X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBfile.java;h=ebc52aaf0aa0643410590de2c330fd5611782160;hb=39b4859e1a1b011af5d06058461db4d075acb578;hp=26d44b1a976a34866baa6ab4b9286a073b3cbb71;hpb=f8ccad28f3a8fc90f4f0a13ec0c8d230dec6b230;p=jalview.git
diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 26d44b1..ebc52aa 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -1,170 +1,257 @@
/*
-* 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview 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 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview 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 Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package MCview;
-import jalview.datamodel.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.FileParse;
+import jalview.io.StructureFile;
+import jalview.util.MessageManager;
-import java.io.*;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
-import java.util.*;
-import java.awt.Color;
+public class PDBfile extends StructureFile
+{
+ private static String CALC_ID_PREFIX = "JalviewPDB";
+ public PDBfile(boolean addAlignmentAnnotations,
+ boolean predictSecondaryStructure, boolean externalSecStr)
+ {
+ super();
+ addSettings(addAlignmentAnnotations, predictSecondaryStructure,
+ externalSecStr);
+ }
-public class PDBfile extends jalview.io.AlignFile {
- public Vector chains;
- public String id;
+ public PDBfile(boolean addAlignmentAnnotations, boolean predictSecStr,
+ boolean externalSecStr, String dataObject,
+ DataSourceType sourceType) throws IOException
+ {
+ super(false, dataObject, sourceType);
+ addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
+ doParse();
+ }
- public PDBfile(String inFile, String inType) throws IOException
- {
- super(inFile, inType);
- }
+ public PDBfile(boolean addAlignmentAnnotations, boolean predictSecStr,
+ boolean externalSecStr, FileParse source) throws IOException
+ {
+ super(false, source);
+ addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
+ doParse();
+ }
- public String print()
- {
- return null;
- }
+ @Override
+ public String print(SequenceI[] seqs, boolean jvSuffix)
+ {
+ return null;
+ }
- public void parse() throws IOException
- {
- try{
- chains = new Vector();
+ @Override
+ public void parse() throws IOException
+ {
+ setDbRefType(DBRefSource.PDB);
+ // TODO set the filename sensibly - try using data source name.
+ setId(safeName(getDataName()));
- PDBChain tmpchain;
- String line;
- boolean modelFlag = false;
- boolean terFlag = false;
+ setChains(new Vector());
+ List rna = new ArrayList();
+ List prot = new ArrayList();
+ PDBChain tmpchain;
+ String line = null;
+ boolean modelFlag = false;
+ boolean terFlag = false;
+ String lastID = "";
- int index = 0;
- while ( (line = nextLine()) != null)
+ int indexx = 0;
+ String atomnam = null;
+ try
+ {
+ while ((line = nextLine()) != null)
+ {
+ if (line.indexOf("HEADER") == 0)
{
- if (line.indexOf("HEADER") == 0)
+ if (line.length() > 62)
{
- 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;
-
- if (line.indexOf("TER") == 0)
- terFlag = true;
-
- if (modelFlag && line.indexOf("ENDMDL") == 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"))
+ String tid;
+ if (line.length() > 67)
{
- continue;
+ tid = line.substring(62, 67).trim();
}
-
- Atom tmpatom = new Atom(line);
- tmpchain = findChain(tmpatom.chain);
- if (tmpchain != null)
+ else
{
- tmpchain.atoms.addElement(tmpatom);
+ tid = line.substring(62).trim();
}
- else
+ if (tid.length() > 0)
{
- tmpchain = new PDBChain(id,tmpatom.chain);
- chains.addElement(tmpchain);
- tmpchain.atoms.addElement(tmpatom);
+ setId(tid);
}
+ continue;
}
- index++;
}
-
- makeResidueList();
- makeCaBondList();
-
- if (id == null)
+ // Were we to do anything with SEQRES - we start it here
+ if (line.indexOf("SEQRES") == 0)
{
- id = inFile.getName();
}
- for (int i = 0; i < chains.size(); i++)
+
+ if (line.indexOf("MODEL") == 0)
{
- 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
+ modelFlag = true;
}
- }catch(OutOfMemoryError er)
- {
- System.out.println("OUT OF MEMORY LOADING PDB FILE");
- throw new IOException("Out of memory loading PDB File");
- }
- }
- public void makeResidueList() {
- for (int i = 0; i < chains.size(); i++) {
- ((PDBChain) chains.elementAt(i)).makeResidueList();
+ if (line.indexOf("TER") == 0)
+ {
+ terFlag = true;
}
- }
- public void makeCaBondList() {
- for (int i = 0; i < chains.size(); i++) {
- ((PDBChain) chains.elementAt(i)).makeCaBondList();
+ if (modelFlag && line.indexOf("ENDMDL") == 0)
+ {
+ break;
}
- }
+ if (line.indexOf("ATOM") == 0
+ || (line.indexOf("HETATM") == 0 && !terFlag))
+ {
+ terFlag = false;
+
+ // Jalview is only interested in CA bonds????
+ atomnam = line.substring(12, 15).trim();
+ if (!atomnam.equals("CA") && !atomnam.equals("P"))
+ {
+ continue;
+ }
- 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);
+ Atom tmpatom = new Atom(line);
+ try
+ {
+ tmpchain = findChain(tmpatom.chain);
+ if (tmpatom.resNumIns.trim().equals(lastID))
+ {
+ // phosphorylated protein - seen both CA and P..
+ continue;
}
+ tmpchain.atoms.addElement(tmpatom);
+ } catch (Exception e)
+ {
+ tmpchain = new PDBChain(getId(), tmpatom.chain);
+ getChains().add(tmpchain);
+ tmpchain.atoms.addElement(tmpatom);
+ }
+ lastID = tmpatom.resNumIns.trim();
}
+ index++;
+ }
- return null;
- }
+ makeResidueList();
+ makeCaBondList();
- public void setChargeColours() {
- for (int i = 0; i < chains.size(); i++) {
- ((PDBChain) chains.elementAt(i)).setChargeColours();
+ if (getId() == null)
+ {
+ setId(inFile.getName());
+ }
+ for (PDBChain chain : getChains())
+ {
+ SequenceI chainseq = postProcessChain(chain);
+ if (isRNA(chainseq))
+ {
+ rna.add(chainseq);
}
- }
-
- public void setColours(jalview.schemes.ColourSchemeI cs) {
- for (int i = 0; i < chains.size(); i++) {
- ((PDBChain) chains.elementAt(i)).setChainColours(cs);
+ else
+ {
+ prot.add(chainseq);
}
+ }
+ if (predictSecondaryStructure)
+ {
+ addSecondaryStructure(rna, prot);
+ }
+ } catch (OutOfMemoryError er)
+ {
+ System.out.println("OUT OF MEMORY LOADING PDB FILE");
+ throw new IOException(MessageManager
+ .getString("exception.outofmemory_loading_pdb_file"));
+ } catch (NumberFormatException ex)
+ {
+ if (line != null)
+ {
+ System.err.println("Couldn't read number from line:");
+ System.err.println(line);
+ }
}
+ markCalcIds();
+ }
+
+ /**
+ * Process a parsed chain to construct and return a Sequence, and add it to
+ * the list of sequences parsed.
+ *
+ * @param chain
+ * @return
+ */
+
+ public static boolean isCalcIdHandled(String calcId)
+ {
+ return calcId != null && (CALC_ID_PREFIX.equals(calcId));
+ }
- public void setChainColours()
+ public static boolean isCalcIdForFile(AlignmentAnnotation alan,
+ String pdbFile)
+ {
+ return alan.getCalcId() != null
+ && CALC_ID_PREFIX.equals(alan.getCalcId())
+ && pdbFile.equals(alan.getProperty("PDBID"));
+ }
+
+ public static String relocateCalcId(String calcId,
+ Hashtable alreadyLoadedPDB) throws Exception
+ {
+ int s = CALC_ID_PREFIX.length(),
+ end = calcId.indexOf(CALC_ID_PREFIX, s);
+ String between = calcId.substring(s, end - 1);
+ return CALC_ID_PREFIX + alreadyLoadedPDB.get(between) + ":"
+ + calcId.substring(end);
+ }
+
+ private void markCalcIds()
+ {
+ for (SequenceI sq : seqs)
{
- for (int i = 0; i < chains.size(); i++)
- {
- ((PDBChain) chains.elementAt(i)).setChainColours(
- Color.getHSBColor(1.0f / (float)i, .4f, 1.0f)
- );
+ if (sq.getAnnotation() != null)
+ {
+ for (AlignmentAnnotation aa : sq.getAnnotation())
+ {
+ String oldId = aa.getCalcId();
+ if (oldId == null)
+ {
+ oldId = "";
+ }
+ aa.setCalcId(CALC_ID_PREFIX);
+ aa.setProperty("PDBID", getId());
+ aa.setProperty("oldCalcId", oldId);
}
+ }
}
+ }
+
}