openpharmacophore.Ligand

class openpharmacophore.Ligand(mol)[source]

Bases: object

Represents a ligand. Wrapper for rdkit Mol object

Methods

`add_conformers`	Add conformers to a ligand.
`add_hydrogens`	Add hydrogens to this ligand.
`draw`	Draw the ligand.
`fix_bond_order`	Fix the bond order of a ligand.
`from_string`	Create a ligand from a smiles, smarts, inchi, pdb block, or mol2 block
`generate_conformers`	Generate conformers for this ligand.
`get_chem_feats`	Find chemical features in this ligand.
`get_chem_feats_with_directionality`	Find chemical features in this ligand.
`get_conformer`	Get the coordinates of the specified conformer
`get_feat_indices`
`has_aromatic_bonds`	Returns true if the ligand has aromatic bonds.
`has_double_bonds`	Returns true if the ligand has double bonds.
`to_rdkit`	Returns the ligand as an rdkit molecule.

Attributes

`feat_ind`
`has_conformers`
`has_hydrogens`	Returns true if the ligand has any hydrogen atoms
`lig_id`	ID of the ligand if it was extracted from a protein.
`n_atoms`
`n_bonds`
`n_conformers`
`n_heavy_atoms`

add_conformers(coords)[source]

Add conformers to a ligand.

Parameters:: coords (puw.Quantity) – A quantity of shape (n_conformers, n_atoms, 3)

add_hydrogens()[source]

Add hydrogens to this ligand. Modifies the ligand in place.

Can only add hydrogens to a ligand that only has one conformer.

draw()[source]: Draw the ligand.

fix_bond_order(smiles)[source]

Fix the bond order of a ligand. This is necessary when a ligand is extracted from a Protein object.

Parameters:: smiles (str) – Smiles of the ligand

classmethod from_string(string, form)[source]

Create a ligand from a smiles, smarts, inchi, pdb block, or mol2 block

Parameters:

string (str) – The string that encodes the ligand
form (str) – Can be “smi”, “smarts”, “inchi”, “mol2”, “pdb”.

Return type:

Ligand

generate_conformers(n_confs)[source]: Generate conformers for this ligand. Removes current conformers if any

get_chem_feats(conf_ind, types=None, indices=False)[source]

Find chemical features in this ligand.

Parameters:

conf_ind (int) – Index of the conformer.
types (set[str], optional) – The chemical features that will be searched for.
indices (bool, default=False) – Whether to store the indices of the atoms in the chemical features.

Return type:

ChemFeatContainer

get_chem_feats_with_directionality(conf_ind, types=None)[source]

Find chemical features in this ligand. Hydrogen bond donors obtained with this method will include information about hydrogen atoms, and aromatic ring will contain their normal vector.

Parameters:

conf_ind (int) – Index of the conformer.
types (set[str], optional) – The chemical features that will be searched for.

Return type:

ChemFeatContainer

get_conformer(conf_ind)[source]

Get the coordinates of the specified conformer

Parameters:: conf_ind (int) – Index of the conformer
Returns:: A quantity of shape (n_atoms, 3)
Return type:: puw.Quantity

has_aromatic_bonds()[source]

Returns true if the ligand has aromatic bonds.

Return type:: bool

has_double_bonds()[source]

Returns true if the ligand has double bonds.

Return type:: bool

property has_hydrogens: bool

Returns true if the ligand has any hydrogen atoms

Return type:: bool

property lig_id: str: ID of the ligand if it was extracted from a protein.

to_rdkit()[source]

Returns the ligand as an rdkit molecule.

Return type:: rdkit.Chem.Mol