X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJmolParser.java;h=45f3d7c918b5353643351543996d9b644043282d;hb=5db8e803feb3d04bf6142d25ded76473ec1cb571;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..45f3d7c 100644 --- a/src/jalview/ext/jmol/JmolParser.java +++ b/src/jalview/ext/jmol/JmolParser.java @@ -20,22 +20,11 @@ */ 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.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 +35,21 @@ 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.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 mc_view.Atom; +import mc_view.PDBChain; +import mc_view.Residue; /** * Import and process files with Jmol for file like PDB, mmCIF @@ -60,7 +61,16 @@ public class JmolParser extends StructureFile implements JmolStatusListener { Viewer viewer = null; - public JmolParser(String inFile, DataSourceType sourceType) + 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); @@ -105,9 +115,10 @@ 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); } @@ -128,8 +139,8 @@ 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 +154,60 @@ 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)"); + 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 { 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 +218,41 @@ public class JmolParser extends StructureFile implements JmolStatusListener { setId(pdbId); setPDBIdAvailable(true); + alphaFoldModel = 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); + String tempFString = null; + if (isAlphafoldModel()) + { + tempFString = "Alphafold Reliability"; + } + + tmpchain = new PDBChain(getId(), tmpatom.chain, tempFString); getChains().add(tmpchain); tmpchain.atoms.addElement(tmpatom); } lastID = tmpatom.resNumIns.trim(); } - xferSettings(); + if (isParseImmediately()) + { + // configure parsing settings from the static singleton + xferSettings(); + } makeResidueList(); makeCaBondList(); @@ -200,7 +269,8 @@ 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); } @@ -214,6 +284,11 @@ public class JmolParser extends StructureFile implements JmolStatusListener } } + private boolean isAlphafoldModel() + { + return alphaFoldModel; + } + private List convertSignificantAtoms(ModelSet ms) { List significantAtoms = new ArrayList(); @@ -340,7 +415,7 @@ 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 @@ -355,10 +430,10 @@ 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') { @@ -585,7 +660,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener * Not implemented - returns null */ @Override - public float[][] functionXY(String functionName, int x, int y) + public double[][] functionXY(String functionName, int x, int y) { return null; } @@ -594,7 +669,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener * Not implemented - returns null */ @Override - public float[][][] functionXYZ(String functionName, int nx, int ny, + public double[][][] functionXYZ(String functionName, int nx, int ny, int nz) { return null;