git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
JAL-1761 backbone type parameter for configuring which atoms are used for superpositi...
[jalview.git]
/
src
/
jalview
/
ext
/
pymol
/
PymolCommands.java
diff --git
a/src/jalview/ext/pymol/PymolCommands.java
b/src/jalview/ext/pymol/PymolCommands.java
index
ae91aa5
..
ed64c00
100644
(file)
--- a/
src/jalview/ext/pymol/PymolCommands.java
+++ b/
src/jalview/ext/pymol/PymolCommands.java
@@
-106,12
+106,13
@@
public class PymolCommands extends StructureCommandsBase
@Override
public List<StructureCommandI> superposeStructures(AtomSpecModel refAtoms,
@Override
public List<StructureCommandI> superposeStructures(AtomSpecModel refAtoms,
- AtomSpecModel atomSpec, boolean isNucleotide)
+ AtomSpecModel atomSpec, AtomSpecType specType)
{
{
+
// https://pymolwiki.org/index.php/Super
List<StructureCommandI> commands = new ArrayList<>();
// https://pymolwiki.org/index.php/Super
List<StructureCommandI> commands = new ArrayList<>();
- String refAtomsAlphaOnly = "("+getAtomSpec(refAtoms, true)+" and (altloc '' or altloc 'a'))";
- String atomSpec2AlphaOnly = "("+getAtomSpec(atomSpec, true)+" and (altloc '' or altloc 'a'))";
+ String refAtomsAlphaOnly = "("+getAtomSpec(refAtoms, specType)+" and (altloc '' or altloc 'a'))";
+ String atomSpec2AlphaOnly = "("+getAtomSpec(atomSpec, specType)+" and (altloc '' or altloc 'a'))";
// pair_fit mobile -> reference
commands.add(new StructureCommand("pair_fit",
atomSpec2AlphaOnly, refAtomsAlphaOnly));
// pair_fit mobile -> reference
commands.add(new StructureCommand("pair_fit",
atomSpec2AlphaOnly, refAtomsAlphaOnly));
@@
-119,8
+120,8
@@
public class PymolCommands extends StructureCommandsBase
/*
* and show superposed residues as cartoon
*/
/*
* and show superposed residues as cartoon
*/
- String refAtomsAll = getAtomSpec(refAtoms, false);
- String atomSpec2All = getAtomSpec(atomSpec, false);
+ String refAtomsAll = getAtomSpec(refAtoms, AtomSpecType.RESIDUE_ONLY);
+ String atomSpec2All = getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY);
commands.add(new StructureCommand("show", "cartoon",
refAtomsAll + " " + atomSpec2All));
commands.add(new StructureCommand("show", "cartoon",
refAtomsAll + " " + atomSpec2All));
@@
-154,7
+155,7
@@
public class PymolCommands extends StructureCommandsBase
* @see https://pymolwiki.org/index.php/Selection_Macros
*/
@Override
* @see https://pymolwiki.org/index.php/Selection_Macros
*/
@Override
- public String getAtomSpec(AtomSpecModel model, boolean alphaOnly)
+ public String getAtomSpec(AtomSpecModel model, AtomSpecType specType)
{
StringBuilder sb = new StringBuilder(64);
boolean first = true;
{
StringBuilder sb = new StringBuilder(64);
boolean first = true;
@@
-185,10
+186,14
@@
public class PymolCommands extends StructureCommandsBase
}
}
sb.append("/");
}
}
sb.append("/");
- if (alphaOnly)
+ if (specType == AtomSpecType.ALPHA)
{
sb.append("CA");
}
{
sb.append("CA");
}
+ if (specType == AtomSpecType.PHOSPHATE)
+ {
+ sb.append("P");
+ }
}
}
return sb.toString();
}
}
return sb.toString();
@@
-262,7
+267,7
@@
public class PymolCommands extends StructureCommandsBase
StringBuilder sb = new StringBuilder(128);
sb.append("p.").append(attributeName).append("='")
.append(attributeValue).append("'");
StringBuilder sb = new StringBuilder(128);
sb.append("p.").append(attributeName).append("='")
.append(attributeValue).append("'");
- String atomSpec = getAtomSpec(atomSpecModel, false);
+ String atomSpec = getAtomSpec(atomSpecModel, AtomSpecType.RESIDUE_ONLY);
return new StructureCommand("iterate", atomSpec, sb.toString());
}
return new StructureCommand("iterate", atomSpec, sb.toString());
}