import MCview.Atom;
import MCview.PDBChain;
+import MCview.Residue;
/**
* Import and process files with Jmol for file like PDB, mmCIF
}
/**
+ * Calls the Jmol library to parse the PDB/mmCIF file, and then inspects the
+ * resulting object model to generate Jalview-style sequences, with secondary
+ * structure annotation added where available (i.e. where it has been computed
+ * by Jmol using DSSP).
+ *
+ * @see jalview.io.AlignFile#parse()
+ */
+ @Override
+ public void parse() throws IOException
+ {
+
+ setChains(new Vector<PDBChain>());
+ Viewer jmolModel = getJmolData();
+ jmolModel.openReader(getDataName(), getDataName(), getReader());
+ waitForScript(jmolModel);
+
+ /*
+ * Convert one or more Jmol Model objects to Jalview sequences
+ */
+ if (jmolModel.ms.mc > 0)
+ {
+ parseBiopolymer(jmolModel.ms);
+ // transformJmolModelToJalview(jmolModel.ms);
+ }
+ }
+
+ /**
* create a headless jmol instance for dataprocessing
*
* @return
return viewer;
}
- private void waitForScript(Viewer jmd)
+ public void transformJmolModelToJalview(ModelSet ms) throws IOException
{
- while (jmd.isScriptExecuting())
+ try
{
- 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)
{
- Thread.sleep(50);
+ 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();
- } catch (InterruptedException x)
+ 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);
+ }
+ 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_mmcif_file"));
}
}
- /**
- * Convert Jmol's secondary structure code to Jalview's, and stored it in the
- * secondary structure arrays at the given sequence position
- *
- * @param proteinStructureSubType
- * @param pos
- * @param secstr
- * @param secstrcode
- */
- protected void setSecondaryStructure(STR proteinStructureSubType,
- int pos, char[] secstr, char[] secstrcode)
+ private List<Atom> convertSignificantAtoms(ModelSet ms)
{
- switch (proteinStructureSubType)
+ List<Atom> significantAtoms = new ArrayList<Atom>();
+ for (org.jmol.modelset.Atom atom : ms.at)
{
- case HELIX310:
- secstr[pos] = '3';
- break;
- case HELIX:
- case HELIXALPHA:
- secstr[pos] = 'H';
- break;
- case HELIXPI:
- secstr[pos] = 'P';
- break;
- case SHEET:
- secstr[pos] = 'E';
- break;
- default:
- secstr[pos] = 0;
+ 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.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.type = 0;
+ significantAtoms.add(curAtom);
+ }
}
+ return significantAtoms;
+ }
- switch (proteinStructureSubType)
+ private void createAnnotation(SequenceI sequence, PDBChain chain,
+ org.jmol.modelset.Atom[] jmolAtoms)
+ {
+ char[] secstr = new char[sequence.getLength()];
+ char[] secstrcode = new char[sequence.getLength()];
+ for (Residue residue : chain.residues)
{
- case HELIX310:
- case HELIXALPHA:
- case HELIXPI:
- case HELIX:
- secstrcode[pos] = 'H';
- break;
- case SHEET:
- secstrcode[pos] = 'E';
- break;
- default:
- secstrcode[pos] = 0;
+
}
+ addSecondaryStructureAnnotation(chain.pdbid, sequence, secstr,
+ secstrcode, chain.id, sequence.getStart());
}
/**
- * Convert any non-standard peptide codes to their standard code table
- * equivalent. (Initial version only does Selenomethionine MSE->MET.)
+ * Process the Jmol BioPolymer array and generate a Jalview sequence for each
+ * chain found (including any secondary structure annotation from DSSP)
*
- * @param threeLetterCode
- * @param seq
- * @param pos
+ * @param ms
+ * @throws IOException
*/
- protected void replaceNonCanonicalResidue(String threeLetterCode,
- char[] seq, int pos)
+ public void parseBiopolymer(ModelSet ms) throws IOException
{
- String canonical = ResidueProperties
- .getCanonicalAminoAcid(threeLetterCode);
- if (canonical != null && !canonical.equalsIgnoreCase(threeLetterCode))
+ int modelIndex = -1;
+ for (Model model : ms.am)
{
- seq[pos] = ResidueProperties.getSingleCharacterCode(canonical);
+ 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;
+ }
}
}
/**
- * Not implemented - returns null
+ * 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
*/
- @Override
- public String print()
+ protected List<Monomer> getMonomers(ModelSet ms, BioModel model)
{
- return null;
+ 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;
}
/**
- * Not implemented
+ * 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
*/
- @Override
- public void setCallbackFunction(String callbackType,
- String callbackFunction)
+ protected List<Integer> getChainLengths(List<Monomer> monomers)
{
- }
+ List<Integer> chainLengths = new ArrayList<Integer>();
+ int lastChainId = -1;
+ int length = 0;
- @Override
- public void notifyCallback(CBK cbType, Object[] data)
- {
- String strInfo = (data == null || data[1] == null ? null : data[1]
- .toString());
- switch (cbType)
+ for (Monomer monomer : monomers)
{
- case ECHO:
- sendConsoleEcho(strInfo);
- break;
- case SCRIPT:
- notifyScriptTermination((String) data[2],
- ((Integer) data[3]).intValue());
- break;
- case MEASURE:
- String mystatus = (String) data[3];
- if (mystatus.indexOf("Picked") >= 0
- || mystatus.indexOf("Sequence") >= 0)
+ int chainId = monomer.chain.chainID;
+ if (chainId != lastChainId && length > 0)
{
- // Picking mode
- sendConsoleMessage(strInfo);
+ /*
+ * change of chain - record the length of the last one
+ */
+ chainLengths.add(length);
+ length = 0;
}
- else if (mystatus.indexOf("Completed") >= 0)
- {
- sendConsoleEcho(strInfo.substring(strInfo.lastIndexOf(",") + 2,
- strInfo.length() - 1));
- }
- break;
- case MESSAGE:
- sendConsoleMessage(data == null ? null : strInfo);
- break;
- case PICK:
- sendConsoleMessage(strInfo);
- break;
- default:
- break;
+ lastChainId = chainId;
+ length++;
+ }
+ if (length > 0)
+ {
+ /*
+ * record the length of the final chain
+ */
+ chainLengths.add(length);
}
- }
-
- String lastConsoleEcho = "";
- private void sendConsoleEcho(String string)
- {
- lastConsoleEcho += string;
- lastConsoleEcho += "\n";
+ return chainLengths;
}
- String lastConsoleMessage = "";
-
- private void sendConsoleMessage(String string)
+ /**
+ * 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)
{
- lastConsoleMessage += string;
- lastConsoleMessage += "\n";
- }
-
- int lastScriptTermination = -1;
+ final int length = monomers.size();
- String lastScriptMessage = "";
+ /*
+ * arrays to hold sequence and secondary structure
+ */
+ char[] seq = new char[length];
+ char[] secstr = new char[length];
+ char[] secstrcode = new char[length];
- private void notifyScriptTermination(String string, int intValue)
- {
- lastScriptMessage += string;
- lastScriptMessage += "\n";
- lastScriptTermination = intValue;
- }
+ /*
+ * populate the sequence and secondary structure arrays
+ */
+ extractJmolChainData(monomers, seq, secstr, secstrcode);
- @Override
- public boolean notifyEnabled(CBK callbackPick)
- {
- switch (callbackPick)
+ /*
+ * 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)
{
- case MESSAGE:
- case SCRIPT:
- case ECHO:
- case LOADSTRUCT:
- case ERROR:
- return true;
- default:
- return false;
+ // Jalview doesn't like residue < 1, so force this to 1
+ System.err.println("Converting chain " + chainId + " first RESNUM ("
+ + firstResNum + ") to 1");
+ firstResNum = 1;
}
- }
- /**
- * Not implemented - returns null
- */
- @Override
- public String eval(String strEval)
- {
- return null;
- }
+ /*
+ * convert any non-gap unknown residues to 'X'
+ */
+ convertNonGapCharacters(seq);
- /**
- * Not implemented - returns null
- */
- @Override
- public float[][] functionXY(String functionName, int x, int y)
- {
- return null;
- }
+ /*
+ * construct and add the Jalview sequence
+ */
+ String seqName = "" + modelTitle + "|" + chainId;
+ int start = firstResNum;
+ int end = firstResNum + length - 1;
- /**
- * Not implemented - returns null
- */
- @Override
- public float[][][] functionXYZ(String functionName, int nx, int ny, int nz)
- {
- return null;
- }
+ SequenceI sq = new Sequence(seqName, seq, start, end);
- /**
- * Not implemented - returns null
- */
- @Override
- public String createImage(String fileName, String imageType,
- Object text_or_bytes, int quality)
- {
- return null;
- }
+ addPdbid(sq, modelTitle, chainId);
- /**
- * Not implemented - returns null
- */
- @Override
- public Map<String, Object> getRegistryInfo()
- {
- return null;
- }
+ addSourceDBref(sq, modelTitle, start, end);
- /**
- * Not implemented
- */
- @Override
- public void showUrl(String url)
- {
- }
+ seqs.add(sq);
- /**
- * Not implemented - returns null
- */
- @Override
- public Dimension resizeInnerPanel(String data)
- {
- return null;
- }
+ /*
+ * add secondary structure predictions (if any)
+ */
+ addSecondaryStructureAnnotation(modelTitle, sq, secstr, secstrcode,
+ chainId, firstResNum);
- @Override
- public Map<String, Object> getJSpecViewProperty(String arg0)
- {
- return null;
}
/**
- * Calls the Jmol library to parse the PDB file, and then inspects the
- * resulting object model to generate Jalview-style sequences, with secondary
- * structure annotation added where available (i.e. where it has been computed
- * by Jmol using DSSP).
+ * 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
*
- * @see jalview.io.AlignFile#parse()
+ * @param monomers
+ * @param seq
+ * @param secstr
+ * @param secstrcode
*/
- @Override
- public void parse() throws IOException
+ protected void extractJmolChainData(List<Monomer> monomers, char[] seq,
+ char[] secstr, char[] secstrcode)
{
+ int pos = 0;
+ for (Monomer monomer : monomers)
+ {
+ seq[pos] = monomer.getGroup1();
- setChains(new Vector<PDBChain>());
- Viewer jmolModel = getJmolData();
- jmolModel.openReader(getDataName(), getDataName(), getReader());
- waitForScript(jmolModel);
+ /*
+ * 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);
- /*
- * Convert one or more Jmol Model objects to Jalview sequences
- */
- if (jmolModel.ms.mc > 0)
- {
- // parseBiopolymer(jmolModel.ms);
- transformJmolModelToJalview(jmolModel.ms);
+ /*
+ * 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++;
}
}
/**
- * Process the Jmol BioPolymer array and generate a Jalview sequence for each
- * chain found (including any secondary structure annotation from DSSP)
+ * Replace any non-gap miscellaneous characters with 'X'
*
- * @param ms
- * @throws IOException
+ * @param seq
+ * @return
*/
- public void parseBiopolymer(ModelSet ms) throws IOException
+ protected void convertNonGapCharacters(char[] seq)
{
- 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);
+ boolean isNa = Comparison.areNucleotide(new char[][] { seq });
+ int[] cinds = isNa ? ResidueProperties.nucleotideIndex
+ : ResidueProperties.aaIndex;
+ int nonGap = isNa ? ResidueProperties.maxNucleotideIndex
+ : ResidueProperties.maxProteinIndex;
- /*
- * now chop up the Monomer list to make Jalview Sequences
- */
- int from = 0;
- for (int length : chainLengths)
+ for (int p = 0; p < seq.length; p++)
+ {
+ if (cinds[seq[p]] == nonGap)
{
- buildSequenceFromChain(monomers.subList(from, from + length),
- modelTitle);
- from += length;
+ seq[p] = 'X';
}
}
}
- public void transformJmolModelToJalview(ModelSet ms)
+ /**
+ * 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)
{
- 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)
+ 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
+ {
+ // TODO: decide if we should dump the datasource to disk
+ entry.setFile(getDataName());
+ }
+
+ sq.addPDBId(entry);
+ }
+
+
+ /**
+ * Helper method that adds an AlignmentAnnotation for secondary structure to
+ * the sequence, provided at least one secondary structure prediction has been
+ * made
+ *
+ * @param modelTitle
+ * @param seq
+ * @param secstr
+ * @param secstrcode
+ * @param chainId
+ * @param firstResNum
+ * @return
+ */
+ protected void addSecondaryStructureAnnotation(String modelTitle,
+ SequenceI sq, char[] secstr, char[] secstrcode, String chainId,
+ int firstResNum)
+ {
+ char[] seq = sq.getSequence();
+ boolean ssFound = false;
+ Annotation asecstr[] = new Annotation[seq.length + firstResNum - 1];
+ for (int p = 0; p < seq.length; p++)
+ {
+ if (secstr[p] >= 'A' && secstr[p] <= 'z')
{
- 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();
+ asecstr[p] = new Annotation(String.valueOf(secstr[p]), null,
+ secstrcode[p], Float.NaN);
+ ssFound = true;
}
- makeResidueList();
- makeCaBondList();
+ }
- if (getId() == null)
+ if (ssFound)
+ {
+ String mt = modelTitle == null ? getDataName() : modelTitle;
+ mt += chainId;
+ AlignmentAnnotation ann = new AlignmentAnnotation(
+ "Secondary Structure", "Secondary Structure for " + mt,
+ asecstr);
+ ann.belowAlignment = true;
+ ann.visible = true;
+ ann.autoCalculated = false;
+ ann.setCalcId(getClass().getName());
+ ann.adjustForAlignment();
+ ann.validateRangeAndDisplay();
+ annotations.add(ann);
+ sq.addAlignmentAnnotation(ann);
+ }
+ }
+
+ private void waitForScript(Viewer jmd)
+ {
+ while (jmd.isScriptExecuting())
+ {
+ try
{
- setId(inFile.getName());
- }
- for (PDBChain chain : getChains())
+ Thread.sleep(50);
+
+ } catch (InterruptedException x)
{
- SequenceI chainseq = postProcessChain(chain);
- if (isRNA(chainseq))
- {
- rna.add(chainseq);
- }
- else
- {
- prot.add(chainseq);
- }
}
- } catch (OutOfMemoryError er)
+ }
+ }
+
+ /**
+ * Convert Jmol's secondary structure code to Jalview's, and stored it in the
+ * secondary structure arrays at the given sequence position
+ *
+ * @param proteinStructureSubType
+ * @param pos
+ * @param secstr
+ * @param secstrcode
+ */
+ protected void setSecondaryStructure(STR proteinStructureSubType,
+ int pos, char[] secstr, char[] secstrcode)
+ {
+ switch (proteinStructureSubType)
{
- System.out
- .println("OUT OF MEMORY LOADING TRANSFORMING JMOL MODEL TO JALVIEW MODEL");
- // throw new IOException(
- // MessageManager
- // .getString("exception.outofmemory_loading_pdb_file"));
+ case HELIX310:
+ secstr[pos] = '3';
+ break;
+ case HELIX:
+ case HELIXALPHA:
+ secstr[pos] = 'H';
+ break;
+ case HELIXPI:
+ secstr[pos] = 'P';
+ break;
+ case SHEET:
+ secstr[pos] = 'E';
+ break;
+ default:
+ secstr[pos] = 0;
+ }
+
+ switch (proteinStructureSubType)
+ {
+ case HELIX310:
+ case HELIXALPHA:
+ case HELIXPI:
+ case HELIX:
+ secstrcode[pos] = 'H';
+ break;
+ case SHEET:
+ secstrcode[pos] = 'E';
+ break;
+ default:
+ secstrcode[pos] = 0;
}
}
- private List<Atom> convertSignificantAtoms(ModelSet ms)
+ private char getSecondayStructure(STR proteinStructureSubType)
{
- List<Atom> significantAtoms = new ArrayList<Atom>();
- for (org.jmol.modelset.Atom atom : ms.at)
+ switch (proteinStructureSubType)
{
- 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);
- }
+ case HELIX310:
+ return '3';
+ case HELIX:
+ case HELIXALPHA:
+ return 'H';
+ case HELIXPI:
+ return 'P';
+ case SHEET:
+ return 'E';
+ default:
+ return 0;
}
- return significantAtoms;
}
/**
- * Helper method to construct a sequence for one chain and add it to the seqs
- * list
+ * Convert any non-standard peptide codes to their standard code table
+ * equivalent. (Initial version only does Selenomethionine MSE->MET.)
*
- * @param monomers
- * a list of all monomers in the chain
- * @param modelTitle
+ * @param threeLetterCode
+ * @param seq
+ * @param pos
*/
- protected void buildSequenceFromChain(List<Monomer> monomers,
- String modelTitle)
+ protected void replaceNonCanonicalResidue(String threeLetterCode,
+ char[] seq, int pos)
{
- final int length = monomers.size();
+ String canonical = ResidueProperties
+ .getCanonicalAminoAcid(threeLetterCode);
+ if (canonical != null && !canonical.equalsIgnoreCase(threeLetterCode))
+ {
+ seq[pos] = ResidueProperties.getSingleCharacterCode(canonical);
+ }
+ }
- /*
- * arrays to hold sequence and secondary structure
- */
- char[] seq = new char[length];
- char[] secstr = new char[length];
- char[] secstrcode = new char[length];
+ /**
+ * Not implemented - returns null
+ */
+ @Override
+ public String print()
+ {
+ return null;
+ }
- /*
- * populate the sequence and secondary structure arrays
- */
- extractJmolChainData(monomers, seq, secstr, secstrcode);
+ /**
+ * Not implemented
+ */
+ @Override
+ public void setCallbackFunction(String callbackType,
+ String callbackFunction)
+ {
+ }
- /*
- * 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)
+ @Override
+ public void notifyCallback(CBK cbType, Object[] data)
+ {
+ String strInfo = (data == null || data[1] == null ? null : data[1]
+ .toString());
+ switch (cbType)
{
- // Jalview doesn't like residue < 1, so force this to 1
- System.err.println("Converting chain " + chainId + " first RESNUM ("
- + firstResNum + ") to 1");
- firstResNum = 1;
+ case ECHO:
+ sendConsoleEcho(strInfo);
+ break;
+ case SCRIPT:
+ notifyScriptTermination((String) data[2],
+ ((Integer) data[3]).intValue());
+ break;
+ case MEASURE:
+ String mystatus = (String) data[3];
+ if (mystatus.indexOf("Picked") >= 0
+ || mystatus.indexOf("Sequence") >= 0)
+ {
+ // Picking mode
+ sendConsoleMessage(strInfo);
+ }
+ else if (mystatus.indexOf("Completed") >= 0)
+ {
+ sendConsoleEcho(strInfo.substring(strInfo.lastIndexOf(",") + 2,
+ strInfo.length() - 1));
+ }
+ break;
+ case MESSAGE:
+ sendConsoleMessage(data == null ? null : strInfo);
+ break;
+ case PICK:
+ sendConsoleMessage(strInfo);
+ break;
+ default:
+ break;
}
+ }
- /*
- * convert any non-gap unknown residues to 'X'
- */
- convertNonGapCharacters(seq);
+ String lastConsoleEcho = "";
- /*
- * construct and add the Jalview sequence
- */
- String seqName = "" + modelTitle + "|" + chainId;
- int start = firstResNum;
- int end = firstResNum + length - 1;
+ private void sendConsoleEcho(String string)
+ {
+ lastConsoleEcho += string;
+ lastConsoleEcho += "\n";
+ }
- SequenceI sq = new Sequence(seqName, seq, start, end);
+ String lastConsoleMessage = "";
- addPdbid(sq, modelTitle, chainId);
+ private void sendConsoleMessage(String string)
+ {
+ lastConsoleMessage += string;
+ lastConsoleMessage += "\n";
+ }
- addSourceDBref(sq, modelTitle, start, end);
+ int lastScriptTermination = -1;
+
+ String lastScriptMessage = "";
- seqs.add(sq);
+ private void notifyScriptTermination(String string, int intValue)
+ {
+ lastScriptMessage += string;
+ lastScriptMessage += "\n";
+ lastScriptTermination = intValue;
+ }
- /*
- * add secondary structure predictions (if any)
- */
- if (isPredictSecondaryStructure())
+ @Override
+ public boolean notifyEnabled(CBK callbackPick)
+ {
+ switch (callbackPick)
{
- addSecondaryStructureAnnotation(modelTitle, sq, secstr, secstrcode,
- chainId, firstResNum);
+ case MESSAGE:
+ case SCRIPT:
+ case ECHO:
+ case LOADSTRUCT:
+ case ERROR:
+ return true;
+ default:
+ return false;
}
-
}
/**
- * Add a source db ref entry for the given sequence.
- *
- * @param sq
- * @param accessionId
- * @param start
- * @param end
+ * Not implemented - returns null
*/
- protected void addSourceDBref(SequenceI sq, String accessionId,
- int start, int end)
+ @Override
+ public String eval(String strEval)
{
- DBRefEntry sourceDBRef = new DBRefEntry();
- sourceDBRef.setAccessionId(accessionId);
- sourceDBRef.setSource(DBRefSource.MMCIF);
- sourceDBRef.setStartRes(start);
- sourceDBRef.setEndRes(end);
- sq.setSourceDBRef(sourceDBRef);
- sq.addDBRef(sourceDBRef);
+ return null;
}
/**
- * Add a PDBEntry giving the source of PDB data to the sequence
- *
- * @param sq
- * @param id
- * @param chainId
+ * Not implemented - returns null
*/
- protected void addPdbid(SequenceI sq, String id, String chainId)
+ @Override
+ public float[][] functionXY(String functionName, int x, int y)
{
- 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
- {
- // TODO: decide if we should dump the datasource to disk
- entry.setFile(getDataName());
- }
-
- sq.addPDBId(entry);
+ return null;
}
/**
- * 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
+ * Not implemented - returns null
*/
- protected void extractJmolChainData(List<Monomer> monomers, char[] seq,
- char[] secstr, char[] secstrcode)
+ @Override
+ public float[][][] functionXYZ(String functionName, int nx, int ny, int nz)
{
- 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++;
- }
+ return null;
}
/**
- * Helper method that adds an AlignmentAnnotation for secondary structure to
- * the sequence, provided at least one secondary structure prediction has been
- * made
- *
- * @param modelTitle
- * @param seq
- * @param secstr
- * @param secstrcode
- * @param chainId
- * @param firstResNum
- * @return
+ * Not implemented - returns null
*/
- protected void addSecondaryStructureAnnotation(String modelTitle,
- SequenceI sq, char[] secstr, char[] secstrcode, String chainId,
- int firstResNum)
+ @Override
+ public String createImage(String fileName, String imageType,
+ Object text_or_bytes, int quality)
{
- char[] seq = sq.getSequence();
- boolean ssFound = false;
- Annotation asecstr[] = new Annotation[seq.length + firstResNum - 1];
- for (int p = 0; p < seq.length; p++)
- {
- if (secstr[p] >= 'A' && secstr[p] <= 'z')
- {
- asecstr[p] = new Annotation(String.valueOf(secstr[p]), null,
- secstrcode[p], Float.NaN);
- ssFound = true;
- }
- }
-
- if (ssFound)
- {
- String mt = modelTitle == null ? getDataName() : modelTitle;
- mt += chainId;
- AlignmentAnnotation ann = new AlignmentAnnotation(
- "Secondary Structure", "Secondary Structure for " + mt,
- asecstr);
- ann.belowAlignment = true;
- ann.visible = true;
- ann.autoCalculated = false;
- ann.setCalcId(getClass().getName());
- ann.adjustForAlignment();
- ann.validateRangeAndDisplay();
- annotations.add(ann);
- sq.addAlignmentAnnotation(ann);
- }
+ return null;
}
/**
- * Replace any non-gap miscellaneous characters with 'X'
- *
- * @param seq
- * @return
+ * Not implemented - returns null
*/
- protected void convertNonGapCharacters(char[] seq)
+ @Override
+ public Map<String, Object> getRegistryInfo()
{
- 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';
- }
- }
+ return null;
}
/**
- * 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
+ * Not implemented
*/
- protected List<Integer> getChainLengths(List<Monomer> monomers)
+ @Override
+ public void showUrl(String url)
{
- 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;
}
/**
- * 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
+ * Not implemented - returns null
*/
- protected List<Monomer> getMonomers(ModelSet ms, BioModel model)
+ @Override
+ public Dimension resizeInnerPanel(String data)
{
- List<Monomer> result = new ArrayList<Monomer>();
- int lastResNo = Integer.MIN_VALUE;
+ return null;
+ }
- 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;
+ @Override
+ public Map<String, Object> getJSpecViewProperty(String arg0)
+ {
+ return null;
}
public boolean isPredictSecondaryStructure()
git://source.jalview.org / jalview.git / commitdiff