On Fri, May 7, 2010 at 1:27 PM, Rajarshi Guha <[email protected]> wrote:
> On May 7, 2010, at 12:32 AM, Egon Willighagen wrote:
>> I'd guess you simply have to calculate the number of implicit hydrogens
>> first?
>
> How would I do that?
CDKHydrogenAdder adder = CDKHydrogenAdder.getInstance(
NoNotificationChemObjectBuilder.getInstance()
);
adder.addImplicitHydrogens(molecule);
(but do atom type perception first)
>>> But if the corresponding SMILES form is read in, and implcit H's are
>>> converted to explicit, H's are added.
>>
>> SMILES on the other hand *does* specify the number of implicit
>> hydrogens (implicitly, of course), but it's part of the standard... so
>> the SmilesParser does atom type detection, calculate number of
>> implicit hydrogens, and actually aromaticity detection too...
>
> No, the parser doesn't do aromaticity detection or atom typing. That has to
> be done separately
Mmmm... this is the code I see in front of me:
public IMolecule parseSmiles(String smiles) throws InvalidSmilesException {
IMolecule molecule = this.parseString(smiles);
// perceive atom types
CDKAtomTypeMatcher matcher =
CDKAtomTypeMatcher.getInstance(molecule.getBuilder());
int i = 0;
for (IAtom atom : molecule.atoms()) {
i++;
try {
IAtomType type = matcher.findMatchingAtomType(molecule, atom);
AtomTypeManipulator.configure(atom, type);
} catch (Exception e) {
System.out.println("Cannot percieve atom type for the
" + i + "th atom: " + atom.getSymbol());
atom.setAtomTypeName("X");
}
}
this.addImplicitHydrogens(molecule);
this.perceiveAromaticity(molecule);
return molecule;
}
Egon
--
Post-doc @ Uppsala University
Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers
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