Welcome to molSimplify’s documentation!
General Information
Descriptions of important folders and file organization:
Classes: generic tools used to manipulate non-periodic molecular structures-
mol3D.py: object used to manipulate non-periodic molecular structure (not just transition metal complexes), composed of atom3D objects-
atom3D.py: object representing a single atom defined by position, identify, etc-
globarvars.py: contains all information about elements in the periodic tableCores: templates for building transition metal complexData: template for coordination for not just octahedral coordinationInformatics: scripts and codes for featurization, revised autocorrelations, transformations of molecular information into numerical vectors, and other ML toolsLigands: database of ligands which are used in molSimplify (if your ligand is not found here, there is a tutorial for adding to the ligand database)-
ligands.dict: contains mappings between ligand name and corresponding structureScripts: codes to write and measure geometries, and write input filespython_nn: bond length information for the very first bond length NN (2017 Chemical Science)sklearn_models: models for static classification of whether a geometry is good or badtf_nn: published models from the groupAPI