X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJmolParser.java;h=c64dac1fd2cb75249fbc98958227beb1c50ad296;hb=beb2fee66dde629e3bbb7febb38d0116e1a64df2;hp=ae8ff7a68c5e5b65e4cb07d9e17ebdb5bd79c369;hpb=d46c8cbd1a5282ede9a0a94471f23ca002cf7df6;p=jalview.git diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java index ae8ff7a..c64dac1 100644 --- a/src/jalview/ext/jmol/JmolParser.java +++ b/src/jalview/ext/jmol/JmolParser.java @@ -20,21 +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.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; @@ -47,6 +38,22 @@ import org.jmol.viewer.Viewer; 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; @@ -61,21 +68,30 @@ public class JmolParser extends StructureFile implements JmolStatusListener { Viewer viewer = null; - private boolean alphaFoldModel; - 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); @@ -96,6 +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()); @@ -115,11 +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); } } @@ -138,7 +161,7 @@ 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 = JalviewJmolBinding.getJmolData(this); // ensure the 'new' (DSSP) not 'old' (Ramachandran) SS method is used viewer.setBooleanProperty("defaultStructureDSSP", true); @@ -152,16 +175,45 @@ public class JmolParser extends StructureFile implements JmolStatusListener } return viewer; } - + public static Regex getNewAlphafoldValidator() { - Regex validator = new Regex("(AF-[A-Z]+[0-9]+[A-Z0-9]+-F1)"); + 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) throws IOException + public void transformJmolModelToJalview(ModelSet ms, + boolean localDoXferSettings) throws IOException { try { @@ -171,7 +223,14 @@ public class JmolParser extends StructureFile implements JmolStatusListener List prot = new ArrayList(); PDBChain tmpchain; String pdbId = (String) ms.getInfo(0, "title"); - String isMMCIF = (String) ms.getInfo(0, "fileType"); + 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) { @@ -182,8 +241,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener { setId(pdbId); setPDBIdAvailable(true); - alphaFoldModel = alphaFold.search(pdbId) && isMMCIF!=null && isMMCIF.equalsIgnoreCase("mmcif"); - + setAlphafoldModel(alphaFold.search(pdbId) && isMMCIF); } List significantAtoms = convertSignificantAtoms(ms); for (Atom tmpatom : significantAtoms) @@ -197,15 +255,23 @@ public class JmolParser extends StructureFile implements JmolStatusListener if (tmpchain != null) { tmpchain.atoms.addElement(tmpatom); - } else + } + else { - tmpchain = new PDBChain(getId(), tmpatom.chain,isAlphafoldModel()); + 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(); } - if (isParseImmediately()) + if (isParseImmediately() && localDoXferSettings) { // configure parsing settings from the static singleton xferSettings(); @@ -232,6 +298,44 @@ public class JmolParser extends StructureFile implements JmolStatusListener 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( @@ -241,11 +345,6 @@ public class JmolParser extends StructureFile implements JmolStatusListener } } - private boolean isAlphafoldModel() - { - return alphaFoldModel; - } - private List convertSignificantAtoms(ModelSet ms) { List significantAtoms = new ArrayList(); @@ -396,8 +495,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener { 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) {