2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.datamodel.AlignmentAnnotation;
24 import jalview.datamodel.DBRefSource;
25 import jalview.datamodel.SequenceI;
26 import jalview.io.FileParse;
27 import jalview.io.StructureFile;
28 import jalview.util.MessageManager;
30 import java.io.IOException;
31 import java.util.ArrayList;
32 import java.util.Hashtable;
33 import java.util.List;
34 import java.util.Vector;
36 public class PDBfile extends StructureFile
38 private static String CALC_ID_PREFIX = "JalviewPDB";
40 public PDBfile(boolean addAlignmentAnnotations,
41 boolean predictSecondaryStructure, boolean externalSecStr)
44 addSettings(addAlignmentAnnotations, predictSecondaryStructure,
48 public PDBfile(boolean addAlignmentAnnotations, boolean predictSecStr,
49 boolean externalSecStr, String dataObject, String protocol)
52 super(false, dataObject, protocol);
53 addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
57 public PDBfile(boolean addAlignmentAnnotations, boolean predictSecStr,
58 boolean externalSecStr, FileParse source) throws IOException
61 addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
72 public void parse() throws IOException
74 setDbRefType(DBRefSource.PDB);
75 // TODO set the filename sensibly - try using data source name.
76 setId(safeName(getDataName()));
78 setChains(new Vector<PDBChain>());
79 List<SequenceI> rna = new ArrayList<SequenceI>();
80 List<SequenceI> prot = new ArrayList<SequenceI>();
83 boolean modelFlag = false;
84 boolean terFlag = false;
88 String atomnam = null;
91 while ((line = nextLine()) != null)
93 if (line.indexOf("HEADER") == 0)
95 if (line.length() > 62)
98 if (line.length() > 67)
100 tid = line.substring(62, 67).trim();
104 tid = line.substring(62).trim();
106 if (tid.length() > 0)
113 // Were we to do anything with SEQRES - we start it here
114 if (line.indexOf("SEQRES") == 0)
118 if (line.indexOf("MODEL") == 0)
123 if (line.indexOf("TER") == 0)
128 if (modelFlag && line.indexOf("ENDMDL") == 0)
132 if (line.indexOf("ATOM") == 0
133 || (line.indexOf("HETATM") == 0 && !terFlag))
137 // Jalview is only interested in CA bonds????
138 atomnam = line.substring(12, 15).trim();
139 if (!atomnam.equals("CA") && !atomnam.equals("P"))
144 Atom tmpatom = new Atom(line);
147 tmpchain = findChain(tmpatom.chain);
148 if (tmpatom.resNumIns.trim().equals(lastID))
150 // phosphorylated protein - seen both CA and P..
153 tmpchain.atoms.addElement(tmpatom);
154 } catch (Exception e)
156 tmpchain = new PDBChain(getId(), tmpatom.chain);
157 getChains().add(tmpchain);
158 tmpchain.atoms.addElement(tmpatom);
160 lastID = tmpatom.resNumIns.trim();
170 setId(inFile.getName());
172 for (PDBChain chain : getChains())
174 SequenceI chainseq = postProcessChain(chain);
184 if (predictSecondaryStructure)
186 addSecondaryStructure(rna, prot);
188 } catch (OutOfMemoryError er)
190 System.out.println("OUT OF MEMORY LOADING PDB FILE");
191 throw new IOException(
193 .getString("exception.outofmemory_loading_pdb_file"));
194 } catch (NumberFormatException ex)
198 System.err.println("Couldn't read number from line:");
199 System.err.println(line);
206 * Process a parsed chain to construct and return a Sequence, and add it to
207 * the list of sequences parsed.
213 public static boolean isCalcIdHandled(String calcId)
215 return calcId != null && (CALC_ID_PREFIX.equals(calcId));
218 public static boolean isCalcIdForFile(AlignmentAnnotation alan,
221 return alan.getCalcId() != null
222 && CALC_ID_PREFIX.equals(alan.getCalcId())
223 && pdbFile.equals(alan.getProperty("PDBID"));
226 public static String relocateCalcId(String calcId,
227 Hashtable<String, String> alreadyLoadedPDB) throws Exception
229 int s = CALC_ID_PREFIX.length(), end = calcId
230 .indexOf(CALC_ID_PREFIX, s);
231 String between = calcId.substring(s, end - 1);
232 return CALC_ID_PREFIX + alreadyLoadedPDB.get(between) + ":"
233 + calcId.substring(end);
236 private void markCalcIds()
238 for (SequenceI sq : seqs)
240 if (sq.getAnnotation() != null)
242 for (AlignmentAnnotation aa : sq.getAnnotation())
244 String oldId = aa.getCalcId();
249 aa.setCalcId(CALC_ID_PREFIX);
250 aa.setProperty("PDBID", getId());
251 aa.setProperty("oldCalcId", oldId);