Reaction Data and Molecular Conformer

A light-weight software package with expertise in handling Reaction Data and Molecular (including transitions states) Conformers.

Installation

The package can be easily installed with conda or mamba with

conda install -c xiaoruidong rdmc

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 -e --no-deps -vv ./;

There are two major modules in RDMC:

rdtools

It has a collections of functions that can be directly operated on to RDKit native objects. Most of them can be regarded as a modified version of a RDKit native operation but with simplified imports, more intuitive usage, and more robustness implementation. They are distributed in submodules, each named by its relevance field and objects. It is best used in cases where efficiency is a major conern and the task you required is relatively simple. Here are some highlights in rdtools:

• viewers in rdtools.view. These viewers greatly extend RDKit's default Ipython 3D viewer, with the capability of viewing animations and interaction with conformers.
• generate_resonance_structures in rdtools.resonance is able to generate resonance structures for radical molecules that is not capable by the original RDKit.
• mol_from_smiles in rdtools.conversion make sure the created molecule has an atom ordering consistent with the atom mapping
• mol_from_xyz supports two backends openbabel as well as xyz2mol for molecule connectivity perception. If both native backends fail (e.g., cannot be sanitized, or wrong charge or multiplicity), rdtools also provided a heuristic fix tool fix_mol in rdtools.fix to help fix the molecules if possible.

rdmc

It can be regarded as a midware between RDKit/rdtools basic operations and complicated workflows. Mol (Previously, RDKitMol) and Reaction are the most important classes.

• Mol (known as RDKitMol previously) is a child class of RWMol, which means that you can directly use it with RDKit's native functions, but also integrated a lot of tools in rdtools, so you can directly use them as class methods. The appended methods not only provides convenience in usage, but also make sure the output molecule objects, if applicable, is still a rdmc.Mol object. While many RDKit functions will just output Chem.Mol which is no longer editable, breaking the flow of your molecule operations.
• Reaction provides intuitive APIs for getting bond analysis, reaction comparison, visualization, etc.

For detailed APIs, please check the documentation.

Demos

Feel free to check demos in the ipython/, some of them are also available on the Google Colab:

• Generate Atom Map for Reactions
• Handle molecule from/to XYZ
• Parse QM Results

Requirements

• To use rdtools, you only needs numpy and rdkit at minimum. You can install optional dependencies: scipy for better resonance structure generation for polycyclic molecules, py3dmol to use the amazing 3D viewers, openbabel to extend rdmc's xyz perception cability.
• To use rdmc, the dependencies are basically the same as rdtools, but we do recommend installing all optional dependencies for a better experience. Besides, to plot curves and figures for data, you can install matplotlib; to play around with the log parsers you should consider install cclib and ipywidgets. And to start computations in conformer_generation, you need to have xtb and orca (which are free to academia) installed to get some serious results.