X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBfile.java;h=f5a0255094f23ab858ddb3bb5b9df9a7e232aad6;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=36eecb8471f24e76b50b4659232b69456c7dd6a5;hpb=1e8006f71404e0afb34bcb2d754abce7f6d3fe25;p=jalview.git
diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 36eecb8..f5a0255 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -1,169 +1,257 @@
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 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.io.AppletFormatAdapter;
-import jalview.datamodel.*;
-
-import java.io.*;
-
-import java.net.*;
-
-import java.util.*;
-import java.awt.Color;
-
-
-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
- {
- chains = new Vector();
-
- PDBChain tmpchain;
- String line;
- boolean modelFlag = false;
- boolean terFlag = false;
-
-
- int index = 0;
- while((line = nextLine())!=null)
- {
- if (line.indexOf("HEADER") == 0)
- {
- id = line.substring(62, 67).trim();
- continue;
- }
-
- 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"))
- {
- continue;
- }
-
- Atom tmpatom = new Atom(line);
- tmpchain = findChain(tmpatom.chain);
- if (tmpchain != null)
- {
- tmpchain.atoms.addElement(tmpatom);
- }
- else
- {
- tmpchain = new PDBChain(tmpatom.chain);
- chains.addElement(tmpchain);
- tmpchain.atoms.addElement(tmpatom);
- }
- }
- index ++;
- }
-
- makeResidueList();
- makeCaBondList();
-
- for (int i = 0; i < chains.size(); i++)
- {
- SequenceI seq = ( (PDBChain) chains.elementAt(i)).
- sequence;
- seq.setName(id + "|" + seq.getName());
- Sequence dataset = new Sequence(seq.
- getName(),
- seq.getSequence().toString(), seq.getStart(), seq.getEnd());
-
- PDBEntry entry = new PDBEntry();
- entry.setId(id);
- entry.setFile(inFile.getAbsolutePath());
-
- seq.setDatasetSequence(dataset);
- dataset.addPDBId(entry);
-
- getSeqs().addElement(seq);
- }
- }
-
- public void makeResidueList() {
- for (int i = 0; i < chains.size(); i++) {
- ((PDBChain) chains.elementAt(i)).makeResidueList();
- }
- }
-
- public void makeCaBondList() {
- for (int i = 0; i < chains.size(); i++) {
- ((PDBChain) chains.elementAt(i)).makeCaBondList();
- }
- }
-
- 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);
- }
- }
-
- 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 setChainColours()
- {
- for (int i = 0; i < chains.size(); i++)
- {
- ((PDBChain) chains.elementAt(i)).setChainColours(
- Color.getHSBColor(1.0f / (float)i, .4f, 1.0f)
- );
- }
- }
-}
+/*
+ * 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.AlignmentAnnotation;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.SequenceI;
+import jalview.io.FileParse;
+import jalview.io.StructureFile;
+import jalview.util.MessageManager;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
+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 PDBfile(boolean addAlignmentAnnotations, boolean predictSecStr,
+ boolean externalSecStr, String dataObject, String protocol)
+ throws IOException
+ {
+ super(false, dataObject, protocol);
+ addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
+ doParse();
+ }
+
+ public PDBfile(boolean addAlignmentAnnotations, boolean predictSecStr,
+ boolean externalSecStr, FileParse source) throws IOException
+ {
+ super(false, source);
+ addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
+ doParse();
+ }
+
+ @Override
+ public String print()
+ {
+ return null;
+ }
+
+ @Override
+ public void parse() throws IOException
+ {
+ setDbRefType(DBRefSource.PDB);
+ // TODO set the filename sensibly - try using data source name.
+ setId(safeName(getDataName()));
+
+ 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 indexx = 0;
+ String atomnam = null;
+ try
+ {
+ while ((line = nextLine()) != null)
+ {
+ if (line.indexOf("HEADER") == 0)
+ {
+ 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)
+ {
+ setId(tid);
+ }
+ 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????
+ atomnam = line.substring(12, 15).trim();
+ if (!atomnam.equals("CA") && !atomnam.equals("P"))
+ {
+ continue;
+ }
+
+ 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++;
+ }
+
+ makeResidueList();
+ makeCaBondList();
+
+ if (getId() == null)
+ {
+ setId(inFile.getName());
+ }
+ for (PDBChain chain : getChains())
+ {
+ SequenceI chainseq = postProcessChain(chain);
+ if (isRNA(chainseq))
+ {
+ rna.add(chainseq);
+ }
+ 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 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)
+ {
+ 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);
+ }
+ }
+ }
+ }
+
+}