More updates to the superb MayaChemTools. A new command line script named PyMOLExtractSelection.py to extract an arbitrary PyMOL selection from a macromolecule and write it out to a file. In addition, the Psi4CalculateEnergy.py and Psi4PerformMinimization.py scripts have been updated to perform these calculations in solution using domain-decomposition-based continuum solvation models. These scripts rely on Psi4 interface to the DDX module to perform the calculations. Two solvation models are supported: COnductor-like Screening MOdel (COSMO) and Polarizable Continuum Model (PCM). A number of enhancements have been made to the PyMOLVisualizeMacromolecules.py script including identification of arbitrary distance contacts between heavy atoms in pocket residues and docked poses, visualization of solvents and inorganics in the pocket around docked poses, and visualization of B factor values for chains.

 

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.

 

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.

 

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.

 

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

 

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.