Re: [Open Babel] Serializing OBMol to memory

[Tim V. <tim...@gm...>]

Hi,

On Fri, Mar 13, 2009 at 9:25 AM,  <ern...@ba...> wrote:
> Hello,
>
>>what would be the preferred method of serializing an OBMol object into
> memory?
>
>>Endianness et al. is not an issue, but the whole data structure should be
> saved.
>
>>I assume that instead of storing e.g. a SMILES string and building the
> OBMol every time it's needed from that string, reading a readymade OBMol
> into memory is faster...?
>
> maybe I shall clarify my question. :-)
>
> I filter many matches of OBMols through a SMARTS pattern in PostgreSQL.
> Within PostgreSQL, every time a function is called - per table row - it
> forgets all that was before. So I have to parse the OBMol _every row_ and
> instantiate the SMARTS Pattern _every row_.
>
> For the SMARTS pattern, there might be a solution of saving a pointer to
> in shared memory between calls to avoid init()-ing it every call, but for
> the parsing of the OBMols I'm still searching for a clever method to avoid
> the parsing and perception steps every time. As parsing and perception can
> be done upon saving the OBMol the first time in the database, a means of
> storing the OBMol, or at least the essential data structures to recreate
> it faster than from a textual format like SMILES, would be great. Is this
> RTFM? I have not found any documentation about serializing OBMol, parts of
> OBMol or something like the fastest input format yet...

I don't think we have an easy way to do this (compared to "pickling" a
class in python). However, do you really need the OBMol each time or
will something like fingerprints to narrow down your search be?

Tim