/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program 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 General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
package MCview;
-import jalview.datamodel.*;
-
import java.io.*;
-
import java.util.*;
-import java.awt.Color;
+import java.awt.*;
-public class PDBfile extends jalview.io.AlignFile {
- public Vector chains;
- public String id;
+import jalview.datamodel.*;
- public PDBfile(String inFile, String inType) throws IOException
+public class PDBfile
+ extends jalview.io.AlignFile
+{
+ public Vector chains;
+ public String id;
+
+ public PDBfile(String inFile, String inType)
+ throws IOException
+ {
+ super(inFile, inType);
+ }
+
+ public String print()
+ {
+ return null;
+ }
+
+ public void parse()
+ throws IOException
+ {
+ try
{
- super(inFile, inType);
- }
+ chains = new Vector();
- public String print()
- {
- return null;
- }
+ PDBChain tmpchain;
+ String line;
+ boolean modelFlag = false;
+ boolean terFlag = false;
- public void parse() throws IOException
- {
- try{
- chains = new Vector();
+ int index = 0;
+ while ( (line = nextLine()) != null)
+ {
+ if (line.indexOf("HEADER") == 0)
+ {
+ id = line.substring(62, 67).trim();
+ continue;
+ }
+ // Were we to do anything with SEQRES - we start it here
+ if (line.indexOf("SEQRES") == 0)
+ {
+ }
+
+ if (line.indexOf("MODEL") == 0)
+ {
+ modelFlag = true;
+ }
- PDBChain tmpchain;
- String line;
- boolean modelFlag = false;
- boolean terFlag = false;
+ if (line.indexOf("TER") == 0)
+ {
+ terFlag = true;
+ }
- int index = 0;
- while ( (line = nextLine()) != null)
+ if (modelFlag && line.indexOf("ENDMDL") == 0)
{
- if (line.indexOf("HEADER") == 0)
+ break;
+ }
+ if (line.indexOf("ATOM") == 0
+ || (line.indexOf("HETATM") == 0 && !terFlag)
+ )
+ {
+ terFlag = false;
+
+ //Jalview is only interested in CA bonds????
+ if (!line.substring(12, 15).trim().equals("CA"))
{
- id = line.substring(62, 67).trim();
continue;
}
- // Were we to do anything with SEQRES - we start it here
- if (line.indexOf("SEQRES") == 0) {
+
+ Atom tmpatom = new Atom(line);
+ tmpchain = findChain(tmpatom.chain);
+ if (tmpchain != null)
+ {
+ tmpchain.atoms.addElement(tmpatom);
}
-
- if (line.indexOf("MODEL") == 0)
- modelFlag = true;
-
- if (line.indexOf("TER") == 0)
- terFlag = true;
-
- if (modelFlag && line.indexOf("ENDMDL") == 0)
- break;
- if (line.indexOf("ATOM") == 0
- || (line.indexOf("HETATM") == 0 && !terFlag)
- )
+ else
{
- terFlag = false;
-
- //Jalview is only interested in CA bonds????
- if (!line.substring(12, 15).trim().equals("CA"))
- {
- continue;
- }
-
- Atom tmpatom = new Atom(line);
- tmpchain = findChain(tmpatom.chain);
- if (tmpchain != null)
- {
- tmpchain.atoms.addElement(tmpatom);
- }
- else
- {
- tmpchain = new PDBChain(id,tmpatom.chain);
- chains.addElement(tmpchain);
- tmpchain.atoms.addElement(tmpatom);
- }
+ tmpchain = new PDBChain(id, tmpatom.chain);
+ chains.addElement(tmpchain);
+ tmpchain.atoms.addElement(tmpatom);
}
- index++;
}
+ index++;
+ }
- makeResidueList();
- makeCaBondList();
+ makeResidueList();
+ makeCaBondList();
- if (id == null)
- {
- id = inFile.getName();
- }
- for (int i = 0; i < chains.size(); i++)
+ if (id == null)
+ {
+ id = inFile.getName();
+ }
+ for (int i = 0; i < chains.size(); i++)
+ {
+ SequenceI dataset = ( (PDBChain) chains.elementAt(i)).
+ sequence;
+ dataset.setName(id + "|" + dataset.getName());
+ PDBEntry entry = new PDBEntry();
+ entry.setId(id);
+ if (inFile != null)
{
- SequenceI dataset = ( (PDBChain) chains.elementAt(i)).
- sequence;
- dataset.setName(id + "|" + dataset.getName());
- PDBEntry entry = new PDBEntry();
- entry.setId(id);
- if (inFile != null)
- entry.setFile(inFile.getAbsolutePath());
- dataset.addPDBId(entry);
- getSeqs().addElement(dataset.deriveSequence()); // PDBChain objects maintain reference to dataset
+ entry.setFile(inFile.getAbsolutePath());
}
- }catch(OutOfMemoryError er)
- {
- System.out.println("OUT OF MEMORY LOADING PDB FILE");
- throw new IOException("Out of memory loading PDB File");
+ dataset.addPDBId(entry);
+ getSeqs().addElement(dataset.deriveSequence()); // PDBChain objects maintain reference to dataset
}
}
-
- public void makeResidueList() {
- for (int i = 0; i < chains.size(); i++) {
- ((PDBChain) chains.elementAt(i)).makeResidueList();
- }
+ catch (OutOfMemoryError er)
+ {
+ System.out.println("OUT OF MEMORY LOADING PDB FILE");
+ throw new IOException("Out of memory loading PDB File");
}
+ }
- public void makeCaBondList() {
- for (int i = 0; i < chains.size(); i++) {
- ((PDBChain) chains.elementAt(i)).makeCaBondList();
- }
+ public void makeResidueList()
+ {
+ for (int i = 0; i < chains.size(); i++)
+ {
+ ( (PDBChain) chains.elementAt(i)).makeResidueList();
}
+ }
- public PDBChain findChain(String id) {
- for (int i = 0; i < chains.size(); i++) {
- if (((PDBChain) chains.elementAt(i)).id.equals(id)) {
- return (PDBChain) chains.elementAt(i);
- }
- }
+ public void makeCaBondList()
+ {
+ for (int i = 0; i < chains.size(); i++)
+ {
+ ( (PDBChain) chains.elementAt(i)).makeCaBondList();
+ }
+ }
- return null;
+ public PDBChain findChain(String id)
+ {
+ for (int i = 0; i < chains.size(); i++)
+ {
+ if ( ( (PDBChain) chains.elementAt(i)).id.equals(id))
+ {
+ return (PDBChain) chains.elementAt(i);
+ }
}
- public void setChargeColours() {
- for (int i = 0; i < chains.size(); i++) {
- ((PDBChain) chains.elementAt(i)).setChargeColours();
- }
+ return null;
+ }
+
+ public void setChargeColours()
+ {
+ for (int i = 0; i < chains.size(); i++)
+ {
+ ( (PDBChain) chains.elementAt(i)).setChargeColours();
}
+ }
- public void setColours(jalview.schemes.ColourSchemeI cs) {
- for (int i = 0; i < chains.size(); i++) {
- ((PDBChain) chains.elementAt(i)).setChainColours(cs);
- }
+ public void setColours(jalview.schemes.ColourSchemeI cs)
+ {
+ for (int i = 0; i < chains.size(); i++)
+ {
+ ( (PDBChain) chains.elementAt(i)).setChainColours(cs);
}
+ }
- public void setChainColours()
+ public void setChainColours()
+ {
+ for (int i = 0; i < chains.size(); i++)
{
- for (int i = 0; i < chains.size(); i++)
- {
- ((PDBChain) chains.elementAt(i)).setChainColours(
- Color.getHSBColor(1.0f / (float)i, .4f, 1.0f)
- );
- }
+ ( (PDBChain) chains.elementAt(i)).setChainColours(
+ Color.getHSBColor(1.0f / (float) i, .4f, 1.0f)
+ );
}
+ }
}
git://source.jalview.org / jalview.git / blobdiff