hello,
I'm a Bioinformatics student from Frankfurt and currently working on a project
in which I need to add Hydrogens to a PDBfile.
The problem I'm experiencing is that the HydrogenAdder() Class object seems to
be adding too many Hydrogens to the Molecule I've extracted from the pdbfile.
Assuming I've extracted the first model from the 1fjs.pdb file.
InputStream pdbfile =
this.getClass().getClassLoader().getResourceAsStream("1FJS.pdb");
IChemObjectReader file = new PDBReader(new InputStreamReader(pdbfile));
ChemFile oFile = (ChemFile) file.read(new ChemFile());
IChemSequence Seq = oFile.getChemSequence(0);
IChemModel model = Seq.getChemModel(0);
SetOfMolecules MOL = (SetOfMolecules) model.getSetOfMolecules();
Molecule mole = (Molecule) MOL.getMolecule(0);
System.out.println("before h2add:");
System.out.println(mole.getAtomCount());
HydrogenAdder H_adder = new HydrogenAdder();
try {
H_adder.addExplicitHydrogensToSatisfyValency(lala);}
catch (CDKException ex) {
ex.printStackTrace();}
catch (IOException ex) {
ex.printStackTrace();}
catch (ClassNotFoundException ex) {
ex.printStackTrace();}
System.out.println("after h2add:");
System.out.println(mole.getAtomCount());
//
This is my output
before h2add:
2475
after h2add:
5927
I compared these results with the pymol h_add() method and received the
following...:
PyMOL>print cmd.count_atoms()
2475
PyMOL>cmd.h_add()
PyMOL>print cmd.count_atoms()
5062
... meaning my java code must be adding about 900 additional Hydrogens
(assuming the correctness of the pymol results).
Is there a mistake in my java code? Or have I forgotten something?
I'd be thankful for every hint I can get.
Cheers, Daniel
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