Hi again,
first a short update if anyone is interested:
Not very surprisingly Java serialization is quite useless. I tried it (HSQLDB
has a special column type for this) but to keep it simple, it is considerably
slower than just reading the Molfiles.
Not to mentioned that the serialized form seems to use a large amount of disk
space.
So back to storing properties. How do you store aromaticty? Just Yes/no per
molecule? Isn't that covered by the fingerprint? (an hence useless)
As far as i understood, each Atom and Bond that are part of an aromatic system
have the according flag set. This is probably relevant in graph-matching and
hence when creating a molecule, aromaticity must be detected. So every aromatic
Atom and bond per molecule would have to be stored in the database so that this
calculation is not needed anymore. Of course that would be a stupid idea to do
so. Ideally it should be in the Molfile but it's not.
Creating AtomContainers seems to be pretty straight forward, not much to
improve. Maybe a light-weight implementation only for structure search would be
an option?
Reagrds,
Thomas
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