Hi all,
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?
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?
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