Revision: 5127
Author: hansonr
Date: 2006-05-16 09:57:38 -0700 (Tue, 16 May 2006)
ViewCVS: http://svn.sourceforge.net/jmol/?rev=5127&view=rev
Log Message:
-----------
bob200603 altloc total flexibility with conformation
-introduces "designer" conformations
load alt/1vwh.cif;color altloc;restrict none;select *;cartoon on
conformation 1 #from altloc = A
conformation 2 #from altloc = B
select 59-64 and (*%,*%A) or 65-70 and (*%,*%B);conformation
# a conformation derived from a mixed set of altlocs.
-multiple file load now working for PDB files
# note that when multiple files are loaded, 1000 is added to each model number
so as to designate which model in which file
load "1vwh" "alt/1vwh.cif" "alt/1vwh.cif";color altloc;restrict none;select
*;cartoon on
model 1001;conformation 1
model 2001;conformation 2
model 0 #display both conformations together
-PDB model numbers in multiple file add 1000 for each file.
so 1001 is file 1, model 1
1002 is file 1, model 2
2003 is file 2, model 3
etc.
see http://www.stolaf.edu/people/hansonr/jmol/test/proto/altloc.htm
Modified Paths:
--------------
branches/bob200603/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
branches/bob200603/Jmol/src/org/jmol/adapter/smarter/CifReader.java
branches/bob200603/Jmol/src/org/jmol/adapter/smarter/PdbReader.java
branches/bob200603/Jmol/src/org/jmol/adapter/smarter/SmarterJmolAdapter.java
branches/bob200603/Jmol/src/org/jmol/adapter/smarter/Structure.java
branches/bob200603/Jmol/src/org/jmol/api/JmolAdapter.java
branches/bob200603/Jmol/src/org/jmol/viewer/Atom.java
branches/bob200603/Jmol/src/org/jmol/viewer/Eval.java
branches/bob200603/Jmol/src/org/jmol/viewer/Frame.java
branches/bob200603/Jmol/src/org/jmol/viewer/Mmset.java
branches/bob200603/Jmol/src/org/jmol/viewer/Model.java
branches/bob200603/Jmol/src/org/jmol/viewer/ModelManager.java
branches/bob200603/Jmol/src/org/jmol/viewer/Token.java
branches/bob200603/Jmol/src/org/jmol/viewer/Viewer.java
Modified:
branches/bob200603/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
2006-05-16 03:01:48 UTC (rev 5126)
+++ branches/bob200603/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
2006-05-16 16:57:38 UTC (rev 5127)
@@ -67,8 +67,6 @@
float[] pdbScaleMatrix;
float[] pdbScaleTranslate;
- String[] pdbStructureRecords;
-
AtomSetCollection(String fileTypeName) {
this.fileTypeName = fileTypeName;
// set the default PATH properties as defined in the SmarterJmolAdapter
@@ -85,17 +83,20 @@
*/
AtomSetCollection(AtomSetCollection[] array) {
this("Array");
+ setAtomSetCollectionAuxiliaryInfo("isMultiFile", Boolean.TRUE);
for (int i = 0; i < array.length; i++) {
- appendAtomSetCollection(array[i]);
+ appendAtomSetCollection(i, array[i]);
}
}
/**
* Appends an AtomSetCollection
*
+ * @param collectionIndex collection index for new model number
* @param collection AtomSetCollection to append
*/
- protected void appendAtomSetCollection(AtomSetCollection collection) {
+ protected void appendAtomSetCollection(int collectionIndex,
+ AtomSetCollection collection) {
// Initialisations
int existingAtomsCount = atomCount;
@@ -116,16 +117,29 @@
newCloneAtom(collection.atoms[clonedAtoms]);
clonedAtoms++;
}
+
+ // auxiliary info
+ atomSetAuxiliaryInfo[currentAtomSetIndex] =
collection.atomSetAuxiliaryInfo[atomSetNum];
+
+ //Structures: We must incorporate any global structures (modelIndex ==
-1) into this model
+ //explicitly. Whew! This is because some cif _data structures have
multiple PDB models (1skt)
+ for (int i = 0; i < collection.structureCount; i++)
+ if (collection.structures[i].modelIndex == atomSetNum
+ || collection.structures[i].modelIndex == -1)
+ addStructure(collection.structures[i]);
+
+ // names and numbers
+ atomSetNames[currentAtomSetIndex] = collection.atomSetNames[atomSetNum];
+ atomSetNumbers[currentAtomSetIndex] = ((collectionIndex + 1) * 1000)
+ + collection.atomSetNumbers[atomSetNum];
}
-
// Clone bonds
for (int bondNum = 0; bondNum < collection.bondCount; bondNum++) {
Bond bond = collection.bonds[bondNum];
- addNewBond(
- bond.atomIndex1 + existingAtomsCount,
- bond.atomIndex2 + existingAtomsCount,
- bond.order);
+ addNewBond(bond.atomIndex1 + existingAtomsCount, bond.atomIndex2
+ + existingAtomsCount, bond.order);
}
+
}
protected void finalize() {
@@ -137,7 +151,6 @@
atoms = null;
bonds = null;
notionalUnitcell = pdbScaleMatrix = pdbScaleTranslate = null;
- pdbStructureRecords = null;
symmetries = null;
}
@@ -304,6 +317,8 @@
if (structureCount == structures.length)
structures = (Structure[])AtomSetCollectionReader.setLength(structures,
structureCount + 32);
+ structure.modelIndex = currentAtomSetIndex;
+ System.out.println("AtomSetColl. addStructure " + structureCount+"
:"+structure.modelIndex+" "+structure.structureType+"
"+structure.startSequenceNumber);
structures[structureCount++] = structure;
}
Modified: branches/bob200603/Jmol/src/org/jmol/adapter/smarter/CifReader.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/adapter/smarter/CifReader.java
2006-05-16 03:01:48 UTC (rev 5126)
+++ branches/bob200603/Jmol/src/org/jmol/adapter/smarter/CifReader.java
2006-05-16 16:57:38 UTC (rev 5127)
@@ -41,7 +41,6 @@
int desiredModelNumber;
int modelNumber = 0;
-
boolean normalize = true;
boolean iHaveAppliedSymmetry = false;
BufferedReader reader;
@@ -156,6 +155,8 @@
thisDataSetName = (line.length() < 6 ? "" : line.substring(5).trim());
if (thisDataSetName.length() > 0) {
if (atomSetCollection.currentAtomSetIndex >= 0) {
+ // note that there can be problems with multi-data mmCIF sets each with
+ // multiple models; and we could be loading multiple files!
atomSetCollection.newAtomSet();
atomSetCollection.setCollectionName("<collection of "
+ (atomSetCollection.currentAtomSetIndex + 1) + " models>");
@@ -328,6 +329,7 @@
void processAtomSiteLoopBlock() throws Exception {
// logger.log("processAtomSiteLoopBlock()-------------------------");
int currentModelNO = -1;
+ boolean isPDB = false;
int[] fieldTypes = new int[100]; // should be enough
boolean[] atomPropertyReferenced = new boolean[ATOM_PROPERTY_MAX];
int fieldCount = parseLoopParameters(atomFields, atomFieldMap, fieldTypes,
@@ -447,6 +449,7 @@
altLocIds += alternateLocationID;
break;
case GROUP_PDB:
+ isPDB = true;
if ("HETATM".equals(field))
atom.isHetero = true;
break;
@@ -474,6 +477,8 @@
atomSetCollection.addAtomWithMappedName(atom);
}
}
+ if (isPDB)
+ atomSetCollection.setAtomSetAuxiliaryInfo("isPDB", new Boolean(isPDB));
}
void disableField(int fieldCount, int[] fieldTypes, int fieldIndex) {
Modified: branches/bob200603/Jmol/src/org/jmol/adapter/smarter/PdbReader.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/adapter/smarter/PdbReader.java
2006-05-16 03:01:48 UTC (rev 5126)
+++ branches/bob200603/Jmol/src/org/jmol/adapter/smarter/PdbReader.java
2006-05-16 16:57:38 UTC (rev 5127)
@@ -40,7 +40,6 @@
String spaceGroup;
float[] notionalUnitcell = new float[6];
String altLocIds = "";
-
final Hashtable htFormul = new Hashtable();
String currentGroup3;
@@ -49,8 +48,8 @@
AtomSetCollection readAtomSetCollection(BufferedReader reader) throws
Exception {
atomSetCollection = new AtomSetCollection("pdb");
+ atomSetCollection.setAtomSetCollectionAuxiliaryInfo("isPDB", Boolean.TRUE);
- atomSetCollection.pdbStructureRecords = new String[32];
initialize();
while ((line = reader.readLine()) != null) {
lineLength = line.length();
@@ -347,7 +346,8 @@
// this should probably call Structure.validateAndAllocate
// in order to check validity of parameters
- Structure structure = new Structure(structureType, startChainID,
+ // 0 here is just a placeholder; actual model number is set in
addStructure()
+ Structure structure = new Structure(0, structureType, startChainID,
startSequenceNumber,
startInsertionCode, endChainID,
endSequenceNumber, endInsertionCode);
Modified:
branches/bob200603/Jmol/src/org/jmol/adapter/smarter/SmarterJmolAdapter.java
===================================================================
---
branches/bob200603/Jmol/src/org/jmol/adapter/smarter/SmarterJmolAdapter.java
2006-05-16 03:01:48 UTC (rev 5126)
+++
branches/bob200603/Jmol/src/org/jmol/adapter/smarter/SmarterJmolAdapter.java
2006-05-16 16:57:38 UTC (rev 5127)
@@ -332,6 +332,9 @@
return true;
}
+ public int getModelIndex() {
+ return structure.modelIndex;
+ }
public String getStructureType() {
return structure.structureType;
}
Modified: branches/bob200603/Jmol/src/org/jmol/adapter/smarter/Structure.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/adapter/smarter/Structure.java
2006-05-16 03:01:48 UTC (rev 5126)
+++ branches/bob200603/Jmol/src/org/jmol/adapter/smarter/Structure.java
2006-05-16 16:57:38 UTC (rev 5127)
@@ -31,12 +31,14 @@
char endChainID;
int endSequenceNumber;
char endInsertionCode;
+ int modelIndex;
Structure() { }
- Structure(String structureType,
+ Structure(int modelIndex, String structureType,
char startChainID, int startSequenceNumber, char
startInsertionCode,
char endChainID, int endSequenceNumber, char endInsertionCode) {
+ this.modelIndex = modelIndex;
this.structureType = structureType;
this.startChainID = startChainID;
this.startSequenceNumber = startSequenceNumber;
Modified: branches/bob200603/Jmol/src/org/jmol/api/JmolAdapter.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/api/JmolAdapter.java 2006-05-16
03:01:48 UTC (rev 5126)
+++ branches/bob200603/Jmol/src/org/jmol/api/JmolAdapter.java 2006-05-16
16:57:38 UTC (rev 5127)
@@ -431,6 +431,7 @@
public abstract class StructureIterator {
public abstract boolean hasNext();
+ public abstract int getModelIndex();
public abstract String getStructureType();
public abstract char getStartChainID();
public abstract int getStartSequenceNumber();
Modified: branches/bob200603/Jmol/src/org/jmol/viewer/Atom.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/viewer/Atom.java 2006-05-16
03:01:48 UTC (rev 5126)
+++ branches/bob200603/Jmol/src/org/jmol/viewer/Atom.java 2006-05-16
16:57:38 UTC (rev 5127)
@@ -759,8 +759,9 @@
int getModelTagNumber() {
if (group == null)
return 0;
- if (group.chain.frame.isPDB) {
+ if (group.chain.model.isPDB) {
try {
+ System.out.println("Atom.getModelTagNumber");
return Integer.parseInt(group.chain.model.modelTag);
} finally {}
}
Modified: branches/bob200603/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/viewer/Eval.java 2006-05-16
03:01:48 UTC (rev 5126)
+++ branches/bob200603/Jmol/src/org/jmol/viewer/Eval.java 2006-05-16
16:57:38 UTC (rev 5127)
@@ -2277,8 +2277,13 @@
}
void conformation() throws ScriptException {
- checkLength2();
- BitSet bsConformations = viewer.setConformation(intParameter(1) - 1);
+ BitSet bsConformations;
+ if (statementLength == 1) {
+ bsConformations = viewer.setConformation();
+ } else {
+ checkLength2();
+ bsConformations = viewer.setConformation(intParameter(1) - 1);
+ }
boolean addHbonds = viewer.hbondsAreVisible();
viewer.setShapeSize(JmolConstants.SHAPE_HSTICKS, 0, bsConformations);
if (addHbonds)
Modified: branches/bob200603/Jmol/src/org/jmol/viewer/Frame.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/viewer/Frame.java 2006-05-16
03:01:48 UTC (rev 5126)
+++ branches/bob200603/Jmol/src/org/jmol/viewer/Frame.java 2006-05-16
16:57:38 UTC (rev 5127)
@@ -49,6 +49,7 @@
// if (modelSetTypeName == "xyz")
final String modelSetTypeName;
final boolean isPDB;
+ final boolean isMultiFile;
final Mmset mmset;
final Graphics3D g3d;
// the maximum BondingRadius seen in this set of atoms
@@ -185,13 +186,11 @@
// NOTE: these strings are interned and are lower case
// therefore, we can do == comparisions against string constants
// if (modelSetTypeName == "xyz") { }
- this.modelSetTypeName = fileTypeName.toLowerCase().intern();
- this.isPDB = (this.modelSetTypeName == "pdb")
- || (this.modelSetTypeName == "array");
+ modelSetTypeName = fileTypeName.toLowerCase().intern();
mmset = new Mmset(this);
- this.frameRenderer = viewer.getFrameRenderer();
- this.g3d = viewer.getGraphics3D();
+ frameRenderer = viewer.getFrameRenderer();
+ g3d = viewer.getGraphics3D();
loadShape(JmolConstants.SHAPE_BALLS);
loadShape(JmolConstants.SHAPE_STICKS);
@@ -210,6 +209,9 @@
* need to be transformed to fit in the crystal cell
****************************************************************/
+ isMultiFile = mmset.getModelSetAuxiliaryInfoBoolean("isMultiFile");
+ isPDB = mmset.getModelSetAuxiliaryInfoBoolean("isPDB");
+
//THESE TWO LINES ARE INCORRECT -- ASSUMES SINGLE-MODEL FILE --
//these are only used to generate a unit cell, not fractional coord.
//they should be incorporated into modelAuxiliaryInfo
@@ -239,8 +241,10 @@
Properties modelProperties = adapter.getAtomSetProperties(clientFile, i);
Hashtable modelAuxiliaryInfo = adapter.getAtomSetAuxiliaryInfo(
clientFile, i);
+ boolean isPDBModel = (isPDB || mmset.getModelAuxiliaryInfoBoolean(i,
+ "isPDB"));
setModelNameNumberProperties(i, modelName, modelNumber, modelProperties,
- modelAuxiliaryInfo);
+ modelAuxiliaryInfo, isPDBModel);
}
for (JmolAdapter.AtomIterator iterAtom = adapter
@@ -275,7 +279,7 @@
}
}
-
+
// define turns LAST. (pulled by the iterator first)
// so that if they overlap they get overwritten:
@@ -284,22 +288,24 @@
if (iterStructure != null)
while (iterStructure.hasNext()) {
if (!iterStructure.getStructureType().equals("turn"))
- defineStructure(iterStructure.getStructureType(), iterStructure
- .getStartChainID(), iterStructure.getStartSequenceNumber(),
- iterStructure.getStartInsertionCode(), iterStructure
- .getEndChainID(), iterStructure.getEndSequenceNumber(),
- iterStructure.getEndInsertionCode());
+ defineStructure(iterStructure.getModelIndex(), iterStructure
+ .getStructureType(), iterStructure.getStartChainID(),
+ iterStructure.getStartSequenceNumber(), iterStructure
+ .getStartInsertionCode(), iterStructure.getEndChainID(),
+ iterStructure.getEndSequenceNumber(), iterStructure
+ .getEndInsertionCode());
}
iterStructure = adapter.getStructureIterator(clientFile);
if (iterStructure != null)
while (iterStructure.hasNext()) {
if (iterStructure.getStructureType().equals("turn"))
- defineStructure(iterStructure.getStructureType(), iterStructure
- .getStartChainID(), iterStructure.getStartSequenceNumber(),
- iterStructure.getStartInsertionCode(), iterStructure
- .getEndChainID(), iterStructure.getEndSequenceNumber(),
- iterStructure.getEndInsertionCode());
+ defineStructure(iterStructure.getModelIndex(), iterStructure
+ .getStructureType(), iterStructure.getStartChainID(),
+ iterStructure.getStartSequenceNumber(), iterStructure
+ .getStartInsertionCode(), iterStructure.getEndChainID(),
+ iterStructure.getEndSequenceNumber(), iterStructure
+ .getEndInsertionCode());
}
doUnitcellStuff();
@@ -685,7 +691,7 @@
}
}
- void defineStructure(String structureType, char startChainID,
+ void defineStructure(int modelIndex, String structureType, char startChainID,
int startSequenceNumber, char startInsertionCode,
char endChainID, int endSequenceNumber,
char endInsertionCode) {
@@ -695,7 +701,7 @@
+ " startchainid" + startChainID + " statseq" + startSequenceNumber
+ " endchain" + endChainID + " endseq" + endSequenceNumber);
*/
- mmset.defineStructure(structureType, startChainID, startSequenceNumber,
+ mmset.defineStructure(modelIndex, structureType, startChainID,
startSequenceNumber,
startInsertionCode, endChainID, endSequenceNumber, endInsertionCode);
}
@@ -813,9 +819,10 @@
void setModelNameNumberProperties(int modelIndex, String modelName,
int modelNumber,
Properties modelProperties,
- Hashtable modelAuxiliaryInfo) {
+ Hashtable modelAuxiliaryInfo,
+ boolean isPDB) {
mmset.setModelNameNumberProperties(modelIndex, modelName, modelNumber,
- modelProperties, modelAuxiliaryInfo);
+ modelProperties, modelAuxiliaryInfo, isPDB);
}
////////////////////////////////////////////////////////////////
@@ -1362,9 +1369,11 @@
////////////////////////////////////////////////////////////////
void doAutobond() {
// perform bonding if necessary
-
+ // to do this right, we would do it PER MODEL in the PDB, but it's not
clear
+ // how to specify that. For now -- if multifile, then just rebond.
if (viewer.getAutoBond() && getModelSetProperty("noautobond") == null) {
- if ((bondCount == 0) || (isPDB && (bondCount < (atomCount / 2))))
+ if ((bondCount == 0) || isMultiFile
+ || (isPDB && (bondCount < (atomCount / 2))))
rebond(false);
}
}
Modified: branches/bob200603/Jmol/src/org/jmol/viewer/Mmset.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/viewer/Mmset.java 2006-05-16
03:01:48 UTC (rev 5126)
+++ branches/bob200603/Jmol/src/org/jmol/viewer/Mmset.java 2006-05-16
16:57:38 UTC (rev 5127)
@@ -50,7 +50,7 @@
this.frame = frame;
}
- void defineStructure(String structureType, char startChainID,
+ void defineStructure(int modelIndex, String structureType, char startChainID,
int startSequenceNumber, char startInsertionCode,
char endChainID, int endSequenceNumber,
char endInsertionCode) {
@@ -63,7 +63,7 @@
if (structureCount == structures.length)
structures = (Structure[]) Util
.setLength(structures, structureCount + 10);
- structures[structureCount++] = new Structure(structureType, startChainID,
+ structures[structureCount++] = new Structure(modelIndex, structureType,
startChainID,
Group.getSeqcode(startSequenceNumber, startInsertionCode), endChainID,
Group.getSeqcode(endSequenceNumber, endInsertionCode));
}
@@ -220,7 +220,8 @@
void setModelNameNumberProperties(int modelIndex, String modelName,
int modelNumber,
Properties modelProperties,
- Hashtable modelAuxiliaryInfo) {
+ Hashtable modelAuxiliaryInfo,
+ boolean isPDB) {
modelNames[modelIndex] = modelName;
modelNumbers[modelIndex] = modelNumber;
this.modelProperties[modelIndex] = modelProperties;
@@ -228,17 +229,24 @@
models[modelIndex] = new Model(this, modelIndex, modelName);
String altLocs = (String) getModelAuxiliaryInfo(modelIndex, "altLocs");
models[modelIndex].setNAltLocs(altLocs == null ? 0 : altLocs.length());
+ models[modelIndex].isPDB = isPDB;
}
int getAltLocCountInModel(int modelIndex) {
return models[modelIndex].nAltLocs;
}
private void propogateSecondaryStructure() {
+ // issue arises with multiple file loading and multi-_data mmCIF files
+ // that structural information may be model-specific
+
for (int i = structureCount; --i >= 0;) {
Structure structure = structures[i];
+ System.out.println("Mmset.propogate " +structure.modelIndex+"
"+structure.type +" "+ structure.startChainID +" "+ structure.startSeqcode + "
"+structure.endSeqcode);
for (int j = modelCount; --j >= 0;)
- models[j].addSecondaryStructure(structure.type, structure.startChainID,
- structure.startSeqcode, structure.endChainID,
structure.endSeqcode);
+ if (structure.modelIndex == j || structure.modelIndex == -1)
+ models[j].addSecondaryStructure(structure.type,
+ structure.startChainID, structure.startSeqcode,
+ structure.endChainID, structure.endSeqcode);
}
}
@@ -314,9 +322,11 @@
int startSeqcode;
char endChainID;
int endSeqcode;
+ int modelIndex;
- Structure(String typeName, char startChainID, int startSeqcode,
+ Structure(int modelIndex, String typeName, char startChainID, int
startSeqcode,
char endChainID, int endSeqcode) {
+ this.modelIndex = modelIndex;
this.typeName = typeName;
this.startChainID = startChainID;
this.startSeqcode = startSeqcode;
Modified: branches/bob200603/Jmol/src/org/jmol/viewer/Model.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/viewer/Model.java 2006-05-16
03:01:48 UTC (rev 5126)
+++ branches/bob200603/Jmol/src/org/jmol/viewer/Model.java 2006-05-16
16:57:38 UTC (rev 5127)
@@ -34,7 +34,7 @@
int firstMolecule;
int moleculeCount;
int nAltLocs;
-
+ boolean isPDB = false;
private int chainCount = 0;
private Chain[] chains = new Chain[8];
@@ -68,7 +68,7 @@
void addSecondaryStructure(byte type,
char startChainID, int startSeqcode,
char endChainID, int endSeqcode) {
- //System.out.println("MODEL addSecondary (from file) " + type);
+ System.out.println("MODEL addSecondary (from file) " + modelIndex+" "+type
+ startChainID + " "+startSeqcode + " " + endSeqcode);
for (int i = polymerCount; --i >= 0; ) {
Polymer polymer = polymers[i];
polymer.addSecondaryStructure(type, startChainID, startSeqcode,
Modified: branches/bob200603/Jmol/src/org/jmol/viewer/ModelManager.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/viewer/ModelManager.java
2006-05-16 03:01:48 UTC (rev 5126)
+++ branches/bob200603/Jmol/src/org/jmol/viewer/ModelManager.java
2006-05-16 16:57:38 UTC (rev 5127)
@@ -145,6 +145,10 @@
return frame == null ? false : frame.isPDB;
}
+ boolean isPDB(int modelIndex) {
+ return frame == null ? false : frame.mmset.getModel(modelIndex).isPDB;
+ }
+
int getModelCount() {
return (frame == null) ? 0 : frame.getModelCount();
}
@@ -922,12 +926,11 @@
}
Vector getAllAtomInfo(BitSet bs) {
- boolean isPDB = frame.isPDB;
Vector V = new Vector();
int atomCount = viewer.getAtomCount();
for (int i = 0; i < atomCount; i++)
- if (bs.get(i))
- V.add(getAtomInfo(i, isPDB));
+ if (bs.get(i))
+ V.add(getAtomInfoLong(i));
return V;
}
@@ -942,7 +945,7 @@
info.put("sym", getElementSymbol(i));
}
- Hashtable getAtomInfo(int i, boolean isPDB) {
+ Hashtable getAtomInfoLong(int i) {
Atom atom = frame.getAtomAt(i);
Hashtable info = new Hashtable();
getAtomIdentityInfo(i, info);
@@ -969,8 +972,7 @@
info.put("translucent", new Boolean(isTranslucent));
info.put("formalCharge", new Integer(atom.getFormalCharge()));
info.put("partialCharge", new Float(atom.getPartialCharge()));
-
- if (isPDB) {
+ if (isPDB(atom.modelIndex)) {
info.put("resname", atom.getGroup3());
info.put("resno", atom.getSeqcodeString());
char chainID = atom.getChainID();
@@ -1374,6 +1376,11 @@
frame.recalculateStructure(bsSelected);
}
+ BitSet setConformation(int modelIndex, BitSet bsConformation) {
+ frame.setConformation(modelIndex, bsConformation);
+ return bsConformation;
+ }
+
BitSet setConformation(int modelIndex, int conformationIndex) {
if (frame == null)
return null;
@@ -1384,12 +1391,14 @@
continue;
String altLocs = frame.getAltLocListInModel(i);
BitSet bsConformation = getModelAtomBitSet(i);
+ System.out.println("\nmodelmanager.setconf. a "+i+" "+bsConformation);
if (conformationIndex >= 0)
for (int c = frame.getAltLocCountInModel(i); --c >= 0;)
if (c != conformationIndex)
bsConformation.andNot(frame.getSpecAlternate(altLocs.substring(c,
c + 1)));
if (bsConformation.length() > 0) {
+ System.out.println("modelmanager.setconf. b "+i+" "+bsConformation);
frame.setConformation(i, bsConformation);
bsResult.or(bsConformation);
}
Modified: branches/bob200603/Jmol/src/org/jmol/viewer/Token.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/viewer/Token.java 2006-05-16
03:01:48 UTC (rev 5126)
+++ branches/bob200603/Jmol/src/org/jmol/viewer/Token.java 2006-05-16
16:57:38 UTC (rev 5127)
@@ -536,7 +536,7 @@
"centerat", new Token(centerAt, varArgCount, "centerat"),
"isosurface", new Token(isosurface,varArgCount,"isosurface"),
"getproperty", new Token(getproperty,varArgCount, "getproperty"),
- "conformation", new Token(conformation, 1, "conformation"),
+ "conformation", new Token(conformation,varArgCount, "conformation"),
// setparams
"ambient", new Token(ambient, "ambient"),
Modified: branches/bob200603/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/viewer/Viewer.java 2006-05-16
03:01:48 UTC (rev 5126)
+++ branches/bob200603/Jmol/src/org/jmol/viewer/Viewer.java 2006-05-16
16:57:38 UTC (rev 5127)
@@ -1628,6 +1628,13 @@
return modelManager.getAllStateInfo(bs);
}
+ public BitSet setConformation() {
+ // user has selected some atoms, now this sets that as a conformation
+ // with the effect of rewriting the cartoons to match
+
+ return modelManager.setConformation(getDisplayModelIndex(),
getSelectionSet());
+ }
+
public BitSet setConformation(int conformationIndex) {
return modelManager.setConformation(getDisplayModelIndex(),
conformationIndex);
}
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