xyz2mol has now been implented in RDKit

raw_mol = Chem.MolFromXYZFile('acetate.xyz')
mol = Chem.Mol(raw_mol)
rdDetermineBonds.DetermineBonds(mol,charge=-1)

Convert Cartesian coordinates to one or more molecular graphs

Given Cartesian coordinates in the form of a .xyz file, the code constructs a list of one or more molecular graphs. In cases where there are several possible resonance forms xyz2mol returns a list of all, otherwise just a list of one.

This code is based on the work of DOI: 10.1002/bkcs.10334

Yeonjoon Kim and Woo Youn Kim
"Universal Structure Conversion Method for Organic Molecules:
From Atomic Connectivity to Three-Dimensional Geometry"
Bull. Korean Chem. Soc.
2015, Vol. 36, 1769-1777

Setup

Depends on rdkit, numpy, and networkx. Easiest to setup via anaconda/conda:

conda install -c conda-forge xyz2mol

Setup for a standalone enviroment is avaliable via Makefile. To setup and test simply clone the project and make.

git clone https://github.com/jensengroup/xyz2mol

and then run the following the the xyz2mol folder

make
make test

Note, it is also possible to run the code without the networkx dependencies, but is slower.

Example usage

Read in xyz file and print out the SMILES, but don't incode the chirality.

xyz2mol.py examples/chiral_stereo_test.xyz --ignore-chiral

Read in xyz file and print out the SDF format, save it in a file

xyz2mol.py examples/chiral_stereo_test.xyz -o sdf > save_file.sdf

Read in xyz file with a charge and print out the SMILES

xyz2mol.py examples/acetate.xyz --charge -1

Dependencies:

rdkit # (version 2019.9.1 or later needed for huckel option)
networkx