Re: [Rdkit-discuss] RDKit and organometallics
Thank you for the tips.
In a lng and dumb workflow, I was able to load a sample molecule.
* Downloaded a sample .cif structure from CCDC
https://www.ccdc.cam.ac.uk/structures/search?id=doi:10.5517/ccdc.csd.cc1m9hgw=DataCite
* Used OpenBabel to convert my .cif to .mol V3000 (the converted .mol fails
to load in RDKit)
* I was only able to load the molecule getting the .mol2 file provided in
the same CCDC link and converting such .mol2 to .mol V3000 using OpenBabel (the
.mol2 itself wasn't read by RDKit).
Attached is my converted .mol V3000
--
Henrique C. S. Junior
From: Michal Krompiec
Sent: Tuesday, November 13, 2018 11:16
To: malgorzata.wer...@molecularhealth.com
Cc: henrique...@outlook.com; RDKit Discuss
Subject: Re: [Rdkit-discuss] RDKit and organometallics
Isn't this patch already incorporated in the master branch?
On Tue, 13 Nov 2018 at 12:35, Malgorzata Werner
mailto:malgorzata.wer...@molecularhealth.com>>
wrote:
Hi Henrique,
You could try using v3000 sd files.
Here's a blog about this:
https://www.wildcardconsulting.dk/useful-information/how-to-solve-problems-with-coordinate-bonds-in-rdkit/<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.wildcardconsulting.dk%2Fuseful-information%2Fhow-to-solve-problems-with-coordinate-bonds-in-rdkit%2F=02%7C01%7C%7C3da7193ebdb349b124fa08d6496a30e9%7C84df9e7fe9f640afb435%7C1%7C0%7C636777117763691235=hUC0cFUlbd6sEATeJ3Ma7SR9%2BXIA5PXc6rJLWb6VnXo%3D=0>
Best,
Malgorzata
From: Henrique Castro mailto:henrique...@outlook.com>>
Sent: 13 November 2018 11:57:34
To:
rdkit-discuss@lists.sourceforge.net<mailto:rdkit-discuss@lists.sourceforge.net>
Subject: [Rdkit-discuss] RDKit and organometallics
Dear colleagues,
I know that this is probably a dumb question, but since my searches showed no
clarifying results I'm asking here anyway.
I'm planning to use RDKit on my Ph.D. thesis, but my field of research is
inorganic chemistry and molecular magnetism. That means that I'm dealing with
organometallics (transition metals, lanthanides, actinides...). So far I was
unable to import even a single structure to my RDKit test with different error
messages like those (they are all the same structure, that is attached here):
m = Chem.MolFromMolFile('st1.pdb')
RDKit WARNING: [08:36:40] CTAB version string invalid at line 4
m = Chem.MolFromMolFile('st1.sdf')
RDKit ERROR: [08:51:30] Explicit valence for atom # 1 N, 4, is greater than
permitted
m = Chem.MolFromMolFile('st1.mol2')
RDKit WARNING: [08:52:15] Counts line too short: 'SMALL' on line4
Based on this, I'd like to as for hints on how to deal with molecules with
"unusual" valences like the ones we deal in inorganic chemistry.
Thanks in advance
--
Henrique C. S. Junior
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Re: [Rdkit-discuss] RDKit and organometallics
Isn't this patch already incorporated in the master branch?
On Tue, 13 Nov 2018 at 12:35, Malgorzata Werner <
malgorzata.wer...@molecularhealth.com> wrote:
> Hi Henrique,
>
> You could try using v3000 sd files.
>
> Here's a blog about this:
> https://www.wildcardconsulting.dk/useful-information/how-to-solve-problems-with-coordinate-bonds-in-rdkit/
>
>
>
> Best,
>
> Malgorzata
>
> --
> *From:* Henrique Castro
> *Sent:* 13 November 2018 11:57:34
> *To:* rdkit-discuss@lists.sourceforge.net
> *Subject:* [Rdkit-discuss] RDKit and organometallics
>
> Dear colleagues,
> I know that this is probably a dumb question, but since my searches showed
> no clarifying results I'm asking here anyway.
> I'm planning to use RDKit on my Ph.D. thesis, but my field of research is
> inorganic chemistry and molecular magnetism. That means that I'm dealing
> with organometallics (transition metals, lanthanides, actinides...). So far
> I was unable to import even a single structure to my RDKit test with
> different error messages like those (they are all the same structure, that
> is attached here):
>
> m = Chem.MolFromMolFile('st1.pdb')
> RDKit WARNING: [08:36:40] CTAB version string invalid at line 4
>
> m = Chem.MolFromMolFile('st1.sdf')
> RDKit ERROR: [08:51:30] Explicit valence for atom # 1 N, 4, is greater
> than permitted
>
> m = Chem.MolFromMolFile('st1.mol2')
> RDKit WARNING: [08:52:15] Counts line too short: 'SMALL' on line4
>
> Based on this, I'd like to as for hints on how to deal with molecules with
> "unusual" valences like the ones we deal in inorganic chemistry.
>
> Thanks in advance
>
>
> --
> Henrique C. S. Junior
>
> ___
> Rdkit-discuss mailing list
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> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
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Re: [Rdkit-discuss] RDKit and organometallics
Hi Henrique,
You could try using v3000 sd files.
Here's a blog about this:
https://www.wildcardconsulting.dk/useful-information/how-to-solve-problems-with-coordinate-bonds-in-rdkit/
Best,
Malgorzata
From: Henrique Castro
Sent: 13 November 2018 11:57:34
To: rdkit-discuss@lists.sourceforge.net
Subject: [Rdkit-discuss] RDKit and organometallics
Dear colleagues,
I know that this is probably a dumb question, but since my searches showed no
clarifying results I'm asking here anyway.
I'm planning to use RDKit on my Ph.D. thesis, but my field of research is
inorganic chemistry and molecular magnetism. That means that I'm dealing with
organometallics (transition metals, lanthanides, actinides...). So far I was
unable to import even a single structure to my RDKit test with different error
messages like those (they are all the same structure, that is attached here):
m = Chem.MolFromMolFile('st1.pdb')
RDKit WARNING: [08:36:40] CTAB version string invalid at line 4
m = Chem.MolFromMolFile('st1.sdf')
RDKit ERROR: [08:51:30] Explicit valence for atom # 1 N, 4, is greater than
permitted
m = Chem.MolFromMolFile('st1.mol2')
RDKit WARNING: [08:52:15] Counts line too short: 'SMALL' on line4
Based on this, I'd like to as for hints on how to deal with molecules with
"unusual" valences like the ones we deal in inorganic chemistry.
Thanks in advance
--
Henrique C. S. Junior
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[Rdkit-discuss] RDKit and organometallics
Dear colleagues,
I know that this is probably a dumb question, but since my searches showed no
clarifying results I'm asking here anyway.
I'm planning to use RDKit on my Ph.D. thesis, but my field of research is
inorganic chemistry and molecular magnetism. That means that I'm dealing with
organometallics (transition metals, lanthanides, actinides...). So far I was
unable to import even a single structure to my RDKit test with different error
messages like those (they are all the same structure, that is attached here):
m = Chem.MolFromMolFile('st1.pdb')
RDKit WARNING: [08:36:40] CTAB version string invalid at line 4
m = Chem.MolFromMolFile('st1.sdf')
RDKit ERROR: [08:51:30] Explicit valence for atom # 1 N, 4, is greater than
permitted
m = Chem.MolFromMolFile('st1.mol2')
RDKit WARNING: [08:52:15] Counts line too short: 'SMALL' on line4
Based on this, I'd like to as for hints on how to deal with molecules with
"unusual" valences like the ones we deal in inorganic chemistry.
Thanks in advance
--
Henrique C. S. Junior
st1.mol
Description: st1.mol
st1.mol2
Description: st1.mol2
st1.pdb
Description: st1.pdb
st1.sdf
Description: st1.sdf
st1.xyz
Description: st1.xyz
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