-/*\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
-package MCview;\r
-\r
-import jalview.datamodel.*;\r
-\r
-import java.io.*;\r
-\r
-import java.net.*;\r
-\r
-import java.util.*;\r
-\r
-\r
-public class PDBfile extends jalview.io.FileParse {\r
- public Vector chains = new Vector();\r
- Vector lineArray = new Vector();\r
-\r
- public PDBfile(String[] lines) {\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
- super(inFile, inType);\r
-\r
- String line;\r
- this.lineArray = new Vector();\r
-\r
- BufferedReader dataIn;\r
-\r
- if (inType.equals("File")) {\r
- dataIn = new BufferedReader(new FileReader(inFile));\r
- }\r
- else {\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
-\r
- noLines = lineArray.size();\r
-\r
- parse();\r
- }\r
-\r
- public void parse() {\r
- for (int i = 0; i < lineArray.size(); i++) {\r
- StringTokenizer str = new StringTokenizer(lineArray.elementAt(i)\r
- .toString());\r
-\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
-\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:" +\r
- lineArray.elementAt(i).toString());\r
- }\r
- }\r
- }\r
- }\r
-\r
- makeResidueList();\r
- makeCaBondList();\r
-\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
-\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
-\r
- return null;\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
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.analysis.AlignSeq;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.io.FileParse;
+import jalview.util.MessageManager;
+
+import java.awt.Color;
+import java.io.IOException;
+import java.lang.reflect.Constructor;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
+public class PDBfile extends jalview.io.AlignFile
+{
+ private static String CALC_ID_PREFIX = "JalviewPDB";
+
+ public Vector<PDBChain> chains;
+
+ public String id;
+
+ /**
+ * set to true to add derived sequence annotations (temp factor read from
+ * file, or computed secondary structure) to the alignment
+ */
+ private boolean visibleChainAnnotation = false;
+
+ /*
+ * Set true to predict secondary structure (using JMol for protein, Annotate3D
+ * for RNA)
+ */
+ private boolean predictSecondaryStructure = true;
+
+ /*
+ * Set true (with predictSecondaryStructure=true) to predict secondary
+ * structure using an external service (currently Annotate3D for RNA only)
+ */
+ private boolean externalSecondaryStructure = false;
+
+ public PDBfile(boolean addAlignmentAnnotations,
+ boolean predictSecondaryStructure, boolean externalSecStr)
+ {
+ super();
+ this.visibleChainAnnotation = addAlignmentAnnotations;
+ this.predictSecondaryStructure = predictSecondaryStructure;
+ this.externalSecondaryStructure = externalSecStr;
+ }
+
+ public PDBfile(boolean addAlignmentAnnotations,
+ boolean predictSecondaryStructure, boolean externalSecStr,
+ String file, String protocol) throws IOException
+ {
+ super(false, file, protocol);
+ this.visibleChainAnnotation = addAlignmentAnnotations;
+ this.predictSecondaryStructure = predictSecondaryStructure;
+ this.externalSecondaryStructure = externalSecStr;
+ doParse();
+ }
+
+ public PDBfile(boolean addAlignmentAnnotations,
+ boolean predictSecondaryStructure, boolean externalSecStr,
+ FileParse source) throws IOException
+ {
+ super(false, source);
+ this.visibleChainAnnotation = addAlignmentAnnotations;
+ this.predictSecondaryStructure = predictSecondaryStructure;
+ this.externalSecondaryStructure = externalSecStr;
+ doParse();
+ }
+
+ public String print()
+ {
+ return null;
+ }
+
+ public void parse() throws IOException
+ {
+ // TODO set the filename sensibly - try using data source name.
+ id = safeName(getDataName());
+
+ chains = 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)
+ {
+ id = 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);
+ 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
+ {
+ tmpchain = new PDBChain(id, tmpatom.chain);
+ chains.addElement(tmpchain);
+ tmpchain.atoms.addElement(tmpatom);
+ }
+ lastID = tmpatom.resNumIns.trim();
+ }
+ index++;
+ }
+
+ makeResidueList();
+ makeCaBondList();
+
+ if (id == null)
+ {
+ id = inFile.getName();
+ }
+ for (PDBChain chain : chains)
+ {
+ SequenceI chainseq = postProcessChain(chain);
+ if (isRNA(chainseq))
+ {
+ rna.add(chainseq);
+ }
+ else
+ {
+ prot.add(chainseq);
+ }
+ }
+ if (predictSecondaryStructure)
+ {
+ predictSecondaryStructure(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();
+ }
+
+ /**
+ * Predict secondary structure for RNA and/or protein sequences and add as
+ * annotations
+ *
+ * @param rnaSequences
+ * @param proteinSequences
+ */
+ protected void predictSecondaryStructure(List<SequenceI> rnaSequences,
+ List<SequenceI> proteinSequences)
+ {
+ /*
+ * Currently using Annotate3D for RNA, but only if the 'use external
+ * prediction' flag is set
+ */
+ if (externalSecondaryStructure && rnaSequences.size() > 0)
+ {
+ try
+ {
+ processPdbFileWithAnnotate3d(rnaSequences);
+ } catch (Exception x)
+ {
+ System.err.println("Exceptions when dealing with RNA in pdb file");
+ x.printStackTrace();
+
+ }
+ }
+
+ /*
+ * Currently using JMol PDB parser for peptide
+ */
+ if (proteinSequences.size() > 0)
+ {
+ try
+ {
+ processPdbFileWithJmol(proteinSequences);
+ } catch (Exception x)
+ {
+ System.err
+ .println("Exceptions from Jmol when processing data in pdb file");
+ x.printStackTrace();
+ }
+ }
+ }
+
+ /**
+ * Process a parsed chain to construct and return a Sequence, and add it to
+ * the list of sequences parsed.
+ *
+ * @param chain
+ * @return
+ */
+ protected SequenceI postProcessChain(PDBChain chain)
+ {
+ SequenceI dataset = chain.sequence;
+ dataset.setName(id + "|" + dataset.getName());
+ PDBEntry entry = new PDBEntry();
+ entry.setId(id);
+ entry.setType(PDBEntry.Type.PDB);
+ entry.setProperty(new Hashtable());
+ if (chain.id != null)
+ {
+ // entry.getProperty().put("CHAIN", chains.elementAt(i).id);
+ entry.setChainCode(String.valueOf(chain.id));
+ }
+ if (inFile != null)
+ {
+ entry.setFile(inFile.getAbsolutePath());
+ }
+ else
+ {
+ // TODO: decide if we should dump the datasource to disk
+ entry.setFile(getDataName());
+ }
+ dataset.addPDBId(entry);
+ // PDBChain objects maintain reference to dataset
+ SequenceI chainseq = dataset.deriveSequence();
+ seqs.addElement(chainseq);
+
+ AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
+
+ if (chainannot != null && visibleChainAnnotation)
+ {
+ for (int ai = 0; ai < chainannot.length; ai++)
+ {
+ chainannot[ai].visible = visibleChainAnnotation;
+ annotations.addElement(chainannot[ai]);
+ }
+ }
+ return chainseq;
+ }
+
+ 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", id);
+ aa.setProperty("oldCalcId", oldId);
+ }
+ }
+ }
+ }
+
+ private void processPdbFileWithJmol(List<SequenceI> prot)
+ throws Exception
+ {
+ try
+ {
+ Class cl = Class.forName("jalview.ext.jmol.PDBFileWithJmol");
+ if (cl != null)
+ {
+ final Constructor constructor = cl
+ .getConstructor(new Class[] { FileParse.class });
+ final Object[] args = new Object[] { new FileParse(getDataName(),
+ type) };
+ Object jmf = constructor.newInstance(args);
+ AlignmentI al = new Alignment((SequenceI[]) cl.getMethod(
+ "getSeqsAsArray", new Class[] {}).invoke(jmf));
+ cl.getMethod("addAnnotations", new Class[] { AlignmentI.class })
+ .invoke(jmf, al);
+ for (SequenceI sq : al.getSequences())
+ {
+ if (sq.getDatasetSequence() != null)
+ {
+ sq.getDatasetSequence().getAllPDBEntries().clear();
+ }
+ else
+ {
+ sq.getAllPDBEntries().clear();
+ }
+ }
+ replaceAndUpdateChains(prot, al, AlignSeq.PEP, false);
+ }
+ } catch (ClassNotFoundException q)
+ {
+ }
+ }
+
+ private void replaceAndUpdateChains(List<SequenceI> prot, AlignmentI al,
+ String pep, boolean b)
+ {
+ List<List<? extends Object>> replaced = AlignSeq
+ .replaceMatchingSeqsWith(seqs, annotations, prot, al, pep,
+ false);
+ for (PDBChain ch : chains)
+ {
+ int p = 0;
+ for (SequenceI sq : (List<SequenceI>) replaced.get(0))
+ {
+ p++;
+ if (sq == ch.sequence || sq.getDatasetSequence() == ch.sequence)
+ {
+ p = -p;
+ break;
+ }
+ }
+ if (p < 0)
+ {
+ p = -p - 1;
+ // set shadow entry for chains
+ ch.shadow = (SequenceI) replaced.get(1).get(p);
+ ch.shadowMap = ((AlignSeq) replaced.get(2).get(p))
+ .getMappingFromS1(false);
+ }
+ }
+ }
+
+ private void processPdbFileWithAnnotate3d(List<SequenceI> rna)
+ throws Exception
+ {
+ // System.out.println("this is a PDB format and RNA sequence");
+ // note: we use reflection here so that the applet can compile and run
+ // without the HTTPClient bits and pieces needed for accessing Annotate3D
+ // web service
+ try
+ {
+ Class cl = Class.forName("jalview.ws.jws1.Annotate3D");
+ if (cl != null)
+ {
+ // TODO: use the PDB ID of the structure if one is available, to save
+ // bandwidth and avoid uploading the whole structure to the service
+ Object annotate3d = cl.getConstructor(new Class[] {}).newInstance(
+ new Object[] {});
+ AlignmentI al = ((AlignmentI) cl.getMethod("getRNAMLFor",
+ new Class[] { FileParse.class }).invoke(annotate3d,
+ new Object[] { new FileParse(getDataName(), type) }));
+ for (SequenceI sq : al.getSequences())
+ {
+ if (sq.getDatasetSequence() != null)
+ {
+ if (sq.getDatasetSequence().getAllPDBEntries() != null)
+ {
+ sq.getDatasetSequence().getAllPDBEntries().clear();
+ }
+ }
+ else
+ {
+ if (sq.getAllPDBEntries() != null)
+ {
+ sq.getAllPDBEntries().clear();
+ }
+ }
+ }
+ replaceAndUpdateChains(rna, al, AlignSeq.DNA, false);
+ }
+ } catch (ClassNotFoundException x)
+ {
+ // ignore classnotfounds - occurs in applet
+ }
+ ;
+ }
+
+ /**
+ * make a friendly ID string.
+ *
+ * @param dataName
+ * @return truncated dataName to after last '/'
+ */
+ private String safeName(String dataName)
+ {
+ int p = 0;
+ while ((p = dataName.indexOf("/")) > -1 && p < dataName.length())
+ {
+ dataName = dataName.substring(p + 1);
+ }
+ return dataName;
+ }
+
+ public void makeResidueList()
+ {
+ for (int i = 0; i < chains.size(); i++)
+ {
+ chains.elementAt(i).makeResidueList(visibleChainAnnotation);
+ }
+ }
+
+ public void makeCaBondList()
+ {
+ for (int i = 0; i < chains.size(); i++)
+ {
+ chains.elementAt(i).makeCaBondList();
+ }
+ }
+
+ public PDBChain findChain(String id)
+ {
+ for (int i = 0; i < chains.size(); i++)
+ {
+ if (chains.elementAt(i).id.equals(id))
+ {
+ return chains.elementAt(i);
+ }
+ }
+
+ return null;
+ }
+
+ public void setChargeColours()
+ {
+ for (int i = 0; i < chains.size(); i++)
+ {
+ chains.elementAt(i).setChargeColours();
+ }
+ }
+
+ public void setColours(jalview.schemes.ColourSchemeI cs)
+ {
+ for (int i = 0; i < chains.size(); i++)
+ {
+ chains.elementAt(i).setChainColours(cs);
+ }
+ }
+
+ public void setChainColours()
+ {
+ for (int i = 0; i < chains.size(); i++)
+ {
+ // divide by zero --> infinity --> 255 ;-)
+ chains.elementAt(i).setChainColours(
+ Color.getHSBColor(1.0f / i, .4f, 1.0f));
+ }
+ }
+
+ public static boolean isRNA(SequenceI seq)
+ {
+ for (char c : seq.getSequence())
+ {
+ if ((c != 'A') && (c != 'C') && (c != 'G') && (c != 'U'))
+ {
+ return false;
+ }
+ }
+
+ return true;
+
+ }
+}
git://source.jalview.org / jalview.git / blobdiff