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HELP!!Read PDB files

P: 35
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  1. PDBReader reader1 = new PDBReader(new FileReader("M5250.pdb"));
  2. IChemFile content1=(IChemFile)reader1.read((IChemObject)new org.openscience.cdk.ChemFile());
  3. IAtomContainer[] c1 = ChemFileManipulator.getAllAtomContainers(content1);
  4. Fingerprinter fp1 = new Fingerprinter();
  5. BitSet fingerprint1 = fp1.getFingerprint(c1[0]);
  6. System.out.println(fingerprint1);
There is no problem in compiling. However, I got these statements when
executing:
Did not recognize PDB atom type: MOL.C1
Did not recognize PDB atom type: MOL.C2
Did not recognize PDB atom type: MOL.O3
Did not recognize PDB atom type: MOL.N4
Did not recognize PDB atom type: MOL.C5
Did not recognize PDB atom type: MOL.C6
Did not recognize PDB atom type: MOL.C7
Did not recognize PDB atom type: MOL.C8
Did not recognize PDB atom type: MOL.N9
Did not recognize PDB atom type: MOL.H10
Did not recognize PDB atom type: MOL.C11
Did not recognize PDB atom type: MOL.C12
Did not recognize PDB atom type: MOL.C13
Did not recognize PDB atom type: MOL.C14
Did not recognize PDB atom type: MOL.C15
Did not recognize PDB atom type: MOL.C16
Did not recognize PDB atom type: MOL.O17
Did not recognize PDB atom type: MOL.C18
In addtion, the fingeprint is wrong when I printed it out. Is there another simpler way for readin pdb file?
Jan 9 '07 #1
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