def mol2_to_dataframe(klifs_download_path, species, kinase_name, pdb_id, alt=None, chain=None):
"""
Get water structural data content (mol2 file) from local file.
Parameters
----------
klifs_download_path : pathlib.Path or str
Path to folder where KLIFS_download folder lives.
species : str
Species.
kinase_name : str
Kinase name.
pdb_id : str
PDB ID.
alt : str
Alternate model ID.
chain : str
Chain ID.
Returns
-------
pandas.DataFrame
Water structural data.
"""
mol2_file = _mol2_path('water', klifs_download_path, species, kinase_name, pdb_id, alt, chain)
structure_df = _mol2_file_to_dataframe(mol2_file)
return structure_df.df
def mol2_to_rdkit_mol(klifs_download_path,
species,
kinase_name,
pdb_id,
alt=None,
chain=None,
compute2d=True):
"""
Get ligand structural data content (mol2 file) from local file.
Parameters
----------
klifs_download_path : pathlib.Path or str
Path to folder where KLIFS_download folder lives.
species : str
Species.
kinase_name : str
Kinase name.
pdb_id : str
PDB ID.
alt : str
Alternate model ID.
chain : str
Chain ID.
compute2d : bool
Compute 2D coordinates for ligand (default).
Returns
-------
rdkit.Chem.rdchem.Mol
Ligand structural data.
"""
mol2_file = _mol2_path('ligand', klifs_download_path, species, kinase_name,
pdb_id, alt, chain)
mol = _mol2_file_to_rdkit_mol(str(mol2_file), compute2d)
return mol