*/
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;
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
{
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);
@Override
public void parse() throws IOException
{
+ parse(true);
+ }
+
+ @Override
+ public void parse(boolean doXferSettings) throws IOException
+ {
setChains(new Vector<PDBChain>());
Viewer jmolModel = getJmolData();
jmolModel.openReader(getDataName(), getDataName(), getReader());
// }
// ;
// 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);
}
}
* 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)
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<SequenceI> rna = new ArrayList<SequenceI>();
List<SequenceI> prot = new ArrayList<SequenceI>();
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)
{
{
setId(pdbId);
setPDBIdAvailable(true);
+ setAlphafoldModel(alphaFold.search(pdbId) && isMMCIF);
}
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(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();
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(
/**
* 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
{
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)
{
git://source.jalview.org / jalview.git / blobdiff