import org.jmol.modelset.ModelSet;
import org.jmol.viewer.Viewer;
+import com.stevesoft.pat.Regex;
+
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
{
}
return viewer;
}
+
+ public static Regex getNewAlphafoldValidator()
+ {
+ Regex validator = new Regex("(AF-[A-Z]+[0-9]+[A-Z0-9]+-F1)");
+ validator.setIgnoreCase(true);
+ return validator;
+ }
+
public void transformJmolModelToJalview(ModelSet ms) 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");
+ String isMMCIF = (String) ms.getInfo(0, "fileType");
if (pdbId == null)
{
{
setId(pdbId);
setPDBIdAvailable(true);
+ alphaFoldModel = alphaFold.search(pdbId) && isMMCIF!=null && isMMCIF.equalsIgnoreCase("mmcif");
+
}
List<Atom> significantAtoms = convertSignificantAtoms(ms);
for (Atom tmpatom : significantAtoms)
tmpchain.atoms.addElement(tmpatom);
} else
{
- tmpchain = new PDBChain(getId(), tmpatom.chain);
+ tmpchain = new PDBChain(getId(), tmpatom.chain,isAlphafoldModel());
getChains().add(tmpchain);
tmpchain.atoms.addElement(tmpatom);
}
}
}
+ private boolean isAlphafoldModel()
+ {
+ return alphaFoldModel;
+ }
+
private List<Atom> convertSignificantAtoms(ModelSet ms)
{
List<Atom> significantAtoms = new ArrayList<Atom>();
/**
* 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