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,
59 FileParse source) throws IOException
62 addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
73 public void parse() throws IOException
75 setDbRefType(DBRefSource.PDB);
76 // TODO set the filename sensibly - try using data source name.
77 setId(safeName(getDataName()));
79 setChains(new Vector<PDBChain>());
80 List<SequenceI> rna = new ArrayList<SequenceI>();
81 List<SequenceI> prot = new ArrayList<SequenceI>();
84 boolean modelFlag = false;
85 boolean terFlag = false;
89 String atomnam = null;
92 while ((line = nextLine()) != null)
94 if (line.indexOf("HEADER") == 0)
96 if (line.length() > 62)
99 if (line.length() > 67)
101 tid = line.substring(62, 67).trim();
105 tid = line.substring(62).trim();
107 if (tid.length() > 0)
114 // Were we to do anything with SEQRES - we start it here
115 if (line.indexOf("SEQRES") == 0)
119 if (line.indexOf("MODEL") == 0)
124 if (line.indexOf("TER") == 0)
129 if (modelFlag && line.indexOf("ENDMDL") == 0)
133 if (line.indexOf("ATOM") == 0
134 || (line.indexOf("HETATM") == 0 && !terFlag))
138 // Jalview is only interested in CA bonds????
139 atomnam = line.substring(12, 15).trim();
140 if (!atomnam.equals("CA") && !atomnam.equals("P"))
145 Atom tmpatom = new Atom(line);
148 tmpchain = findChain(tmpatom.chain);
149 if (tmpatom.resNumIns.trim().equals(lastID))
151 // phosphorylated protein - seen both CA and P..
154 tmpchain.atoms.addElement(tmpatom);
155 } catch (Exception e)
157 tmpchain = new PDBChain(getId(), tmpatom.chain);
158 getChains().add(tmpchain);
159 tmpchain.atoms.addElement(tmpatom);
161 lastID = tmpatom.resNumIns.trim();
171 setId(inFile.getName());
173 for (PDBChain chain : getChains())
175 SequenceI chainseq = postProcessChain(chain);
185 if (predictSecondaryStructure)
187 addSecondaryStructure(rna, prot);
189 } catch (OutOfMemoryError er)
191 System.out.println("OUT OF MEMORY LOADING PDB FILE");
192 throw new IOException(
194 .getString("exception.outofmemory_loading_pdb_file"));
195 } catch (NumberFormatException ex)
199 System.err.println("Couldn't read number from line:");
200 System.err.println(line);
209 * Process a parsed chain to construct and return a Sequence, and add it to
210 * the list of sequences parsed.
216 public static boolean isCalcIdHandled(String calcId)
218 return calcId != null && (CALC_ID_PREFIX.equals(calcId));
221 public static boolean isCalcIdForFile(AlignmentAnnotation alan,
224 return alan.getCalcId() != null
225 && CALC_ID_PREFIX.equals(alan.getCalcId())
226 && pdbFile.equals(alan.getProperty("PDBID"));
229 public static String relocateCalcId(String calcId,
230 Hashtable<String, String> alreadyLoadedPDB) throws Exception
232 int s = CALC_ID_PREFIX.length(), end = calcId
233 .indexOf(CALC_ID_PREFIX, s);
234 String between = calcId.substring(s, end - 1);
235 return CALC_ID_PREFIX + alreadyLoadedPDB.get(between) + ":"
236 + calcId.substring(end);
239 private void markCalcIds()
241 for (SequenceI sq : seqs)
243 if (sq.getAnnotation() != null)
245 for (AlignmentAnnotation aa : sq.getAnnotation())
247 String oldId = aa.getCalcId();
252 aa.setCalcId(CALC_ID_PREFIX);
253 aa.setProperty("PDBID", getId());
254 aa.setProperty("oldCalcId", oldId);