-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-\r
-package MCview;\r
-\r
-import jalview.datamodel.*;\r
-import java.io.*;\r
-import java.net.*;\r
-import java.util.*;\r
-\r
-\r
-public class PDBfile extends jalview.io.FileParse {\r
-\r
- public Vector chains = new Vector();\r
-\r
- Vector lineArray = new Vector();\r
-\r
- public PDBfile(String [] lines)\r
- {\r
- for(int i=0; i<lines.length; i++)\r
- lineArray.addElement(lines[i]);\r
-\r
- noLines = lineArray.size();\r
- parse();\r
- }\r
-\r
- public PDBfile(String inFile, String inType) throws IOException {\r
-\r
- super(inFile,inType);\r
-\r
- String line;\r
- this.lineArray = new Vector();\r
- BufferedReader dataIn;\r
-\r
- if (inType.equals("File"))\r
- dataIn = new BufferedReader(new FileReader( inFile ));\r
-\r
- else\r
- {\r
- URL url = new URL(inFile);\r
- this.fileSize = 0;\r
- dataIn = new BufferedReader(new InputStreamReader(url.openStream()));\r
- }\r
-\r
- while ((line = dataIn.readLine()) != null) {\r
- lineArray.addElement(line);\r
- }\r
- noLines = lineArray.size();\r
-\r
- parse();\r
-\r
-}\r
-\r
-\r
- public void parse() {\r
-\r
- for (int i = 0; i < lineArray.size(); i++) {\r
- StringTokenizer str = new StringTokenizer(lineArray.elementAt(i).toString());\r
- if (str.hasMoreTokens()) {\r
- String inStr = str.nextToken();\r
-\r
- if (inStr.indexOf("ATOM") != -1) {\r
- try {\r
- myAtom tmpatom = new myAtom(str);\r
- if (findChain(tmpatom.chain) != null) {\r
- // System.out.println("Adding to chain " + tmpatom.chain);\r
- findChain(tmpatom.chain).atoms.addElement(tmpatom);\r
- } else {\r
- // System.out.println("Making chain " + tmpatom.chain);\r
- PDBChain tmpchain = new PDBChain(tmpatom.chain);\r
- chains.addElement(tmpchain);\r
- tmpchain.atoms.addElement(tmpatom);\r
- }\r
- } catch(NumberFormatException e) {\r
- System.err.println("Caught" + e);\r
- System.err.println("Record not added to PDB model:"+lineArray.elementAt(i).toString());\r
- }\r
- }\r
- }\r
- }\r
- makeResidueList();\r
- makeCaBondList();\r
- // for (int i=0; i < chains.size() ; i++) {\r
- // String pog = ((PDBChain)chains.elementAt(i)).print();\r
- // System.out.println(pog);\r
- // }\r
- }\r
-\r
- public void makeResidueList() {\r
- for (int i=0; i < chains.size() ; i++) {\r
- ((PDBChain)chains.elementAt(i)).makeResidueList();\r
- }\r
- }\r
- public void makeCaBondList() {\r
- for (int i=0; i < chains.size() ; i++) {\r
- ((PDBChain)chains.elementAt(i)).makeCaBondList();\r
- }\r
- }\r
-\r
- public PDBChain findChain(String id) {\r
- for (int i=0; i < chains.size(); i++) {\r
- // System.out.println("ID = " + id + " " +((PDBChain)chains.elementAt(i)).id);\r
- if (((PDBChain)chains.elementAt(i)).id.equals(id)) {\r
- return (PDBChain)chains.elementAt(i);\r
- }\r
- }\r
- return null;\r
- }\r
-\r
-\r
- public void setChargeColours() {\r
- for (int i=0; i < chains.size(); i++) {\r
- ((PDBChain)chains.elementAt(i)).setChargeColours();\r
- }\r
- }\r
-\r
- public void setHydrophobicityColours() {\r
- for (int i=0; i < chains.size(); i++) {\r
- ((PDBChain)chains.elementAt(i)).setHydrophobicityColours();\r
- }\r
- }\r
-\r
- public void colourBySequence(Sequence seq) {\r
-//SMJS TODO\r
-// int max = seq.maxchain;\r
-// if (seq.maxchain != -1) {\r
-// ((PDBChain)chains.elementAt(max)).colourBySequence(seq);\r
-// }\r
- }\r
-\r
- public void setChainColours() {\r
- for (int i=0; i < chains.size(); i++) {\r
- ((PDBChain)chains.elementAt(i)).setChainColours();\r
- }\r
- }\r
- public static void main(String[] args) {\r
- try {\r
- PDBfile pdb = new PDBfile("enkp1.pdb","File");\r
- } catch(IOException e) {\r
- System.out.println(e);\r
- e.printStackTrace();\r
- System.exit(0);\r
- }\r
- }\r
-}\r
-\r
-\r
-\r
+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ * 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.DataSourceType;
+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,
+ DataSourceType sourceType)
+ throws IOException
+ {
+ super(false, dataObject, sourceType);
+ 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(SequenceI[] seqs, boolean jvSuffix)
+ {
+ 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<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 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<String, String> 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);
+ }
+ }
+ }
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff