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MayaChemTools

Additions to MayaChemTools

 

A couple of new scripts have been added to the excellent MayaChemTools growing collection of Perl and Python scripts, modules, and classes to support a variety of day-to-day computational discovery needs.

RDKitFilterTorsionLibraryAlerts.py - Filter torsion library alerts Direct Link

And

Psi4CalculateInteractionEnergy.py - Calculate interaction energy Direct Link.

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New additions to MayaChemTools

 

There have been a couple of new additions to the fabulous list of tools and scripts on MayaChemTools.

MayaChemTools is a growing collection of Perl and Python scripts, modules, and classes to support a variety of day-to-day computational discovery needs.

o Psi4GenerateConstrainedConformers.py http://www.mayachemtools.org/docs/scripts/html/Psi4GenerateConstrainedConformers.html>

o Psi4PerformConstrainedMinimization.py http://www.mayachemtools.org/docs/scripts/html/Psi4PerformConstrainedMinimization.html.

o Psi4PerformTorsionScan.py http://www.mayachemtools.org/docs/scripts/html/Psi4PerformTorsionScan.html.

These scripts rely on the presence of Psi4 https://psicode.org/ and RDKit in your environment. In addition, the script RDKitPerformTorsionScan.py http://www.mayachemtools.org/index.html for further details.

MayaChemTools is free software; you can redistribute it and/or modify it under the terms of the GNU LGPL as published by the Free Software Foundation.

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Update to MayaChemTools

 

MayaChemTools is an ever increasing collection of python and perl scripts that support cheminformatics and computational chemistry.

The latest addition are based on PSI4 an open-source quantum chemistry package.

PSI4 provides a wide variety of quantum chemical methods using state-of-the-art numerical methods and algorithms. Several parts of the code feature shared-memory parallelization to run efficiently on multi-core machines. An advanced parser written in Python allows the user input to have a very simple style for routine computations, but it can also automate very complex tasks with ease.

The command line Python scripts based on Psi4 provide functionality for the following tasks:

  • Calculation of single point energies
  • Calculation of molecular properties and partial charges
  • Performing structure minimization
  • Generating molecular conformations
  • Visualizing frontier molecular orbitals and dual descriptors
  • Visualizing electrostatic potential on densities and molecular surfaces

MayaChemTools is free software; you can redistribute it and/or modify it under the terms of the GNU LGPL as published by the Free Software Foundation.

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Update to MayaChemTools

 

I just heard that the following command line scripts available as part of MayaChemTools package now have implemented multiprocessing functionality.

o RDKitCalculateMolecularDescriptors.py

o RDKitCalculatePartialCharges.py

o RDKitGenerateConformers.py

o RDKitFilterChEMBLAlerts.py

o RDKitFilterPAINS.py

o RDKitPerformMinimization.py

o RDKitRemoveSalts.py

o RDKitSearchSMARTS.py


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MayaChemtools

 

MayaChemTools now includes a collection of python scripts for PyMol

The command line Python scripts based on PyMOL provide functionality for the following tasks:

Aligning macromolecules Splitting macromolecules into chains and ligands Listing information about macromolecules Calculation of physicochemical properties Comparison of marcromolecules based on RMSD Conversion between different ligand file formats Visualizing X-ray electron density and cryo-EM density Visualizing macromolecules in terms of chains, ligands, and ligand binding pockets

MayaChemTools is a growing collection of Perl and Python scripts, modules, and classes to support a variety of day-to-day computational discovery needs.


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MayaChemTools Update

MayaChemTools has been updated. Read More...
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