dpet.data package

Submodules

dpet.data.api_client module

class dpet.data.api_client.APIClient

Bases: object

close_session()

download_response_content(response, save_path)

perform_get_request(url, headers=None)

dpet.data.coord module

dpet.data.coord.calc_chain_dihedrals(xyz, norm=False)

dpet.data.coord.contact_probability_map(traj, scheme='ca', contact='all', threshold=0.8)

dpet.data.coord.create_consecutive_indices_matrix(ca_indices): This function gets the CA indices of (L,) shape and create all possible 4 consecutive indices with the shape (L-3, 4)

dpet.data.coord.dict_phi_psi_normal_cases(dict_phi_psi)

dpet.data.coord.get_contact_map(dmap, threshold=0.8, pseudo_count=0.01): Gets a trajectory of distance maps with shape (N, L, L) and returns a (L, L) contact probability map.

dpet.data.coord.get_distance_matrix(xyz): Gets an ensemble of xyz conformations with shape (N, L, 3) and returns the corresponding distance matrices with shape (N, L, L).

dpet.data.coord.site_specific_order_parameter(ca_xyz_dict: dict) → dict

Computes site-specific order parameters for a set of protein conformations. :param ca_xyz_dict: A dictionary where keys represent unique identifiers for proteins, :type ca_xyz_dict: dict :param and values are 3D arrays containing the coordinates of alpha-carbon: :type and values are 3D arrays containing the coordinates of alpha-carbon: CA

Returns:: A dictionary where keys are the same protein identifiers provided in ca_xyz_dict, and values are one-dimensional arrays containing the site-specific order parameters computed for each residue of the protein.
Return type:: dict

dpet.data.coord.split_dictionary_phipsiangles(features_dict)

dpet.data.coord.ss_measure_disorder(features_dict: dict): This function accepts the dictionary of phi-psi arrays which is saved in featurized_data attribute and as an output provide flexibility parameter for each residue in the ensemble Note: this function only works on phi/psi feature

dpet.data.extract_tar_gz module

dpet.data.extract_tar_gz.extract_tar_gz(tar_gz_file: str, output_dir: str, new_name: str)

dpet.data.topology module

Work with topologies of protein systems.

dpet.data.topology.get_ca_topology(sequence: str, bead_name: str = 'CA') → Topology: input: amino acid sequence. output: a mdtraj topology with one bead per residue.

dpet.data.topology.slice_traj_to_com(traj: Trajectory) → Trajectory