cg_openmm.ensembles.ens_build

Functions

get_ensemble(cgmodel[, ensemble_size, ...])	Given a coarse grained model, this function generates an ensemble of high energy configurations and, by default, saves this ensemble to the foldamers/ensembles database for future reference/use, if a high-energy ensemble with these settings does not already exist.
get_ensemble_data(cgmodel, ensemble_directory)	Given a CGModel() class object and an 'ensemble_directory', this function reads the PDB files within that directory, as well as any energy data those files contain.
get_ensemble_directory(cgmodel[, ensemble_type])	Given a CGModel() class object, this function uses its attributes to assign an ensemble directory name.
get_ensembles(cgmodel, native_structure[, ...])	Given a native structure as input, this function builds both native and nonnative ensembles.
get_ensembles_from_replica_positions(...[, ...])	Given a coarse grained model and replica positions, this function: 1) decorrelates the samples, 2) clusters the samples with MSMBuilder, and 3) generates native and nonnative ensembles based upon the RMSD positions of decorrelated samples.
get_native_ensemble(cgmodel, native_structure)	Given a native structure as input, this function builds a "native" ensemble of structures.
get_native_structure(replica_positions, ...)	Given replica exchange run positions and energies, this function identifies the "native" structure, calculated as the structure with the lowest reduced potential energy.
get_nonnative_ensemble(cgmodel, native_structure)	Given a native structure as input, this function builds a "nonnative" ensemble of structures.
get_pdb_list(ensemble_directory)	Given an 'ensemble_directory', this function retrieves a list of the PDB files within it.
improve_ensemble(energy, positions, ...)	Given an energy and positions for a single pose, as well as the same data for a reference ensemble, this function "improves" the quality of the ensemble by identifying poses with the lowest potential energy.
test_energy(energy)	Given an energy, this function determines if that energy is too large to be "physical".
write_ensemble_pdb(cgmodel[, ensemble_directory])	Given a CGModel() class object that contains positions, this function writes a PDB file for the coarse grained model, using those positions.
z_score(nonnative_ensemble_energies, ...)	Given a set of nonnative and native ensemble energies, this function computes the Z-score (for a set of model parameters).