import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
-import jalview.io.AlignFile;
import jalview.io.FileParse;
+import jalview.io.StructureFile;
import jalview.schemes.ResidueProperties;
import jalview.util.Comparison;
import jalview.util.MessageManager;
import java.io.IOException;
import java.util.ArrayList;
-import java.util.Collection;
import java.util.Hashtable;
import java.util.List;
import java.util.Map;
+import java.util.Vector;
import javajs.awt.Dimension;
import org.jmol.modelsetbio.Monomer;
import org.jmol.viewer.Viewer;
+import MCview.Atom;
import MCview.PDBChain;
/**
- * Import and process files with Jmol for file like PDB, mmCIF
+ * Import and process files with Jmol for file like PDB, mmCIF
*
* @author jprocter
*
*/
-public class JmolParser extends AlignFile implements
- JmolStatusListener
+public class JmolParser extends StructureFile implements JmolStatusListener
{
Viewer viewer = null;
- private Collection<PDBChain> chains;
-
- /*
- * Set true to predict secondary structure (using JMol for protein, Annotate3D
- * for RNA)
- */
- private boolean predictSecondaryStructure = true;
-
- public JmolParser(String inFile, String type) throws IOException
+ public JmolParser(boolean addAlignmentAnnotations,
+ boolean predictSecondaryStructure, 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
super(fp);
}
+ public JmolParser(String inFile, String type) throws IOException
+ {
+ super(inFile, type);
+ }
+
public JmolParser()
{
}
public void parse() throws IOException
{
- chains = new ArrayList<PDBChain>();
+ setChains(new Vector<PDBChain>());
Viewer jmolModel = getJmolData();
jmolModel.openReader(getDataName(), getDataName(), getReader());
waitForScript(jmolModel);
*/
if (jmolModel.ms.mc > 0)
{
- parseBiopolymers(jmolModel.ms);
+ // parseBiopolymer(jmolModel.ms);
+ transformJmolModelToJalview(jmolModel.ms);
}
}
* @param ms
* @throws IOException
*/
- public void parseBiopolymers(ModelSet 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
+ * 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);
int from = 0;
for (int length : chainLengths)
{
- buildSequenceFromChain(monomers.subList(from, from + length), modelTitle);
+ buildSequenceFromChain(monomers.subList(from, from + length),
+ modelTitle);
from += length;
}
}
}
+ public void transformJmolModelToJalview(ModelSet ms)
+ {
+ try
+ {
+ String lastID = "";
+ List<SequenceI> rna = new ArrayList<SequenceI>();
+ List<SequenceI> prot = new ArrayList<SequenceI>();
+ PDBChain tmpchain;
+ String pdbId = (String) ms.getInfo(0, "title");
+ setId(pdbId);
+ List<Atom> significantAtoms = convertSignificantAtoms(ms);
+ for (Atom tmpatom : significantAtoms)
+ {
+ try
+ {
+ tmpchain = findChain(tmpatom.chain);
+ if (tmpatom.resNumIns.trim().equals(lastID))
+ {
+ // phosphorylated protein - seen both CA and P..
+ continue;
+ }
+ tmpchain.atoms.addElement(tmpatom);
+ } catch (Exception e)
+ {
+ tmpchain = new PDBChain(pdbId, tmpatom.chain);
+ getChains().add(tmpchain);
+ tmpchain.atoms.addElement(tmpatom);
+ }
+ lastID = tmpatom.resNumIns.trim();
+ }
+ makeResidueList();
+ makeCaBondList();
+
+ if (getId() == null)
+ {
+ setId(inFile.getName());
+ }
+ for (PDBChain chain : getChains())
+ {
+ SequenceI chainseq = postProcessChain(chain);
+ if (isRNA(chainseq))
+ {
+ rna.add(chainseq);
+ }
+ else
+ {
+ prot.add(chainseq);
+ }
+ }
+ } catch (OutOfMemoryError er)
+ {
+ System.out
+ .println("OUT OF MEMORY LOADING TRANSFORMING JMOL MODEL TO JALVIEW MODEL");
+ // throw new IOException(
+ // MessageManager
+ // .getString("exception.outofmemory_loading_pdb_file"));
+ }
+ }
+
+ private List<Atom> convertSignificantAtoms(ModelSet ms)
+ {
+ List<Atom> significantAtoms = new ArrayList<Atom>();
+ for (org.jmol.modelset.Atom atom : ms.at)
+ {
+ if (atom.getAtomName().equalsIgnoreCase("CA")
+ || atom.getAtomName().equalsIgnoreCase("P"))
+ {
+ Atom curAtom = new Atom(atom.x, atom.y, atom.z);
+ curAtom.atomIndex = atom.getIndex();
+ curAtom.chain = atom.getChainIDStr();
+ curAtom.insCode = atom.group.getInsertionCode();
+ curAtom.name = atom.getAtomName();
+ curAtom.number = atom.getAtomNumber();
+ curAtom.resName = atom.getGroup3(true);
+ curAtom.resNumber = atom.getResno();
+ curAtom.occupancy = ms.occupancies != null ? ms.occupancies[atom
+ .getIndex()] : Float.valueOf(atom.getOccupancy100());
+ curAtom.resNumIns = "" + curAtom.resNumber + curAtom.insCode;
+ curAtom.tfactor = 0;
+ curAtom.type = 0;
+ significantAtoms.add(curAtom);
+ }
+ }
+ return significantAtoms;
+ }
+
/**
* Helper method to construct a sequence for one chain and add it to the seqs
* list
* a list of all monomers in the chain
* @param modelTitle
*/
- protected void buildSequenceFromChain(List<Monomer> monomers, String modelTitle)
+ protected void buildSequenceFromChain(List<Monomer> monomers,
+ String modelTitle)
{
final int length = monomers.size();
/*
* construct and add the Jalview sequence
*/
- String seqName = "" + modelTitle + "|"
- + chainId;
+ String seqName = "" + modelTitle + "|" + chainId;
int start = firstResNum;
int end = firstResNum + length - 1;
seqs.add(sq);
- addChainMetaData(sq, monomers, chainId);
-
/*
* add secondary structure predictions (if any)
*/
if (isPredictSecondaryStructure())
{
addSecondaryStructureAnnotation(modelTitle, sq, secstr, secstrcode,
- chainId, firstResNum);
+ chainId, firstResNum);
}
}
- public void addChainMetaData(SequenceI sq, List<Monomer> monomers,
- String chainId)
- {
- for (char res : sq.getSequence())
- {
-
- }
- }
-
/**
* Add a source db ref entry for the given sequence.
*
sq.addDBRef(sourceDBRef);
}
-
/**
* Add a PDBEntry giving the source of PDB data to the sequence
*
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
+ * 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
+ * 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);
* @return
*/
protected void addSecondaryStructureAnnotation(String modelTitle,
- SequenceI sq, char[] secstr, char[] secstrcode,
- String chainId, int firstResNum)
+ SequenceI sq, char[] secstr, char[] secstrcode, String chainId,
+ int firstResNum)
{
char[] seq = sq.getSequence();
boolean ssFound = false;
}
}
-
/**
* 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
if (group instanceof Monomer)
{
/*
- * ignore alternate residue at same position
- * example: 1ejg has residues A:LEU, B:ILE at RESNUM=25
+ * ignore alternate residue at same position example: 1ejg has
+ * residues A:LEU, B:ILE at RESNUM=25
*/
int resNo = group.getResno();
if (lastResNo != resNo)
this.predictSecondaryStructure = predictSecondaryStructure;
}
- public Collection<PDBChain> getChains()
- {
- return chains;
- }
-
- public void setChains(Collection<PDBChain> chains)
- {
- this.chains = chains;
- }
-
}
git://source.jalview.org / jalview.git / blobdiff