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[Jmol-commits] CVS: Jmol/src/org/openscience/jmol/viewer/protein PdbChain.java,NONE,1.1 PdbResidue.java,NONE,1.1 PdbAtom.java,1.5,1.6 PdbMolecule.java,1.5,1.6
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From: Michael T H. <mic...@us...> - 2003-10-29 23:27:10
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Update of /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/protein
In directory sc8-pr-cvs1:/tmp/cvs-serv24327/src/org/openscience/jmol/viewer/protein
Modified Files:
PdbAtom.java PdbMolecule.java
Added Files:
PdbChain.java PdbResidue.java
Log Message:
added classes PdbChain & PdbResidue + reimplemented Trace
--- NEW FILE: PdbChain.java ---
/* $RCSfile: PdbChain.java,v $
* $Author: michaelthoward $
* $Date: 2003/10/29 23:27:07 $
* $Revision: 1.1 $
*
* Copyright (C) 2002-2003 The Jmol Development Team
*
* Contact: jmo...@li...
*
* This library is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public
* License as published by the Free Software Foundation; either
* version 2.1 of the License, or (at your option) any later version.
*
* This library is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
* Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public
* License along with this library; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
* 02111-1307 USA.
*/
package org.openscience.jmol.viewer.protein;
import org.openscience.jmol.viewer.*;
import org.openscience.jmol.viewer.datamodel.Atom;
import java.util.Hashtable;
public class PdbChain {
public char chainID;
int residueCount;
PdbResidue[] residues = new PdbResidue[16];
PdbResidue[] mainchain;
public PdbChain(char chainID) {
this.chainID = chainID;
}
void freeze() {
if (residueCount != residues.length) {
PdbResidue[] t = new PdbResidue[residueCount];
System.arraycopy(residues, 0, t, 0, residueCount);
residues = t;
}
System.out.println("chain: " + chainID + " has length=" + residues.length);
}
void addResidue(PdbResidue residue) {
if (residueCount == residues.length) {
PdbResidue[] t = new PdbResidue[residueCount * 2];
System.arraycopy(residues, 0, t, 0, residueCount);
residues = t;
}
residues[residueCount++] = residue;
}
int mainchainHelper(boolean addResidues) {
int mainchainCount = 0;
outer:
for (int i = residueCount; --i >= 0; ) {
PdbResidue residue = residues[i];
int[] mainchainIndices = residue.mainchainIndices;
if (mainchainIndices == null)
continue;
for (int j = 4; --j >=0; )
if (mainchainIndices[j] == -1)
continue outer;
if (addResidues)
mainchain[mainchainCount] = residue;
++mainchainCount;
}
return mainchainCount;
}
PdbResidue[] getMainchain() {
if (mainchain == null) {
int mainchainCount = mainchainHelper(false);
if (mainchainCount == residueCount) {
mainchain = residues;
} else {
mainchain = new PdbResidue[mainchainCount];
if (mainchainCount > 0)
mainchainHelper(true);
}
}
return mainchain;
}
void propogateSecondaryStructure(byte type, int startResidueNumber, int endResidueNumber) {
System.out.println("chainID=" + chainID + " type=" + type + " " + startResidueNumber + "->"
+ endResidueNumber);
for (int i = residueCount; --i >= 0; ) {
PdbResidue residue = residues[i];
int resNumber = residue.resNumber;
if (resNumber >= startResidueNumber && resNumber <= endResidueNumber)
residue.setStructureType(type);
}
}
}
--- NEW FILE: PdbResidue.java ---
/* $RCSfile: PdbResidue.java,v $
* $Author: michaelthoward $
* $Date: 2003/10/29 23:27:07 $
* $Revision: 1.1 $
*
* Copyright (C) 2002-2003 The Jmol Development Team
*
* Contact: jmo...@li...
*
* This library is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public
* License as published by the Free Software Foundation; either
* version 2.1 of the License, or (at your option) any later version.
*
* This library is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
* Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public
* License along with this library; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
* 02111-1307 USA.
*/
package org.openscience.jmol.viewer.protein;
import org.openscience.jmol.viewer.*;
import java.util.Hashtable;
public class PdbResidue {
public final static byte STRUCTURE_NONE = 0;
public final static byte STRUCTURE_HELIX = 1;
public final static byte STRUCTURE_SHEET = 2;
public final static byte STRUCTURE_TURN = 3;
public char chainID;
public short resNumber;
public short resid;
public byte structureType = STRUCTURE_NONE;
int[] mainchainIndices;
public PdbResidue(char chainID, int resNumber, String residue3) {
this.chainID = chainID;
this.resNumber = (short) resNumber;
resid = lookupResid(residue3);
}
public void setStructureType(byte structureType) {
this.structureType = structureType;
}
public boolean isResidue(String residue3) {
return residueNames3[resid].equalsIgnoreCase(residue3);
}
public String getResidue3() {
return residueNames3[resid];
}
public int getResidueNumber() {
return resNumber;
}
public short getResID() {
return resid;
}
public boolean isResidueNameMatch(String strWildcard) {
if (strWildcard.length() != 3) {
System.err.println("residue wildcard length != 3");
return false;
}
String strResidue = residueNames3[resid];
for (int i = 0; i < 3; ++i) {
char charWild = strWildcard.charAt(i);
if (charWild == '?')
continue;
if (charWild != strResidue.charAt(i))
return false;
}
return true;
}
public int getResno() {
return resNumber;
}
public char getChainID() {
return chainID;
}
private static Hashtable htResidue = new Hashtable();
static String[] residueNames3 = new String[128];
static short residMax = 0;
static {
for (int i = 0; i < JmolConstants.predefinedResidueNames3.length; ++i)
addResidueName(JmolConstants.predefinedResidueNames3[i]);
}
synchronized static short addResidueName(String name) {
if (residMax == residueNames3.length) {
String[] t;
t = new String[residMax * 2];
System.arraycopy(residueNames3, 0, t, 0, residMax);
residueNames3 = t;
}
short resid = residMax++;
residueNames3[resid] = name;
htResidue.put(name, new Short(resid));
return resid;
}
static short lookupResid(String strRes3) {
Short boxedResid = (Short)htResidue.get(strRes3);
if (boxedResid != null)
return boxedResid.shortValue();
return addResidueName(strRes3);
}
PdbAtom newPdbAtom(int atomIndex, String pdbRecord) {
PdbAtom pdbatom = new PdbAtom(this, pdbRecord);
if (pdbatom.atomid <= 3) {
if (mainchainIndices == null) {
mainchainIndices = new int[4];
for (int i = 4; --i >= 0; )
mainchainIndices[i] = -1;
}
if (mainchainIndices[pdbatom.atomid] == -1)
mainchainIndices[pdbatom.atomid] = atomIndex;
}
return pdbatom;
}
public int getAlphaCarbonIndex() {
if (mainchainIndices == null)
return -1;
return mainchainIndices[1];
}
}
Index: PdbAtom.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/protein/PdbAtom.java,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- PdbAtom.java 21 Oct 2003 19:53:20 -0000 1.5
+++ PdbAtom.java 29 Oct 2003 23:27:07 -0000 1.6
@@ -30,23 +30,17 @@
public class PdbAtom {
- public final static byte STRUCTURE_NONE = 0;
- public final static byte STRUCTURE_HELIX = 1;
- public final static byte STRUCTURE_SHEET = 2;
- public final static byte STRUCTURE_TURN = 3;
-
// FIXME mth -- a very quick/dirty/ugly implementation
// just to get some complex queries running
+ public PdbResidue pdbResidue;
public String recordPdb;
- short resid;
short atomid;
int atomNumber;
- public byte structureType = STRUCTURE_NONE;
- public PdbAtom(String recordPdb) {
+ public PdbAtom(PdbResidue pdbResidue, String recordPdb) {
+ this.pdbResidue = pdbResidue;
this.recordPdb = recordPdb;
- resid = lookupResid(recordPdb.substring(17, 20));
atomid = lookupAtomid(recordPdb.substring(12, 16));
atomNumber = -999999;
try {
@@ -60,7 +54,7 @@
}
public boolean isResidue(String residue) {
- return recordPdb.regionMatches(true, 17, residue, 0, 3);
+ return pdbResidue.isResidue(residue);
}
public String getName() {
@@ -68,20 +62,15 @@
}
public String getResidue() {
- return residueNames3[resid];
+ return pdbResidue.getResidue3();
}
public int getResidueNumber() {
- int num = -1;
- try {
- num = Integer.parseInt(recordPdb.substring(22, 26).trim());
- } catch (NumberFormatException e)
- {}
- return num;
+ return pdbResidue.getResidueNumber();
}
public short getResID() {
- return resid;
+ return pdbResidue.resid;
}
public short getAtomID() {
@@ -97,19 +86,7 @@
}
public boolean isResidueNameMatch(String strWildcard) {
- if (strWildcard.length() != 3) {
- System.err.println("residue wildcard length != 3");
- return false;
- }
- String strResidue = getResidue();
- for (int i = 0; i < 3; ++i) {
- char charWild = strWildcard.charAt(i);
- if (charWild == '?')
- continue;
- if (charWild != strResidue.charAt(i))
- return false;
- }
- return true;
+ return pdbResidue.isResidueNameMatch(strWildcard);
}
public boolean isAtomNameMatch(String strPattern) {
@@ -131,13 +108,7 @@
}
public int getResno() {
- int chain = 0;
- try {
- chain = Integer.parseInt(recordPdb.substring(22, 26).trim());
- } catch (NumberFormatException e) {
- System.out.println("Resno is not an integer:" + recordPdb);
- }
- return chain;
+ return pdbResidue.getResno();
}
public int getTemperature() {
@@ -156,14 +127,18 @@
return recordPdb.charAt(21);
}
- public void setStructureType(byte structureType) {
- this.structureType = structureType;
- }
-
public int getAtomNumber() {
return atomNumber;
}
+ public void setStructureType(byte type) {
+ pdbResidue.structureType = type;
+ }
+
+ public int getProteinStructureType() {
+ return pdbResidue.structureType;
+ }
+
/*
"N", "N", // 0
"CA", "C\u03B1",
@@ -270,34 +245,4 @@
return boxedAtomid.shortValue();
return addAtomName(strAtom);
}
-
- private static Hashtable htResidue = new Hashtable();
- static String[] residueNames3 = new String[128];
- static short residMax = 0;
-
- static {
- for (int i = 0; i < JmolConstants.predefinedResidueNames3.length; ++i)
- addResidueName(JmolConstants.predefinedResidueNames3[i]);
- }
-
- synchronized static short addResidueName(String name) {
- if (residMax == residueNames3.length) {
- String[] t;
- t = new String[residMax * 2];
- System.arraycopy(residueNames3, 0, t, 0, residMax);
- residueNames3 = t;
- }
- short resid = residMax++;
- residueNames3[resid] = name;
- htResidue.put(name, new Short(resid));
- return resid;
- }
-
- short lookupResid(String strRes3) {
- Short boxedResid = (Short)htResidue.get(strRes3);
- if (boxedResid != null)
- return boxedResid.shortValue();
- return addResidueName(strRes3);
- }
-
}
Index: PdbMolecule.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/protein/PdbMolecule.java,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- PdbMolecule.java 7 Oct 2003 18:43:37 -0000 1.5
+++ PdbMolecule.java 29 Oct 2003 23:27:07 -0000 1.6
@@ -26,6 +26,7 @@
import org.openscience.jmol.viewer.datamodel.Frame;
import org.openscience.jmol.viewer.datamodel.Atom;
+import javax.vecmath.Point3f;
import java.util.Hashtable;
import java.util.Vector;
@@ -41,42 +42,42 @@
this.structureRecords = structureRecords;
}
- public void finalize(int atomCount, Atom[] atoms) {
- propogateAtomStructure(atomCount, atoms);
+ public void freeze() {
+ System.out.println("PdbMolecule.freeze() called");
+ if (chainCount != chains.length) {
+ PdbChain[] t = new PdbChain[chainCount];
+ System.arraycopy(chains, 0, t, 0, chainCount);
+ chains = t;
+ }
+ System.out.println("chainCount=" + chainCount);
+ for (int i = chainCount; --i >= 0; )
+ chains[i].freeze();
+ propogateSecondaryStructure();
}
- private void propogateAtomStructure(int atomCount, Atom[] atoms) {
+ private void propogateSecondaryStructure() {
if (structureRecords == null)
return;
-
- Hashtable ht = new Hashtable();
- for (int i = atomCount; --i >= 0; ) {
- PdbAtom pdbatom = atoms[i].pdbAtom;
- if (pdbatom == null)
- continue;
- int residueNum = pdbatom.getResidueNumber();
- Integer boxed = new Integer(residueNum);
- Vector v = (Vector)ht.get(boxed);
- if (v == null)
- ht.put(boxed, v = new Vector());
- v.addElement(pdbatom);
- }
-
for (int i = structureRecords.length; --i >= 0; ) {
String structure = structureRecords[i];
- byte type = PdbAtom.STRUCTURE_NONE;
+ byte type = PdbResidue.STRUCTURE_NONE;
+ int chainIDIndex = 19;
int startIndex = 0;
int endIndex = 0;
if (structure.startsWith("HELIX ")) {
- type = PdbAtom.STRUCTURE_HELIX;
+ System.out.println("HELIX");
+ type = PdbResidue.STRUCTURE_HELIX;
startIndex = 21;
endIndex = 33;
} else if (structure.startsWith("SHEET ")) {
- type = PdbAtom.STRUCTURE_SHEET;
+ System.out.println("SHEET");
+ type = PdbResidue.STRUCTURE_SHEET;
+ chainIDIndex = 21;
startIndex = 22;
endIndex = 33;
} else if (structure.startsWith("TURN ")) {
- type = PdbAtom.STRUCTURE_TURN;
+ System.out.println("TURN");
+ type = PdbResidue.STRUCTURE_TURN;
startIndex = 20;
endIndex = 31;
} else
@@ -88,95 +89,117 @@
start = Integer.parseInt(structure.substring(startIndex, startIndex + 4).trim());
end = Integer.parseInt(structure.substring(endIndex, endIndex + 4).trim());
} catch (NumberFormatException e) {
- System.out.println("number format exception");
+ System.out.println("secondary structure record error");
continue;
}
-
- for (int j = start; j <= end; ++j) {
- Vector v = (Vector)ht.get(new Integer(j));
- if (v == null)
- continue;
- for (int k = v.size(); --k >= 0; ) {
- PdbAtom pdbatom = (PdbAtom)v.elementAt(k);
- pdbatom.setStructureType(type);
- }
+
+ System.out.println("start=" + start + " end=" + end);
+
+ PdbChain chain = getPdbChain(structure.charAt(chainIDIndex));
+ if (chain == null) {
+ System.out.println("secondary structure record error");
+ continue;
}
+ chain.propogateSecondaryStructure(type, start, end);
}
}
- char chainCurrent;
- int alphaCountCurrent;
- Atom[] alphasCurrent;
-
int chainCount = 0;
- char[] chainIDs;
- Atom[][] chains;
+ PdbChain[] chains = new PdbChain[8];
- public Atom[][] getAlphaChains() {
- if (chains == null)
- buildAlphaChains();
- return chains;
- }
-
- void buildAlphaChains() {
- initializeAlphaChains();
- int atomCount = frame.getAtomCount();
- for (int i = 0; i < atomCount; ++i) {
- Atom atom = frame.getAtomAt(i);
- PdbAtom pdbAtom = atom.pdbAtom;
- if (pdbAtom == null || pdbAtom.getAtomID() != 1) // FIXME!! needs a symbol
- continue;
- addAlpha(atom);
- }
- finalizeAlphaChains();
+ public int getChainCount() {
+ return chainCount;
+ }
+
+ public PdbResidue[] getMainchain(int chainIndex) {
+ return chains[chainIndex].getMainchain();
+ }
+
+ /*
+ Point3f[][] midpointsChains;
+
+ public Point3f[][] getMidpointsChains() {
+ calcMidpoints();
+ return midpointsChains;
}
- void initializeAlphaChains() {
- chainCount = 0;
- chainIDs = new char[8];
- chains = new Atom[8][];
+ public Point3f[] getMidpointsChain(int chainIndex) {
+ calcMidpoints();
+ return midpointsChains[chainIndex];
+ }
+ */
- alphaCountCurrent = 0;
- alphasCurrent = new Atom[64];
- chainCurrent = '\u0000';
+ /*
+ void calcMidpoints() {
+ // buildAlphaChains();
+ midpointsChains = new Point3f[chainIDCount][];
+ for (int i = chainIDCount; --i >= 0; ) {
+ Atom[] alphaChain = alphaChains[i];
+ int chainLength = alphaChain.length;
+ calcMidpoints(alphaChain, midpointsChains[i] = new Point3f[chainLength + 1]);
+ }
}
- void addAlpha(Atom atom) {
- char chain = atom.pdbAtom.getChainID();
- if (chain != chainCurrent) {
- if (alphaCountCurrent > 0)
- addCurrentChain();
- alphaCountCurrent = 0;
- chainCurrent = chain;
+ void calcMidpoints(Atom[] alphas, Point3f[] midpoints) {
+ int chainLength = alphas.length;
+ Point3f atomPrevious = alphas[0].point3f;
+ midpoints[0] = atomPrevious;
+ for (int i = 1; i < chainLength; ++i) {
+ Point3f mid = midpoints[i] = new Point3f(atomPrevious);
+ atomPrevious = alphas[i].point3f;
+ mid.add(atomPrevious);
+ mid.scale(0.5f);
}
- if (alphaCountCurrent == alphasCurrent.length) {
- Atom[] t = new Atom[alphaCountCurrent * 2];
- System.arraycopy(alphasCurrent, 0, t, 0, alphaCountCurrent);
- alphasCurrent = t;
+ midpoints[chainLength] = atomPrevious;
+ }
+ */
+
+ PdbChain getPdbChain(char chainID) {
+ for (int i = chainCount; --i >= 0; ) {
+ PdbChain chain = chains[i];
+ if (chain.chainID == chainID)
+ return chain;
}
- alphasCurrent[alphaCountCurrent++] = atom;
+ return null;
}
- void addCurrentChain() {
+ PdbChain getOrAllocPdbChain(char chainID) {
+ PdbChain chain = getPdbChain(chainID);
+ if (chain != null)
+ return chain;
if (chainCount == chains.length) {
- Atom[][] t = new Atom[chainCount * 2][];
+ PdbChain[] t = new PdbChain[chainCount * 2];
System.arraycopy(chains, 0, t, 0, chainCount);
chains = t;
}
- Atom[] newChain = new Atom[alphaCountCurrent];
- System.arraycopy(alphasCurrent, 0, newChain, 0, alphaCountCurrent);
- chains[chainCount] = newChain;
- chainIDs[chainCount++] = chainCurrent;
+ return chains[chainCount++] = new PdbChain(chainID);
}
- void finalizeAlphaChains() {
- if (alphaCountCurrent != 0)
- addCurrentChain();
- if (chainCount != chains.length) {
- Atom[][] t = new Atom[chainCount][];
- System.arraycopy(chains, 0, t, 0, chainCount);
- chains = t;
+
+ char chainIDCurrent = '\uFFFF';
+ int resNumberCurrent = -1;
+ PdbResidue pdbResidueCurrent;
+
+ PdbResidue allocResidue(char chainID, int resNumber, String residue3) {
+ PdbChain chain = getOrAllocPdbChain(chainID);
+ PdbResidue residue = new PdbResidue(chainID, resNumber, residue3);
+ chain.addResidue(residue);
+ return residue;
+ }
+
+ public PdbAtom getPdbAtom(int atomIndex, String pdbRecord) {
+ try {
+ char chainID = pdbRecord.charAt(21);
+ int resNumber = Integer.parseInt(pdbRecord.substring(22, 26).trim());
+ if (chainID != chainIDCurrent || resNumber != resNumberCurrent) {
+ pdbResidueCurrent = allocResidue(chainID, resNumber, pdbRecord.substring(17, 20));
+ chainIDCurrent = chainID;
+ resNumberCurrent = resNumber;
+ }
+ return pdbResidueCurrent.newPdbAtom(atomIndex, pdbRecord);
+ } catch (NumberFormatException e) {
+ System.out.println("bad residue number in: " + pdbRecord);
}
- alphasCurrent = null;
+ return null;
}
}
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