import java.io.IOException;
import java.util.ArrayList;
import java.util.Hashtable;
+import java.util.List;
import java.util.Vector;
public class PDBfile extends jalview.io.AlignFile
{
- public Vector chains;
+ public Vector<PDBChain> chains;
public String id;
*/
boolean VisibleChainAnnotation = false;
- boolean processSecondaryStructure=true;
-
+ boolean processSecondaryStructure = true;
+
+ boolean externalSecondaryStructure = false;
public PDBfile(boolean visibleChainAnnotation,
- boolean processSecondaryStructure)
+ boolean processSecondaryStructure, boolean externalSecStr)
{
super();
VisibleChainAnnotation = visibleChainAnnotation;
this.processSecondaryStructure = processSecondaryStructure;
+ this.externalSecondaryStructure = externalSecStr;
}
public PDBfile(boolean visibleChainAnnotation,
- boolean processSecondaryStructure, String file, String protocol) throws IOException
+ boolean processSecondaryStructure, boolean externalSecStr,
+ String file, String protocol) throws IOException
{
super(false, file, protocol);
VisibleChainAnnotation = visibleChainAnnotation;
this.processSecondaryStructure = processSecondaryStructure;
+ this.externalSecondaryStructure = externalSecStr;
doParse();
}
public PDBfile(boolean visibleChainAnnotation,
- boolean processSecondaryStructure, FileParse source) throws IOException
+ boolean processSecondaryStructure, boolean externalSecStr,
+ FileParse source) throws IOException
{
super(false, source);
VisibleChainAnnotation = visibleChainAnnotation;
this.processSecondaryStructure = processSecondaryStructure;
+ this.externalSecondaryStructure = externalSecStr;
doParse();
}
}
for (int i = 0; i < chains.size(); i++)
{
- SequenceI dataset = ((PDBChain) chains.elementAt(i)).sequence;
+ SequenceI dataset = chains.elementAt(i).sequence;
dataset.setName(id + "|" + dataset.getName());
PDBEntry entry = new PDBEntry();
entry.setId(id);
entry.setProperty(new Hashtable());
- if (((PDBChain) chains.elementAt(i)).id != null)
+ if (chains.elementAt(i).id != null)
{
- entry.getProperty().put("CHAIN",
- ((PDBChain) chains.elementAt(i)).id);
+ entry.getProperty().put("CHAIN", chains.elementAt(i).id);
}
if (inFile != null)
{
AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
- if (chainannot != null)
+ if (chainannot != null && VisibleChainAnnotation)
{
for (int ai = 0; ai < chainannot.length; ai++)
{
}
if (processSecondaryStructure)
{
- if (rna.size() > 0)
- {
- try
- {
- processPdbFileWithAnnotate3d(rna);
- } catch (Exception x)
+ if (externalSecondaryStructure && rna.size() > 0)
{
- System.err
- .println("Exceptions when dealing with RNA in pdb file");
- x.printStackTrace();
+ try
+ {
+ processPdbFileWithAnnotate3d(rna);
+ } catch (Exception x)
+ {
+ System.err
+ .println("Exceptions when dealing with RNA in pdb file");
+ x.printStackTrace();
+ }
}
- }
- ;
- if (prot.size() > 0)
- {
- try
+ ;
+ if (prot.size() > 0)
{
- processPdbFileWithJmol(prot);
- } catch (Exception x)
- {
- System.err
- .println("Exceptions from Jmol when processing data in pdb file");
- x.printStackTrace();
+ try
+ {
+ processPdbFileWithJmol(prot);
+ } catch (Exception x)
+ {
+ System.err
+ .println("Exceptions from Jmol when processing data in pdb file");
+ x.printStackTrace();
+ }
}
}
- }
} catch (OutOfMemoryError er)
{
System.out.println("OUT OF MEMORY LOADING PDB FILE");
markCalcIds();
}
- private static String calcIdPrefix = "JalviewPDB:";
+ private static String calcIdPrefix = "JalviewPDB";
public static boolean isCalcIdHandled(String calcId)
{
- return calcId != null
- && (calcId.startsWith(calcIdPrefix) && calcId.indexOf(
- calcIdPrefix,
- calcIdPrefix.length() + 1) > -1);
+ return calcId != null && (calcIdPrefix.equals(calcId));
}
- public static boolean isCalcIdForFile(String calcId, String pdbFile)
+
+ public static boolean isCalcIdForFile(AlignmentAnnotation alan,
+ String pdbFile)
{
- return (calcId != null && calcId.startsWith(calcIdPrefix + pdbFile
- + ":" + calcIdPrefix));
+ return alan.getCalcId() != null
+ && calcIdPrefix.equals(alan.getCalcId())
+ && pdbFile.equals(alan.getProperty("PDBID"));
}
public static String relocateCalcId(String calcId,
{
for (SequenceI sq : seqs)
{
- for (AlignmentAnnotation aa : sq.getAnnotation())
+ if (sq.getAnnotation() != null)
{
- String oldId = aa.getCalcId();
- if (oldId == null)
+ for (AlignmentAnnotation aa : sq.getAnnotation())
{
- oldId = "";
+ String oldId = aa.getCalcId();
+ if (oldId == null)
+ {
+ oldId = "";
+ }
+ aa.setCalcId(calcIdPrefix);
+ aa.setProperty("PDBID", id);
+ aa.setProperty("oldCalcId", oldId);
}
- aa.setCalcId("JalviewPDB:" + id + ":JalviewPDB:" + oldId);
}
}
}
+
private void processPdbFileWithJmol(ArrayList<SequenceI> prot)
throws Exception
{
{
if (sq.getDatasetSequence() != null)
{
- if (sq.getDatasetSequence().getPDBId() != null)
- {
- sq.getDatasetSequence().getPDBId().clear();
- }
+ sq.getDatasetSequence().getPDBId().clear();
}
else
{
- if (sq.getPDBId() != null)
- {
- sq.getPDBId().clear();
- }
+ sq.getPDBId().clear();
}
}
- AlignSeq.replaceMatchingSeqsWith(seqs, annotations, prot, al, AlignSeq.PEP, false);
+ replaceAndUpdateChains(prot, al, AlignSeq.PEP, false);
}
} catch (ClassNotFoundException q)
{
}
}
+ private void replaceAndUpdateChains(ArrayList<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(ArrayList<SequenceI> rna)
throws Exception
{
{
if (sq.getPDBId() != null)
{
- sq.getDatasetSequence().getPDBId().clear();
+ sq.getPDBId().clear();
}
}
}
- AlignSeq.replaceMatchingSeqsWith(seqs, annotations, rna, al, AlignSeq.DNA, false);
+ replaceAndUpdateChains(rna, al, AlignSeq.DNA, false);
}
} catch (ClassNotFoundException x)
{
{
for (int i = 0; i < chains.size(); i++)
{
- ((PDBChain) chains.elementAt(i)).makeResidueList();
+ chains.elementAt(i).makeResidueList(VisibleChainAnnotation);
}
}
{
for (int i = 0; i < chains.size(); i++)
{
- ((PDBChain) chains.elementAt(i)).makeCaBondList();
+ chains.elementAt(i).makeCaBondList();
}
}
{
for (int i = 0; i < chains.size(); i++)
{
- if (((PDBChain) chains.elementAt(i)).id.equals(id))
+ if (chains.elementAt(i).id.equals(id))
{
- return (PDBChain) chains.elementAt(i);
+ return chains.elementAt(i);
}
}
{
for (int i = 0; i < chains.size(); i++)
{
- ((PDBChain) chains.elementAt(i)).setChargeColours();
+ chains.elementAt(i).setChargeColours();
}
}
{
for (int i = 0; i < chains.size(); i++)
{
- ((PDBChain) chains.elementAt(i)).setChainColours(cs);
+ chains.elementAt(i).setChainColours(cs);
}
}
{
for (int i = 0; i < chains.size(); i++)
{
- ((PDBChain) chains.elementAt(i)).setChainColours(Color.getHSBColor(
- 1.0f / i, .4f, 1.0f));
+ chains.elementAt(i).setChainColours(
+ Color.getHSBColor(1.0f / i, .4f, 1.0f));
}
}