Thread: [Rdkit-discuss] Impose conformation of molecule substructure?

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rdkit-discuss

[Rdkit-discuss] Impose conformation of molecule substructure?

From: Kurt T. <kur...@ar...> - 2024-09-12 16:10:33

Attachments: Outlook-Logo Desc

Hi All -

I would like to enumerate a virtual library of a compound family we have a crystal structure of, where I want to model structures of multiple substituents at a single site. What I would like to do is enforce that the constant part of the molecule assume the conformation in the crystal structure and enumerate just conformers for the new substituent added. Does anyone have a  suggestion for how to achieve this in rdkit?

Thanks,
Kurt




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 Dr Kurt Thorn

Chief Technology Officer

+1.609.423.1571 (US Office)

+1.415.298.3495 (US Mobile)

kur...@ar...<mailto:kur...@ar...>

www.arrepath.com<http://www.arrepath.com/>



ArrePath Inc.

303A College Road East

Princeton, NJ 08540

U.S.

Re: [Rdkit-discuss] Impose conformation of molecule substructure?

From: Stephen R. <s.d...@go...> - 2024-09-12 16:40:53

Attachments: Outlook-Logo

Hi Kurt,

The Vernalis KNIME community contribution has a node "Templated Conformer
Generator (RDKit)" (see https://hub.knime.com/n/wK3RJiystQYq5M9w ) which
will do exactly this.  If you don't want to do it in KNIME, then you can
see the relevant bits of the Java source at:

https://github.com/vernalis/vernalis-knime-nodes/blob/d125b97ad2841133622150c168472168547c4ff3/com.vernalis.knime.chem.pmi/src/com/vernalis/knime/chem/pmi/nodes/confs/rdkitgenerate/RdkitConfgenNodeModel.java#L441-L465

and in particular at:

https://github.com/vernalis/vernalis-knime-nodes/blob/d125b97ad2841133622150c168472168547c4ff3/com.vernalis.knime.chem.pmi/src/com/vernalis/knime/chem/pmi/nodes/confs/rdkitgenerate/RdkitConfgenNodeModel.java#L688-L809

Steve



On Thu, 12 Sept 2024 at 17:13, Kurt Thorn <kur...@ar...> wrote:

> Hi All -
>
> I would like to enumerate a virtual library of a compound family we have a
> crystal structure of, where I want to model structures of multiple
> substituents at a single site. What I would like to do is enforce that the
> constant part of the molecule assume the conformation in the crystal
> structure and enumerate just conformers for the new substituent added. Does
> anyone have a  suggestion for how to achieve this in rdkit?
>
> Thanks,
> Kurt
>
>
>
> *[image: Logo Description automatically generated]*
>
>  *Dr Kurt Thorn*
>
> *Chief Technology Officer*
>
> +1.609.423.1571 (US Office)
>
> +1.415.298.3495 (US Mobile)
>
> kur...@ar...
>
> www.arrepath.com
>
>
>
> *ArrePath Inc.*
>
> 303A College Road East
>
> Princeton, NJ 08540
>
> U.S.
>
>
> _______________________________________________
> Rdkit-discuss mailing list
> Rdk...@li...
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>

Re: [Rdkit-discuss] Impose conformation of molecule substructure?

From: Kurt T. <kur...@ar...> - 2024-09-12 17:26:29

Attachments: Outlook-Logo

Thanks Stephen!

That code pointed me to the key "coordMap" parameter for fixing atom coordinates.

Kurt
________________________________
From: Stephen Roughley <s.d...@go...>
Sent: Thursday, September 12, 2024 9:40 AM
To: Kurt Thorn <kur...@ar...>
Cc: rdk...@li... <rdk...@li...>
Subject: Re: [Rdkit-discuss] Impose conformation of molecule substructure?

Hi Kurt,

The Vernalis KNIME community contribution has a node "Templated Conformer Generator (RDKit)" (see https://hub.knime.com/n/wK3RJiystQYq5M9w ) which will do exactly this.  If you don't want to do it in KNIME, then you can see the relevant bits of the Java source at:

https://github.com/vernalis/vernalis-knime-nodes/blob/d125b97ad2841133622150c168472168547c4ff3/com.vernalis.knime.chem.pmi/src/com/vernalis/knime/chem/pmi/nodes/confs/rdkitgenerate/RdkitConfgenNodeModel.java#L441-L465

and in particular at:

https://github.com/vernalis/vernalis-knime-nodes/blob/d125b97ad2841133622150c168472168547c4ff3/com.vernalis.knime.chem.pmi/src/com/vernalis/knime/chem/pmi/nodes/confs/rdkitgenerate/RdkitConfgenNodeModel.java#L688-L809

Steve

On Thu, 12 Sept 2024 at 17:13, Kurt Thorn <kur...@ar...<mailto:kur...@ar...>> wrote:
Hi All -

I would like to enumerate a virtual library of a compound family we have a crystal structure of, where I want to model structures of multiple substituents at a single site. What I would like to do is enforce that the constant part of the molecule assume the conformation in the crystal structure and enumerate just conformers for the new substituent added. Does anyone have a  suggestion for how to achieve this in rdkit?

Thanks,
Kurt

[Logo    Description automatically generated]

 Dr Kurt Thorn

Chief Technology Officer

+1.609.423.1571 (US Office)

+1.415.298.3495 (US Mobile)

kur...@ar...<mailto:kur...@ar...>

www.arrepath.com<http://www.arrepath.com/>

ArrePath Inc.

303A College Road East

Princeton, NJ 08540

U.S.

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Re: [Rdkit-discuss] Impose conformation of molecule substructure?

From: Manish S. <ms...@sa...> - 2024-09-12 18:14:45

Attachments: image003.jpg

Hi Kurt,

 

You might find the following scripts helpful for enumerating compounds and
align them to a reference molecule:

 

o RDKitEnumerateCompoundLibrary.py
<http://www.mayachemtools.org/docs/scripts/html/RDKitEnumerateCompoundLibrar
y.html> 

o RDKitPerformPositionalAnalogueScan.py
<http://www.mayachemtools.org/docs/scripts/html/RDKitPerformPositionalAnalog
ueScan.html> 

o RDKitGenerateConstrainedConformers.py
<http://www.mayachemtools.org/docs/scripts/html/RDKitGenerateConstrainedConf
ormers.html> 

o RDKitPerformConstrainedMinimization.py
<http://www.mayachemtools.org/docs/scripts/html/RDKitPerformConstrainedMinim
ization.html> 

 

Let me know of any further questions.

 

Thanks,

Manish

 

 

From: Kurt Thorn <kur...@ar...> 
Sent: Thursday, September 12, 2024 8:50 AM
To: rdk...@li...
Subject: [Rdkit-discuss] Impose conformation of molecule substructure?

 

Hi All -

 

I would like to enumerate a virtual library of a compound family we have a
crystal structure of, where I want to model structures of multiple
substituents at a single site. What I would like to do is enforce that the
constant part of the molecule assume the conformation in the crystal
structure and enumerate just conformers for the new substituent added. Does
anyone have a  suggestion for how to achieve this in rdkit?

 

Thanks,

Kurt

 

 



 Dr Kurt Thorn

Chief Technology Officer

+1.609.423.1571 (US Office)

+1.415.298.3495 (US Mobile)

kur...@ar... <mailto:kur...@ar...> 

www.arrepath.com <http://www.arrepath.com/> 

 

ArrePath Inc.

303A College Road East

Princeton, NJ 08540

U.S.