ProteinComponent

class openfe.setup.system.ProteinComponent(rdkit: Mol, name='')

Bases: ExplicitMoleculeComponent

Component representing the contents of a PDB file, such as a protein.

In comparison to a SmallMoleculeComponent, this representation additionally contains information relating to the residue and chain information. This is achievable by having the MonomerInfo attributes present on each atom of the input RDKit molecule, which is done when reading from either PDB or .mae file inputs.

Note

This class is a read-only representation of a protein, if you want to edit the molecule do this in an appropriate toolkit before creating an instance from this class.

Parameters:

• rdkit (rdkit.Mol) – rdkit representation of the protein

• name (str, optional) – of the protein, by default “”

Methods

from_pdb_file	Create ProteinComponent from PDB-formatted file.
from_pdbx_file	Create ProteinComponent from PDBX-formatted file.
to_openmm_positions	serialize the positions to openmm.unit.Quantity ! only one frame at the moment!
to_openmm_topology	Convert to an openmm Topology object
to_pdb_file	serialize protein to pdb file.
to_pdbx_file	serialize protein to pdbx file.

classmethod from_json(json_str)

classmethod from_pdb_file(pdb_file: str, name: str = '')

Create ProteinComponent from PDB-formatted file.

Parameters:

• pdb_file (str) – path to the pdb file.

• name (str, optional) – name of the input protein, by default “”

Returns:

the deserialized molecule

Return type:

ProteinComponent

classmethod from_pdbx_file(pdbx_file: str, name='')

Create ProteinComponent from PDBX-formatted file.

Parameters:

• pdbxfile (str) – path to the pdb file.

• name (str, optional) – name of the input protein, by default “”

Returns:

the deserialized molecule

Return type:

ProteinComponent

classmethod from_rdkit(rdkit: Mol, name: str = '')

Create a Component, copying from an RDKit Mol

property name: str

property smiles: str

to_json()

to_openmm_positions() → Quantity

serialize the positions to openmm.unit.Quantity ! only one frame at the moment!

Returns:

Quantity containing protein atom positions

Return type:

omm_unit.Quantity

to_openmm_topology() → Topology

Convert to an openmm Topology object

Returns:

resulting topology obj.

Return type:

openmm.app.Topology

to_pdb_file(out_path: str | bytes | PathLike[str] | PathLike[bytes] | TextIOBase) → str

serialize protein to pdb file.

Parameters:

out_path (Union[str, bytes, PathLike[str], PathLike[bytes], TextIOBase]) – provide path or any string based stream (e.g. FileIO ) to the resulting file

Returns:

string path to the resulting pdb.

Return type:

str

to_pdbx_file(out_path: str | bytes | PathLike[str] | PathLike[bytes] | TextIOBase) → str

serialize protein to pdbx file.

Parameters:

out_path (Union[str, bytes, PathLike[str], PathLike[bytes], TextIOBase]) – provide path or FileIO to the resulting file

Returns:

string path to the resulting pdbx.

Return type:

str

to_rdkit() → Mol

Return an RDKit copied representation of this molecule

property total_charge

Net formal charge for the Component, if defined.