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JAL-629 whittling down options for successful tests
[jalview.git]
/
src
/
mc_view
/
PDBfile.java
diff --git
a/src/mc_view/PDBfile.java
b/src/mc_view/PDBfile.java
index
0435def
..
2a89e61
100755
(executable)
--- a/
src/mc_view/PDBfile.java
+++ b/
src/mc_view/PDBfile.java
@@
-20,6
+20,13
@@
*/
package mc_view;
*/
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.datamodel.AlignmentAnnotation;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.SequenceI;
@@
-28,12
+35,6
@@
import jalview.io.FileParse;
import jalview.io.StructureFile;
import jalview.util.MessageManager;
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";
public class PDBfile extends StructureFile
{
private static String CALC_ID_PREFIX = "JalviewPDB";
@@
-51,7
+52,9
@@
public class PDBfile extends StructureFile
DataSourceType sourceType) throws IOException
{
super(false, dataObject, sourceType);
DataSourceType sourceType) throws IOException
{
super(false, dataObject, sourceType);
+ Console.debug("***** PDBfile constructor");
addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
+ Console.debug("***** About to doParse() 1");
doParse();
}
doParse();
}
@@
-60,6
+63,7
@@
public class PDBfile extends StructureFile
{
super(false, source);
addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
{
super(false, source);
addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
+ Console.debug("***** About to doParse() 2");
doParse();
}
doParse();
}
@@
-143,17
+147,19
@@
public class PDBfile extends StructureFile
}
Atom tmpatom = new Atom(line);
}
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);
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);
tmpchain = new PDBChain(getId(), tmpatom.chain);
getChains().add(tmpchain);
tmpchain.atoms.addElement(tmpatom);