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.structure.StructureImportSettings;
29 import jalview.util.MessageManager;
31 import java.io.IOException;
32 import java.util.ArrayList;
33 import java.util.Hashtable;
34 import java.util.List;
35 import java.util.Vector;
37 public class PDBfile extends StructureFile
39 private static String CALC_ID_PREFIX = "JalviewPDB";
41 public PDBfile(boolean addAlignmentAnnotations,
42 boolean predictSecondaryStructure, boolean externalSecStr)
45 addSettings(addAlignmentAnnotations, predictSecondaryStructure,
49 public PDBfile(boolean addAlignmentAnnotations, boolean predictSecStr,
50 boolean externalSecStr, String dataObject, String protocol)
53 super(false, dataObject, protocol);
54 addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
58 public PDBfile(boolean addAlignmentAnnotations, boolean predictSecStr,
59 boolean externalSecStr,
60 FileParse source) throws IOException
63 addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
74 public void parse() throws IOException
76 setDbRefType(DBRefSource.PDB);
77 // TODO set the filename sensibly - try using data source name.
78 setId(safeName(getDataName()));
80 setChains(new Vector<PDBChain>());
81 List<SequenceI> rna = new ArrayList<SequenceI>();
82 List<SequenceI> prot = new ArrayList<SequenceI>();
85 boolean modelFlag = false;
86 boolean terFlag = false;
90 String atomnam = null;
93 while ((line = nextLine()) != null)
95 if (line.indexOf("HEADER") == 0)
97 if (line.length() > 62)
100 if (line.length() > 67)
102 tid = line.substring(62, 67).trim();
106 tid = line.substring(62).trim();
108 if (tid.length() > 0)
115 // Were we to do anything with SEQRES - we start it here
116 if (line.indexOf("SEQRES") == 0)
120 if (line.indexOf("MODEL") == 0)
125 if (line.indexOf("TER") == 0)
130 if (modelFlag && line.indexOf("ENDMDL") == 0)
134 if (line.indexOf("ATOM") == 0
135 || (StructureImportSettings.isProcessHETATMs()
136 && line.indexOf("HETATM") == 0 && !terFlag))
140 // Jalview is only interested in CA bonds????
141 atomnam = line.substring(12, 15).trim();
142 if (!atomnam.equals("CA") && !atomnam.equals("P"))
147 Atom tmpatom = new Atom(line);
150 tmpchain = findChain(tmpatom.chain);
151 if (tmpatom.resNumIns.trim().equals(lastID))
153 // phosphorylated protein - seen both CA and P..
156 tmpchain.atoms.addElement(tmpatom);
157 } catch (Exception e)
159 tmpchain = new PDBChain(getId(), tmpatom.chain);
160 getChains().add(tmpchain);
161 tmpchain.atoms.addElement(tmpatom);
163 lastID = tmpatom.resNumIns.trim();
173 setId(inFile.getName());
175 for (PDBChain chain : getChains())
177 SequenceI chainseq = postProcessChain(chain);
187 if (predictSecondaryStructure)
189 addSecondaryStructure(rna, prot);
191 } catch (OutOfMemoryError er)
193 System.out.println("OUT OF MEMORY LOADING PDB FILE");
194 throw new IOException(
196 .getString("exception.outofmemory_loading_pdb_file"));
197 } catch (NumberFormatException ex)
201 System.err.println("Couldn't read number from line:");
202 System.err.println(line);
211 * Process a parsed chain to construct and return a Sequence, and add it to
212 * the list of sequences parsed.
218 public static boolean isCalcIdHandled(String calcId)
220 return calcId != null && (CALC_ID_PREFIX.equals(calcId));
223 public static boolean isCalcIdForFile(AlignmentAnnotation alan,
226 return alan.getCalcId() != null
227 && CALC_ID_PREFIX.equals(alan.getCalcId())
228 && pdbFile.equals(alan.getProperty("PDBID"));
231 public static String relocateCalcId(String calcId,
232 Hashtable<String, String> alreadyLoadedPDB) throws Exception
234 int s = CALC_ID_PREFIX.length(), end = calcId
235 .indexOf(CALC_ID_PREFIX, s);
236 String between = calcId.substring(s, end - 1);
237 return CALC_ID_PREFIX + alreadyLoadedPDB.get(between) + ":"
238 + calcId.substring(end);
241 private void markCalcIds()
243 for (SequenceI sq : seqs)
245 if (sq.getAnnotation() != null)
247 for (AlignmentAnnotation aa : sq.getAnnotation())
249 String oldId = aa.getCalcId();
254 aa.setCalcId(CALC_ID_PREFIX);
255 aa.setProperty("PDBID", getId());
256 aa.setProperty("oldCalcId", oldId);