cg_openmm.parameters.secondary_structure

Functions

bootstrap_native_contacts_expectation(...[, ...])	Given a cgmodel, native contact definitions, and trajectory file list, this function calculates the fraction of native contacts for all specified frames, and uses a bootstrapping scheme to compute the uncertainties in the Q vs T folding curve.
expectations_fraction_contacts(...[, ...])	Given a .nc output file, temperature list, and number of intermediate states to insert for the temperature list, this function calculates the native contact fraction expectation.
fraction_native_contacts(cgmodel, file_list, ...)	Given a cgmodel, mdtraj trajectory object, and positions for the native structure, this function calculates the fraction of native contacts for the model.
fraction_native_contacts_preloaded(cgmodel, ...)	Given a cgmodel, mdtraj trajectory object, and positions for the native structure, this function calculates the fraction of native contacts for the model.
get_helix_contacts(cgmodel, ...[, ...])	Given a coarse grained model and positions for the native structure this function determines which pairs are native contacts.
get_native_contacts(cgmodel, ...)	Given a coarse grained model, positions for the native structure, and cutoff, this function determines which pairs are native contacts.
optimize_Q_cut(cgmodel, ...[, output_data, ...])	Given a coarse grained model and a native structure as input, optimize both the distance cutoff defining the native contact pairs and the distance tolerance for scanning the trajectory for native contacts.
optimize_Q_cut_1d(cgmodel, ...[, ...])	Given a coarse grained model and a native structure as input, optimize the distance cutoff defining the native contact pairs, with a fixed distance tolerance factor for scanning the trajectory.
optimize_Q_tol_helix(cgmodel, ...[, ...])	Given a coarse grained model and a native structure as input, determine which helical backbone sequences are native contacts, and the optimal distance tolerance for scanning the trajectory for native contacts.
plot_native_contact_fraction(...[, ...])	Given a list of temperatures and corresponding native contact fractions, plot Q vs T.
plot_native_contact_timeseries(Q[, ...])	Given average native contact fractions timeseries for each replica or state, plot Q vs time.