def load_opls(cls, atom_types, pfile_name=None, restrict=None):
'''
Given a parameter file, inport the LJ parameters if possible.
**Parameters**
atom_types: *list, dict, ...*
Atom types from a parsed opls parameter file.
pfile_name: *str*
The name of a parameter file to be parsed. If specified,
then pfile is ignored (you may simply pass None as pfile).
restrict: *list, str, optional*
A list of atom labels to include when loading. If not
specified, everything is loaded.
**Returns**
lj_objs: *list,* :class:`squid.forcefields.lj.LJ`, or *None*
Returns a list of LJ objects if possible, else None.
'''
# Ensure correct pfile format, and that we even need to parse it.
import squid.forcefields.opls as opls_utils
if pfile_name is not None:
atom_types, _, _, _ = opls_utils.parse_pfile(pfile_name)
return [
cls(index=t["index"], sigma=t["vdw_r"], epsilon=t["vdw_e"])
for t in atom_types if check_restriction(t, restrict)
]
def load_opls(cls, atom_types, pfptr=None, restrict=None):
"""
Given a parameter file, importthe Coulomb parameters if possible.
**Parameters**
atom_types: *list,* :class:`structures.Struct`
Atom types from a parsed opls parameter file.
pfptr: *str*
The name of a parameter file to be parsed. If specified,
then pfile is ignored (you may simply pass None as pfile).
**Returns**
coul_objs: *list, Coul*, or *None*
Returns a list of Coul objects if possible, else None.
"""
import squid.forcefields.opls as opls_utils
# Ensure correct pfile format, and that we even need to parse it.
if pfptr is not None:
atom_types, _, _, _ = opls_utils.parse_pfile(pfptr)
return [
cls(index=t.index,
charge=t.charge,
mass=t.mass,
element=(elem_i2s(t.element) if t.element != 0 else "X"))
for t in atom_types if check_restriction(t, restrict)
]
def load_opls(cls, atom_types, pfile_name=None, restrict=None):
'''
Given a parameter file, import the Coulomb parameters if possible.
**Parameters**
atom_types: *list, dict, ...*
Atom types from a parsed opls parameter file.
pfile_name: *str*
The name of a parameter file to be parsed. If specified,
then pfile is ignored (you may simply pass None as pfile).
restrict: *list, str, optional*
A list of atom labels to include when loading. If not
specified, everything is loaded.
**Returns**
coul_objs: *list,* :class:`squid.forcefields.coulomb.Coul`, or *None*
Returns a list of Coul objects if possible, else None.
'''
import squid.forcefields.opls as opls_utils
# Ensure correct pfile format, and that we even need to parse it.
if pfile_name is not None:
atom_types, _, _, _ = opls_utils.parse_pfile(pfile_name)
return [
cls(index=t["index"], charge=t["charge"], mass=t["mass"],
element=(elem_i2s(t["element"]) if t["element"] != 0 else "X"))
for t in atom_types if check_restriction(t, restrict)
]
def load_opls(cls, dihedral_types, pfile_name=None, restrict=None):
'''
Given a parameter file, inport the Dihedral parameters if possible.
**Parameters**
dihedral_types: *list, dict*
Dihedral types from a parsed opls parameter file.
pfile_name: *str*
The name of a parameter file to be parsed. If specified,
then pfile is ignored (you may simply pass None as pfile).
restrict: *list, str, optional*
A list of atom labels to include when loading. If not
specified, everything is loaded.
**Returns**
dihedral_objs: *list, Dihedral*, or *None*
Returns a list of Dihedral objects if possible, else None.
'''
import squid.forcefields.opls as opls_utils
if pfile_name is not None:
_, _, _, dihedral_types = opls_utils.parse_pfile(pfile_name)
return [
cls(indices=t["index2s"], energies=t["e"], equilibs=[])
for t in dihedral_types if check_restriction(
t["index2s"], restrict)
]
def load_opls(cls, dihedral_types, pfptr=None, restrict=None):
"""
Given a parameter file, inport the Dihedral parameters if possible.
**Parameters**
dihedral_types: *list,* :class:`structures.Struct`
Dihedral types from a parsed opls parameter file.
pfptr: *str*
The name of a parameter file to be parsed. If specified,
then pfile is ignored (you may simply pass None as pfile).
**Returns**
dihedral_objs: *list, Dihedral*, or *None*
Returns a list of Dihedral objects if possible, else None.
"""
import squid.forcefields.opls as opls_utils
if pfptr is not None:
_, _, _, dihedral_types = opls_utils.parse_pfile(pfptr)
return [
cls(indices=t.index2s, energies=t.e, equilibs=[])
for t in dihedral_types if check_restriction(t.index2s, restrict)
]
def load_opls(cls, atom_types, pfptr=None, restrict=None):
'''
Given a parameter file, inport the LJ parameters if possible.
**Parameters**
atom_types: *list,* :class:`structures.Struct`
Atom types from a parsed opls parameter file.
pfptr: *str*
The name of a parameter file to be parsed. If specified,
then pfile is ignored (you may simply pass None as pfile).
**Returns**
lj_objs: *list, LJ*, or *None*
Returns a list of LJ objects if possible, else None.
'''
# Ensure correct pfile format, and that we even need to parse it.
import squid.forcefields.opls as opls_utils
if pfptr is not None:
atom_types, _, _, _ = opls_utils.parse_pfile(pfptr)
return [
cls(index=t.index, sigma=t.vdw_r, epsilon=t.vdw_e)
for t in atom_types if check_restriction(t, restrict)
]