openpharmacophore.Protein

class openpharmacophore.Protein(topology, coords)

Bases: object

Represents a protein and optionally its different structures if it comes from a MD trajectory. The protein may contain ligands but is not necessary.

Parameters:

• topology (Topology) – The topology.

• coords (Quantity) – A quantity of shape (n_structures, n_atoms, 3)

Methods

add_hydrogens	Add hydrogens to the protein.
atoms_at_distance	Get the indices of the atoms that are at min_dist <= centroid <= max_dist.
concatenate	Concatenate new residues to this protein.
extract_chain	Extract the chain with given id from the topology.
get_ligand	Extract a ligand assuming there is one.
has_hydrogens
has_ligands
has_solvent_or_ions
ligand_ids
remove_all_ligands	Remove all ligands from this protein.
remove_ligand	Remove a ligand from this protein.
remove_solvent_and_ions	Remove the solvent and ions from this protein.
slice	Obtain a subset of the protein with the specified atoms.

Attributes

coords
n_atoms
n_chains
n_residues
topology

add_hydrogens()

Add hydrogens to the protein.

Assumes that the protein has a single frame.

atoms_at_distance(frame, centroid, max_dist, min_dist=0)

Get the indices of the atoms that are at min_dist <= centroid <= max_dist.

Parameters:

• frame (int) – Frame of the trajectory

• centroid (puw.Quantity) – Shape (1,3)

• max_dist (puw.Quantity) – Scalar

• min_dist (puw.Quantity) – Scalar

Returns:

Array if integers with the indices.

Return type:

np.ndarray

concatenate(topology, coords)

Concatenate new residues to this protein.

Parameters:

• topology (Topology)

• coords (QuantityLike)

extract_chain(chain_id)

Extract the chain with given id from the topology.

Parameters:

chain_id (str or int) – Id of the chain

get_ligand(ligand_id, remove_hyd=False)

Extract a ligand assuming there is one.

Parameters:

• ligand_id (str) – ID of the ligand. ID is composed by pdb id followed by chain name, i.e. “EST:B”.

• remove_hyd (bool) – Whether to remove hydrogens from the ligand.

Returns:

A ligand. Its bond orders may be incorrect.

Return type:

openpharmacophore.Ligand

remove_all_ligands()

Remove all ligands from this protein.

remove_ligand(ligand_id)

Remove a ligand from this protein.

Parameters:

ligand_id (str) – ID of the ligand

remove_solvent_and_ions()

Remove the solvent and ions from this protein.

slice(atoms, frame=None)

Obtain a subset of the protein with the specified atoms.

Parameters:

• atoms (list[int])

• atoms (list[int]) – Indices of the atoms in the sliced protein.

• frame (int, optional) – Frame to extract. If None all frames are extracted.

Returns:

The sliced protein.

Return type:

Protein