CDK 1.5 Traps, Pitfalls, and Common Mistakes

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Egon Willighagen edited this page Jan 1, 2016 · 6 revisions

Some topics that seem to come up a lot. This page will explain how to handle with examples.

implicit hydrogens
atom types
molfile bond order 4
hydrogen suppressing/adding, hydrogen layout
MDLReader vs MDLV2000Reader
SMILES general vs unique
layout vs rendering
Stereo in Molfile (gen2d)
DefaultChemObjectBuilder/SilentChemObjectBuilder
Object reuse (IFingerprinter)
IteratingSDFReader vs Lazy MDLV2000Reader
Interfaces
SDG templates

Interfaces

Whenever possible, use the IChemObject interfaces instead of implementations thereof: use IAtom instead of Atom, etc.