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charmm_writer.py
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charmm_writer.py
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class Charmm:
def __init__(
self,
structure_box_0,
filename_box_0,
structure_box_1=None,
filename_box_1=None,
non_bonded_type="LJ",
forcefield_selection=None,
residues=None,
detect_forcefield_style=True,
gomc_fix_bonds_angles=None,
gomc_fix_bonds=None,
gomc_fix_angles=None,
bead_to_atom_name_dict=None,
fix_residue=None,
fix_residue_in_box=None,
set_residue_pdb_occupancy_to_1=None,
ff_filename=None,
reorder_res_in_pdb_psf=False,
):
# depreciation error that charmm_writer has been depreciated
depreciation_error = (
"The mosdef_gomc 'charmm_writer.py' has been depreciated, and the entire 'charmm_writer.py' "
"file will be removed/deleted soon."
"The this only effects the mosdef-gomc 'charmm_writer' parmed version. The GMSO version, "
"'gmso_charmm_writer.py', has replaced it with more features, so please use this GMSO version."
)
raise ModuleNotFoundError(depreciation_error)