ REMARK 350 BIOMT2 3 -1.000000 0.000000 0.000000 0.00000
+ REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000
-*/
-
-
+ */
+
+ @SuppressWarnings("unchecked")
private void remark350() throws Exception {
- Lst<M4> biomts = null;
- vBiomolecules = new Lst<Map<String,Object>>();
+ Lst<M4> biomts = null;
+ Lst<String> biomtchains = null;
+ vBiomolecules = new Lst<Map<String, Object>>();
biomtChainAtomCounts = new int[255];
String title = "";
String chainlist = "";
@@ -668,15 +675,14 @@
Logger.info("biomolecule " + id + ": number of transforms: "
+ nBiomt);
info = new Hashtable<String, Object>();
- biomts = new Lst<M4>();
id = line.substring(line.indexOf(":") + 1).trim();
-
title = line.trim();
info.put("name", "biomolecule " + id);
- info.put("molecule", id.length() == 3 ? id :
Integer.valueOf(parseIntStr(id)));
+ info.put("molecule",
+ id.length() == 3 ? id : Integer.valueOf(parseIntStr(id)));
info.put("title", title);
- info.put("chains", "");
- info.put("biomts", biomts);
+ info.put("chains", biomtchains = new Lst<String>());
+ info.put("biomts", biomts = new Lst<M4>());
vBiomolecules.addLast(info);
nBiomt = 0;
//continue; need to allow for next IF, in case this is a
reconstruction
@@ -693,14 +699,16 @@
appendLoadNote("found biomolecule " + id + ": " + list);
chainlist = ":" + list.replace(' ', ':');
needLine = false;
- while (readHeader(true) != null && line.indexOf("BIOMT") < 0 &&
line.indexOf("350") == 7)
+ while (readHeader(true) != null && line.indexOf("BIOMT") < 0
+ && line.indexOf("350") == 7)
chainlist += ":" + line.substring(11).trim().replace(' ', ':');
- if (checkFilterKey("BIOMOLECULE " + id + ";") ||
checkFilterKey("BIOMOLECULE=" + id + ";")) {
- setFilter(filter.replace(':', '_') + chainlist);
+ chainlist += ";";
+ if (checkFilterKey("BIOMOLECULE " + id + ";")
+ || checkFilterKey("BIOMOLECULE=" + id + ";")) {
+ setFilter(filter + chainlist);
Logger.info("filter set to \"" + filter + "\"");
thisBiomolecule = info;
}
- info.put("chains", chainlist);
continue;
}
/*
@@ -723,10 +731,13 @@
mat[15] = 1;
M4 m4 = new M4();
m4.setA(mat);
- if (m4.equals(mIdent))
+ if (m4.equals(mIdent)) {
biomts.add(0, m4);
- else
+ biomtchains.add(0, chainlist);
+ } else {
biomts.addLast(m4);
+ biomtchains.addLast(chainlist);
+ }
continue;
}
} catch (Exception e) {
@@ -737,8 +748,7 @@
}
}
if (nBiomt > 0)
- Logger.info("biomolecule " + id + ": number of transforms: "
- + nBiomt);
+ Logger.info("biomolecule " + id + ": number of transforms: " + nBiomt);
}
/*
Modified: branches/v14_2/Jmol/src/org/jmol/adapter/smarter/XtalSymmetry.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/adapter/smarter/XtalSymmetry.java
2015-03-11 23:56:34 UTC (rev 20377)
+++ branches/v14_2/Jmol/src/org/jmol/adapter/smarter/XtalSymmetry.java
2015-03-11 23:56:53 UTC (rev 20378)
@@ -983,8 +983,11 @@
doNormalize = false;
Lst<M4> biomts = (Lst<M4>) thisBiomolecule.get("biomts");
+ Lst<String> biomtchains = (Lst<String>) thisBiomolecule.get("chains");
if (biomts.size() < 2)
return;
+ if (biomtchains.get(0).equals(biomtchains.get(1)))
+ biomtchains = null;
symmetry = null;
// it's not clear to me why you would do this:
if (!Float.isNaN(unitCellParams[0])) // PDB can do this;
@@ -1057,7 +1060,7 @@
}
for (int iAtom = firstSymmetryAtom; iAtom < atomMax; iAtom++)
atoms[iAtom].bsSymmetry = BSUtil.newAndSetBit(0);
- for (int i = 1; i < len; i++) {
+ for (int i = (biomtchains == null ? 1 : 0); i < len; i++) {
if (filter.indexOf("!#") >= 0) {
if (filter.indexOf("!#" + (i + 1) + ";") >= 0)
continue;
@@ -1066,10 +1069,15 @@
continue;
}
M4 mat = biomts.get(i);
- //Vector3f trans = new Vector3f();
+ String chains = (biomtchains == null ? null : biomtchains.get(i));
+
for (int iAtom = firstSymmetryAtom; iAtom < atomMax; iAtom++) {
if (asc.bsAtoms != null && !asc.bsAtoms.get(iAtom))
continue;
+ if (chains != null
+ && chains.indexOf(":" + acr.vwr.getChainIDStr(atoms[iAtom].chainID)
+ + ";") < 0)
+ continue;
try {
int atomSite = atoms[iAtom].atomSite;
Atom atom1;
@@ -1098,6 +1106,13 @@
if (i > 0)
symmetry.addBioMoleculeOperation(mat, false);
}
+ if (biomtchains != null) {
+ if (asc.bsAtoms == null)
+ asc.bsAtoms = BSUtil.newBitSet2(0, asc.ac);
+ for (int iAtom = firstSymmetryAtom; iAtom < atomMax; iAtom++)
+ asc.bsAtoms.clear(iAtom);
+ }
+
noSymmetryCount = atomMax - firstSymmetryAtom;
asc.setCurrentModelInfo("presymmetryAtomIndex",
Integer.valueOf(firstSymmetryAtom));
Modified: branches/v14_2/Jmol/src/org/jmol/modelset/ModelSet.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/modelset/ModelSet.java 2015-03-11
23:56:34 UTC (rev 20377)
+++ branches/v14_2/Jmol/src/org/jmol/modelset/ModelSet.java 2015-03-11
23:56:53 UTC (rev 20378)
@@ -3873,7 +3873,7 @@
protected void calculatePolymers(Group[] groups, int groupCount,
int baseGroupIndex, BS modelsExcluded) {
- if (haveBioModels)
+ if (bioModelset != null) // not using haveBioModels because not frozen yet
bioModelset.calculateAllPolymers(groups, groupCount, baseGroupIndex,
modelsExcluded);
}
Modified: branches/v14_2/Jmol/src/org/jmol/modelsetbio/Resolver.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/modelsetbio/Resolver.java 2015-03-11
23:56:34 UTC (rev 20377)
+++ branches/v14_2/Jmol/src/org/jmol/modelsetbio/Resolver.java 2015-03-11
23:56:53 UTC (rev 20378)
@@ -1254,7 +1254,8 @@
}
static short getGroupIdFor(String group3) {
- group3 = group3.trim();
+ if (group3 != null)
+ group3 = group3.trim();
short groupID = knownGroupID(group3);
return (groupID == -1 ? addGroup3Name(group3) : groupID);
}
Modified: branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties 2015-03-11
23:56:34 UTC (rev 20377)
+++ branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties 2015-03-11
23:56:53 UTC (rev 20378)
@@ -4,8 +4,13 @@
# THIS IS THE RELEASE BRANCH
# BUG FIXES ONLY, PLEASE
-Jmol.___JmolVersion="14.2.13_2015.03.09"
+Jmol.___JmolVersion="14.2.13_2015.03.11"
+bug fix; pdb and mmcif readers not doing biomolecule 2 properly
+bug fix: load filter "bychain" broken
+
+JmolVersion="14.2.13_2015.03.09"
+
bug fix: show state/xxxx does not work
JmolVersion="14.2.13_2015.03.07"
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