X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJmolParser.java;h=c64dac1fd2cb75249fbc98958227beb1c50ad296;hb=beb2fee66dde629e3bbb7febb38d0116e1a64df2;hp=ddf3b1a6639cfaac5b762d1c6d72b165c080906e;hpb=3d0101179759ef157b088ea135423cd909512d9f;p=jalview.git diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java index ddf3b1a..c64dac1 100644 --- a/src/jalview/ext/jmol/JmolParser.java +++ b/src/jalview/ext/jmol/JmolParser.java @@ -20,22 +20,12 @@ */ package jalview.ext.jmol; -import jalview.datamodel.AlignmentAnnotation; -import jalview.datamodel.Annotation; -import jalview.datamodel.PDBEntry; -import jalview.datamodel.SequenceI; -import jalview.io.DataSourceType; -import jalview.io.FileParse; -import jalview.io.StructureFile; -import jalview.schemes.ResidueProperties; -import jalview.structure.StructureImportSettings; -import jalview.util.Format; -import jalview.util.MessageManager; - +import java.io.File; import java.io.IOException; import java.util.ArrayList; import java.util.HashMap; import java.util.List; +import java.util.Locale; import java.util.Map; import java.util.Vector; @@ -46,9 +36,27 @@ import org.jmol.c.STR; import org.jmol.modelset.ModelSet; import org.jmol.viewer.Viewer; -import MCview.Atom; -import MCview.PDBChain; -import MCview.Residue; +import com.stevesoft.pat.Regex; + +import jalview.bin.Console; +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.Annotation; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SequenceI; +import jalview.datamodel.annotations.AlphaFoldAnnotationRowBuilder; +import jalview.datamodel.annotations.AnnotationRowBuilder; +import jalview.io.DataSourceType; +import jalview.io.FileParse; +import jalview.io.StructureFile; +import jalview.schemes.ResidueProperties; +import jalview.structure.StructureImportSettings; +import jalview.util.Format; +import jalview.util.MessageManager; +import jalview.ws.dbsources.EBIAlfaFold; +import mc_view.Atom; +import mc_view.PDBChain; +import mc_view.Residue; /** * Import and process files with Jmol for file like PDB, mmCIF @@ -60,12 +68,30 @@ public class JmolParser extends StructureFile implements JmolStatusListener { Viewer viewer = null; - public JmolParser(String inFile, DataSourceType sourceType) + public JmolParser(boolean immediate, Object inFile, + DataSourceType sourceType) throws IOException + { + // BH 2018 File or String for filename + super(immediate, inFile, sourceType); + + } + + public JmolParser(Object inFile, DataSourceType sourceType) throws IOException { - super(inFile, sourceType); + this(inFile, sourceType, null); } + public JmolParser(Object inFile, DataSourceType sourceType, + StructureImportSettings.TFType tempfacType) throws IOException + { + super(inFile, sourceType, tempfacType); + } + + public JmolParser(FileParse fp, boolean doXferSettings) throws IOException + { + super(fp, doXferSettings); + } public JmolParser(FileParse fp) throws IOException { super(fp); @@ -86,6 +112,12 @@ public class JmolParser extends StructureFile implements JmolStatusListener @Override public void parse() throws IOException { + parse(true); + } + + @Override + public void parse(boolean doXferSettings) throws IOException + { setChains(new Vector()); Viewer jmolModel = getJmolData(); jmolModel.openReader(getDataName(), getDataName(), getReader()); @@ -105,11 +137,12 @@ public class JmolParser extends StructureFile implements JmolStatusListener // } // ; // instead, we distinguish .cif from non-.cif by filename - setStructureFileType(getDataName().toLowerCase().endsWith(".cif") - ? PDBEntry.Type.MMCIF.toString() - : "PDB"); + setStructureFileType( + getDataName().toLowerCase(Locale.ROOT).endsWith(".cif") + ? PDBEntry.Type.MMCIF.toString() + : "PDB"); - transformJmolModelToJalview(jmolModel.ms); + transformJmolModelToJalview(jmolModel.ms, doXferSettings); } } @@ -128,8 +161,8 @@ public class JmolParser extends StructureFile implements JmolStatusListener * params -o (output to sysout) -n (nodisplay) -x (exit when finished) * see http://wiki.jmol.org/index.php/Jmol_Application */ - viewer = (Viewer) JmolViewer.allocateViewer(null, null, null, null, - null, "-x -o -n", this); + + viewer = JalviewJmolBinding.getJmolData(this); // ensure the 'new' (DSSP) not 'old' (Ramachandran) SS method is used viewer.setBooleanProperty("defaultStructureDSSP", true); } catch (ClassCastException x) @@ -143,15 +176,61 @@ public class JmolParser extends StructureFile implements JmolStatusListener return viewer; } - public void transformJmolModelToJalview(ModelSet ms) throws IOException + public static Regex getNewAlphafoldValidator() + { + Regex validator = new Regex("(AF-[A-Z]+[0-9]+[A-Z0-9]+-F1)"); + validator.setIgnoreCase(true); + return validator; + } + + PDBEntry.Type jmolFiletype = null; + + /** + * resolve a jmol filetype string and update the jmolFiletype field + * accordingly + * + * @param jmolIdentifiedFileType + * @return true if filetype was identified as MMCIF, PDB + */ + public boolean updateFileType(String jmolIdentifiedFileType) + { + if (jmolIdentifiedFileType == null + || jmolIdentifiedFileType.trim().equals("")) + { + return false; + } + if ("mmcif".equalsIgnoreCase(jmolIdentifiedFileType)) + { + jmolFiletype = PDBEntry.Type.MMCIF; + return true; + } + if ("pdb".equalsIgnoreCase(jmolIdentifiedFileType)) + { + jmolFiletype = PDBEntry.Type.PDB; + return true; + } + return false; + } + + public void transformJmolModelToJalview(ModelSet ms, + boolean localDoXferSettings) throws IOException { try { + Regex alphaFold = getNewAlphafoldValidator(); String lastID = ""; List rna = new ArrayList(); List prot = new ArrayList(); PDBChain tmpchain; String pdbId = (String) ms.getInfo(0, "title"); + boolean isMMCIF = false; + String jmolFileType_String = (String) ms.getInfo(0, "fileType"); + if (updateFileType(jmolFileType_String)) + { + setStructureFileType(jmolFiletype.toString()); + } + + isMMCIF = PDBEntry.Type.MMCIF.equals(jmolFiletype); if (pdbId == null) { @@ -162,28 +241,41 @@ public class JmolParser extends StructureFile implements JmolStatusListener { setId(pdbId); setPDBIdAvailable(true); + setAlphafoldModel(alphaFold.search(pdbId) && isMMCIF); } List 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(getId(), tmpatom.chain); + AnnotationRowBuilder builder = null; + if (isAlphafoldModel() + || getTemperatureFactorType() == StructureImportSettings.TFType.PLDDT) + { + builder = new AlphaFoldAnnotationRowBuilder(); + } + + tmpchain = new PDBChain(getId(), tmpatom.chain, builder); getChains().add(tmpchain); tmpchain.atoms.addElement(tmpatom); } lastID = tmpatom.resNumIns.trim(); } - xferSettings(); + if (isParseImmediately() && localDoXferSettings) + { + // configure parsing settings from the static singleton + xferSettings(); + } makeResidueList(); makeCaBondList(); @@ -200,11 +292,50 @@ public class JmolParser extends StructureFile implements JmolStatusListener prot.add(chainseq); } - if (StructureImportSettings.isProcessSecondaryStructure()) + // look at local setting for adding secondary tructure + if (predictSecondaryStructure) { createAnnotation(chainseq, chain, ms.at); } } + // if Alphafold, fetch the PAE matrix if doesn't already have one + if (isAlphafoldModel() && !hasPAEMatrix()) + { + try + { + Console.info("Retrieving PAE for " + pdbId); + File paeFile = EBIAlfaFold.fetchAlphaFoldPAE(pdbId, null); + this.setPAEMatrix(paeFile.getAbsolutePath()); + } catch (Throwable t) + { + Console.error("Couldn't get the pAE for " + pdbId, t); + } + } + // add a PAEMatrix if set (either by above or otherwise) + if (hasPAEMatrix()) + { + try + { + Alignment al = new Alignment(prot.toArray(new SequenceI[0])); + EBIAlfaFold.addAlphaFoldPAE(al, new File(this.getPAEMatrix()), 0, + null, false, false, null); + + if (al.getAlignmentAnnotation() != null) + { + for (AlignmentAnnotation alann : al.getAlignmentAnnotation()) + { + annotations.add(alann); + } + } + } catch (Throwable ff) + { + Console.error("Couldn't import PAE Matrix from " + getPAEMatrix(), + ff); + warningMessage += "Couldn't import PAE Matrix" + + getNewlineString() + ff.getLocalizedMessage() + + getNewlineString(); + } + } } catch (OutOfMemoryError er) { System.out.println( @@ -340,7 +471,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener /** * Helper method that adds an AlignmentAnnotation for secondary structure to - * the sequence, provided at least one secondary structure prediction has been + * the sequence, provided at least one secondary structure assignment has been * made * * @param modelTitle @@ -355,17 +486,16 @@ public class JmolParser extends StructureFile implements JmolStatusListener 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') { try { - asecstr[p] = new Annotation(String.valueOf(secstr[p]), null, - secstrcode[p], Float.NaN); + asecstr[p] = new Annotation(null, null, secstrcode[p], Float.NaN); ssFound = true; } catch (Exception e) {