RDMC Documentation#
RDMC (Reaction Data and Molecular Conformer) is an open-source lightweight software package specialized in handling Reaction Data and Molecular (including transition states) Conformers.
It contains various modules and classes (e.g., RDKitMol, Reaction, view) helpful for relevant tasks to make conversion, visualization, manipulation, and analysis of molecules easier.
It also provides solutions to pipelining tasks to achieve high-throughput generating and processing of large amount of molecule/reaction data. It is written in Python and has dependencies only
on popular packages (i.e., numpy, scipy, matplotlib, rdkit, openbabel, py3dmol, ase, networkx, cclib), and you can easily incorporate it into your own Python scripts.
The source code of the RDMC software package is hosted on GitHub, and its binary distribution is available on Anaconda Cloud. The easiest way to install RDMC is to use conda or mamba:
conda install -c xiaoruidong rdmc
Or
mamba install -c xiaoruidong rdmc
conda can be installed by via Anaconda and, mamba can be installed via Mambaforge.
You can also install RDMC from the source code:
git clone https://github.com/xiaoruidong/rdmc
cd RDMC
conda env create -f environment.yml
conda activate rdmc
python -m pip install --no-deps -vv ./
To start with, simply try:
from rdmc import RDKitMol, Reaction
mol = RDKitMol.FromSmiles('CCO')
rxn = Reaction.from_reaction_smiles('CCO>>CC(=O)O')
And see what the mol and rxn are capable of! The full lists of APIs of RDKitMol and Reaction are provided in this documentation.
We also provided a few notebooks (available in \ipython and Colab) to demonstrate the usage of RDMC. Please feel invited to try them out!
RDMC is developed by
Xiaorui Dong (
| 
| 
),Dr. Lagnajit Pattanaik (
| | ),Dr. Shih-Cheng Li (
| | ),Dr. Kevin Spiekermann (
| | ),Hao-Wei Pang (
| | ),Prof. William H. Green (
| )
at Green Research Group at Massachusetts Institute of Technology (MIT). For any questions while using RDMC, please contact us via the GitHub issue page or email us at rdmc_dev@mit.edu.