index.rst

Welcome to molSimplify's documentation!

Installation Citation

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 table
Cores: templates for building transition metal complex
Data: template for coordination for not just octahedral coordination
Informatics: scripts and codes for featurization, revised autocorrelations, transformations of molecular information into numerical vectors, and other ML tools
Ligands: 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 structure
Scripts: codes to write and measure geometries, and write input files
molscontrol: dynamic classifier files
python_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 bad
tf_nn: published models from the group

Classes Scripts Informatics

tutorials/development

View Source Code (GitHub) <https://github.com/hjkgrp/molSimplify> Report an Issue <https://github.com/hjkgrp/molSimplify/issues> Visit Our Research Group Website <https://hjkgrp.mit.edu> Visit Our Interactive Site <https://molsimplify.mit.edu>