API Documentation for pharmacophore

class PharmacophoreGenerator(df_all, ligand_name)

A class for generating pharmacophore features from molecular dynamics (MD) interaction data.

This class processes interaction data from MD simulations and generates pharmacophore features including hydrogen bond donors/acceptors, hydrophobic features etc. exporting them in .pml format.

Parameters:

• df_all (pd.DataFrame) – DataFrame storing the input interaction data.

• ligand_name (str) – Name of the ligand.

• coord_pattern (re.Pattern) – Regular expression pattern for extracting 3D coordinates from strings.

• clouds (dict) – Dictionary containing interaction types and associated 3D coordinates with visualization metadata.

Variables:

complex_name (str) – Name of the complex consisting of ligand name and “_complex”.

to_dict()

Export the interaction cloud as a dictionary.

Returns:

Dictionary representation of the interaction cloud.

Return type:

dict

generate_md_pharmacophore_cloudcenters(output_filename, id_num=0)

Generates pharmacophore from all interactions formed in the MD simulation. A feature is generated for each interaction at the center of all its ocurrences.

Parameters:

• output_filename (str) – Name the of the output .pml file.

• id_num (int) – ID number as an identifier in the PML file. Defaults to 0.

Returns:

None. This function writes output directly to a .pml XML file and does not return anything.

Return type:

None

generate_point_cloud_pml(outname)

Generates pharmacophore point cloud and writes it to a .pml file.

Parameters:

outname (str) – Name of the output .pml file.

Returns:

None. This function writes output directly to a .pml file and does not return anything.

Return type:

None

generate_bindingmode_pharmacophore(dict_bindingmode, outname, id_num=0)

Generates pharmacophore from a binding mode and writes it to a .pml file.

Parameters:

• dict_bindingmode (dict) – Dictionary containing all interactions of the bindingmode and their coresponding ligand and protein coordinates.

• outname (str) – Name of the output .pml file.

• id_num (int) – if multiple id number can enumerate the diferent bindingmodes. Defaults to 0.

Returns:

None. This function writes output directly to a .pml file and does not return anything.

Return type:

None

_generate_clouds()

Process the dataframe with the interactions to extract and categorize ligand/protein interactions.

Returns:

A dict containing interaction types as keys and their 3D coordinates.

Return type:

dict

_format_clouds(interaction_coords)

Add visualization properties (color, radius) to the interactions.

Parameters:

interaction_coords (dict) – Dictionary of raw 3D coordinates grouped by interaction type.

Returns:

Dictionary formatted with interaction type as key, and a dictionary of coordinates, color, and radius as value.

Return type:

dict

_generate_pharmacophore_centers(interactions)

Generates pharmacophore points for interactions that are points such as hydrophobic and ionic interactions.

Parameters:

interactions (list) – List of interactions to generate pharmacophore from.

Returns:

Dict of interactions from which pharmacophore is generated as key and list of coordinates as value.

Return type:

dict

_generate_pharmacophore_vectors(interactions)

Generates pharmacophore points for interactions that are vectors such as hydrogen bond donors or acceptors.

Parameters:

interactions (list) – List of interactions to generate pharmacophore vectors from.

Returns:

Dict of interactions from which pharmacophore is generated as key and list of coordinates as value (first coords are ligand side, second are protein side).

Return type:

dict

_generate_pharmacophore_centers_all_points(interactions)

Generates pharmacophore points for all interactions to generate point cloud.

Parameters:

interactions (list) – List of interactions to generate pharmacophore from.

Returns:

Dict of interactions from which pharmacophore is generated as key and list of coordinates as value.

Return type:

dict