Python interface to chemfiles

This is the documentation for the Python interface to the chemfiles library. This interface uses Numpy, and is compatible with Python 2.7 and 3.4+, and Numpy 1.8 to 1.10.

Installation

Pre-compiled packages

Chemfiles is available as pre-compiled packages for the three main operating systems, both on PyPI and conda. You can install these pre-compiled packages using

# if you use pip
pip install chemfiles

# if you use conda
conda install -c conda-forge chemfiles

In case there is no pre-compiled wheel for your platform available (currently 32 and 64-bit x86/Intel CPU on Linux and Windows are supported, as well as macOS with Intel CPU); then the pip installation will try to build the latest release from source on your machine. In this case, you will need to have a C++ compiler installed, as well as CMake.

Build from sources – development version

You can also install this python module from sources if you have all the dependencies of the C++ library installed on your computer.

git clone https://github.com/chemfiles/chemfiles.py
cd chemfiles.py
git submodule update --init
# Install development dependencies
pip install -r dev-requirements.txt
# Install chemfiles
pip install .
# Optionally run the test suite
tox

User documentation

This section contains example of how to use chemfiles, and the complete interface reference for all the types and subroutines in chemfiles.

• Tutorials
  • Read a single frame
  • Generating a structure
  • Using selections
• Python interface reference
  • Error handling
• Atom class
  • Atom
• Residue class
  • Residue
• Topology class
  • BondOrder
  • Topology
• UnitCell class
  • CellShape
  • UnitCell
• Frame class
  • Frame
• Trajectory class
  • Trajectory
  • MemoryTrajectory
• Selection class
  • Selection