Hi,
I'm trying to add Explicit Hydrogens to a molecule in order to compute
qsar descriptors.
When I'm trying to do that I get an error message "The IAtomType was
null." Traking the error led me to the CDKAtomTypeMatcher and the
following lines in the 'perceiveNitrogens' function:
} else if (atomContainer.getConnectedBondsCount(atom) > 3) {
// FIXME: I don't perceive carbons with more than 3
connections yet
return null;
My compounds have Nitrogens with 4 Bonds. Is there a workaround for this
problem? By the way computing qsar descriptors without adding hydrogens
yields the same error for some descriptor classes.
Özgür
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