Helper functions

Helper functions — prolif.utils

prolif.utils.get_residues_near_ligand(lig, prot, cutoff=6.0)[source]

Detects residues close to a reference ligand

Parameters

  • lig (prolif.molecule.Molecule) – Select residues that are near this ligand

  • prot (prolif.molecule.Molecule) – Protein containing the residues

  • cutoff (float) – If any interatomic distance between the ligand reference points and a residue is below or equal to this cutoff, the residue will be selected

Returns

residues – A list of unique ResidueId that are close to the ligand

Return type

list

prolif.utils.to_bitvectors(df)[source]

Converts an interaction DataFrame to a list of RDKit ExplicitBitVector

Parameters

df (pandas.DataFrame) – A DataFrame where each column corresponds to an interaction between two residues

Returns

bv – A list of ExplicitBitVect for each frame

Return type

list

Example

>>> from rdkit.DataStructs import TanimotoSimilarity
>>> bv = prolif.to_bitvectors(df)
>>> TanimotoSimilarity(bv[0], bv[1])
0.42
prolif.utils.to_dataframe(ifp, interactions, index_col='Frame', dtype=None, drop_empty=True, return_atoms=False)[source]

Converts IFPs to a pandas DataFrame

Parameters

  • ifp (list) – A list of dict in the format {key: bitvector}. “key” is a tuple of ligand and protein ResidueId. “bitvector” is either a numpy.ndarray of bits, or a list of bitarray, ligand atom indices, and protein atom indices. Each dictionnary must also contain an entry that will be used as an index, typically a frame number.

  • interactions (list) – A list of interactions, in the same order as the bitvector.

  • index_col (str) – The dictionnary key that will be used as an index in the DataFrame

  • dtype (object or None) – Cast the input of each bit in the bitvector to this type. If None, keep the data as is. Not compatible with return_atoms=True

  • drop_empty (bool) – Drop columns with only empty values

  • return_atoms (bool) – For each residue pair and interaction, return indices of atoms responsible for the interaction instead of bits

Returns

df – A 3-levels DataFrame where each ligand residue, protein residue, and interaction type are in separate columns

Return type

pandas.DataFrame

Example

>>> df = prolif.to_dataframe(results, fp.interactions.keys(), dtype=int)
>>> print(df)
ligand             LIG1.G
protein             ILE59                  ILE55       TYR93
interaction   Hydrophobic HBAcceptor Hydrophobic Hydrophobic PiStacking
Frame
0                       0          1           0           0          0
...

Changed in version 0.3.2: Moved the return_atoms parameter from the run methods to the dataframe conversion code