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.DataSourceType;
import jalview.io.FileParse;
import jalview.io.StructureFile;
import jalview.schemes.ResidueProperties;
-import jalview.util.Comparison;
+import jalview.util.Format;
import jalview.util.MessageManager;
import java.io.IOException;
import java.util.ArrayList;
-import java.util.Hashtable;
+import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Vector;
-import javajs.awt.Dimension;
-
import org.jmol.api.JmolStatusListener;
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;
-import MCview.PDBChain;
-import MCview.Residue;
+import mc_view.Atom;
+import mc_view.PDBChain;
+import mc_view.Residue;
/**
* Import and process files with Jmol for file like PDB, mmCIF
{
Viewer viewer = null;
- public JmolParser(boolean addAlignmentAnnotations,
- boolean predictSecondaryStructure, boolean externalSecStr,
- String inFile, String type) throws IOException
+ public JmolParser(boolean immediate, Object inFile,
+ DataSourceType sourceType) throws IOException
{
- super(inFile, type);
- this.visibleChainAnnotation = addAlignmentAnnotations;
- this.predictSecondaryStructure = predictSecondaryStructure;
- this.externalSecondaryStructure = externalSecStr;
+ // BH 2018 File or String for filename
+ super(immediate, inFile, sourceType);
}
- public JmolParser(boolean addAlignmentAnnotations,
- boolean predictSecondaryStructure, boolean externalSecStr,
- FileParse fp) throws IOException
+ public JmolParser(Object inFile, DataSourceType sourceType)
+ throws IOException
{
- super(fp);
- this.visibleChainAnnotation = addAlignmentAnnotations;
- this.predictSecondaryStructure = predictSecondaryStructure;
- this.externalSecondaryStructure = externalSecStr;
+ super(inFile, sourceType);
}
public JmolParser(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
{
-
setChains(new Vector<PDBChain>());
Viewer jmolModel = getJmolData();
jmolModel.openReader(getDataName(), getDataName(), getReader());
*/
if (jmolModel.ms.mc > 0)
{
- parseBiopolymer(jmolModel.ms);
- // transformJmolModelToJalview(jmolModel.ms);
+ // ideally we do this
+ // try
+ // {
+ // setStructureFileType(jmolModel.evalString("show _fileType"));
+ // } catch (Exception q)
+ // {
+ // }
+ // ;
+ // instead, we distinguish .cif from non-.cif by filename
+ setStructureFileType(getDataName().toLowerCase().endsWith(".cif")
+ ? PDBEntry.Type.MMCIF.toString()
+ : "PDB");
+
+ transformJmolModelToJalview(jmolModel.ms);
}
}
{
try
{
- viewer = (Viewer) JmolViewer.allocateViewer(null, null, null, null,
- null, "-x -o -n", this);
+ /*
+ * params -o (output to sysout) -n (nodisplay) -x (exit when finished)
+ * see http://wiki.jmol.org/index.php/Jmol_Application
+ */
+
+ viewer = JalviewJmolBinding.getJmolData(this);
// ensure the 'new' (DSSP) not 'old' (Ramachandran) SS method is used
viewer.setBooleanProperty("defaultStructureDSSP", true);
} catch (ClassCastException x)
{
throw new Error(MessageManager.formatMessage(
"error.jmol_version_not_compatible_with_jalview_version",
- new String[] { JmolViewer.getJmolVersion() }), x);
+ new String[]
+ { JmolViewer.getJmolVersion() }), x);
}
}
return viewer;
List<SequenceI> prot = new ArrayList<SequenceI>();
PDBChain tmpchain;
String pdbId = (String) ms.getInfo(0, "title");
- setId(pdbId);
+
+ if (pdbId == null)
+ {
+ setId(safeName(getDataName()));
+ setPDBIdAvailable(false);
+ }
+ else
+ {
+ setId(pdbId);
+ setPDBIdAvailable(true);
+ }
List<Atom> significantAtoms = convertSignificantAtoms(ms);
for (Atom tmpatom : significantAtoms)
{
- try
+ if (tmpatom.resNumIns.trim().equals(lastID))
+ {
+ // phosphorylated protein - seen both CA and P..
+ continue;
+ }
+ tmpchain = findChain(tmpatom.chain);
+ if (tmpchain != null)
{
- 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)
+ } else
{
- tmpchain = new PDBChain(pdbId, tmpatom.chain);
+ tmpchain = new PDBChain(getId(), tmpatom.chain);
getChains().add(tmpchain);
tmpchain.atoms.addElement(tmpatom);
}
lastID = tmpatom.resNumIns.trim();
}
+ if (isParseImmediately())
+ {
+ // configure parsing settings from the static singleton
+ xferSettings();
+ }
+
makeResidueList();
makeCaBondList();
- if (getId() == null)
- {
- setId(inFile.getName());
- }
for (PDBChain chain : getChains())
{
SequenceI chainseq = postProcessChain(chain);
- createAnnotation(chainseq, chain, ms.at);
if (isRNA(chainseq))
{
rna.add(chainseq);
{
prot.add(chainseq);
}
+
+ // look at local setting for adding secondary tructure
+ if (predictSecondaryStructure)
+ {
+ createAnnotation(chainseq, chain, ms.at);
+ }
}
} catch (OutOfMemoryError er)
{
- System.out
- .println("OUT OF MEMORY LOADING TRANSFORMING JMOL MODEL TO JALVIEW MODEL");
- throw new IOException(
- MessageManager
- .getString("exception.outofmemory_loading_mmcif_file"));
+ System.out.println(
+ "OUT OF MEMORY LOADING TRANSFORMING JMOL MODEL TO JALVIEW MODEL");
+ throw new IOException(MessageManager
+ .getString("exception.outofmemory_loading_mmcif_file"));
}
}
private List<Atom> convertSignificantAtoms(ModelSet ms)
{
List<Atom> significantAtoms = new ArrayList<Atom>();
+ HashMap<String, org.jmol.modelset.Atom> chainTerMap = new HashMap<String, org.jmol.modelset.Atom>();
+ org.jmol.modelset.Atom prevAtom = null;
for (org.jmol.modelset.Atom atom : ms.at)
{
if (atom.getAtomName().equalsIgnoreCase("CA")
|| atom.getAtomName().equalsIgnoreCase("P"))
{
+ if (!atomValidated(atom, prevAtom, chainTerMap))
+ {
+ continue;
+ }
Atom curAtom = new Atom(atom.x, atom.y, atom.z);
curAtom.atomIndex = atom.getIndex();
curAtom.chain = atom.getChainIDStr();
- curAtom.insCode = atom.group.getInsertionCode();
+ curAtom.insCode = atom.group.getInsertionCode() == '\000' ? ' '
+ : atom.group.getInsertionCode();
curAtom.name = atom.getAtomName();
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.occupancy = ms.occupancies != null
+ ? ms.occupancies[atom.getIndex()]
+ : Float.valueOf(atom.getOccupancy100());
+ String fmt = new Format("%4i").form(curAtom.resNumber);
+ curAtom.resNumIns = (fmt + curAtom.insCode);
+ curAtom.tfactor = atom.getBfactor100() / 100f;
curAtom.type = 0;
- significantAtoms.add(curAtom);
+ // significantAtoms.add(curAtom);
+ // ignore atoms from subsequent models
+ if (!significantAtoms.contains(curAtom))
+ {
+ significantAtoms.add(curAtom);
+ }
+ prevAtom = atom;
}
}
return significantAtoms;
}
- private void createAnnotation(SequenceI sequence, PDBChain chain,
- org.jmol.modelset.Atom[] jmolAtoms)
+ private boolean atomValidated(org.jmol.modelset.Atom curAtom,
+ org.jmol.modelset.Atom prevAtom,
+ HashMap<String, org.jmol.modelset.Atom> chainTerMap)
{
- char[] secstr = new char[sequence.getLength()];
- char[] secstrcode = new char[sequence.getLength()];
- for (Residue residue : chain.residues)
+ // System.out.println("Atom: " + curAtom.getAtomNumber()
+ // + " Last atom index " + curAtom.group.lastAtomIndex);
+ if (chainTerMap == null || prevAtom == null)
{
-
+ return true;
}
- 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)
+ String curAtomChId = curAtom.getChainIDStr();
+ String prevAtomChId = prevAtom.getChainIDStr();
+ // new chain encoutered
+ if (!prevAtomChId.equals(curAtomChId))
{
- 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)
+ // On chain switch add previous chain termination to xTerMap if not exists
+ if (!chainTerMap.containsKey(prevAtomChId))
{
- buildSequenceFromChain(monomers.subList(from, from + length),
- modelTitle);
- from += length;
+ chainTerMap.put(prevAtomChId, prevAtom);
}
- }
- }
-
- /**
- * 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())
+ // if current atom belongs to an already terminated chain and the resNum
+ // diff < 5 then mark as valid and update termination Atom
+ if (chainTerMap.containsKey(curAtomChId))
{
- Group group = ms.at[groupLeadAtoms].group;
- if (group instanceof Monomer)
+ if (curAtom.getResno() < chainTerMap.get(curAtomChId).getResno())
+ {
+ return false;
+ }
+ if ((curAtom.getResno()
+ - chainTerMap.get(curAtomChId).getResno()) < 5)
{
- /*
- * 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;
+ chainTerMap.put(curAtomChId, curAtom);
+ return true;
}
+ return false;
}
}
- 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)
+ // atom with previously terminated chain encountered
+ else if (chainTerMap.containsKey(curAtomChId))
{
- int chainId = monomer.chain.chainID;
- if (chainId != lastChainId && length > 0)
+ if (curAtom.getResno() < chainTerMap.get(curAtomChId).getResno())
{
- /*
- * change of chain - record the length of the last one
- */
- chainLengths.add(length);
- length = 0;
+ return false;
}
- 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)
- {
- // Jalview doesn't like residue < 1, so force this to 1
- System.err.println("Converting chain " + chainId + " first RESNUM ("
- + firstResNum + ") to 1");
- firstResNum = 1;
- }
-
- /*
- * 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)
+ if ((curAtom.getResno()
+ - chainTerMap.get(curAtomChId).getResno()) < 5)
{
- seq[p] = 'X';
+ chainTerMap.put(curAtomChId, curAtom);
+ return true;
}
+ return false;
}
+ // HETATM with resNum jump > 2
+ return !(curAtom.isHetero()
+ && ((curAtom.getResno() - prevAtom.getResno()) > 2));
}
- /**
- * 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)
+ private void createAnnotation(SequenceI sequence, PDBChain chain,
+ org.jmol.modelset.Atom[] jmolAtoms)
{
- DBRefEntry sourceDBRef = new DBRefEntry();
- sourceDBRef.setAccessionId(accessionId);
- sourceDBRef.setSource(DBRefSource.MMCIF);
- sourceDBRef.setStartRes(start);
- sourceDBRef.setEndRes(end);
- sq.setSourceDBRef(sourceDBRef);
- sq.addDBRef(sourceDBRef);
- }
+ char[] secstr = new char[sequence.getLength()];
+ char[] secstrcode = new char[sequence.getLength()];
- /**
- * 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)
+ // Ensure Residue size equals Seq size
+ if (chain.residues.size() != sequence.getLength())
{
- // entry.getProperty().put("CHAIN", chains.elementAt(i).id);
- entry.setChainCode(String.valueOf(chainId));
+ return;
}
- 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
SequenceI sq, char[] secstr, char[] secstrcode, String chainId,
int firstResNum)
{
- char[] seq = sq.getSequence();
+ int length = sq.getLength();
boolean ssFound = false;
- Annotation asecstr[] = new Annotation[seq.length + firstResNum - 1];
- for (int p = 0; p < seq.length; p++)
+ Annotation asecstr[] = new Annotation[length + firstResNum - 1];
+ for (int p = 0; p < length; p++)
{
if (secstr[p] >= 'A' && secstr[p] <= 'z')
{
- asecstr[p] = new Annotation(String.valueOf(secstr[p]), null,
- secstrcode[p], Float.NaN);
- ssFound = true;
+ try
+ {
+ asecstr[p] = new Annotation(String.valueOf(secstr[p]), null,
+ secstrcode[p], Float.NaN);
+ ssFound = true;
+ } catch (Exception e)
+ {
+ // e.printStackTrace();
+ }
}
}
* @param secstr
* @param secstrcode
*/
- protected void setSecondaryStructure(STR proteinStructureSubType,
- int pos, char[] secstr, char[] secstrcode)
+ protected void setSecondaryStructure(STR proteinStructureSubType, int pos,
+ char[] secstr, char[] secstrcode)
{
switch (proteinStructureSubType)
{
}
}
- 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.)
* Not implemented - returns null
*/
@Override
- public String print()
+ public String print(SequenceI[] seqs, boolean jvSuffix)
{
return null;
}
@Override
public void notifyCallback(CBK cbType, Object[] data)
{
- String strInfo = (data == null || data[1] == null ? null : data[1]
- .toString());
+ String strInfo = (data == null || data[1] == null ? null
+ : data[1].toString());
switch (cbType)
{
case ECHO:
* Not implemented - returns null
*/
@Override
- public float[][][] functionXYZ(String functionName, int nx, int ny, int nz)
+ public float[][][] functionXYZ(String functionName, int nx, int ny,
+ int nz)
{
return null;
}
* Not implemented - returns null
*/
@Override
- public Dimension resizeInnerPanel(String data)
+ public int[] resizeInnerPanel(String data)
{
return null;
}
return predictSecondaryStructure;
}
- public void setPredictSecondaryStructure(boolean predictSecondaryStructure)
+ public void setPredictSecondaryStructure(
+ boolean predictSecondaryStructure)
{
this.predictSecondaryStructure = predictSecondaryStructure;
}
+ public boolean isVisibleChainAnnotation()
+ {
+ return visibleChainAnnotation;
+ }
+
+ public void setVisibleChainAnnotation(boolean visibleChainAnnotation)
+ {
+ this.visibleChainAnnotation = visibleChainAnnotation;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff