schrodinger.protein.natural_analog module

schrodinger.protein.natural_analog.get_canvas_program(program_name) → str
schrodinger.protein.natural_analog.build_natural_analog_dict(ref_res_filename: str, query_res_filename: str) → dict[str, Tuple[str, float]]
Get a dictionary of natural analogs and similarity scores from a

canvas fingerprint matrix

Parameters

  • ref_res_filename – filename of the reference residue database

  • query_res_filename – filename of the query residue database

Returns

dictionary of natural analogs and similarity scores

schrodinger.protein.natural_analog.get_fp_matrix(ref_res_filename: str, query_res_filename: str) → pandas.core.frame.DataFrame

Use canvas fingerprints to get a dataframe of similarity scores

Parameters

  • ref_res_filename – reference residue database filename, which will be used as the matrix columns

  • query_res_filename – query residue database filename, which will be used as the matrix rows

Returns

dataframe of fingerprint similarity scores

schrodinger.protein.natural_analog.write_canvas_fingerprint(residue_file, fp_filename, fingerprint_type='dendritic')
schrodinger.protein.natural_analog.write_canvas_fingerprint_matrix(mx_row_fp_filename: str, mx_col_fp_filename: str, output_filename='sim.csv')
Write a canvas fingerprint matrix which compares the fingerprints of two

residue databases

Parameters

  • mx_row_fp_filename – fingerprint file to use as matrix rows

  • mx_col_fp_filename – fingerprint file to use as matrix columns

  • output_filename – filename of the output matrix

schrodinger.protein.natural_analog.read_canvas_fingerprint_matrix(fp_mx_filename: str) → pandas.core.frame.DataFrame

Read a canvas fingerprint matrix csv

Parameters

fp_mx_filename – fingerprint matrix filename

Returns

fingerprint matrix dataframe

schrodinger.protein.natural_analog.apply_natural_analog_props(st: schrodinger.structure._structure.Structure, natural_analog_dict: dict[str, Tuple[str, float]])

Apply the natural analog and similarity score properties to a structure containing a single residue

Parameters

  • st – structure containing a single residue

  • natural_analog_dict – dictionary mapping residue names to natural analogs and similarity scores

schrodinger.protein.natural_analog.write_natural_analog_res_db(residue_structures: Iterable[schrodinger.structure._structure.Structure], output_filename: str, natural_analog_dict: dict[str, Tuple[str, float]])
Write a new residue database with the natural analog and similarity score

as properties.

Parameters

  • residue_structures – list of residue structures

  • output_filename – filename of the output residue database

  • natural_analog_dict – dictionary mapping residue names to natural analogs and similarity scores