Yeah, this is definitely a bug.
@Ling: thanks for raising it.
@Ivan: thanks for simplifying the example!
I created a github issue here: https://github.com/rdkit/rdkit/issues/4674
-greg
On Thu, Nov 4, 2021 at 11:33 PM Ivan Tubert-Brohman <
ivan.tubert-broh...@schrodinger.com> wrote:
> That does
Re: your second issue with the 2D depiction, especially for these kinds of
bicyclic structures, the Schrödinger coordgen that is a part of RDKit gives
better looking results(at the cost of a somewhat longer running time). You
can turn it on using:
from rdkit.Chem import rdDepictor
rdDepictor.SetPre
That does seem like a bug. You can also see it without involving
DeleteSubstructs, by starting from different SMILES representations of the
same molecule:
>>> m1 = Chem.MolFromSmiles('FC12C31C32F')
>>> m2 = Chem.MolFromSmiles('C12C31C32')
>>> m3 = Chem.MolFromSmiles('C1CC2C3C(C1)C23')
Hi Tim,
You might also consider using chemfp, which has this sort of functionality
available through its toolkit wrapper API:
from chemfp import rdkit_toolkit as T
import itertools
with T.read_ids_and_molecules("chembl_28.sdf.gz") as reader:
loc = reader.location
for id, mol in itertools.
Thanks Paolo, that's fantastic.
The first option was what I needed.
Tim
On Thu, Nov 4, 2021 at 4:36 PM Paolo Tosco
wrote:
> Hi Tim,
>
> if you need access to the original text, you'll have to do the chunking
> yourself, e.g.:
>
> import gzip
>
> def molgen(hnd):
> mol_text_tmp = ""
> whi
Hi Tim,
if you need access to the original text, you'll have to do the chunking
yourself, e.g.:
import gzip
def molgen(hnd):
mol_text_tmp = ""
while 1:
line = hnd.readline()
if not line:
return
line = line.decode("utf-8")
mol_text_tmp += line
I am needing to access the text of each record of a SDF, as well as
creating a mol instance.
I was successfully doing this using SDMolSupplier.GetItemText().
Then I needed to switch to handling gzipped SD files, and SDMolSupplier can
only take a file name in its constructor.
ForwardSDMolSupplier ca
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