*/
package mc_view;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
+import jalview.bin.Console;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.SequenceI;
import jalview.io.StructureFile;
import jalview.util.MessageManager;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Vector;
-
public class PDBfile extends StructureFile
{
private static String CALC_ID_PREFIX = "JalviewPDB";
DataSourceType sourceType) throws IOException
{
super(false, dataObject, sourceType);
+ Console.debug("***** PDBfile constructor");
addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
+ Console.debug("***** About to doParse() 1");
doParse();
}
{
super(false, source);
addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
+ Console.debug("***** About to doParse() 2");
doParse();
}
}
Atom tmpatom = new Atom(line);
- 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
{
+ // PDBfile never handles alphafold models
tmpchain = new PDBChain(getId(), tmpatom.chain);
getChains().add(tmpchain);
tmpchain.atoms.addElement(tmpatom);