Python binding for the chemfiles library
![Documentation](https://img.shields.io/badge/docs-latest-brightgreen.svg)
Chemfiles is a library for reading and writing molecular trajectory files. These
files are created by your favorite theoretical chemistry program, and contains
information about atomic or residues names and positions. Chemfiles offers
abstraction on top of these formats, and a consistent interface for loading and
saving data to these files.
This repository contains the Python binding for the chemfiles library. This
binding is created with the ctypes module, calling directly the C interface of
chemfiles, and thus is compatible with Python 2 and 3, and with all versions of
Numpy.
Installation
You can use your favorite package manager (conda
or pip
) to install
pre-built versions of Chemfiles, that support Linux/Windows/macOS, and Python
2.7 and 3.
# Using pip
pip install chemfiles
# Using conda
conda install -c conda-forge chemfiles
Source compilation
You can install this python module from sources if you have all the
dependencies of the C++ chemfiles library installed on your computer.
git clone https://github.com/chemfiles/chemfiles.py
cd chemfiles.py
git submodule update --init
pip install -r dev-requirements.txt
pip install .
tox
Usage example
Here is a simple usage example for the chemfiles
module. Please see the
examples
folder for more examples.
from chemfiles import Trajectory, Frame
trajectory = Trajectory("filename.xyz")
frame = trajectory.read()
print(f"There are {len(frame.atoms)} atoms in the frame")
positions = frame.positions()
Bug reports, feature requests
Please report any bug you find and any feature you may want as a github
issue.