/*
- * 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
+ * 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.
- *
- * 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.
- *
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package MCview;
-import java.io.*;
-import java.util.*;
+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.awt.*;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
-import jalview.datamodel.*;
-
-public class PDBfile
- extends jalview.io.AlignFile
+public class PDBfile extends StructureFile
{
- public Vector chains;
- public String id;
+ 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(String inFile, String inType)
- throws IOException
+ public PDBfile(boolean addAlignmentAnnotations, boolean predictSecStr,
+ boolean externalSecStr, FileParse source) throws IOException
{
- super(inFile, inType);
+ super(false, source);
+ addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
+ doParse();
}
+ @Override
public String print()
{
return null;
}
- public void parse()
- throws IOException
+ @Override
+ public void parse() throws IOException
{
- try
- {
- chains = new Vector();
+ 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<PDBChain>());
+ List<SequenceI> rna = new ArrayList<SequenceI>();
+ List<SequenceI> prot = new ArrayList<SequenceI>();
+ 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)
{
- 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)
+ {
+ setId(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;
}
Atom tmpatom = new Atom(line);
- tmpchain = findChain(tmpatom.chain);
- if (tmpchain != null)
+ try
{
+ tmpchain = findChain(tmpatom.chain);
+ if (tmpatom.resNumIns.trim().equals(lastID))
+ {
+ // phosphorylated protein - seen both CA and P..
+ continue;
+ }
tmpchain.atoms.addElement(tmpatom);
- }
- else
+ } catch (Exception e)
{
- tmpchain = new PDBChain(id, tmpatom.chain);
- chains.addElement(tmpchain);
+ tmpchain = new PDBChain(getId(), tmpatom.chain);
+ getChains().add(tmpchain);
tmpchain.atoms.addElement(tmpatom);
}
+ lastID = tmpatom.resNumIns.trim();
}
index++;
}
makeResidueList();
makeCaBondList();
- if (id == null)
+ if (getId() == null)
{
- id = inFile.getName();
+ setId(inFile.getName());
}
- for (int i = 0; i < chains.size(); i++)
+ for (PDBChain chain : getChains())
{
- SequenceI dataset = ( (PDBChain) chains.elementAt(i)).
- sequence;
- dataset.setName(id + "|" + dataset.getName());
- PDBEntry entry = new PDBEntry();
- entry.setId(id);
- if (inFile != null)
+ SequenceI chainseq = postProcessChain(chain);
+ if (isRNA(chainseq))
{
- entry.setFile(inFile.getAbsolutePath());
+ rna.add(chainseq);
+ }
+ else
+ {
+ prot.add(chainseq);
}
- dataset.addPDBId(entry);
- getSeqs().addElement(dataset.deriveSequence()); // PDBChain objects maintain reference to dataset
}
- }
- catch (OutOfMemoryError er)
+ if (predictSecondaryStructure)
+ {
+ addSecondaryStructure(rna, prot);
+ }
+ } 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++)
+ throw new IOException(
+ MessageManager
+ .getString("exception.outofmemory_loading_pdb_file"));
+ } catch (NumberFormatException ex)
{
- ( (PDBChain) chains.elementAt(i)).makeResidueList();
+ if (line != null)
+ {
+ System.err.println("Couldn't read number from line:");
+ System.err.println(line);
+ }
}
+ markCalcIds();
}
- public void makeCaBondList()
- {
- for (int i = 0; i < chains.size(); i++)
- {
- ( (PDBChain) chains.elementAt(i)).makeCaBondList();
- }
- }
+ /**
+ * Process a parsed chain to construct and return a Sequence, and add it to
+ * the list of sequences parsed.
+ *
+ * @param chain
+ * @return
+ */
- public PDBChain findChain(String id)
+ public static boolean isCalcIdHandled(String calcId)
{
- for (int i = 0; i < chains.size(); i++)
- {
- if ( ( (PDBChain) chains.elementAt(i)).id.equals(id))
- {
- return (PDBChain) chains.elementAt(i);
- }
- }
-
- return null;
+ return calcId != null && (CALC_ID_PREFIX.equals(calcId));
}
- public void setChargeColours()
+ public static boolean isCalcIdForFile(AlignmentAnnotation alan,
+ String pdbFile)
{
- for (int i = 0; i < chains.size(); i++)
- {
- ( (PDBChain) chains.elementAt(i)).setChargeColours();
- }
+ return alan.getCalcId() != null
+ && CALC_ID_PREFIX.equals(alan.getCalcId())
+ && pdbFile.equals(alan.getProperty("PDBID"));
}
- public void setColours(jalview.schemes.ColourSchemeI cs)
+ public static String relocateCalcId(String calcId,
+ Hashtable<String, String> alreadyLoadedPDB) throws Exception
{
- for (int i = 0; i < chains.size(); i++)
- {
- ( (PDBChain) chains.elementAt(i)).setChainColours(cs);
- }
+ 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);
}
- public void setChainColours()
+ private void markCalcIds()
{
- for (int i = 0; i < chains.size(); i++)
+ for (SequenceI sq : seqs)
{
- ( (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);
+ }
+ }
}
}
+
}
git://source.jalview.org / jalview.git / blobdiff