Hello Giovanni,
have you tried using the ForwardSDMolSupplier with sanitize = False and
/ or strictParsing = False ?
This should at least reduce the number of cases where molecules are not
accepted. You would then have to sanitize the structures yourself
afterwards and handle possible errors explicitly.
If that doesn't solve your problem, I would consider to write my own
parser that just ignores everything looking like a CTAB.
Hope this helps,
Nils
Am 13.04.2022 um 18:15 schrieb Giovanni Tricarico:
Hello,
I am using rdkit to read data from SD files.
My goal is to extract both the molecules and their associated properties
(which for our purposes are separate entities) from the SDF.
[For 100% clarity: by ‘properties’ I don’t mean calculated properties or
atom or bond properties, but the text properties that were saved in the
SDF with each molecule, i.e. those that you get when you do
mol.GetPropsAsDict() ].
After several tests I found that Chem.ForwardSDMolSupplier does what I need.
But there is an issue.
When Chem.ForwardSDMolSupplier decides that a molecule is not OK, i.e.
when it says it is None, the SDF record is lost:
I cannot access its Props; I cannot save the failed SDF record for later
inspection.
[Or at least, I don’t know how to do it, hence this question].
At most I can collect the indices of the records that fail.
> Would anyone be able to suggest how to save to a text file (which an
SDF essentially already is) the SDF records for which
Chem.ForwardSDMolSupplier returns a None?
> Even better, could the properties associated to the failed molecules
be read independently? In theory the properties are in a separate part
of the CTAB, so even when the atoms, bonds, etc. have a problem, the
properties might still be OK.
(Note: PandasTools.LoadSDF gives the same issue, it does not even store
in the DataFrame the records for which the molecule is None, and in any
case it cannot be used with the kind of SDF’s I am handling, as it uses
an enormous amount of memory for the molecules – hence the decision to
use Chem.ForwardSDMolSupplier and pickle the molecules as soon as they
are read).
Thanks
This e-mail and its attachment(s) (if any) may contain confidential
and/or proprietary information and is intended for its addressee(s)
only. Any unauthorized use of the information contained herein
(including, but not limited to, alteration, reproduction, communication,
distribution or any other form of dissemination) is strictly prohibited.
If you are not the intended addressee, please notify the originator
promptly and delete this e-mail and its attachment(s) (if any)
subsequently. Neither Galapagos nor any of its affiliates shall be
liable for direct, special, indirect or consequential damages arising
from alteration of the contents of this message (by a third party) or as
a result of a virus being passed on.
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
