public List<StructureCommandI> superposeStructures(AtomSpecModel refAtoms,
AtomSpecModel atomSpec, AtomSpecType specType)
{
-
+
// https://pymolwiki.org/index.php/Super
List<StructureCommandI> commands = new ArrayList<>();
- String refAtomsAlphaOnly = "("+getAtomSpec(refAtoms, specType)+" and (altloc '' or altloc 'a'))";
- String atomSpec2AlphaOnly = "("+getAtomSpec(atomSpec, specType)+" 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
// crashes when undo is enabled on 2.5.2 (incentive)
commands.add(new StructureCommand("undo_disable"));
- commands.add(new StructureCommand("pair_fit",
- atomSpec2AlphaOnly, refAtomsAlphaOnly));
+ commands.add(new StructureCommand("pair_fit", atomSpec2AlphaOnly,
+ refAtomsAlphaOnly));
commands.add(new StructureCommand("undo_enable"));
-
+
/*
* and show superposed residues as cartoon
*/