Revision: 20960
http://sourceforge.net/p/jmol/code/20960
Author: hansonr
Date: 2016-02-15 01:27:16 +0000 (Mon, 15 Feb 2016)
Log Message:
-----------
Jmol.___JmolVersion="14.4.2_2016.02.14"
FEATURE CHANGE: JSmol default for Info._disableInitialConsole changed to true
-- no longer necessary with JSmol_spinner.gif
new feature: j2s/img/JSmol_spinner.gif implemented (Angel Herraez)
-- as default for Info._appletLoadingImage
-- use Info._appletLoadingImage = "none" to disable
new feature: j2s/img/cursor_wait.gif animation implemented
bug fix: EBI assembly CIF files that are multi-model files will be by chain,
not by model.
-- result was that each chain became a new model
-- for example: see
http://www.ebi.ac.uk/pdbe/static/entry/download/2lev-assembly-1.cif.gz
bug fix: XmlMolProReader does not recognize FILTER "NOMO"
bug fix: JSmol has never shown cursors
Modified Paths:
--------------
branches/v14_4/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java
branches/v14_4/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
branches/v14_4/Jmol/src/org/jmol/adapter/smarter/AtomIterator.java
branches/v14_4/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
branches/v14_4/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
branches/v14_4/Jmol/src/org/jmol/adapter/smarter/Structure.java
branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
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/adapter/smarter/AtomIterator.java
trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
trunk/Jmol/src/org/jmol/adapter/smarter/Structure.java
trunk/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
2016-02-14 19:27:32 UTC (rev 20959)
+++ branches/v14_4/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java
2016-02-15 01:27:16 UTC (rev 20960)
@@ -91,7 +91,7 @@
private int configurationPtr = Integer.MIN_VALUE;
private boolean useAuthorChainID = true;
- private String thisDataSetName = "", lastDataSetName;
+ protected String thisDataSetName = "", lastDataSetName;
private String chemicalName = "";
private String thisStructuralFormula = "";
private String thisFormula = "";
@@ -1043,7 +1043,7 @@
continue;
}
}
- String assemblyId = null;
+ String componentId = null;
String strChain = null;
String id = null;
int seqID = 0;
@@ -1137,7 +1137,7 @@
atom.group3 = field;
break;
case ASYM_ID:
- assemblyId = field;
+ componentId = field;
if (!useAuthorChainID)
setChainID(atom, strChain = field);
break;
@@ -1264,10 +1264,10 @@
}
if (atom.elementSymbol == null && atom.atomName != null)
atom.getElementSymbol();
- if (!filterCIFAtom(atom, assemblyId))
+ if (!filterCIFAtom(atom, componentId))
continue;
setAtomCoord(atom);
- if (isMMCIF && !processSubclassAtom(atom, assemblyId, strChain))
+ if (isMMCIF && !processSubclassAtom(atom, componentId, strChain))
continue;
if (asc.iSet < 0)
nextAtomSet();
@@ -1316,10 +1316,10 @@
return true;
}
- protected boolean filterCIFAtom(Atom atom, String assemblyId) {
+ protected boolean filterCIFAtom(Atom atom, String componentId) {
if (!filterAtom(atom, -1))
return false;
- if (filterAssembly && filterReject(filter, "$", assemblyId))
+ if (filterAssembly && filterReject(filter, "$", componentId))
return false;
if (configurationPtr > 0) {
if (!disorderAssembly.equals(lastDisorderAssembly)) {
Modified: branches/v14_4/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
2016-02-14 19:27:32 UTC (rev 20959)
+++ branches/v14_4/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
2016-02-15 01:27:16 UTC (rev 20960)
@@ -164,6 +164,50 @@
}
+ private boolean requiresSorting;
+
+ /**
+ * issue here is that mmCIF assembly atoms can be in different blocks by
chain:
+ * Model1:Chain1 Model2:Chain1 Model1:Chain2 Model2:Chain2 ... and so
assigned
+ * to too many atom sets.
+ *
+ */
+ protected void sortAssemblyModels() {
+ int natoms = asc.ac;
+ int lastSet = -1;
+ Atom[] atoms = asc.atoms;
+ Atom[] newAtoms = new Atom[natoms];
+ String[] ids = PT.split("," + modelStrings + ",", ",,");
+ BS bsAtomsNew = (asc.bsAtoms == null ? null : BS.newN(asc.bsAtoms.size()));
+ for (int im = 1, n = 0; im < ids.length; im++) {
+ String sModel = ids[im];
+ int modelIndex = -1;
+ for (int is = 0; is < asc.atomSetCount; is++) {
+ int ia0 = asc.getAtomSetAtomIndex(is);
+ int ia1 = ia0 + asc.getAtomSetAtomCount(is);
+ String am = "" + modelMap.get("_" + is);
+ if (am.equals(sModel)) {
+ if (modelIndex < 0 && (modelIndex = is) > lastSet)
+ lastSet = is;
+ for (int i = ia0; i < ia1; i++) {
+ if (bsAtomsNew == null || asc.bsAtoms.get(i)) {
+ if (bsAtomsNew != null)
+ bsAtomsNew.set(n);
+ atoms[i].atomSetIndex = modelIndex;
+ newAtoms[n++] = atoms[i];
+ }
+ }
+ }
+ }
+
+ }
+ asc.atoms = newAtoms;
+ asc.bsAtoms = bsAtomsNew;
+ if (++lastSet < asc.atomSetCount)
+ asc.atomSetCount = lastSet;
+ }
+
+
@Override
protected boolean finalizeSubclass() throws Exception {
if (byChain && !isBiomolecule)
@@ -172,7 +216,7 @@
if (!isCourseGrained && asc.ac == nAtoms) {
asc.removeCurrentAtomSet();
} else {
- if ((dssr != null || validation != null || addedData != null) &&
!isCourseGrained) {
+ if ((dssr != null || validation != null || addedData != null) &&
!isCourseGrained && !requiresSorting) {
MMCifValidationParser vs = ((MMCifValidationParser)
getInterface("org.jmol.adapter.readers.cif.MMCifValidationParser"))
.set(this);
String note = null;
@@ -204,6 +248,8 @@
asc.xtalSymmetry = null;
}
}
+ if (requiresSorting)
+ sortAssemblyModels();
return true;
}
@@ -1110,16 +1156,31 @@
return true;
}
+ private String modelStrings = "";
+
@Override
protected int checkPDBModelField(int modelField, int currentModelNo) throws
Exception {
// the model field value is only used if
// it is indicated AFTER the file name in the load command,
// not if we have a MODEL keyword before the file name.
- //
+
fieldProperty(modelField);
int modelNo = parseIntStr(field);
if (modelNo != currentModelNo) {
- if (iHaveDesiredModel && asc.atomSetCount > 0) {
+ boolean isAssembly = (thisDataSetName != null &&
thisDataSetName.indexOf("-assembly-") >= 0);
+ if (isAssembly) {
+ // Files such as
http://www.ebi.ac.uk/pdbe/static/entry/download/2lev-assembly-1.cif.gz
+ // may require sorting if there are multiple models, since the models
are by chain, not by model.
+
+ useFileModelNumbers = true;
+ String key = "," + modelNo + ",";
+ if (modelStrings.indexOf(key) >= 0) {
+ requiresSorting = true;
+ } else {
+ modelStrings += key;
+ }
+ }
+ if (iHaveDesiredModel && asc.atomSetCount > 0 && !isAssembly) {
parser.skipLoop(false);
// but only this atom loop
skipping = false;
Modified: branches/v14_4/Jmol/src/org/jmol/adapter/smarter/AtomIterator.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/adapter/smarter/AtomIterator.java
2016-02-14 19:27:32 UTC (rev 20959)
+++ branches/v14_4/Jmol/src/org/jmol/adapter/smarter/AtomIterator.java
2016-02-15 01:27:16 UTC (rev 20960)
@@ -46,7 +46,7 @@
AtomIterator(AtomSetCollection asc) {
ac = asc.ac;
- atoms = asc.atoms;
+ atoms = asc.atoms;
bsAtoms = asc.bsAtoms;
iatom = 0;
}
Modified:
branches/v14_4/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
2016-02-14 19:27:32 UTC (rev 20959)
+++ branches/v14_4/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
2016-02-15 01:27:16 UTC (rev 20960)
@@ -92,6 +92,7 @@
public int atomSetCount;
public int iSet = -1;
+
public int[] atomSetNumbers = new int[16];
public int[] atomSetAtomIndexes = new int[16];
public int[] atomSetAtomCounts = new int[16];
Modified:
branches/v14_4/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
===================================================================
---
branches/v14_4/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
2016-02-14 19:27:32 UTC (rev 20959)
+++
branches/v14_4/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
2016-02-15 01:27:16 UTC (rev 20960)
@@ -195,6 +195,7 @@
protected boolean forcePacked;
public float packingError = 0.02f;
+
// private state variables
private SB loadNote = new SB();
Modified: branches/v14_4/Jmol/src/org/jmol/adapter/smarter/Structure.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/adapter/smarter/Structure.java
2016-02-14 19:27:32 UTC (rev 20959)
+++ branches/v14_4/Jmol/src/org/jmol/adapter/smarter/Structure.java
2016-02-15 01:27:16 UTC (rev 20960)
@@ -66,7 +66,7 @@
this.substructureType = substructureType;
if (structureID == null)
return;
- setModels(modelIndex, 0);
+ modelStartEnd[0] = modelStartEnd[1] = modelIndex;
this.structureID = structureID;
this.strandCount = strandCount; // 1 for sheet initially; 0 for helix or
turn
this.serialID = serialID;
@@ -86,9 +86,4 @@
atomStartEnd[1] = iend;
}
- public void setModels(int model1, int model2) {
- modelStartEnd[0] = model1;
- modelStartEnd[1] = (model2 == 0 ? model1 : model2);
- }
-
}
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2016-02-14
19:27:32 UTC (rev 20959)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2016-02-15
01:27:16 UTC (rev 20960)
@@ -7,15 +7,21 @@
# see also http://chemapps.stolaf.edu/jmol/zip for daily updates
-Jmol.___JmolVersion="14.5.2_2016.02.14"
+Jmol.___JmolVersion="14.4.2_2016.02.14"
FEATURE CHANGE: JSmol default for Info._disableInitialConsole changed to true
- -- no longer necessary with JSmol_spinner.gif
+ -- no longer necessary with JSmol_spinner.gif
-new feature: j2s/img/JSmol_spinner.gif implemented as default for
Info._appletLoadingImage
+new feature: j2s/img/JSmol_spinner.gif implemented (Angel Herraez)
+ -- as default for Info._appletLoadingImage
+ -- use Info._appletLoadingImage = "none" to disable
new feature: j2s/img/cursor_wait.gif animation implemented
+bug fix: EBI assembly CIF files that are multi-model files will be by chain,
not by model.
+ -- result was that each chain became a new model
+ -- for example: see
http://www.ebi.ac.uk/pdbe/static/entry/download/2lev-assembly-1.cif.gz
+
bug fix: XmlMolProReader does not recognize FILTER "NOMO"
bug fix: JSmol has never shown cursors
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java 2016-02-14
19:27:32 UTC (rev 20959)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java 2016-02-15
01:27:16 UTC (rev 20960)
@@ -91,7 +91,7 @@
private int configurationPtr = Integer.MIN_VALUE;
private boolean useAuthorChainID = true;
- private String thisDataSetName = "", lastDataSetName;
+ protected String thisDataSetName = "", lastDataSetName;
private String chemicalName = "";
private String thisStructuralFormula = "";
private String thisFormula = "";
@@ -1043,7 +1043,7 @@
continue;
}
}
- String assemblyId = null;
+ String componentId = null;
String strChain = null;
String id = null;
int seqID = 0;
@@ -1137,7 +1137,7 @@
atom.group3 = field;
break;
case ASYM_ID:
- assemblyId = field;
+ componentId = field;
if (!useAuthorChainID)
setChainID(atom, strChain = field);
break;
@@ -1264,10 +1264,10 @@
}
if (atom.elementSymbol == null && atom.atomName != null)
atom.getElementSymbol();
- if (!filterCIFAtom(atom, assemblyId))
+ if (!filterCIFAtom(atom, componentId))
continue;
setAtomCoord(atom);
- if (isMMCIF && !processSubclassAtom(atom, assemblyId, strChain))
+ if (isMMCIF && !processSubclassAtom(atom, componentId, strChain))
continue;
if (asc.iSet < 0)
nextAtomSet();
@@ -1316,10 +1316,10 @@
return true;
}
- protected boolean filterCIFAtom(Atom atom, String assemblyId) {
+ protected boolean filterCIFAtom(Atom atom, String componentId) {
if (!filterAtom(atom, -1))
return false;
- if (filterAssembly && filterReject(filter, "$", assemblyId))
+ if (filterAssembly && filterReject(filter, "$", componentId))
return false;
if (configurationPtr > 0) {
if (!disorderAssembly.equals(lastDisorderAssembly)) {
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
2016-02-14 19:27:32 UTC (rev 20959)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
2016-02-15 01:27:16 UTC (rev 20960)
@@ -164,6 +164,50 @@
}
+ private boolean requiresSorting;
+
+ /**
+ * issue here is that mmCIF assembly atoms can be in different blocks by
chain:
+ * Model1:Chain1 Model2:Chain1 Model1:Chain2 Model2:Chain2 ... and so
assigned
+ * to too many atom sets.
+ *
+ */
+ protected void sortAssemblyModels() {
+ int natoms = asc.ac;
+ int lastSet = -1;
+ Atom[] atoms = asc.atoms;
+ Atom[] newAtoms = new Atom[natoms];
+ String[] ids = PT.split("," + modelStrings + ",", ",,");
+ BS bsAtomsNew = (asc.bsAtoms == null ? null : BS.newN(asc.bsAtoms.size()));
+ for (int im = 1, n = 0; im < ids.length; im++) {
+ String sModel = ids[im];
+ int modelIndex = -1;
+ for (int is = 0; is < asc.atomSetCount; is++) {
+ int ia0 = asc.getAtomSetAtomIndex(is);
+ int ia1 = ia0 + asc.getAtomSetAtomCount(is);
+ String am = "" + modelMap.get("_" + is);
+ if (am.equals(sModel)) {
+ if (modelIndex < 0 && (modelIndex = is) > lastSet)
+ lastSet = is;
+ for (int i = ia0; i < ia1; i++) {
+ if (bsAtomsNew == null || asc.bsAtoms.get(i)) {
+ if (bsAtomsNew != null)
+ bsAtomsNew.set(n);
+ atoms[i].atomSetIndex = modelIndex;
+ newAtoms[n++] = atoms[i];
+ }
+ }
+ }
+ }
+
+ }
+ asc.atoms = newAtoms;
+ asc.bsAtoms = bsAtomsNew;
+ if (++lastSet < asc.atomSetCount)
+ asc.atomSetCount = lastSet;
+ }
+
+
@Override
protected boolean finalizeSubclass() throws Exception {
if (byChain && !isBiomolecule)
@@ -172,7 +216,7 @@
if (!isCourseGrained && asc.ac == nAtoms) {
asc.removeCurrentAtomSet();
} else {
- if ((dssr != null || validation != null || addedData != null) &&
!isCourseGrained) {
+ if ((dssr != null || validation != null || addedData != null) &&
!isCourseGrained && !requiresSorting) {
MMCifValidationParser vs = ((MMCifValidationParser)
getInterface("org.jmol.adapter.readers.cif.MMCifValidationParser"))
.set(this);
String note = null;
@@ -204,6 +248,8 @@
asc.xtalSymmetry = null;
}
}
+ if (requiresSorting)
+ sortAssemblyModels();
return true;
}
@@ -1110,16 +1156,31 @@
return true;
}
+ private String modelStrings = "";
+
@Override
protected int checkPDBModelField(int modelField, int currentModelNo) throws
Exception {
// the model field value is only used if
// it is indicated AFTER the file name in the load command,
// not if we have a MODEL keyword before the file name.
- //
+
fieldProperty(modelField);
int modelNo = parseIntStr(field);
if (modelNo != currentModelNo) {
- if (iHaveDesiredModel && asc.atomSetCount > 0) {
+ boolean isAssembly = (thisDataSetName != null &&
thisDataSetName.indexOf("-assembly-") >= 0);
+ if (isAssembly) {
+ // Files such as
http://www.ebi.ac.uk/pdbe/static/entry/download/2lev-assembly-1.cif.gz
+ // may require sorting if there are multiple models, since the models
are by chain, not by model.
+
+ useFileModelNumbers = true;
+ String key = "," + modelNo + ",";
+ if (modelStrings.indexOf(key) >= 0) {
+ requiresSorting = true;
+ } else {
+ modelStrings += key;
+ }
+ }
+ if (iHaveDesiredModel && asc.atomSetCount > 0 && !isAssembly) {
parser.skipLoop(false);
// but only this atom loop
skipping = false;
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomIterator.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/AtomIterator.java 2016-02-14
19:27:32 UTC (rev 20959)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomIterator.java 2016-02-15
01:27:16 UTC (rev 20960)
@@ -46,7 +46,7 @@
AtomIterator(AtomSetCollection asc) {
ac = asc.ac;
- atoms = asc.atoms;
+ atoms = asc.atoms;
bsAtoms = asc.bsAtoms;
iatom = 0;
}
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
2016-02-14 19:27:32 UTC (rev 20959)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
2016-02-15 01:27:16 UTC (rev 20960)
@@ -92,6 +92,7 @@
public int atomSetCount;
public int iSet = -1;
+
public int[] atomSetNumbers = new int[16];
public int[] atomSetAtomIndexes = new int[16];
public int[] atomSetAtomCounts = new int[16];
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
2016-02-14 19:27:32 UTC (rev 20959)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
2016-02-15 01:27:16 UTC (rev 20960)
@@ -195,6 +195,7 @@
protected boolean forcePacked;
public float packingError = 0.02f;
+
// private state variables
private SB loadNote = new SB();
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Structure.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/Structure.java 2016-02-14
19:27:32 UTC (rev 20959)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/Structure.java 2016-02-15
01:27:16 UTC (rev 20960)
@@ -66,7 +66,7 @@
this.substructureType = substructureType;
if (structureID == null)
return;
- setModels(modelIndex, 0);
+ modelStartEnd[0] = modelStartEnd[1] = modelIndex;
this.structureID = structureID;
this.strandCount = strandCount; // 1 for sheet initially; 0 for helix or
turn
this.serialID = serialID;
@@ -86,9 +86,4 @@
atomStartEnd[1] = iend;
}
- public void setModels(int model1, int model2) {
- modelStartEnd[0] = model1;
- modelStartEnd[1] = (model2 == 0 ? model1 : model2);
- }
-
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2016-02-14 19:27:32 UTC
(rev 20959)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2016-02-15 01:27:16 UTC
(rev 20960)
@@ -67,12 +67,18 @@
Jmol.___JmolVersion="14.5.2_2016.02.14"
FEATURE CHANGE: JSmol default for Info._disableInitialConsole changed to true
- -- no longer necessary with JSmol_spinner.gif
+ -- no longer necessary with JSmol_spinner.gif
-new feature: j2s/img/JSmol_spinner.gif implemented as default for
Info._appletLoadingImage
+new feature: j2s/img/JSmol_spinner.gif implemented (Angel Herraez)
+ -- as default for Info._appletLoadingImage
+ -- use Info._appletLoadingImage = "none" to disable
new feature: j2s/img/cursor_wait.gif animation implemented
+bug fix: EBI assembly CIF files that are multi-model files will be by chain,
not by model.
+ -- result was that each chain became a new model
+ -- for example: see
http://www.ebi.ac.uk/pdbe/static/entry/download/2lev-assembly-1.cif.gz
+
bug fix: XmlMolProReader does not recognize FILTER "NOMO"
bug fix: JSmol has never shown cursors
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