Hi,
we would like to store compounds in our database as InChIs. Problem is
that the round-trip to inchi and back changes the compound structure
(IAtomContainer) for about 40 percent of our structures, i.e. mol !=
mol.fromInchi(mol.toInchi)
As an example: CC(=O)N becomes CC(=N)O (See code below). Even adding
explicit Hs does not change anything in this example (i.e., use
CC(=O)N([H])[H] as input).
How come the bond information is not stored? Can I circumvent that?
Kind regards,
Martin
String smi = "CC(=O)N";
IAtomContainer mol = new
SmilesParser(SilentChemObjectBuilder.getInstance()).parseSmiles(smi);
System.out.println(new SmilesGenerator().create(mol));
String inchi =
InChIGeneratorFactory.getInstance().getInChIGenerator(mol).getInchi();
System.out.println(inchi);
mol =
InChIGeneratorFactory.getInstance().getInChIToStructure(inchi,
SilentChemObjectBuilder.getInstance())
.getAtomContainer();
System.out.println(new SmilesGenerator().create(mol));
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