cgexplore.forcefields.ForceField

class cgexplore.forcefields.ForceField(identifier, prefix, present_beads, bond_targets, angle_targets, torsion_targets, nonbonded_targets, vdw_bond_cutoff, verbose=True)

Bases: object

Define a CG ForceField.

Parameters:

• identifier (str) – String idenifier of the forcefield.

• prefix (str) – Prefix for the forcefield for file saving.

• present_beads (Sequence[CgBead]) – The CgBeads that are present in the model.

• bond_targets (Sequence[TargetBond | TargetMartiniBond]) – Target bond classes to find and assign. See systems_optimisation.utilities for an example.

• angle_targets (Sequence[TargetAngle | TargetCosineAngle | TargetMartiniAngle]) – Target angle classes to find and assign. See systems_optimisation.utilities for an example.

• torsion_targets (Sequence[TargetTorsion | TargetMartiniTorsion]) – Target torsion classes to find and assign. See systems_optimisation.utilities for an example.

• nonbonded_targets (Sequence[TargetNonbonded]) – Target nonbonded term classes to find and assign. See systems_optimisation.utilities for an example.

• vdw_bond_cutoff (int) – How many bonds between excluded beads from nonbonded terms.

• verbose (bool) – True if cgexplore should inform the user about what it assigns.

Methods

assign_terms	Assign forcefield terms to molecule.
get_all_possible_terms	Check if there are missing terms in forcefield.
get_bead_library	Get beads in forcefield.
get_forcefield_dictionary	Get the underlying forcefield dict.
get_hr_file_name	Get human-readable file name.
get_identifier	Get forcefield identifier.
get_prefix	Get forcefield prefix.
get_present_beads	Get beads present.
get_targets	Get targets of forcefield.
get_vdw_bond_cutoff	Get vdW bond cutoff of forcefield.
write_human_readable	Write forcefield definition to human-readable file.

assign_terms(molecule, name, output_dir)

Assign forcefield terms to molecule.

Parameters:

• molecule (Molecule)

• name (str)

• output_dir (Path)

Return type:

AssignedSystem

get_all_possible_terms(molecule)

Check if there are missing terms in forcefield.

Parameters:

molecule (Molecule)

Return type:

None

get_bead_library()

Get beads in forcefield.

Return type:

BeadLibrary

get_forcefield_dictionary()

Get the underlying forcefield dict.

Return type:

dict[str, str | dict]

get_hr_file_name()

Get human-readable file name.

Return type:

str

get_identifier()

Get forcefield identifier.

Return type:

str

get_prefix()

Get forcefield prefix.

Return type:

str

get_present_beads()

Get beads present.

Return type:

Sequence[CgBead]

get_targets()

Get targets of forcefield.

Return type:

dict

get_vdw_bond_cutoff()

Get vdW bond cutoff of forcefield.

Return type:

int

write_human_readable(output_dir)

Write forcefield definition to human-readable file.

Parameters:

output_dir (Path)

Return type:

None