utilsΒΆ

Container for other sub-modules with lower-level functions. They are exposed, tested, and documented, so feel free to use them in your workflow as needed.

residue_and_atom

Deal with residues, atoms, and their names, mostly.

bonds

Simple operations with bonds between the residues of an mdtraj.Topology

str_and_dict

Functions for manipulating strings and dictionaries, also a bit of IO.

COM

Functions related to Center-Of-Mass (COM) computations

lists

Miscellaneous operations on list or list-like objects ..

contact_matrix

Functions related to contact-map operations (WIP)

sequence

Functions for and around sequence alignment