dcatoolkit

Collection of useful modules and representations for managing DCA output data.

Major Sections

Representations

• Use Pairs to load lists, tuples, sets, and ndarrays with the correct orientation of elements. This will allow you to yield integer pairs that can be mirrored (where y becomes x and vice versa) and to subset various pairs.
• Use DirectInformationData to create 3-column structured ndarrays that can be sorted by "DI", mapped to a protein with a ResidueAlignment, and used to generate output for other programs (including UCSF Chimera)
• Use ResidueAlignment to generate a reference map. Indices of one sequence of characters can be linked to their corresponding indices of the other sequence of characters. The dictionaries produced, domain-to-protein and protein-to-domain, allow for forward mapping and backmapping.
• Use StructureInformation to find contacts in a protein structure and find atomic information related to specific pairs of interest.

Analytics

• Use MSATools to load in Multiple Sequence Alignment (MSA) data and provide functionality including generating frequency statistics on "gappiness" in the MSA and filtering and cleaning MSAs.

Diagram of Hidden Markov Machine & Direct Coupling Analysis Pipeline