*/
package jalview.ext.jmol;
+import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
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.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;
{
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);
@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());
? PDBEntry.Type.MMCIF.toString()
: "PDB");
- transformJmolModelToJalview(jmolModel.ms);
+ transformJmolModelToJalview(jmolModel.ms, doXferSettings);
}
}
return false;
}
- public void transformJmolModelToJalview(ModelSet ms) throws IOException
+ public void transformJmolModelToJalview(ModelSet ms,
+ boolean localDoXferSettings) throws IOException
{
try
{
{
setId(pdbId);
setPDBIdAvailable(true);
- alphaFoldModel = alphaFold.search(pdbId) && isMMCIF;
-
+ setAlphafoldModel(alphaFold.search(pdbId) && isMMCIF);
}
List<Atom> significantAtoms = convertSignificantAtoms(ms);
for (Atom tmpatom : significantAtoms)
else
{
AnnotationRowBuilder builder = null;
- String tempFString = null;
- if (isAlphafoldModel())
+ if (isAlphafoldModel()
+ || getTemperatureFactorType() == StructureImportSettings.TFType.PLDDT)
{
builder = new AlphaFoldAnnotationRowBuilder();
}
}
lastID = tmpatom.resNumIns.trim();
}
- if (isParseImmediately())
+ if (isParseImmediately() && localDoXferSettings)
{
// configure parsing settings from the static singleton
xferSettings();
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(
+ jalview.bin.Console.outPrintln(
"OUT OF MEMORY LOADING TRANSFORMING JMOL MODEL TO JALVIEW MODEL");
throw new IOException(MessageManager
.getString("exception.outofmemory_loading_mmcif_file"));
}
}
- private boolean isAlphafoldModel()
- {
- return alphaFoldModel;
- }
-
private List<Atom> convertSignificantAtoms(ModelSet ms)
{
List<Atom> significantAtoms = new ArrayList<Atom>();
org.jmol.modelset.Atom prevAtom,
HashMap<String, org.jmol.modelset.Atom> chainTerMap)
{
- // System.out.println("Atom: " + curAtom.getAtomNumber()
+ // jalview.bin.Console.outPrintln("Atom: " + curAtom.getAtomNumber()
// + " Last atom index " + curAtom.group.lastAtomIndex);
if (chainTerMap == null || prevAtom == null)
{
{
int length = sq.getLength();
boolean ssFound = false;
- Annotation asecstr[] = new Annotation[length + firstResNum - 1];
+ Annotation asecstr[] = new Annotation[length + (firstResNum-sq.getStart())];
for (int p = 0; p < length; p++)
{
if (secstr[p] >= 'A' && secstr[p] <= 'z')