cgexplore.forcefields.MartiniForceField¶

class cgexplore.forcefields.MartiniForceField(identifier, prefix, present_beads, bond_targets, angle_targets, torsion_targets, constraints, vdw_bond_cutoff)[source]¶

Bases: ForceField

Class defining a Martini Forcefield.

Methods

assign_terms

Assign forcefield terms to molecule.

Parameters:

identifier (str)
prefix (str)
present_beads (Sequence[CgBead])
bond_targets (Sequence[TargetBond | TargetMartiniBond])
angle_targets (Sequence[TargetAngle | TargetMartiniAngle])
torsion_targets (Sequence[TargetTorsion | TargetMartiniTorsion])
constraints (Sequence[tuple[int, int]])
vdw_bond_cutoff (int)

assign_terms(molecule, name, output_dir)[source]¶

Assign forcefield terms to molecule.

Parameters:

molecule (Molecule)
name (str)
output_dir (Path)

Return type:

MartiniSystem

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