This package provides tools for analyzing and exploring contacts (residue-residue and atom-atom) from a trajectory generated by molecular dynamics. It builds on the excellent tools provided by MDTraj.

Contacts can be an important tool for defining (meta)stable states in processes involving biomolecules. For example, an analysis of contacts can be particularly useful when defining bound states during a binding processes between proteins, DNA, and small molecules (such as potential drugs).

The contacts analyzed by contact_map can be either intermolecular or intramolecular, and can be analyzed on a residue-residue basis or an atom-atom basis.

This package makes it very easy to answer questions like:

  • What contacts are present in a trajectory?

  • Which contacts are most common in a trajectory?

  • What is the difference between the frequency of contacts in one trajectory and another? (Or with a specific frame, such as a PDB entry.)

  • For a particular residue-residue contact pair of interest, which atoms are most frequently in contact?

It also facilitates visualization of the contact matrix, with colors representing the fraction of trajectory time that the contact was present.

contact_map is an open source project, released under the GNU LGPL, version 2.1 or (at your option) any later version. Development takes place in public at; your contributions would be welcome!

If you have suggestions or bug reports, please raise an issue on our GitHub issues page.