Documentation

Warning

Documentation sites are Work in progress

This is the documentation of the three core classes that users will be interacting with:

  1. PyCoM

  2. CoMAnalysis

Quick Summary

pycom.interface.PyCom.find([...])

Find proteins in the database that match the given criteria.

pycom.interface.PyCom.load_matrices(df[, ...])

Only for PyComLocal: Load the coevolution matrices into memory

pycom.interface.PyCom.paginate(df, page[, ...])

Only for PyComLocal: Paginate a DataFrame that is generated by PyCom.find().

pycom.interface.PyCom.get_data_loader()

Returns the PyComDataLoader object that is used to load additional data into the dataframe.

pycom.interface.PyCom.get_biological_process_list()

Retrieves the list of all biological processes in the database.

pycom.interface.PyCom.get_cellular_component_list()

Retrieves the list of all cellular components in the database.

pycom.interface.PyCom.get_cofactor_list()

Retrieves the list of all cofactors in the database.

pycom.interface.PyCom.get_disease_list()

Retrieves the list of all diseases in the database.

pycom.interface.PyCom.get_developmental_stage_list()

Retrieves the list of all developmental stages in the database.

pycom.interface.PyCom.get_domain_list()

Retrieves the list of all domains in the database.

pycom.interface.PyCom.get_ligand_list()

Retrieves the list of all ligands in the database.

pycom.interface.PyCom.get_molecular_function_list()

Retrieves the list of all molecular functions in the database.

pycom.interface.PyCom.get_organism_list()

Retrieves the list of all organisms in the database.

pycom.interface.PyCom.get_ptm_list()

Retrieves the list of all post-translational modifications in the database.

pycom.analysis.CoMAnalysis.add_contact_predictions(df)

Takes in a datafrmae containing coevolution matrices ('matrix' column) and adds a column with contact predictions ('contact_matrix' column).

pycom.analysis.CoMAnalysis.scaled_matrix_to_contact_predictions(...)

Takes in a scaled coevolution matrix and returns a contact prediction matrix

pycom.analysis.CoMAnalysis.get_top_contacts_from_coevolution(...)

returns 'N' top scoring residues as a dataframe

pycom.analysis.CoMAnalysis.get_residue_frequencies(...)

Calculate the residue frequencies count from the top_scoring_residue pairs list

pycom.analysis.CoMAnalysis.calculate_scaled_coevolution_matrix(matrix)

Scales coevolution matrix by average :param matrix: :return: scaled_matrix

pycom.analysis.CoMAnalysis.get_top_scoring_residues(matrix)

returns top scoring residues using percentile cut-off

pycom.analysis.CoMAnalysis.scale_and_normalise_coevolution_matrices(df)

scales coevolution matrix by average, set all values <average to 0 --> S scale S by max of all S in the data frame and add additional column of normalised matrices :param df: :param normalise_matrix: :return: data frame with normalised and scaled coevolution matrix columns

pycom.analysis.CoMAnalysis.save_top_scoring_residue_pairs(df)

Extract top percentile (default: 90) pairs from the chosen matrix and write them in sorted order to an ASCII txt file

Class Documentation