Direct Coupling Analysis for Python

mfDCA implementation, adapted from MATLAB version (http://dca.rice.edu/portal/dca/)

Direct Coupling Analysis was developed using MATLAB. This is a python port.

Unit testing Readme and script details output differences from original MATLAB script.

Installation:

Simplest is:

pip install git+https://github.com/utdal/py-mfdca.git

Or:

git clone https://github.com/utdal/py-mfdca.git
pip install py-mfdca

Which will also download the unit testing.

Example Usage:

from dca.dca_class import dca
protein_family = dca('sequence_file')
protein_family.mean_field()
protein_family.DI # contains DI scores for each pair
protein_family.couplings # NxNxqxq matrix of couplings (eij)
protein_family.localfields # Nxq matrix of localfields (h)
protein_family.compute_Hamiltonian('sequence_file') # returns (Hamiltonians,sequence_headers) for input sequences

Runtimes, Random MSA Average of 2 (M1 Pro, 16GB RAM):

Sequence Length	# of sequences	Runtime (s)
100	1,000	2.2
300	1,000	5.4
500	1,000	21
100	10,000	0.7
300	10,000	6.7
500	10,000	24.1
100	100,000	98.5
300	100,000	266.8
500	100,000	391