Quickstart

Everything in the AFRC is accessed through an AnalyticalFRC object, built from an amino acid sequence. More examples are in the demo directory.

from afrc import AnalyticalFRC

protein = AnalyticalFRC('MASNDYTQQATQSYGAYPTQPGQGYSQQSSQPYGQQSYSGYSQSTDTSGYGQSSYSSYGQSQNTGYGTQSTPQGYG')

# mean dimensions, all in Angstroms
mean_re = protein.get_mean_end_to_end_distance()
mean_rg = protein.get_mean_radius_of_gyration()
mean_rh = protein.get_mean_hydrodynamic_radius()

# distributions are returned as (distances, probabilities)
re_distances, re_probabilities = protein.get_end_to_end_distribution()
rg_distances, rg_probabilities = protein.get_radius_of_gyration_distribution()

# internal scaling profile: [|i-j|, mean distance] for every separation
internal_scaling = protein.get_internal_scaling()

# contact fractions at a 15 A threshold for every pair of residues
contact_map = protein.get_contact_map(15.0)

# 1000 3D conformations (one bead per residue), written as ens.pdb + ens.xtc
# (the XTC needs mdtraj), and a report on how well they reproduce the model
xyz = protein.save_ensemble('ens', n=1000, seed=1)
print(protein.check_ensemble(xyz).format())

Residue indices start at 0. See Analytical Flory Random Coil for the full set of methods, and Command-line tools for generating ensembles from the command line with afrc-ensemble.