Hi Curt,
On Fri, Jul 10, 2015 at 11:40 PM, Curt Fischer <[email protected]>
wrote:
>
> I use rdkit through its Python API. As part of an iterative computation
> on a molecule, I have to repeatedly remove different combinations of bonds
> from it. I noticed that the calls to Chem.EditableMol() to create the em,
> to em.GetMol() to get back the new molecule, and to em.RemoveBonds() to
> remove the bonds were taking the most time in my code that loops over
> different combinations of bonds. To speed things up, I though about
> storing copies of intermediate ems in a dictionary, but unfortunately no
> methods for pickling EditableMol() objects seems to be available.
>
> For example, this code...
>
> trp_inchi =
>> 'InChI=1S/C11H12N2O2/c12-9(11(14)15)5-7-6-13-10-4-2-1-3-8(7)10/h1-4,6,9,13H,5,12H2,(H,14,15)/t9-/m0/s1'
>> trp = Chem.MolFromInchi(trp_inchi)
>> e_trp = Chem.EditableMol(trp)
>> from copy import copy, deepcopy
>> for mol in [trp, e_trp]:
>> try:
>> copy(mol); print '%s can be copied' % mol
>> deepcopy(mol); print '%s can be deep copied' % mol
>> mol.ToBinary(); print '%s can be serialized by converting to
>> binary' % mol
>> except RuntimeError:
>> print 'These methods are not available for %s' % mol
>
>
> ...results in
>
> <rdkit.Chem.rdchem.Mol object at 0x11334ee60> can be copied
>> <rdkit.Chem.rdchem.Mol object at 0x11334ee60> can be deep copied
>> <rdkit.Chem.rdchem.Mol object at 0x11334ee60> can be serialized by
>> converting to binary
>> These methods are not available for <rdkit.Chem.rdchem.EditableMol object
>> at 0x11334f7e0>
>
>
> Is there an easy way to "roll my own" serialization or pickle method for
> this class, if I have extremely limited knowledge of C++ but an OK to good
> knowledge of Python?
>
The last release of the RDKit included a new class, RWMol, that should be
useable for what you want to do. There's a bit of explanation in the
documentation:
http://rdkit.org/docs/GettingStartedInPython.html#editing-molecules
but basically you can just treat an RWMol as a normal Mol object.
If you want a normal Mol object, you can do the conversion directly:
nm = Chem.Mol(rwmol)
EditableMols will eventually be deprecated and shouldn't be used any more
in new code.
> Also, I'm new to the rdkit community and hope I'm sending my message to
> the right place. Would rdkit-devel be better for this sort of question?
>
rdkit-discuss is the right place for this kind of thing.
Best,
-greg
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