MayaChemTools is a growing collection of Perl and Python scripts, modules,
and classes to support a variety of day-to-day computational discovery needs.
The core set of command line Perl scripts available in the current release
of MayaChemTools has no external dependencies and provide functionality
for the following tasks:
- Manipulation and analysis of data in SD, CSV/TSV, sequence/alignments, and PDB files
- Listing information about data in SD, CSV/TSV, Sequence/Alignments, PDB, and fingerprints files
- Calculation of a key set of physicochemical properties, such as molecular weight, hydrogen bond donors and acceptors, logP, and topological polar surface area
- Generation of 2D fingerprints corresponding to atom neighborhoods, atom types, E-state indices, extended connectivity, MACCS keys, path lengths, topological atom pairs, topological atom triplets, topological atom torsions, topological pharmacophore atom pairs, and topological pharmacophore atom triplets
- Generation of 2D fingerprints with atom types corresponding to atomic invariants, DREIDING, E-state, functional class, MMFF94, SLogP, SYBYL, TPSA and UFF
- Similarity searching and calculation of similarity matrices using available 2D fingerprints
- Listing properties of elements in the periodic table, amino acids, and nucleic acids
- Exporting data from relational database tables into text files
The command line Python scripts based on RDKit provide functionality for the
following tasks:
- Calculation of molecular descriptors and partial charges
- Comparison of 3D molecules based on RMSD and shape
- Conversion between different molecular file formats
- Enumeration of compound libraries, stereoisomers, and tautomers
- Filtering molecules using SMARTS, PAINS, torsion library, and names of functional groups
- Filtering molecules using torsion library alerts and estimated torsion strain energy library alerts
- Generation of graph and atomic molecular frameworks
- Generation of images for molecules
- Performing structure minimization and conformation generation based on distance geometry and forcefields
- Performing R group decomposition
- Performing torsion scan
- Picking and clustering molecules based on 2D fingerprints and various clustering methodologies
- Positional analogue scanning
- Removal of duplicate molecules and salts from molecules
- Standardizing molecules
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
- Mutating amino acids and nucleic acids
- Generating Ramachandran plots
- Visualizing X-ray electron density and cryo-EM density
- Visualizing macromolecules in terms of chains, ligands, and ligand binding pockets
- Visualizing cavities and pockets in macromolecules
- Visualizing macromolecular interfaces
- Visualizing surface and buried residues in macromolecules
- Visualizing docked poses and trajectories for macromolecules
- Visualizing pockets in macromolecules detected by an open source package named Fpocket
The command line Python scripts based on Psi4 provide functionality for the
following tasks:
- Calculation of single point energies
- Calculation of interaction energies
- Calculation of molecular properties and partial charges
- Performing structure minimization
- Generating molecular conformations
- Performing torsion scan
- Visualizing frontier molecular orbitals and dual descriptors
- Visualizing electrostatic potential on densities and molecular surfaces
The command line Python scripts based on AutoDock Vina
provide functionality for the following tasks:
- Performing rigid and flexible docking
- Scoring molecules
In addition, a command line Python script based on TMAP
provides functionality functionality to visualize chemspaces.
Review the documentation 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.
