mofbuilder.md.LinkerForceFieldGenerator#

class mofbuilder.md.LinkerForceFieldGenerator(comm=None, ostream=None)[source]#

Bases: object

Forcefield generation and mapping for linker molecules in MOFs.

Handles optimization (with QM/xtb), reintroduction of missing bonds, and mapping of existing forcefields onto new linker instances.

Parameters:

  • comm (Any)

  • ostream (veloxchem.outputstream.OutputStream | None)

comm#

MPI communicator (defaults to MPI.COMM_WORLD).

Type:

Any

rank#

MPI process rank.

Type:

int

nodes#

Number of MPI processes.

Type:

int

ostream#

Output stream for logging.

Type:

OutputStream

linker_optimization#

Whether to optimize linker geometry.

Type:

bool

optimize_drv#

Optimization method, ‘xtb’ or ‘qm’.

Type:

str

linker_ff_name#

Name for linker forcefield.

Type:

str

linker_residue_name#

Residue name for linker in topology.

Type:

str

resp_charges#

Whether to use RESP charges.

Type:

bool

linker_fake_edge#

If True, treats X-X as fake edges.

Type:

bool

linker_charge#

Net charge of linker molecule.

Type:

int

linker_multiplicity#

Multiplicity for linker molecule.

Type:

int

target_directory#

Directory where output files will be written.

Type:

Optional[str]

save_files#

Whether to save output structures.

Type:

bool

src_linker_forcefield_itpfile#

Path to reference linker .itp.

Type:

Optional[str]

src_linker_molecule#

Reference linker molecule object.

Type:

Optional[Molecule]

dest_linker_molecule#

Reconnected linker molecule (after-building).

Type:

Optional[Molecule]

dest_molecule_connectivity_matrix#

Connectivity matrix for MOF-linked linker.

Type:

Optional[np.ndarray]

linker_itp_path#

Path to generated linker .itp file.

Type:

Optional[Path]

free_opt_linker_mol#

Free optimized linker molecule (QM or xtb).

Type:

Optional[Molecule]

_debug#

Print debug output if True.

Type:

bool

_reconnect_linker_molecule()[source]#

Generates a VeloxChem Molecule from input coordinates, rebuilding X-X bonds.

generate_reconnected_molecule_forcefield()[source]#

Generates a GROMACS forcefield (.itp) for the reconnected linker.

Parameters:

linker_mol_data (ndarray | None)

Return type:

None

_reconnect()[source]#

Build missing X-X or x-x bonds between linker ends.

_xtb_optimize()[source]#

Optimize a molecule using the xtb backend.

_dft_optimize()[source]#

Optimize a molecule with DFT.

_find_isomorphism_and_mapping()[source]#

Find atom mapping between two isomorphic molecules.

map_existing_forcefield()[source]#

Maps existing forcefield (.itp) from source to a reconnected/new linker instance.

Parameters:

linker_mol_data (ndarray | None)

Return type:

None

generate_reconnected_molecule_forcefield(linker_mol_data=None)[source]#

Generates the forcefield and .itp file for a reconnected linker molecule.

Parameters:

linker_mol_data (Optional[np.ndarray]) – Data array for the linker. If None, does nothing.

Returns:

None

Return type:

None

map_existing_forcefield(linker_mol_data=None)[source]#

Maps an existing linker forcefield from reference (.itp) onto the built linker in a MOF.

Parameters:

linker_mol_data (Optional[np.ndarray]) – Coordinates array of the reconnected linker.

Returns:

None

Return type:

None