Other libraries for reading trajectories

If chemfiles does not provide what you are looking for, here are some other libraries for reading and/or writing trajectories, and the main differencies with chemfiles.

VMD Molfile plugins

VMD is a molecular visualisation program. A set of plugins distributed separatly provide read and write ability for around 60 differents formats.

VMD molfiles plugins are written in C, and do not provide other documentation than the source code (which is very readable, I must say). It is pretty difficult to use it from other languages than C or C++.

Majors differencies

  • More formats than chemfiles;
  • No automatic format regognition;
  • Does not support a variable number of atoms;
  • Not multi-language;
  • Poor documentation for first start. You need to read other software to understand what’s going on.

OpenBabel

OpenBabel is the swiss army knife for converting trajectories from one format to another. It support over 110 file format.

The library is written in C++, and provide Perl, Python, Java and Ruby bindings. It also provide stand-alone tools for conversions and analysis of trajectories.

Majors differencies

  • More formats than chemfiles;
  • Provide analysis tools, SMILES matching and database searching;
  • OpenBabel is distributed under the GNU Public Licence, which might make it harder to use by other softwares: the other software must be GPL softwares;
  • OpenBabel is a complex tool, and provide many public classes. I could not find what I was looking for easily.

MDTraj

MDTraj is a Python library for Molecular Dynamics trajectories reading and analysis.

Majors differencies

  • Provide analysis tools;
  • Only usable from Python;
  • Distributed under the Library GNU Public Licence, which mean that you can use the code in non-GPL software, but must redistribute the library under GPL.

MDAnalysis

MDAnalysis is a Python library for Molecular Dynamics trajectories reading and analysis.

Majors differencies

  • Provide analysis tools;
  • Only usable from Python;
  • MDAnalysis is distributed under the GNU Public Licence, which might make it harder to use by other softwares: the other software must be GPL softwares;