stk.PdbWriter

class stk.PdbWriter[source]

Bases: object

A writer class for .pdb files.

Examples

Writing to a File with a Unit Cell

This writer can write to a file with the unit cell included for periodic molecules. Note that this always assumes P1 space group.

import stk

bb1 = stk.BuildingBlock('BrCCBr', [stk.BromoFactory()])
bb2 = stk.BuildingBlock(
    smiles='BrCC(CBr)CBr',
    functional_groups=[stk.BromoFactory()],
)
topology_graph = stk.cof.PeriodicHoneycomb(
    building_blocks=(bb1, bb2),
    lattice_size=(3, 3, 1),
)
construction_result = topology_graph.construct()
cof = (
    stk.ConstructedMolecule.init_from_construction_result(
        construction_result=construction_result,
    )
)
writer = stk.PdbWriter()
writer.write(
    molecule=cof,
    path='cof.pdb',
    periodic_info=construction_result.get_periodic_info(),
)

Methods

`to_string`	Get a `.pdb` file format string of molecule.
`write`	Write molecule to `.pdb` file format.

to_string(molecule, atom_ids=None, periodic_info=None)[source]

Get a .pdb file format string of molecule.

Parameters:

molecule (Molecule) – Molecule to write to .pdb format.
atom_ids (int | Iterable[int] | None) – The atom ids of atoms to write. Can be a single int, if a single atom is to be used, or None, if all atoms are to be used.
periodic_info (PeriodicInfo | None) – Information about the periodic cell.

Returns:

A string holding the content of a .pdf file.

Return type:

str

write(molecule, path, atom_ids=None, periodic_info=None)[source]

Write molecule to .pdb file format.

Parameters:

molecule (Molecule) – Molecule to write to .pdb format.
path (Path | str) – The full path to the file being written.
atom_ids (int | Iterable[int] | None) – The atom ids of atoms to write. Can be a single int, if a single atom is to be used, or None, if all atoms are to be used.
periodic_info (PeriodicInfo | None) – Information about the periodic cell.

Return type:

None