Revision: 18344
http://sourceforge.net/p/jmol/code/18344
Author: hansonr
Date: 2013-06-18 06:26:20 +0000 (Tue, 18 Jun 2013)
Log Message:
-----------
___JmolVersion="13.1.17_dev_2013.06.18"
new feature: upgrade to allow multicharacter chain specs. See 1bgl_1bgm.cif
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/CifReader.java
trunk/Jmol/src/org/jmol/adapter/readers/more/Mol2Reader.java
trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlXsdReader.java
trunk/Jmol/src/org/jmol/adapter/smarter/Atom.java
trunk/Jmol/src/org/jmol/adapter/smarter/AtomIterator.java
trunk/Jmol/src/org/jmol/adapter/smarter/Structure.java
trunk/Jmol/src/org/jmol/adapter/smarter/StructureIterator.java
trunk/Jmol/src/org/jmol/api/JmolAdapter.java
trunk/Jmol/src/org/jmol/api/JmolAdapterAtomIterator.java
trunk/Jmol/src/org/jmol/api/JmolAdapterStructureIterator.java
trunk/Jmol/src/org/jmol/modelset/Atom.java
trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
trunk/Jmol/src/org/jmol/modelset/Chain.java
trunk/Jmol/src/org/jmol/modelset/Group.java
trunk/Jmol/src/org/jmol/modelset/Model.java
trunk/Jmol/src/org/jmol/modelset/ModelLoader.java
trunk/Jmol/src/org/jmol/modelset/ModelSet.java
trunk/Jmol/src/org/jmol/modelsetbio/AlphaPolymer.java
trunk/Jmol/src/org/jmol/modelsetbio/AminoPolymer.java
trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java
trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java
trunk/Jmol/src/org/jmol/modelsetbio/Monomer.java
trunk/Jmol/src/org/jmol/script/ScriptCompilationTokenParser.java
trunk/Jmol/src/org/jmol/script/ScriptCompiler.java
trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
trunk/Jmol/src/org/jmol/smiles/SmilesAtom.java
trunk/Jmol/src/org/jmol/smiles/SmilesGenerator.java
trunk/Jmol/src/org/jmol/util/JmolNode.java
trunk/Jmol/src/org/jmol/viewer/ColorManager.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/PropertyManager.java
trunk/Jmol/src/org/jmol/viewer/StateCreator.java
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/CifReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/CifReader.java
2013-06-17 22:35:26 UTC (rev 18343)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/CifReader.java
2013-06-18 06:26:20 UTC (rev 18344)
@@ -848,10 +848,7 @@
assemblyId = firstChar;
break;
case AUTH_ASYM_ID:
- if (field.length() > 1)
- Logger.warn("Don't know how to deal with chains more than 1 char: "
- + field);
- atom.chainID = firstChar;
+ atom.chainID = viewer.getChainID(field);
break;
case SEQ_ID:
atom.sequenceNumber = parseIntStr(field);
Modified: trunk/Jmol/src/org/jmol/adapter/readers/more/Mol2Reader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/more/Mol2Reader.java
2013-06-17 22:35:26 UTC (rev 18343)
+++ trunk/Jmol/src/org/jmol/adapter/readers/more/Mol2Reader.java
2013-06-18 06:26:20 UTC (rev 18344)
@@ -103,7 +103,7 @@
}
lastSequenceNumber = Integer.MAX_VALUE;
- chainID = 'A' - 1;
+ chainID = 64; // 'A' - 1;
readLine();
line += " 0 0 0 0 0 0";
atomCount = parseIntStr(line);
@@ -155,7 +155,7 @@
}
private int lastSequenceNumber = Integer.MAX_VALUE;
- private char chainID = 'A' - 1;
+ private int chainID = 64; // 'A' - 1
private void readAtoms(int atomCount) throws Exception {
// 1 Cs 0.0000 4.1230 0.0000 Cs 1 RES1 0.0000
@@ -179,8 +179,8 @@
if (tokens.length > 6) {
atom.sequenceNumber = parseIntStr(tokens[6]);
if (atom.sequenceNumber < lastSequenceNumber) {
- if (chainID == 'Z')
- chainID = 'a' - 1;
+ if (chainID == 90) //'Z'
+ chainID = 96;//'a' - 1;
chainID++;
}
lastSequenceNumber = atom.sequenceNumber;
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
2013-06-17 22:35:26 UTC (rev 18343)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
2013-06-18 06:26:20 UTC (rev 18344)
@@ -1105,13 +1105,13 @@
return;
int istart = -1;
int iend = -1;
- char ichain = '\0';
+ int ichain = 0;
Atom[] atoms = atomSetCollection.getAtoms();
BS bsSeq = null;
BS bsAtom = pymolScene.getSSMapAtom(ssType);
int n = atomCount + 1;
int seqNo = -1;
- char thischain = '\0';
+ int thischain = 0;
int imodel = -1;
int thismodel = -1;
for (int i = atomCount0; i < n; i++) {
Modified: trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlXsdReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlXsdReader.java
2013-06-17 22:35:26 UTC (rev 18343)
+++ trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlXsdReader.java
2013-06-18 06:26:20 UTC (rev 18344)
@@ -89,7 +89,7 @@
atom.atomName = atts.get("ID");
atom.atomSerial = ++iAtom;
if (iChain >= 0)
- atom.chainID = (char) ((iChain - 1)%26 + 'A');
+ atom.chainID = (iChain - 1)%26 + 'A';
atom.group3 = "UNK";
if (iGroup == 0)
iGroup = 1;
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Atom.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/Atom.java 2013-06-17 22:35:26 UTC
(rev 18343)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/Atom.java 2013-06-18 06:26:20 UTC
(rev 18344)
@@ -24,12 +24,10 @@
package org.jmol.adapter.smarter;
-
import org.jmol.util.BS;
import org.jmol.util.P3;
import org.jmol.util.Quadric;
-
public class Atom extends P3 implements Cloneable {
public int atomSetIndex;
public int atomIndex;
@@ -48,7 +46,7 @@
public float radius = Float.NaN;
public boolean isHetero;
public int atomSerial = Integer.MIN_VALUE;
- public char chainID = '\0';
+ public int chainID;
public char alternateLocationID = '\0';
public String group3;
public int sequenceNumber = Integer.MIN_VALUE;
@@ -307,5 +305,4 @@
vectorY *= vibScale;
vectorZ *= vibScale;
}
-
}
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomIterator.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/AtomIterator.java 2013-06-17
22:35:26 UTC (rev 18343)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomIterator.java 2013-06-18
06:26:20 UTC (rev 18344)
@@ -162,8 +162,8 @@
}
@Override
- public char getChainID() {
- return JmolAdapter.canonizeChainID(atom.chainID);
+ public int getChainID() {
+ return atom.chainID;
}
@Override
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Structure.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/Structure.java 2013-06-17
22:35:26 UTC (rev 18343)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/Structure.java 2013-06-18
06:26:20 UTC (rev 18344)
@@ -34,9 +34,9 @@
public int strandCount;
- public char startChainID = '\0';
+ public int startChainID;
public char startInsertionCode = '\0';
- public char endChainID = '\0';
+ public int endChainID;
public char endInsertionCode = '\0';
public int startSequenceNumber;
public int endSequenceNumber;
@@ -68,8 +68,8 @@
}
- public void set(char startChainID, int startSequenceNumber, char
startInsertionCode,
- char endChainID, int endSequenceNumber, char endInsertionCode, int
istart, int iend) {
+ public void set(int startChainID, int startSequenceNumber, char
startInsertionCode,
+ int endChainID, int endSequenceNumber, char endInsertionCode, int
istart, int iend) {
this.startChainID = startChainID;
this.startSequenceNumber = startSequenceNumber;
this.startInsertionCode = startInsertionCode;
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/StructureIterator.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/StructureIterator.java
2013-06-17 22:35:26 UTC (rev 18343)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/StructureIterator.java
2013-06-18 06:26:20 UTC (rev 18344)
@@ -77,8 +77,8 @@
}
@Override
- public char getStartChainID() {
- return JmolAdapter.canonizeChainID(structure.startChainID);
+ public int getStartChainID() {
+ return structure.startChainID;
}
@Override
@@ -92,8 +92,8 @@
}
@Override
- public char getEndChainID() {
- return JmolAdapter.canonizeChainID(structure.endChainID);
+ public int getEndChainID() {
+ return structure.endChainID;
}
@Override
Modified: trunk/Jmol/src/org/jmol/api/JmolAdapter.java
===================================================================
--- trunk/Jmol/src/org/jmol/api/JmolAdapter.java 2013-06-17 22:35:26 UTC
(rev 18343)
+++ trunk/Jmol/src/org/jmol/api/JmolAdapter.java 2013-06-18 06:26:20 UTC
(rev 18344)
@@ -419,17 +419,14 @@
// range-checking routines
/////////////////////////////////////////////////////////////////
- public final static char canonizeAlphaDigit(char ch) {
- if ((ch >= 'A' && ch <= 'Z') ||
- (ch >= 'a' && ch <= 'z') ||
- (ch >= '0' && ch <= '9'))
- return ch;
- return '\0';
+ private final static char canonizeAlphaDigit(char ch) {
+ return ((ch >= 'A' && ch <= 'Z') || (ch >= 'a' && ch <= 'z')
+ || (ch >= '0' && ch <= '9') ? ch : '\0');
}
- public final static char canonizeChainID(char chainID) {
- return canonizeAlphaDigit(chainID);
- }
+// public final static char canonizeChainID(char chainID) {
+// return canonizeAlphaDigit(chainID);
+// }
public final static char canonizeInsertionCode(char insertionCode) {
return canonizeAlphaDigit(insertionCode);
Modified: trunk/Jmol/src/org/jmol/api/JmolAdapterAtomIterator.java
===================================================================
--- trunk/Jmol/src/org/jmol/api/JmolAdapterAtomIterator.java 2013-06-17
22:35:26 UTC (rev 18343)
+++ trunk/Jmol/src/org/jmol/api/JmolAdapterAtomIterator.java 2013-06-18
06:26:20 UTC (rev 18344)
@@ -106,8 +106,8 @@
return Integer.MIN_VALUE;
}
- public char getChainID() {
- return '\0';
+ public int getChainID() {
+ return 0;
}
public char getAlternateLocationID() {
Modified: trunk/Jmol/src/org/jmol/api/JmolAdapterStructureIterator.java
===================================================================
--- trunk/Jmol/src/org/jmol/api/JmolAdapterStructureIterator.java
2013-06-17 22:35:26 UTC (rev 18343)
+++ trunk/Jmol/src/org/jmol/api/JmolAdapterStructureIterator.java
2013-06-18 06:26:20 UTC (rev 18344)
@@ -42,13 +42,13 @@
public abstract int getStrandCount();
- public abstract char getStartChainID();
+ public abstract int getStartChainID();
public abstract int getStartSequenceNumber();
public abstract char getStartInsertionCode();
- public abstract char getEndChainID();
+ public abstract int getEndChainID();
public abstract int getEndSequenceNumber();
Modified: trunk/Jmol/src/org/jmol/modelset/Atom.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/Atom.java 2013-06-17 22:35:26 UTC (rev
18343)
+++ trunk/Jmol/src/org/jmol/modelset/Atom.java 2013-06-18 06:26:20 UTC (rev
18344)
@@ -25,6 +25,8 @@
package org.jmol.modelset;
+import java.util.Map;
+
import org.jmol.api.SymmetryInterface;
import org.jmol.atomdata.RadiusData;
import org.jmol.atomdata.RadiusData.EnumType;
@@ -875,12 +877,12 @@
// for atom picking
if (useChimeFormat) {
String group3 = getGroup3(true);
- char chainID = getChainID();
+ int chainID = getChainID();
P3 pt = getFractionalCoordPt(true);
return "Atom: " + (group3 == null ? getElementSymbol() : getAtomName())
+ " " + getAtomNumber()
+ (group3 != null && group3.length() > 0 ?
(isHetero() ? " Hetero: " : " Group: ") + group3 + " " +
getResno()
- + (chainID != 0 && chainID != ' ' ? " Chain: " + chainID : "")
+ + (chainID != 0 && chainID != 32 ? " Chain: " +
group.chain.getIDStr() : "")
: "")
+ " Model: " + getModelNumber()
+ " Coordinates: " + x + " " + y + " " + z
@@ -904,10 +906,10 @@
String seqcodeString = getSeqcodeString();
if (seqcodeString != null)
info.append(seqcodeString);
- char chainID = getChainID();
- if (chainID != 0 && chainID != ' ') {
+ int chainID = getChainID();
+ if (chainID != 0 && chainID != 32) {
info.append(":");
- info.appendC(chainID);
+ info.append(getChainIDStr());
}
if (!allInfo)
return info.toString();
@@ -1036,10 +1038,14 @@
return group.getGroupParameter(tok);
}
- public char getChainID() {
+ public int getChainID() {
return group.chain.chainID;
}
+ public String getChainIDStr() {
+ return group.chain.getIDStr();
+ }
+
public int getSurfaceDistance100() {
return group.chain.model.modelSet.getSurfaceDistance100(index);
}
@@ -1385,8 +1391,7 @@
case T.atomtype:
return atom.getAtomType();
case T.chain:
- ch = atom.getChainID();
- return (ch == '\0' ? "" : "" + ch);
+ return atom.getChainIDStr();
case T.sequence:
return atom.getGroup1('?');
case T.group1:
Modified: trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2013-06-17
22:35:26 UTC (rev 18343)
+++ trunk/Jmol/src/org/jmol/modelset/AtomCollection.java 2013-06-18
06:26:20 UTC (rev 18344)
@@ -241,7 +241,7 @@
}
public String getAtomChain(int i) {
- return "" + atoms[i].getChainID();
+ return atoms[i].getChainIDStr();
}
public Quadric[] getEllipsoid(int i) {
@@ -2078,7 +2078,7 @@
bs.set(i);
break;
case T.spec_chain:
- return BSUtil.copy(getChainBits((char) ((Integer) specInfo).intValue()));
+ return BSUtil.copy(getChainBits(((Integer) specInfo).intValue()));
case T.spec_seqcode:
return BSUtil.copy(getSeqcodeBits(((Integer) specInfo).intValue(),
true));
case T.hetero:
@@ -2423,15 +2423,15 @@
return (!isEmpty || returnEmpty ? bs : null);
}
- protected BS getChainBits(char chainId) {
+ protected BS getChainBits(int chainID) {
boolean caseSensitive = viewer.getBoolean(T.chaincasesensitive);
- if (!caseSensitive)
- chainId = Character.toUpperCase(chainId);
+ if (!caseSensitive)
+ chainID = Character.toUpperCase(chainID);
BS bs = new BS();
BS bsDone = BSUtil.newBitSet(atomCount);
for (int i = bsDone.nextClearBit(0); i < atomCount; i =
bsDone.nextClearBit(i + 1)) {
Chain chain = atoms[i].getChain();
- if (chainId == (caseSensitive ? chain.chainID :
Character.toUpperCase(chain.chainID))) {
+ if (chainID == (caseSensitive ? chain.chainID :
Character.toUpperCase(chain.chainID))) {
chain.setAtomBitSet(bs);
bsDone.or(bs);
} else {
Modified: trunk/Jmol/src/org/jmol/modelset/Chain.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/Chain.java 2013-06-17 22:35:26 UTC (rev
18343)
+++ trunk/Jmol/src/org/jmol/modelset/Chain.java 2013-06-18 06:26:20 UTC (rev
18344)
@@ -28,7 +28,7 @@
public final class Chain {
public Model model;
- public char chainID = '\0';
+ public int chainID;
public boolean isDna, isRna;
int groupCount;
@@ -39,7 +39,7 @@
return model.modelSet.atoms[index];
}
- Chain(Model model, char chainID) {
+ Chain(Model model, int chainID) {
this.model = model;
this.chainID = chainID;
}
@@ -124,4 +124,8 @@
for (int i = 0; i < groupCount; i++)
groups[i].selectAtoms(bs);
}
+
+ public String getIDStr() {
+ return (chainID == 0 ? "" : chainID < 256 ? "" + (char) chainID : (String)
model.modelSet.viewer.chainMap.get(Integer.valueOf(chainID)));
+ }
}
Modified: trunk/Jmol/src/org/jmol/modelset/Group.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/Group.java 2013-06-17 22:35:26 UTC (rev
18343)
+++ trunk/Jmol/src/org/jmol/modelset/Group.java 2013-06-18 06:26:20 UTC (rev
18344)
@@ -177,7 +177,7 @@
return groupID;
}
- public final char getChainID() {
+ public final int getChainID() {
return chain.chainID;
}
Modified: trunk/Jmol/src/org/jmol/modelset/Model.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/Model.java 2013-06-17 22:35:26 UTC (rev
18343)
+++ trunk/Jmol/src/org/jmol/modelset/Model.java 2013-06-18 06:26:20 UTC (rev
18344)
@@ -261,7 +261,7 @@
return (i < chainCount ? chains[i] : null);
}
- Chain getChain(char chainID) {
+ Chain getChain(int chainID) {
for (int i = chainCount; --i >= 0;) {
Chain chain = chains[i];
if (chain.chainID == chainID)
@@ -428,9 +428,8 @@
}
/**
- * create a new structure, being careful to not
- * overwrite existing structure.
- *
+ * create a new structure, being careful to not overwrite existing structure.
+ *
* @param type
* @param structureID
* @param serialID
@@ -439,14 +438,18 @@
* @param startSeqcode
* @param endChainID
* @param endSeqcode
- * @param istart starting atom index
- * @param iend ending atom index
- * @param bsAssigned already assigned
+ * @param istart
+ * starting atom index
+ * @param iend
+ * ending atom index
+ * @param bsAssigned
+ * already assigned
*/
public void addSecondaryStructure(EnumStructure type, String structureID,
int serialID, int strandCount,
- char startChainID, int startSeqcode,
- char endChainID, int endSeqcode, int
istart, int iend, BS bsAssigned) {
+ int startChainID, int startSeqcode,
+ int endChainID, int endSeqcode, int istart,
+ int iend, BS bsAssigned) {
}
/**
@@ -508,7 +511,7 @@
* @param bs
* @param caseSensitive
*/
- public void selectSeqcodeRange(int seqcodeA, int seqcodeB, char chainID,
+ public void selectSeqcodeRange(int seqcodeA, int seqcodeB, int chainID,
BS bs, boolean caseSensitive) {
}
@@ -544,4 +547,4 @@
return null;
}
-}
+ }
Modified: trunk/Jmol/src/org/jmol/modelset/ModelLoader.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelLoader.java 2013-06-17 22:35:26 UTC
(rev 18343)
+++ trunk/Jmol/src/org/jmol/modelset/ModelLoader.java 2013-06-18 06:26:20 UTC
(rev 18344)
@@ -239,7 +239,7 @@
private int currentModelIndex;
private Model currentModel;
- private char currentChainID = '\0';
+ private int currentChainID = 0;
private Chain currentChain;
private int currentGroupSequenceNumber;
private char currentGroupInsertionCode = '\0';
@@ -843,7 +843,7 @@
htAtomMap.put(atomUid, atom);
}
- private void checkNewGroup(JmolAdapter adapter, char chainID,
+ private void checkNewGroup(JmolAdapter adapter, int chainID,
String group3, int groupSequenceNumber,
char groupInsertionCode, boolean addH) {
String group3i = (group3 == null ? null : group3.intern());
@@ -879,7 +879,7 @@
}
}
- private Chain getOrAllocateChain(Model model, char chainID) {
+ private Chain getOrAllocateChain(Model model, int chainID) {
//Logger.debug("chainID=" + chainID + " -> " + (chainID + 0));
Chain chain = model.getChain(chainID);
if (chain != null)
@@ -1023,9 +1023,9 @@
private void defineStructure(int modelIndex, EnumStructure subType,
String structureID, int serialID,
- int strandCount, char startChainID,
+ int strandCount, int startChainID,
int startSequenceNumber,
- char startInsertionCode, char endChainID,
+ char startInsertionCode, int endChainID,
int endSequenceNumber, char endInsertionCode,
int istart, int iend, BS bsAssigned) {
EnumStructure type = (subType == EnumStructure.NOT ? EnumStructure.NONE :
subType);
@@ -1240,14 +1240,13 @@
throw new NullPointerException();
int modelIndex = modelSet.atoms[firstAtomIndex].modelIndex;
- Group group = null;
- if (group3 != null && jbr != null) {
- group = jbr.distinguishAndPropagateGroup(chain, group3, seqcode,
- firstAtomIndex, maxAtomIndex, modelIndex, specialAtomIndexes,
modelSet.atoms);
- }
+ Group group = (group3 == null || jbr == null ? null : jbr
+ .distinguishAndPropagateGroup(chain, group3, seqcode, firstAtomIndex,
+ maxAtomIndex, modelIndex, specialAtomIndexes, modelSet.atoms));
String key;
if (group == null) {
- group = new Group().setGroup(chain, group3, seqcode, firstAtomIndex,
lastAtomIndex);
+ group = new Group().setGroup(chain, group3, seqcode, firstAtomIndex,
+ lastAtomIndex);
key = "o>";
} else {
key = (group.isProtein() ? "p>" : group.isNucleic() ? "n>" : group
Modified: trunk/Jmol/src/org/jmol/modelset/ModelSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2013-06-17 22:35:26 UTC
(rev 18343)
+++ trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2013-06-18 06:26:20 UTC
(rev 18344)
@@ -320,14 +320,15 @@
*/
public BS getAtomBits(int tokType, Object specInfo) {
switch (tokType) {
+ default:
+ return BSUtil.andNot(getAtomBitsMaybeDeleted(tokType, specInfo), viewer
+ .getDeletedAtoms());
case T.spec_model:
int modelNumber = ((Integer) specInfo).intValue();
int modelIndex = getModelNumberIndex(modelNumber, true, true);
return (modelIndex < 0 && modelNumber > 0 ? new BS()
: viewer.getModelUndeletedAtomsBitSet(modelIndex));
}
- return BSUtil.andNot(getAtomBitsMaybeDeleted(tokType, specInfo), viewer
- .getDeletedAtoms());
}
public String getAtomLabel(int i) {
Modified: trunk/Jmol/src/org/jmol/modelsetbio/AlphaPolymer.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/AlphaPolymer.java 2013-06-17
22:35:26 UTC (rev 18343)
+++ trunk/Jmol/src/org/jmol/modelsetbio/AlphaPolymer.java 2013-06-18
06:26:20 UTC (rev 18344)
@@ -70,8 +70,8 @@
@Override
public void addStructure(EnumStructure type, String structureID,
- int serialID, int strandCount, char startChainID,
- int startSeqcode, char endChainID, int endSeqcode,
int istart, int iend, BS bsAssigned) {
+ int serialID, int strandCount, int startChainID,
+ int startSeqcode, int endChainID, int endSeqcode,
int istart, int iend, BS bsAssigned) {
if (istart >= 0 && (monomers[0].firstAtomIndex > iend ||
monomers[monomerCount - 1].lastAtomIndex < istart))
return;
int indexStart, indexEnd;
Modified: trunk/Jmol/src/org/jmol/modelsetbio/AminoPolymer.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/AminoPolymer.java 2013-06-17
22:35:26 UTC (rev 18343)
+++ trunk/Jmol/src/org/jmol/modelsetbio/AminoPolymer.java 2013-06-18
06:26:20 UTC (rev 18344)
@@ -1167,8 +1167,9 @@
}
private String dumpSummary(char[] labels) {
- char id = monomers[0].getLeadAtom().getChainID();
- String prefix = (id == '\0' ? "" : String.valueOf(id) + ":");
+ Atom a = monomers[0].getLeadAtom();
+ int id = a.getChainID();
+ String prefix = (id == 0 ? "" : a.getChainIDStr() + ":");
SB sb = new SB();
char lastChar = '\0';
char insCode1 = '\0';
Modified: trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java 2013-06-17 22:35:26 UTC
(rev 18343)
+++ trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java 2013-06-18 06:26:20 UTC
(rev 18344)
@@ -92,8 +92,8 @@
@Override
public void addSecondaryStructure(EnumStructure type,
String structureID, int serialID, int strandCount,
- char startChainID, int startSeqcode,
- char endChainID, int endSeqcode, int istart, int
iend, BS bsAssigned) {
+ int startChainID, int startSeqcode,
+ int endChainID, int endSeqcode, int istart, int
iend, BS bsAssigned) {
for (int i = bioPolymerCount; --i >= 0; )
bioPolymers[i].addStructure(type, structureID, serialID, strandCount,
startChainID, startSeqcode,
endChainID, endSeqcode, istart, iend,
bsAssigned);
@@ -299,12 +299,12 @@
}
@Override
- public void selectSeqcodeRange(int seqcodeA, int seqcodeB, char chainID,
+ public void selectSeqcodeRange(int seqcodeA, int seqcodeB, int chainID,
BS bs, boolean caseSensitive) {
- char ch;
+ int id;
for (int i = chainCount; --i >= 0;)
- if (chainID == (ch = chains[i].chainID) || chainID == '\t' ||
!caseSensitive
- && chainID == Character.toUpperCase(ch))
+ if (chainID == -1 || chainID == (id = chains[i].chainID) ||
!caseSensitive
+ && chainID == Character.toUpperCase(id))
for (int index = 0; index >= 0;)
index = chains[i].selectSeqcodeRange(index, seqcodeA, seqcodeB, bs);
}
@@ -658,14 +658,12 @@
.isNaN(atoms[i].getGroupParameter(T.psi))))
continue;
}
- char ch = atoms[i].getChainID();
- if (ch == 0)
- ch = ' ';
+ String ch = atoms[i].getChainIDStr();
if (bs == null) {
bs = new BS();
res1 = atoms[i].getResno();
group1 = atoms[i].getGroup3(false);
- chain1 = "" + ch;
+ chain1 = ch;
}
type = atoms[i].getProteinStructureType();
subtype = atoms[i].getProteinStructureSubType();
@@ -674,7 +672,7 @@
lastId = id;
res2 = atoms[i].getResno();
group2 = atoms[i].getGroup3(false);
- chain2 = "" + ch;
+ chain2 = ch;
iLastAtom = i;
}
if (n > 0)
Modified: trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java 2013-06-17 22:35:26 UTC
(rev 18343)
+++ trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java 2013-06-18 06:26:20 UTC
(rev 18344)
@@ -123,10 +123,10 @@
return leadAtomIndices;
}
- protected int getIndex(char chainID, int seqcode) {
+ protected int getIndex(int chainID, int seqcode) {
int i;
for (i = monomerCount; --i >= 0;)
- if (monomers[i].getChainID() == chainID)
+ if (monomers[i].chain.chainID == chainID)
if (monomers[i].getSeqcode() == seqcode)
break;
return i;
@@ -1014,8 +1014,8 @@
*/
public void addStructure(EnumStructure type, String structureID,
int serialID, int strandCount,
- char startChainID, int startSeqcode,
- char endChainID, int endSeqcode, int
istart, int iend, BS bsAssigned) {
+ int startChainID, int startSeqcode,
+ int endChainID, int endSeqcode, int
istart, int iend, BS bsAssigned) {
// overridden by each subclass
}
Modified: trunk/Jmol/src/org/jmol/modelsetbio/Monomer.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/Monomer.java 2013-06-17 22:35:26 UTC
(rev 18343)
+++ trunk/Jmol/src/org/jmol/modelsetbio/Monomer.java 2013-06-18 06:26:20 UTC
(rev 18344)
@@ -283,8 +283,7 @@
public Map<String, Object> getMyInfo() {
Map<String, Object> info = getGroupInfo(groupIndex);
- char chainID = chain.chainID;
- info.put("chain", (chainID == '\0' ? "" : "" + chainID));
+ info.put("chain", chain.getIDStr());
int seqNum = getSeqNumber();
char insCode = getInsertionCode();
if (seqNum > 0)
@@ -430,13 +429,13 @@
}
public String getUniqueID() {
- char cid = getChainID();
+ int cid = getChainID();
Atom a = getLeadAtom();
String id = (a == null ? "" : "_" + a.getModelIndex()) + "_" + getResno()
- + (cid == '\0' ? "" : "" + cid);
- cid = (a == null ? '\0' : getLeadAtom().getAlternateLocationID());
- if (cid != '\0')
- id += cid;
+ + (cid == 0 ? "" : "_" + cid);
+ char aid = (a == null ? '\0' : getLeadAtom().getAlternateLocationID());
+ if (aid != '\0')
+ id += "_" + aid;
return id;
}
Modified: trunk/Jmol/src/org/jmol/script/ScriptCompilationTokenParser.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptCompilationTokenParser.java
2013-06-17 22:35:26 UTC (rev 18343)
+++ trunk/Jmol/src/org/jmol/script/ScriptCompilationTokenParser.java
2013-06-18 06:26:20 UTC (rev 18344)
@@ -1158,32 +1158,39 @@
return T.tv(T.spec_seqcode, seqvalue, Integer.valueOf(seqcode));
}
+ /**
+ * [:] [term]
+ * [:] [*]
+ * [:] [0-9]
+ * [:] [?]
+ *
+ * @param tok
+ * @return true if chain
+ */
private boolean clauseChainSpec(int tok) {
if (tok == T.colon) {
tokenNext();
tok = tokPeek();
if (isSpecTerminator(tok))
- return generateResidueSpecCode(T.tv(T.spec_chain, '\0',
+ return generateResidueSpecCode(T.tv(T.spec_chain, 0,
"spec_chain"));
}
- char chain;
+ int chain;
switch (tok) {
case T.times:
return (getToken() != null);
case T.integer:
getToken();
int val = theToken.intValue;
- if (val < 0 || val > 9)
+ if (val < 0 || val > 9999)
return error(ERROR_invalidChainSpecification);
- chain = (char) ('0' + val);
+ chain = viewer.getChainID("" + val);
break;
default:
String strChain = "" + getToken().value;
- if (strChain.length() != 1)
- return error(ERROR_invalidChainSpecification);
- chain = strChain.charAt(0);
- if (chain == '?')
+ if (strChain.equals("?"))
return true;
+ chain = viewer.getChainID(strChain);
break;
}
return generateResidueSpecCode(T.tv(T.spec_chain, chain,
Modified: trunk/Jmol/src/org/jmol/script/ScriptCompiler.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptCompiler.java 2013-06-17 22:35:26 UTC
(rev 18343)
+++ trunk/Jmol/src/org/jmol/script/ScriptCompiler.java 2013-06-18 06:26:20 UTC
(rev 18344)
@@ -871,8 +871,10 @@
ident = identLC;
theToken = null;
- } else if (ident.length() == 1) {
+ } else if (ident.length() == 1 || lastToken.tok == T.colon) {
// hack to support case sensitive alternate locations and chains
+ // but now with reading of multicharacter chains, how does that
+ // work?
// if an identifier is a single character long, then
// allocate a new Token with the original character preserved
if ((theToken = T.getTokenFromName(ident)) == null
Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2013-06-17 22:35:26 UTC
(rev 18343)
+++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2013-06-18 06:26:20 UTC
(rev 18344)
@@ -460,13 +460,13 @@
return sc;
}
- static SB getContextTrace(ScriptContext sc, SB sb, boolean isTop) {
+ static SB getContextTrace(Viewer viewer, ScriptContext sc, SB sb, boolean
isTop) {
if (sb == null)
sb = new SB();
sb.append(getErrorLineMessage(sc.functionName, sc.scriptFileName,
- sc.lineNumbers[sc.pc], sc.pc,
ScriptEvaluator.statementAsString(sc.statement, (isTop ? sc.iToken : 9999),
false)));
+ sc.lineNumbers[sc.pc], sc.pc,
ScriptEvaluator.statementAsString(viewer, sc.statement, (isTop ? sc.iToken :
9999), false)));
if (sc.parentContext != null)
- getContextTrace(sc.parentContext, sb, false);
+ getContextTrace(viewer, sc.parentContext, sb, false);
return sb;
}
@@ -549,7 +549,7 @@
*/
public String getNextStatement() {
return (pc < aatoken.length ? getErrorLineMessage(functionName,
scriptFileName,
- getLinenumber(null), pc, statementAsString(aatoken[pc], -9999,
+ getLinenumber(null), pc, statementAsString(viewer, aatoken[pc], -9999,
logMessages)) : "");
}
@@ -624,7 +624,7 @@
String s = (ifLevel > 0 ? " ".substring(0,
ifLevel * 2) : "");
strbufLog.append(s).append(
- statementAsString(st, iToken, logMessages));
+ statementAsString(viewer, st, iToken, logMessages));
viewer.scriptStatus(strbufLog.toString());
} else {
String cmd = getCommand(pc, false, false);
@@ -2851,7 +2851,7 @@
}
} else {
sb.append(getErrorLineMessage(context.functionName,
context.scriptFileName,
- getLinenumber(context), context.pc, statementAsString(
+ getLinenumber(context), context.pc, statementAsString(viewer,
context.statement, -9999, logMessages)));
}
context = context.parentContext;
@@ -2864,7 +2864,7 @@
}
} else {
sb.append(getErrorLineMessage(functionName, scriptFileName,
- getLinenumber(null), pc, statementAsString(st, -9999,
+ getLinenumber(null), pc, statementAsString(viewer, st, -9999,
logMessages)));
}
@@ -2893,7 +2893,7 @@
sx.message = "";
return;
}
- String s = ScriptEvaluator.getContextTrace(getScriptContext(), null,
true).toString();
+ String s = ScriptEvaluator.getContextTrace(viewer, getScriptContext(),
null, true).toString();
while (thisContext != null && !thisContext.isTryCatch)
popContext(false, false);
sx.message += s;
@@ -3311,7 +3311,7 @@
return str.toString();
}
- static String statementAsString(T[] statement, int iTok,
+ static String statementAsString(Viewer viewer, T[] statement, int iTok,
boolean doLogMessages) {
if (statement.length == 0)
return "";
@@ -3424,7 +3424,7 @@
continue;
case T.spec_chain:
sb.append("*:");
- sb.appendC((char) token.intValue);
+ sb.append(viewer.getChainIDStr(token.intValue));
continue;
case T.spec_alternate:
sb.append("*%");
@@ -3860,10 +3860,10 @@
}
int chainID = (pc + 3 < code.length && code[pc + 2].tok == T.opAND
&& code[pc + 3].tok == T.spec_chain ? code[pc + 3].intValue
- : 9);
+ : -1);
rpn.addXBs(getAtomBits(T.spec_seqcode_range, new int[] {
getSeqCode(instruction), getSeqCode(code[++pc]), chainID }));
- if (chainID != 9)
+ if (chainID != -1)
pc += 2;
break;
case T.cell:
@@ -4363,8 +4363,8 @@
}
private static int getSeqCode(T instruction) {
- return (instruction.intValue != Integer.MAX_VALUE ? Group.getSeqcodeFor(
- instruction.intValue, ' ') : ((Integer) instruction.value).intValue());
+ return (instruction.intValue == Integer.MAX_VALUE ? ((Integer)
instruction.value).intValue()
+ : Group.getSeqcodeFor(instruction.intValue, ' '));
}
/*
@@ -10235,7 +10235,7 @@
String msg = null;
if (slen == 1) {
if (!chk)
- msg = getContextTrace(getScriptContext(), null, true).toString();
+ msg = getContextTrace(viewer, getScriptContext(), null,
true).toString();
} else {
msg = parameterExpressionString(1, 0);
}
Modified: trunk/Jmol/src/org/jmol/smiles/SmilesAtom.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesAtom.java 2013-06-17 22:35:26 UTC
(rev 18343)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesAtom.java 2013-06-18 06:26:20 UTC
(rev 18344)
@@ -709,10 +709,14 @@
return 0;
}
- public char getChainID() {
- return '\0';
+ public int getChainID() {
+ return 0;
}
+ public String getChainIDStr() {
+ return "";
+ }
+
static String getAtomLabel(int atomicNumber, int isotopeNumber, int valence,
int charge, int nH, boolean isAromatic,
String stereo) {
Modified: trunk/Jmol/src/org/jmol/smiles/SmilesGenerator.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesGenerator.java 2013-06-17 22:35:26 UTC
(rev 18343)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesGenerator.java 2013-06-18 06:26:20 UTC
(rev 18344)
@@ -121,9 +121,9 @@
end = null;
len = 0;
if (bioStructureName.length() > 0) {
- char id = a.getChainID();
- if (id != '\0') {
- s = "//* chain " + id + " " + bioStructureName + " " +
a.getResno() + " *// ";
+ int id = a.getChainID();
+ if (id != 0) {
+ s = "//* chain " + a.getChainIDStr() + " " + bioStructureName +
" " + a.getResno() + " *// ";
len = s.length();
sb.append(s);
}
@@ -195,14 +195,14 @@
private void addBracketedBioName(SB sb, JmolNode a, String atomName) {
sb.append("[");
if (atomName != null) {
- char chChain = a.getChainID();
+ String chain = a.getChainIDStr();
sb.append(a.getGroup3(false));
if (!atomName.equals(".0"))
sb.append(atomName).append("#").appendI(a.getElementNumber());
sb.append("//* ").appendI(
a.getResno());
- if (chChain != '\0')
- sb.append(":").appendC(chChain);
+ if (chain.length() > 0)
+ sb.append(":").append(chain);
sb.append(" *//");
} else {
sb.append(Elements.elementNameFromNumber(a.getElementNumber()));
Modified: trunk/Jmol/src/org/jmol/util/JmolNode.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/JmolNode.java 2013-06-17 22:35:26 UTC (rev
18343)
+++ trunk/Jmol/src/org/jmol/util/JmolNode.java 2013-06-18 06:26:20 UTC (rev
18344)
@@ -54,7 +54,8 @@
public String getGroup1(char c0);
public String getGroup3(boolean allowNull);
public int getResno();
- public char getChainID();
+ public int getChainID();
+ public String getChainIDStr();
public int getOffsetResidueAtom(String name, int offset);
public boolean getCrossLinkLeadAtomIndexes(JmolList<Integer> vReturn);
public void getGroupBits(BS bs);
Modified: trunk/Jmol/src/org/jmol/viewer/ColorManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/ColorManager.java 2013-06-17 22:35:26 UTC
(rev 18343)
+++ trunk/Jmol/src/org/jmol/viewer/ColorManager.java 2013-06-18 06:26:20 UTC
(rev 18344)
@@ -245,11 +245,12 @@
argb = atom.getProteinStructureSubType().getColor();
break;
case StaticConstants.PALETTE_CHAIN:
- int chain = atom.getChainID() & 0x1F;
+ int chain = atom.getChainID();
if (chain < 0)
chain = 0;
- if (chain >= JC.argbsChainAtom.length)
- chain = chain % JC.argbsChainAtom.length;
+ else if (chain >= 256)
+ chain -= 256;
+ chain = chain % JC.argbsChainAtom.length;
argb = (atom.isHetero() ? JC.argbsChainHetero
: JC.argbsChainAtom)[chain];
break;
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-06-17 22:35:26 UTC
(rev 18343)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-06-18 06:26:20 UTC
(rev 18344)
@@ -9,8 +9,10 @@
# The quotes above look odd for a parameter file, but they are
# important for the JavaScript version of Jmol.
-___JmolVersion="13.1.17_dev_2013.06.17"
+___JmolVersion="13.1.17_dev_2013.06.18"
+new feature: upgrade to allow multicharacter chain specs. See 1bgl_1bgm.cif
+
bug fix: invertSelected on trajectory causes nullPointerException
bug fix: POLYHEDRA with faceCenterOffset not saved in state properly; EDGES
option nonfunctional
Modified: trunk/Jmol/src/org/jmol/viewer/PropertyManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/PropertyManager.java 2013-06-17 22:35:26 UTC
(rev 18343)
+++ trunk/Jmol/src/org/jmol/viewer/PropertyManager.java 2013-06-18 06:26:20 UTC
(rev 18344)
@@ -675,7 +675,8 @@
String names = "";
String sep = "";
Group lastGroup = null;
- char chainlast = '\0';
+ int iChainLast = 0;
+ String sChainLast = null;
String reslist = "";
String model = "";
int resnolast = Integer.MAX_VALUE;
@@ -686,25 +687,26 @@
continue;
lastGroup = atom.group;
int resno = atom.getResno();
- char chain = atom.getChainID();
+ int chain = atom.getChainID();
if (resnolast != resno - 1) {
if (reslist.length() != 0 && resnolast != resnofirst)
reslist += "-" + resnolast;
- chain = '\1';
+ chain = -1;
resnofirst = resno;
}
model = "/" + ms.getModelNumberDotted(atom.modelIndex);
- if (chainlast != '\0' && chain != chainlast)
- reslist += ":" + chainlast + model;
- if (chain == '\1')
+ if (iChainLast != 0 && chain != iChainLast)
+ reslist += ":" + sChainLast + model;
+ if (chain == -1)
reslist += " " + resno;
resnolast = resno;
- chainlast = atom.getChainID();
+ iChainLast = atom.getChainID();
+ sChainLast = atom.getChainIDStr();
names += sep + atom.getGroup3(false);
sep = "-";
}
reslist += (resnofirst == resnolast ? "" : "-" + resnolast)
- + (chainlast == '\0' ? "" : ":" + chainlast) + model;
+ + (iChainLast == 0 ? "" : ":" + sChainLast) + model;
ligand.put("groupNames", names);
ligand.put("residueList", reslist.substring(1));
}
@@ -1060,7 +1062,7 @@
private String getChimeInfoA(Atom[] atoms, int tok, BS bs) {
SB info = new SB();
info.append("\n");
- char id;
+ int id;
String s = "";
Chain clast = null;
Group glast = null;
@@ -1069,7 +1071,7 @@
if (bs != null)
for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
id = atoms[i].getChainID();
- s = (id == '\0' ? " " : "" + id);
+ s = (id == 0 ? " " : atoms[i].getChainIDStr());
switch (tok) {
case T.chain:
break;
@@ -1190,9 +1192,8 @@
info.put("resno", Integer.valueOf(seqNum));
if (insCode != 0)
info.put("insertionCode", "" + insCode);
- char chainID = atom.getChainID();
info.put("name", ms.getAtomName(i));
- info.put("chain", (chainID == '\0' ? "" : "" + chainID));
+ info.put("chain", atom.getChainIDStr());
info.put("atomID", Integer.valueOf(atom.atomID));
info.put("groupID", Integer.valueOf(atom.getGroupID()));
if (atom.alternateLocationID != '\0')
@@ -1336,8 +1337,8 @@
private static void getAtomResidueInfo(SB info, Atom atom) {
info.append("[").append(atom.getGroup3(false)).append("]").append(
atom.getSeqcodeString()).append(":");
- char id = atom.getChainID();
- info.append(id == '\0' ? " " : "" + id);
+ int id = atom.getChainID();
+ info.append(id == 0 ? " " : atom.getChainIDStr());
}
}
Modified: trunk/Jmol/src/org/jmol/viewer/StateCreator.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/StateCreator.java 2013-06-17 22:35:26 UTC
(rev 18343)
+++ trunk/Jmol/src/org/jmol/viewer/StateCreator.java 2013-06-18 06:26:20 UTC
(rev 18344)
@@ -585,8 +585,7 @@
return commands.toString();
}
- private String getVariableState(StateManager.GlobalSettings global,
- SB sfunc) {
+ private String getVariableState(StateManager.GlobalSettings global, SB
sfunc) {
String[] list = new String[global.htBooleanParameterFlags.size()
+ global.htNonbooleanParameterValues.size()];
SB commands = new SB();
@@ -650,9 +649,9 @@
// label defaults
- viewer.loadShape(JC.SHAPE_LABELS);
- commands
- .append(getDefaultLabelState((Labels)
viewer.shapeManager.shapes[JC.SHAPE_LABELS]));
+ if (viewer.shapeManager.getShape(JC.SHAPE_LABELS) != null)
+ commands
+ .append(getDefaultLabelState((Labels)
viewer.shapeManager.shapes[JC.SHAPE_LABELS]));
// structure defaults
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2013-06-17 22:35:26 UTC (rev
18343)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2013-06-18 06:26:20 UTC (rev
18344)
@@ -2786,6 +2786,8 @@
}
stateManager.clear(global);
tempArray.clear();
+ chainMap.clear();
+ chainList.clear();
colorManager.clear();
definedAtomSets.clear();
dataManager.clear();
@@ -5662,7 +5664,7 @@
case T.cartoonrockets:
return global.cartoonRockets;
case T.chaincasesensitive:
- return global.chainCaseSensitive;
+ return global.chainCaseSensitive || chainList.size() > 0;
case T.debugscript:
return global.debugScript;
case T.defaultstructuredssp:
@@ -7648,19 +7650,11 @@
return gdata.getColorArgbOrGray(modelSet.getAtomColix(i));
}
- String getAtomChain(int i) {
- return modelSet.getAtomChain(i);
- }
-
@Override
public int getAtomModelIndex(int i) {
return modelSet.atoms[i].modelIndex;
}
- String getAtomSequenceCode(int i) {
- return modelSet.atoms[i].getSeqcodeString();
- }
-
@Override
public float getBondRadius(int i) {
return modelSet.getBondRadius(i);
@@ -10048,4 +10042,36 @@
return modelSet.getBsBranches(dihedralList);
}
+ /**
+ * Create a unique integer for any chain string.
+ * Note that if there are any chains that are more than
+ * a single character, chainCaseSensitive is automatically set TRUE
+ *
+ *
+ * @param id < 256 is just the character of a single-character
+ * chain id; >= 256 indicates a list pointer into
+ * chainList.
+ * @return i
+ */
+ public int getChainID(String id) {
+ Integer iboxed = (Integer) chainMap.get(id);
+ if (iboxed != null)
+ return iboxed.intValue();
+ int i = id.charAt(0);
+ if (id.length() > 1) {
+ i = 256 + chainList.size();
+ chainList.addLast(id);
+ }
+ iboxed = Integer.valueOf(i);
+ chainMap.put(iboxed, id);
+ chainMap.put(id, iboxed);
+ return i;
+ }
+
+ public String getChainIDStr(int id) {
+ return (String) chainMap.get(Integer.valueOf(id));
+ }
+
+ public Map<Object, Object> chainMap = new Hashtable<Object, Object>();
+ public JmolList<String> chainList = new JmolList<String>();
}
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