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

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. Technically, this is done 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.

Parameters:

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

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

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.

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

to_openmm_topology() → Topology

Convert to an openmm Topology object

Returns:

resulting topology obj.

Return type:

openmm.app.Topology

to_openmm_positions() → Quantity

serialize the positions to openmm.unit.Quantity

Note

Currently only one frame/model is given

Returns:

Quantity containing protein atom positions

Return type:

omm_unit.Quantity

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], io.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], io.TextIOBase]) – provide path or FileIO to the resulting file

Returns:

string path to the resulting pdbx.

Return type:

str

classmethod from_json(json_str)

Generate an instance from JSON keyed chain representation.

Can provide either a filepath/filelike as file, or JSON content via content.

Parameters:

• file – A filepath or filelike object to read JSON data from.

• content – A string to read JSON data from.

See also

to_json

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

Create a Component, copying from an RDKit Mol

property name: str

property smiles: str

to_json()

Generate a JSON keyed chain representation.

This will be writen to the filepath or filelike object if passed.

Parameters:

file – A filepath or filelike object to write the JSON to.

Returns:

A minimal JSON representation of the object if file is None; else None.

Return type:

str

See also

from_json

to_rdkit() → Mol

Return an RDKit copied representation of this molecule

property total_charge

Net formal charge for the Component, if defined.