I'm trying to read in a small molecule PDB file using CDK 1.3.5. My
code looks like:
if (pdbReader == null)
pdbReader = new PDBReader();
pdbReader.setReader(new FileReader(pdbFile));
System.out.println("setReader");
IChemFile cf = (IChemFile)pdbReader.read(new ChemFile());
System.out.println("read " + cf.getChemSequenceCount());
IChemSequence s = cf.getChemSequence(0);
System.out.println("getChemSequence " + s.getChemModelCount());
IChemModel model = s.getChemModel(0);
System.out.println("getChemModel");
IMoleculeSet ms = model.getMoleculeSet();
System.out.println("getMoleculeSet " + ms.getMoleculeCount());
IMolecule m = ms.getMolecule(0);
System.out.println("getMolecule " + m);
and the output I get is:
setReader
read 1
getChemSequence 1
getChemModel
getMoleculeSet 0
getMolecule null
So it appears that the file (attached to this message) was read, but no
molecule was created. Any suggestions on how to approach this problem
is greatly appreciated.
Conrad
ATOM 1 C1 UNK 1 49.590 37.569 23.009 1.00 25.00
ATOM 2 N2 UNK 1 50.783 36.881 23.524 1.00 25.00
ATOM 3 C3 UNK 1 48.434 36.602 22.921 1.00 25.00
ATOM 4 C4 UNK 1 49.898 38.197 21.636 1.00 25.00
ATOM 5 C5 UNK 1 51.687 37.555 24.230 1.00 25.00
ATOM 6 O6 UNK 1 47.474 36.769 21.926 1.00 25.00
ATOM 7 O7 UNK 1 48.342 35.681 23.716 1.00 25.00
ATOM 8 C8 UNK 1 48.617 38.780 21.011 1.00 25.00
ATOM 9 O9 UNK 1 52.749 36.941 24.689 1.00 25.00
ATOM 10 O10 UNK 1 51.526 38.744 24.449 1.00 25.00
ATOM 11 C11 UNK 1 47.484 37.783 20.971 1.00 25.00
ATOM 12 C12 UNK 1 53.693 37.706 25.442 1.00 25.00
ATOM 13 O13 UNK 1 46.605 37.863 20.129 1.00 25.00
ATOM 14 C14 UNK 1 54.228 38.829 24.586 1.00 25.00
ATOM 15 C15 UNK 1 55.370 38.628 23.802 1.00 25.00
ATOM 16 C16 UNK 1 53.582 40.071 24.577 1.00 25.00
ATOM 17 C17 UNK 1 55.866 39.669 23.008 1.00 25.00
ATOM 18 C18 UNK 1 54.078 41.112 23.783 1.00 25.00
ATOM 19 C19 UNK 1 55.220 40.912 22.999 1.00 25.00
ATOM 20 H20 UNK 1 49.320 38.384 23.696 1.00 25.00
ATOM 21 H21 UNK 1 50.914 35.906 23.344 1.00 25.00
ATOM 22 H22 UNK 1 50.630 39.009 21.758 1.00 25.00
ATOM 23 H23 UNK 1 50.300 37.428 20.961 1.00 25.00
ATOM 24 H24 UNK 1 48.290 39.646 21.604 1.00 25.00
ATOM 25 H25 UNK 1 48.833 39.093 19.978 1.00 25.00
ATOM 26 H26 UNK 1 53.203 38.137 26.328 1.00 25.00
ATOM 27 H27 UNK 1 54.531 37.065 25.752 1.00 25.00
ATOM 28 H28 UNK 1 55.870 37.667 23.809 1.00 25.00
ATOM 29 H29 UNK 1 52.698 40.227 25.184 1.00 25.00
ATOM 30 H30 UNK 1 56.751 39.514 22.401 1.00 25.00
ATOM 31 H31 UNK 1 53.578 42.074 23.776 1.00 25.00
ATOM 32 H32 UNK 1 55.605 41.718 22.384 1.00 25.00
CONECT 1 2 3 4 20
CONECT 2 1 5 21
CONECT 3 1 6 7
CONECT 4 1 8 22 23
CONECT 5 2 9 10
CONECT 6 3 11
CONECT 7 3
CONECT 8 4 11 24 25
CONECT 9 5 12
CONECT 10 5
CONECT 11 6 13 8
CONECT 12 9 14 26 27
CONECT 13 11
CONECT 14 12 15 16
CONECT 15 14 17 28
CONECT 16 14 18 29
CONECT 17 15 19 30
CONECT 18 16 19 31
CONECT 19 17 18 32
CONECT 20 1
CONECT 21 2
CONECT 22 4
CONECT 23 4
CONECT 24 8
END
CONECT 25 8
CONECT 26 12
CONECT 27 12
CONECT 28 15
CONECT 29 16
CONECT 30 17
CONECT 31 18
CONECT 32 19
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