Why there is a counter between parentheses there, I don't know, but in case
there's no option to remove it, you might just manually remove it using a
regex to remove anything between parentheses on a line that starts with >
for example:
from rdkit import Chem
import re
from io import StringIO
m = Chem.MolFromSmiles("CCC")
m.SetProp("pKa","3.3")
sio = StringIO()
with Chem.SDWriter(sio) as o:
o.write(m)
sio.seek(0)
with open("temp3.sdf", "w") as f:
for line in sio.readlines():
f.write(re.sub(r'^>(.*?)\((.*?)\)', r'>\1', line))
best wishes
wim
On Tue, Sep 26, 2023 at 1:20 AM Ling Chan <[email protected]> wrote:
> Dear Colleagues,
>
> I noticed that when writing out molecules using SDWriter() , the
> properties fields are followed by something like "(1)" , "(2)". I mean, the
> sdf looks like:
>
> propane
> RDKit 3D
>
> 3 2 0 0 0 0 0 0 0 0999 V2000
> 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 1.4280 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 1.9040 1.3000 -0.3480 C 0 0 0 0 0 0 0 0 0 0 0 0
> 1 2 1 0
> 2 3 1 0
> M END
> > <pKa> (1)
> 4.0999999
>
> > <logP> (1)
> 2
>
> $$$$
>
> Just wonder what was the rationale behind this extra "(1)" on the property
> field lines (pKa and logP in the above example)?
>
> And is there a way to get rid of these? I am not sure if this extra "(1)"
> is part of the standard sd format.
>
> Thank you!
>
> Regards,
> Ling
>
>
> ---------------------------------------------------------------------------------------------------
>
> To create an sdf, you can do something like:
>
> >>> from rdkit import Chem
> >>> m = Chem.MolFromSmiles("CCC")
> >>> m.SetProp("pKa","3.3")
> >>> with Chem.SDWriter("temp3.sdf") as o:
> ... o.write(m)
>
> Or use Chem.SDMolSupplier() to get mols from another sdf.
>
>
>
>
> _______________________________________________
> Rdkit-discuss mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
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