/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 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
import java.awt.*;
import jalview.datamodel.*;
+import jalview.io.FileParse;
-public class PDBfile
- extends jalview.io.AlignFile
+public class PDBfile extends jalview.io.AlignFile
{
public Vector chains;
+
public String id;
/**
* set to true to add chain alignment annotation as visible annotation.
*/
- boolean VisibleChainAnnotation=false;
- public PDBfile(String inFile, String inType)
- throws IOException
+ boolean VisibleChainAnnotation = false;
+
+ public PDBfile(String inFile, String inType) throws IOException
{
super(inFile, inType);
}
+ public PDBfile(FileParse source) throws IOException
+ {
+ super(source);
+ }
+
public String print()
{
return null;
}
- public void parse()
- throws IOException
+ public void parse() throws IOException
{
+ // TODO set the filename sensibly
+ id = (inFile == null || inFile.getName()==null || inFile.getName().length()==0) ? "PDBFILE" : inFile.getName();
try
{
chains = new Vector();
String line;
boolean modelFlag = false;
boolean terFlag = false;
+ String lastID="";
int index = 0;
- while ( (line = nextLine()) != null)
+ String atomnam=null;
+ while ((line = nextLine()) != null)
{
if (line.indexOf("HEADER") == 0)
{
- id = line.substring(62, 67).trim();
- continue;
+ if (line.length()>62)
+ {
+ String tid;
+ if (line.length()>67) {
+ tid = line.substring(62, 67).trim();
+ } else {
+ tid=line.substring(62).trim();
+ }
+ if (tid.length()>0)
+ {
+ id = tid;
+ }
+ continue;
+ }
}
// Were we to do anything with SEQRES - we start it here
if (line.indexOf("SEQRES") == 0)
break;
}
if (line.indexOf("ATOM") == 0
- || (line.indexOf("HETATM") == 0 && !terFlag)
- )
+ || (line.indexOf("HETATM") == 0 && !terFlag))
{
terFlag = false;
- //Jalview is only interested in CA bonds????
- if (!line.substring(12, 15).trim().equals("CA"))
+ // Jalview is only interested in CA bonds????
+ atomnam = line.substring(12, 15).trim();
+ if (!atomnam.equals("CA") && !atomnam.equals("P"))
{
continue;
}
tmpchain = findChain(tmpatom.chain);
if (tmpchain != null)
{
+ if (tmpatom.resNumIns.trim().equals(lastID))
+ {
+ // phosphorylated protein - seen both CA and P..
+ continue;
+ }
tmpchain.atoms.addElement(tmpatom);
}
else
chains.addElement(tmpchain);
tmpchain.atoms.addElement(tmpatom);
}
+ lastID = tmpatom.resNumIns.trim();
}
index++;
}
}
for (int i = 0; i < chains.size(); i++)
{
- SequenceI dataset = ( (PDBChain) chains.elementAt(i)).
- sequence;
+ SequenceI dataset = ((PDBChain) chains.elementAt(i)).sequence;
dataset.setName(id + "|" + dataset.getName());
PDBEntry entry = new PDBEntry();
entry.setId(id);
entry.setFile(inFile.getAbsolutePath());
}
dataset.addPDBId(entry);
- SequenceI chainseq = dataset.deriveSequence(); // PDBChain objects maintain reference to dataset
+ SequenceI chainseq = dataset.deriveSequence(); // PDBChain objects
+ // maintain reference to
+ // dataset
seqs.addElement(chainseq);
AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
- if (chainannot!=null)
+ if (chainannot != null)
{
- for (int ai=0; ai<chainannot.length; ai++)
+ for (int ai = 0; ai < chainannot.length; ai++)
{
- chainannot[ai].visible=VisibleChainAnnotation;
+ chainannot[ai].visible = VisibleChainAnnotation;
annotations.addElement(chainannot[ai]);
}
}
}
- }
- catch (OutOfMemoryError er)
+ } catch (OutOfMemoryError er)
{
System.out.println("OUT OF MEMORY LOADING PDB FILE");
throw new IOException("Out of memory loading PDB File");
{
for (int i = 0; i < chains.size(); i++)
{
- ( (PDBChain) chains.elementAt(i)).makeResidueList();
+ ((PDBChain) chains.elementAt(i)).makeResidueList();
}
}
{
for (int i = 0; i < chains.size(); i++)
{
- ( (PDBChain) chains.elementAt(i)).makeCaBondList();
+ ((PDBChain) chains.elementAt(i)).makeCaBondList();
}
}
{
for (int i = 0; i < chains.size(); i++)
{
- if ( ( (PDBChain) chains.elementAt(i)).id.equals(id))
+ if (((PDBChain) chains.elementAt(i)).id.equals(id))
{
return (PDBChain) chains.elementAt(i);
}
{
for (int i = 0; i < chains.size(); i++)
{
- ( (PDBChain) chains.elementAt(i)).setChargeColours();
+ ((PDBChain) chains.elementAt(i)).setChargeColours();
}
}
{
for (int i = 0; i < chains.size(); i++)
{
- ( (PDBChain) chains.elementAt(i)).setChainColours(cs);
+ ((PDBChain) chains.elementAt(i)).setChainColours(cs);
}
}
{
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