[Rdkit-discuss] Availability of new and updated command line scripts

[Manish Sud]

Hi All,

 

I'll like to share with you the availability of the following new and
updated command line scripts:

 

o RDKitFilterTorsionStrainEnergyAlerts.py
  - New

o RDKitFilterTorsionLibraryAlerts.py
  - Updated

o Psi4CalculatePartialCharges.py
  - Updated

 

These scripts rely on the presence of RDKit and Psi4 in your environment.

 

The RDKitFilterTorsionStrainEnergyAlerts.py script provides functionality to
filter strained docked poses or conformers for estimated torsion strain
energy   alerts. This
script is a result of collaborative effort between Pat and me. I thank John
Irwin (UCSF) for entertaining my inquiries regarding the strain energy
library.

 

The RDKitFilterTorsionLibraryAlerts.py script has been updated to use the
latest version of the torsion library
 . I thank Patrick Penner
(U. of Hamburg) for providing additional details regarding the
implementation of the updated torsion library. The
Psi4CalculatePartialCharges.py script now supports the calculation of RESP
  partial atomic charges
employing RESP plugin for Psi4.

 

Your feedback is welcome.

 

Thanks,

Manish

___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] Find structures with "non-organic" atoms

[Manish Sud]

Hi Rafael,

 

You might find the RDKitSearchSMARTS.py 
  script 
helpful for filtering molecules using the SMARTS pattern Pat has provided in 
his response.

 

For example:

 

% RDKitSearchSMARTS.py -p 
'[!#1;!C;!O;!N;!S;!P;!F;!Cl;!Br;!I;!c;!o;!n;!s;!p;!Na;!K;!Mg;!Ca;!Li]' -i 
Sample.smi -o SampleOut.smi --outfileFiltered yes 

 

% RDKitSearchSMARTS.py -n yes -p 
'[!#1;!C;!O;!N;!S;!P;!F;!Cl;!Br;!I;!c;!o;!n;!s;!p;!Na;!K;!Mg;!Ca;!Li]' -i 
Sample.sdf -o SampleOutNotOrganic.sdf

 

Manish

 

 

From: Patrick Walters  
Sent: Saturday, March 5, 2022 6:17 PM
To: Rafael L 
Cc: rdkit-discuss 
Subject: Re: [Rdkit-discuss] Find structures with "non-organic" atoms

 

Here's what I use. 

 

not_organic_pat = 
Chem.MolFromSmarts("[!#1;!C;!O;!N;!S;!P;!F;!Cl;!Br;!I;!c;!o;!n;!s;!p;!Na;!K;!Mg;!Ca;!Li]")
cisplatin = Chem.MolFromSmiles("[NH3+]-[Pt-2](Cl)(Cl)[NH3+]")
cisplatin.HasSubstructMatch(not_organic_pat)

 

 

 

On Sat, Mar 5, 2022 at 8:08 PM Rafael L via Rdkit-discuss 
mailto:rdkit-discuss@lists.sourceforge.net> > wrote:

Dear all, I remember having used some SMARTS-based function to flag structures 
containing "non-organic" atoms. It seems that there is a knime node for that 
(https://forum.knime.com/t/rdkit-molecule-substructure-filter-incorrectly-matches-aromatic-sulfur-atoms-molecule-as-metal-containing-compounds/12935),
 but I wasn't able to find any Python implementations. Does anyone know where 
to find it?

Thanks in advance


 

--

Rafael da Fonseca Lameiro

PhD Student - Medicinal and Biological Chemistry Group (NEQUIMED)

São Carlos Institute of Chemistry - University of São Paulo - Brazil

     
 https://orcid.org/-0003-4466-2682

___
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

[Rdkit-discuss] Availability of new command line scripts

[Manish Sud]

Hi All,

 

I'll like to share with you the availability of the following new command
line scripts:

 

o RDKitFilterTorsionLibraryAlerts.py
 

o Psi4CalculateInteractionEnergy.py
 

 

These scripts rely on the presence of RDKit and Psi4 in your environment.

 

The RDKitFilterTorsioLibraryAlerts.py script provides functionality to
filter strained docked poses or conformers for Torsion Library
  alerts. This script is
a result of collaborative effort between Pat
  and me. In addition, I
thank Wolfgang Guba (Roche) and Patrick Penner (U. of Hamburg) for providing
additional details regarding the implementation of the Torsion Library.

 

Your feedback is welcome.

 

Thanks.

Manish

 

___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

[Rdkit-discuss] Availability of new command line Psi4 scripts powered by RDKit

[Manish Sud]

Hi All,

 

I'll like to share with you the availability of the following new command
line scripts:

 

o Psi4GenerateConstrainedConformers.py
 

o Psi4PerformConstrainedMinimization.py
 

o Psi4PerformTorsionScan.py



 

These scripts rely on the presence of Psi4   and RDKit
in your environment. In addition, the script RDKitPerformTorsionScan.py
  has been enhanced to support multiprocessing at the level of torsion
angles during the torsion scan. Please visit MayaChemTools
  for further details.

 

Your feedback is welcome.

 

Thanks,

Manish

 

___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] Availability of new command line Psi4 scripts powered by RDKit

[Manish Sud]

Hi JW,

 

Yes, I do. It’s on the list of things to do. It would be similar to the current 
script RDKitPerformTorsionScan.py 
<http://mayachemtools.org/docs/scripts/html/RDKitPerformTorsionScan.html> , but 
use Psi4 on the backend.

 

Thanks,

Manish

 

From: JW Feng  
Sent: Wednesday, April 21, 2021 10:04 AM
To: Manish Sud 
Cc: RDKit Discuss 
Subject: Re: [Rdkit-discuss] Availability of new command line Psi4 scripts 
powered by RDKit

 

Hi Manish,

 

This is great. I used Psi4 extensively for torsional scans while at Denali. Do 
you plan to include scripts for torsional scans? 

 

Best,

 

JW

 

On Wed, Apr 21, 2021 at 9:11 AM Manish Sud mailto:m...@san.rr.com> > wrote:

Hi All,

 

I'll like to share with you the availability of the following new command line 
Python scripts based on Psi4:

 

o Psi4CalculateEnergy.py

o Psi4CalculatePartialCharges.py

o Psi4CalculateProperties.py

o Psi4GenerateConformers.py

o Psi4PerformMinimization.py

o Psi4VisualizeDualDescriptors.py

o Psi4VisualizeElectrostaticPotential.py

o Psi4VisualizeFrontierOrbitals.py

 

These scripts rely on the availability of Psi4 and RDKit in your environment. 
The RDKit is used for a variety of tasks including reading and writing 
molecules, generating initial 3D coordinates and conformers of molecules, and 
removing similar conformers. In addition, multiprocessing functionality is 
available across all the scripts.

 

Some of you might find these scripts useful. Please visit  
www.MayaChemTools.org <http://www.MayaChemTools.org>  for further details.

 

Your feedback is welcome.

 

Thanks,

Manish

___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net 
<mailto: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

[Rdkit-discuss] Availability of a new command line script

[Manish Sud]

Hi All,

 

A new command line script named RDKitPerformPositionalAnalogueScan.py
  is now available as part of MayaChemTools package. Positional
Analogue Scanning is recently reviewed in an article by Pennington et. al.
  Pat wrote a blog post
  about it. The new script extends Pat's work. In addition to
replacing and attaching atoms, a set of options is available to attach
SMILES, run reactions, and perform tandem scanning.

 

Your feedback is welcome.

 

Thanks,

Manish

 

___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

[Rdkit-discuss] Availability of command line scripts

[Manish Sud]

Hi All,

 

I'll like to share with you the availability of the following new command
line scripts:

 

o RDKitAlignMolecules.py

o RDKitCalculateEnergy.py

o RDKitGenerateConstrainedConformers.py

o RDKitPerformConstrainedMinimization.py

o RDKitRemoveInvalidMolecules.py

 

Please visit www.MayaChemTools.org   for
additional details and to download the package.

 

Your feedback is welcome. 

 

Thanks,

Manish

 

___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

[Rdkit-discuss] Updates to multiprocessing functionality in command line scripts

[Manish Sud]

Hi All,

 

Just to let you know, I've updated multiprocessing functionality in the
following command line scripts available as part of MayaChemTools package:

 

o RDKitCalculateMolecularDescriptors.py

o RDKitCalculatePartialCharges.py

o RDKitFilterChEMBLAlerts.py

o RDKitFilterPAINS.py

o RDKitGenerateConformers.py

o RDKitPerformMinimization.py

o RDKitRemoveSalts.py

o RDKitSearchFunctionalGroups.py

o RDKitSearchSMARTS.py

 

The changes are made to sort out some multiprocessing issues for running
these scripts in Python 3.7 environment. In addition, a handful of other
modifications have been made to improve performance. The latest release is
available at www.MayaChemTools.org  .

 

Your feedback is welcome.

 

Thanks,

Manish

 

___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

[Rdkit-discuss] Availability of multiprocessing functionality in command line scripts

[Manish Sud]

Hi All,

 

I've implemented multiprocessing functionality in the following command line
scripts available as part of MayaChemTools package:

 

o RDKitCalculateMolecularDescriptors.py

o RDKitCalculatePartialCharges.py

o RDKitGenerateConformers.py

o RDKitFilterChEMBLAlerts.py

o RDKitFilterPAINS.py

o RDKitPerformMinimization.py

o RDKitRemoveSalts.py

o RDKitSearchSMARTS.py

 

Please visit www.MayaChemTools.org   for
further details.

 

Let me know of any questions/comments.

 

Thanks,

Manish

___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

[Rdkit-discuss] Availability of additional command line scripts

[Manish Sud]

Hi All,

 

I'll like to share with you the availability of the following new command
line scripts, being distributed as part of MayaChemTools package:

 

o RDKitCalculatePartialCharges.py

o RDKitDrawMoleculesAndDataTable.py

o RDKitPerformRGroupDecomposition.py

o RDKitRemoveSalts.py

 

In addition, RDKitDrawMolecules.py script now supports generation of a HTML
file containing in line SVG drawing of molecules in a table. A handful of
changes have been made to other scripts to improve performance.

 

Please visit www.MayaChemTools.org <http://www.MayaChemTools.org>  for
additional details and to download the package.

 

Your feedback is welcome. 

 

Manish Sud

 

--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

[Rdkit-discuss] Availability of command line scripts

[Manish Sud]

Hi All,

I'll like to share with you the availability of the following command line 
scripts:

RDKitCalculateMolecularDescriptors.py
RDKitCalculateRMSD.py
RDKitClusterMolecules.py
RDKitCompareMoleculeShapes.py
RDKitConvertFileFormat.py
RDKitDrawMolecules.py
RDKitEnumerateCompoundLibrary.py
RDKitEnumerateStereoisomers.py
RDKitFilterPAINS.py
RDKitGenerateConformers.py
RDKitGenerateMolecularFrameworks.py
RDKitPerformMinimization.py
RDKitPickDiverseMolecules.py
RDKitRemoveDuplicateMolecules.py
RDKitSearchFunctionalGroups.py
RDKitSearchSMARTS.py

These scripts are distributed as part of MayaChemTools, a growing collection of 
command line Perl and Python scripts to support a variety of day-to-day 
computational discovery needs.

The scripts have been tested using the latest release of RDKit available for 
both Anaconda2 and Anaconda3. They appear to work as expected, as far as I can 
tell. An extensive set of documentation is also available for the scripts.

Please visit www.MayaChemTools.org for additional details and to download the 
package.

Your feedback is welcome. 

Happy scripting,
Manish Sud 

Email: m...@san.rr.com
URL: www.MayaChemTools.org


--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss