import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
-import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.io.FileParse;
import jalview.io.StructureFile;
import jalview.schemes.ResidueProperties;
-import jalview.util.Comparison;
+import jalview.structure.StructureViewSettings;
import jalview.util.MessageManager;
import java.io.IOException;
import java.util.ArrayList;
-import java.util.Hashtable;
import java.util.List;
import java.util.Map;
import java.util.Vector;
import org.jmol.api.JmolViewer;
import org.jmol.c.CBK;
import org.jmol.c.STR;
-import org.jmol.modelset.Group;
-import org.jmol.modelset.Model;
import org.jmol.modelset.ModelSet;
-import org.jmol.modelsetbio.BioModel;
-import org.jmol.modelsetbio.BioPolymer;
-import org.jmol.modelsetbio.Monomer;
import org.jmol.viewer.Viewer;
import MCview.Atom;
{
Viewer viewer = null;
- public JmolParser(boolean addAlignmentAnnotations,
- boolean predictSecondaryStructure, boolean externalSecStr,
- String inFile, String type) throws IOException
+ public JmolParser(boolean addAlignmentAnnotations, boolean predictSecStr,
+ boolean externalSecStr, String inFile, String type)
+ throws IOException
{
super(inFile, type);
- this.visibleChainAnnotation = addAlignmentAnnotations;
- this.predictSecondaryStructure = predictSecondaryStructure;
- this.externalSecondaryStructure = externalSecStr;
- }
-
- public JmolParser(boolean addAlignmentAnnotations,
- boolean predictSecondaryStructure, boolean externalSecStr,
- FileParse fp) throws IOException
- {
- super(fp);
- this.visibleChainAnnotation = addAlignmentAnnotations;
- this.predictSecondaryStructure = predictSecondaryStructure;
- this.externalSecondaryStructure = externalSecStr;
}
- public JmolParser(FileParse fp) throws IOException
+ public JmolParser(boolean addAlignmentAnnotations, boolean predictSecStr,
+ boolean externalSecStr, FileParse fp) throws IOException
{
super(fp);
}
- public JmolParser(String inFile, String type) throws IOException
- {
- super(inFile, type);
- }
-
public JmolParser()
{
}
@Override
public void parse() throws IOException
{
-
+ String dataName = getDataName();
+ if (dataName.endsWith(".cif"))
+ {
+ setDbRefType(DBRefSource.MMCIF);
+ }
+ else
+ {
+ setDbRefType(DBRefSource.PDB);
+ }
setChains(new Vector<PDBChain>());
Viewer jmolModel = getJmolData();
jmolModel.openReader(getDataName(), getDataName(), getReader());
*/
if (jmolModel.ms.mc > 0)
{
- parseBiopolymer(jmolModel.ms);
- // transformJmolModelToJalview(jmolModel.ms);
+ transformJmolModelToJalview(jmolModel.ms);
}
}
}
lastID = tmpatom.resNumIns.trim();
}
+ xferSettings();
+
makeResidueList();
makeCaBondList();
for (PDBChain chain : getChains())
{
SequenceI chainseq = postProcessChain(chain);
- createAnnotation(chainseq, chain, ms.at);
if (isRNA(chainseq))
{
rna.add(chainseq);
{
prot.add(chainseq);
}
+
+ if (StructureViewSettings.isPredictSecondaryStructure())
+ {
+ createAnnotation(chainseq, chain, ms.at);
+ }
}
} catch (OutOfMemoryError er)
{
curAtom.number = atom.getAtomNumber();
curAtom.resName = atom.getGroup3(true);
curAtom.resNumber = atom.getResno();
- curAtom.ss = getSecondayStructure(atom.group
- .getProteinStructureSubType());
curAtom.occupancy = ms.occupancies != null ? ms.occupancies[atom
.getIndex()] : Float.valueOf(atom.getOccupancy100());
curAtom.resNumIns = "" + curAtom.resNumber + curAtom.insCode;
- // curAtom.tfactor = atom.group.;
+ curAtom.tfactor = atom.getBfactor100() / 100f;
curAtom.type = 0;
significantAtoms.add(curAtom);
}
{
char[] secstr = new char[sequence.getLength()];
char[] secstrcode = new char[sequence.getLength()];
- for (Residue residue : chain.residues)
- {
-
- }
- addSecondaryStructureAnnotation(chain.pdbid, sequence, secstr,
- secstrcode, chain.id, sequence.getStart());
- }
-
- /**
- * Process the Jmol BioPolymer array and generate a Jalview sequence for each
- * chain found (including any secondary structure annotation from DSSP)
- *
- * @param ms
- * @throws IOException
- */
- public void parseBiopolymer(ModelSet ms) throws IOException
- {
- int modelIndex = -1;
- for (Model model : ms.am)
- {
- modelIndex++;
- String modelTitle = (String) ms.getInfo(modelIndex, "title");
- /*
- * Chains can span BioPolymers, so first make a flattened list, and then
- * work out the lengths of chains present
- */
- List<Monomer> monomers = getMonomers(ms, (BioModel) model);
- List<Integer> chainLengths = getChainLengths(monomers);
-
- /*
- * now chop up the Monomer list to make Jalview Sequences
- */
- int from = 0;
- for (int length : chainLengths)
- {
- buildSequenceFromChain(monomers.subList(from, from + length),
- modelTitle);
- from += length;
- }
- }
- }
-
- /**
- * Returns a flattened list of Monomer (residues) in order, across all
- * BioPolymers in the model. This simplifies assembling chains which span
- * BioPolymers. The result omits any alternate residues reported for the same
- * sequence position (RESNUM value).
- *
- * @param ms
- * @param model
- * @return
- */
- protected List<Monomer> getMonomers(ModelSet ms, BioModel model)
- {
- List<Monomer> result = new ArrayList<Monomer>();
- int lastResNo = Integer.MIN_VALUE;
-
- for (BioPolymer bp : model.bioPolymers)
- {
- for (int groupLeadAtoms : bp.getLeadAtomIndices())
- {
- Group group = ms.at[groupLeadAtoms].group;
- if (group instanceof Monomer)
- {
- /*
- * ignore alternate residue at same position example: 1ejg has
- * residues A:LEU, B:ILE at RESNUM=25
- */
- int resNo = group.getResno();
- if (lastResNo != resNo)
- {
- result.add((Monomer) group);
- }
- lastResNo = resNo;
- }
- }
- }
- return result;
- }
-
- /**
- * Scans the list of Monomers (residue models), inspecting the chain id for
- * each, and returns an array whose length is the number of chains, and values
- * the length of each chain
- *
- * @param monomers
- * @return
- */
- protected List<Integer> getChainLengths(List<Monomer> monomers)
- {
- List<Integer> chainLengths = new ArrayList<Integer>();
- int lastChainId = -1;
- int length = 0;
-
- for (Monomer monomer : monomers)
- {
- int chainId = monomer.chain.chainID;
- if (chainId != lastChainId && length > 0)
- {
- /*
- * change of chain - record the length of the last one
- */
- chainLengths.add(length);
- length = 0;
- }
- lastChainId = chainId;
- length++;
- }
- if (length > 0)
- {
- /*
- * record the length of the final chain
- */
- chainLengths.add(length);
- }
-
- return chainLengths;
- }
-
- /**
- * Helper method to construct a sequence for one chain and add it to the seqs
- * list
- *
- * @param monomers
- * a list of all monomers in the chain
- * @param modelTitle
- */
- protected void buildSequenceFromChain(List<Monomer> monomers,
- String modelTitle)
- {
- final int length = monomers.size();
- /*
- * arrays to hold sequence and secondary structure
- */
- char[] seq = new char[length];
- char[] secstr = new char[length];
- char[] secstrcode = new char[length];
-
- /*
- * populate the sequence and secondary structure arrays
- */
- extractJmolChainData(monomers, seq, secstr, secstrcode);
-
- /*
- * grab chain code and start position from first residue;
- */
- String chainId = monomers.get(0).chain.getIDStr();
- int firstResNum = monomers.get(0).getResno();
- if (firstResNum < 1)
+ // Ensure Residue size equals Seq size
+ if (chain.residues.size() != sequence.getLength())
{
- // Jalview doesn't like residue < 1, so force this to 1
- System.err.println("Converting chain " + chainId + " first RESNUM ("
- + firstResNum + ") to 1");
- firstResNum = 1;
+ return;
}
-
- /*
- * convert any non-gap unknown residues to 'X'
- */
- convertNonGapCharacters(seq);
-
- /*
- * construct and add the Jalview sequence
- */
- String seqName = "" + modelTitle + "|" + chainId;
- int start = firstResNum;
- int end = firstResNum + length - 1;
-
- SequenceI sq = new Sequence(seqName, seq, start, end);
-
- addPdbid(sq, modelTitle, chainId);
-
- addSourceDBref(sq, modelTitle, start, end);
-
- seqs.add(sq);
-
- /*
- * add secondary structure predictions (if any)
- */
- addSecondaryStructureAnnotation(modelTitle, sq, secstr, secstrcode,
- chainId, firstResNum);
-
- }
-
- /**
- * Scans the list of (Jmol) Monomer objects, and adds the residue for each to
- * the sequence array, and any converted secondary structure prediction to the
- * secondary structure arrays
- *
- * @param monomers
- * @param seq
- * @param secstr
- * @param secstrcode
- */
- protected void extractJmolChainData(List<Monomer> monomers, char[] seq,
- char[] secstr, char[] secstrcode)
- {
- int pos = 0;
- for (Monomer monomer : monomers)
- {
- seq[pos] = monomer.getGroup1();
-
- /*
- * JAL-1828 replace a modified amino acid with its standard equivalent
- * (e.g. MSE with MET->M) to maximise sequence matching
- */
- replaceNonCanonicalResidue(monomer.getGroup3(), seq, pos);
-
- /*
- * if Jmol has derived a secondary structure prediction for this position,
- * convert it to Jalview equivalent and save it
- */
- setSecondaryStructure(monomer.getProteinStructureSubType(), pos,
- secstr, secstrcode);
- pos++;
- }
- }
-
- /**
- * Replace any non-gap miscellaneous characters with 'X'
- *
- * @param seq
- * @return
- */
- protected void convertNonGapCharacters(char[] seq)
- {
- boolean isNa = Comparison.areNucleotide(new char[][] { seq });
- int[] cinds = isNa ? ResidueProperties.nucleotideIndex
- : ResidueProperties.aaIndex;
- int nonGap = isNa ? ResidueProperties.maxNucleotideIndex
- : ResidueProperties.maxProteinIndex;
-
- for (int p = 0; p < seq.length; p++)
- {
- if (cinds[seq[p]] == nonGap)
- {
- seq[p] = 'X';
- }
- }
- }
-
- /**
- * Add a source db ref entry for the given sequence.
- *
- * @param sq
- * @param accessionId
- * @param start
- * @param end
- */
- protected void addSourceDBref(SequenceI sq, String accessionId,
- int start, int end)
- {
- DBRefEntry sourceDBRef = new DBRefEntry();
- sourceDBRef.setAccessionId(accessionId);
- sourceDBRef.setSource(DBRefSource.MMCIF);
- sourceDBRef.setStartRes(start);
- sourceDBRef.setEndRes(end);
- sq.setSourceDBRef(sourceDBRef);
- sq.addDBRef(sourceDBRef);
- }
-
- /**
- * Add a PDBEntry giving the source of PDB data to the sequence
- *
- * @param sq
- * @param id
- * @param chainId
- */
- protected void addPdbid(SequenceI sq, String id, String chainId)
- {
- PDBEntry entry = new PDBEntry();
- entry.setId(id);
- entry.setType(PDBEntry.Type.MMCIF);
- entry.setProperty(new Hashtable());
- if (chainId != null)
- {
- // entry.getProperty().put("CHAIN", chains.elementAt(i).id);
- entry.setChainCode(String.valueOf(chainId));
- }
- if (inFile != null)
- {
- entry.setFile(inFile.getAbsolutePath());
- }
- else
+ int annotIndex = 0;
+ for (Residue residue : chain.residues)
{
- // TODO: decide if we should dump the datasource to disk
- entry.setFile(getDataName());
+ Atom repAtom = residue.getAtoms().get(0);
+ STR proteinStructureSubType = jmolAtoms[repAtom.atomIndex].group
+ .getProteinStructureSubType();
+ setSecondaryStructure(proteinStructureSubType, annotIndex, secstr,
+ secstrcode);
+ ++annotIndex;
}
-
- sq.addPDBId(entry);
+ addSecondaryStructureAnnotation(chain.pdbid, sequence, secstr,
+ secstrcode, chain.id, sequence.getStart());
}
-
/**
* Helper method that adds an AlignmentAnnotation for secondary structure to
* the sequence, provided at least one secondary structure prediction has been
{
if (secstr[p] >= 'A' && secstr[p] <= 'z')
{
+ try
+ {
asecstr[p] = new Annotation(String.valueOf(secstr[p]), null,
secstrcode[p], Float.NaN);
ssFound = true;
+ } catch (Exception e)
+ {
+ // e.printStackTrace();
+ }
}
}
}
}
- private char getSecondayStructure(STR proteinStructureSubType)
- {
- switch (proteinStructureSubType)
- {
- case HELIX310:
- return '3';
- case HELIX:
- case HELIXALPHA:
- return 'H';
- case HELIXPI:
- return 'P';
- case SHEET:
- return 'E';
- default:
- return 0;
- }
- }
-
/**
* Convert any non-standard peptide codes to their standard code table
* equivalent. (Initial version only does Selenomethionine MSE->MET.)
this.predictSecondaryStructure = predictSecondaryStructure;
}
+ public boolean isVisibleChainAnnotation()
+ {
+ return visibleChainAnnotation;
+ }
+
+ public void setVisibleChainAnnotation(boolean visibleChainAnnotation)
+ {
+ this.visibleChainAnnotation = visibleChainAnnotation;
+ }
+
}