def _dihedral_types_from_pmd(structure, dihedral_types_member_map=None):
"""Convert ParmEd dihedral types to GMSO DihedralType.
This function take in a Parmed Structure, iterate through its
dihedral_types and rb_torsion_types, create a corresponding
GMSO.DihedralType, and finally return a dictionary containing all
pairs of pmd.Dihedraltype (or pmd.RBTorsionType) and GMSO.DihedralType
Parameters
----------
structure: pmd.Structure
Parmed Structure that needed to be converted.
dihedral_types_member_map: optional, dict, default=None
The member types (atomtype string) for each atom associated with the dihedral_types the structure
Returns
-------
pmd_top_dihedraltypes : dict
A dictionary linking a pmd.DihedralType or pmd.RBTorsionType
object to its corresponding GMSO.DihedralType object.
"""
pmd_top_dihedraltypes = dict()
dihedral_types_member_map = _assert_dict(
dihedral_types_member_map, "dihedral_types_member_map"
)
for dihedraltype in structure.dihedral_types:
dihedral_params = {
"k": (dihedraltype.phi_k * u.Unit("kcal / mol")),
"phi_eq": (dihedraltype.phase * u.degree),
"n": dihedraltype.per * u.dimensionless,
}
member_types = dihedral_types_member_map.get(id(dihedraltype))
top_dihedraltype = gmso.DihedralType(
parameters=dihedral_params, member_types=member_types
)
pmd_top_dihedraltypes[dihedraltype] = top_dihedraltype
for dihedraltype in structure.rb_torsion_types:
dihedral_params = {
"c0": (dihedraltype.c0 * u.Unit("kcal/mol")),
"c1": (dihedraltype.c1 * u.Unit("kcal/mol")),
"c2": (dihedraltype.c2 * u.Unit("kcal/mol")),
"c3": (dihedraltype.c3 * u.Unit("kcal/mol")),
"c4": (dihedraltype.c4 * u.Unit("kcal/mol")),
"c5": (dihedraltype.c5 * u.Unit("kcal/mol")),
}
member_types = dihedral_types_member_map.get(id(dihedraltype))
top_dihedraltype = gmso.DihedralType(
parameters=dihedral_params,
expression="c0 * cos(phi)**0 + c1 * cos(phi)**1 + "
+ "c2 * cos(phi)**2 + c3 * cos(phi)**3 + c4 * cos(phi)**4 + "
+ "c5 * cos(phi)**5",
independent_variables="phi",
member_types=member_types,
)
pmd_top_dihedraltypes[dihedraltype] = top_dihedraltype
return pmd_top_dihedraltypes
def _dihedral_types_from_pmd(structure, dihedral_types_member_map=None):
""" Helper function to convert GMSO DihedralType
This function take in a Parmed Structure, iterate through its
dihedral_types and rb_torsion_types, create a corresponding
GMSO.DihedralType, and finally return a dictionary containing all
pairs of pmd.Dihedraltype (or pmd.RBTorsionType) and GMSO.DihedralType
Parameters
----------
structure: pmd.Structure
Parmed Structure that needed to be converted.
dihedral_types_member_map: optional, dict, default=None
The member types (atomtype string) for each atom associated with the dihedral_types the structure
Returns
-------
pmd_top_dihedraltypes : dict
A dictionary linking a pmd.DihedralType or pmd.RBTorsionType
object to its corresponding GMSO.DihedralType object.
"""
pmd_top_dihedraltypes = dict()
dihedral_types_member_map = _assert_dict(dihedral_types_member_map,
'dihedral_types_member_map')
for dihedraltype in structure.dihedral_types:
dihedral_params = {
'k': (dihedraltype.phi_k * u.Unit('kcal / mol')),
'phi_eq': (dihedraltype.phase * u.degree),
'n': dihedraltype.per * u.dimensionless
}
member_types = dihedral_types_member_map.get(id(dihedraltype))
top_dihedraltype = gmso.DihedralType(parameters=dihedral_params,
member_types=member_types)
pmd_top_dihedraltypes[dihedraltype] = top_dihedraltype
for dihedraltype in structure.rb_torsion_types:
dihedral_params = {
'c0': (dihedraltype.c0 * u.Unit('kcal/mol')),
'c1': (dihedraltype.c1 * u.Unit('kcal/mol')),
'c2': (dihedraltype.c2 * u.Unit('kcal/mol')),
'c3': (dihedraltype.c3 * u.Unit('kcal/mol')),
'c4': (dihedraltype.c4 * u.Unit('kcal/mol')),
'c5': (dihedraltype.c5 * u.Unit('kcal/mol')),
}
member_types = dihedral_types_member_map.get(id(dihedraltype))
top_dihedraltype = gmso.DihedralType(
parameters=dihedral_params,
expression='c0 * cos(phi)**0 + c1 * cos(phi)**1 + ' +
'c2 * cos(phi)**2 + c3 * cos(phi)**3 + c4 * cos(phi)**4 + ' +
'c5 * cos(phi)**5',
independent_variables='phi',
member_types=member_types)
pmd_top_dihedraltypes[dihedraltype] = top_dihedraltype
return pmd_top_dihedraltypes
def _dihedral_types_from_pmd(structure):
""" Helper function to convert GMSO DihedralType
This function take in a Parmed Structure, iterate through its
dihedral_types and rb_torsion_types, create a corresponding
GMSO.DihedralType, and finally return a dictionary containing all
pairs of pmd.Dihedraltype (or pmd.RBTorsionType) and GMSO.DihedralType
Parameter
----------
structure: pmd.Structure
Parmed Structure that needed to be converted.
Return
------
pmd_top_dihedraltypes : dict
A dictionary linking a pmd.DihedralType or pmd.RBTorsionType
object to its corresponding GMSO.DihedralType object.
"""
pmd_top_dihedraltypes = dict()
for dihedraltype in structure.dihedral_types:
dihedral_params = {
'k': (dihedraltype.phi_k * u.Unit('kcal / mol')),
'phi_eq': (dihedraltype.phase * u.degree),
'n': dihedraltype.per * u.dimensionless
}
top_dihedraltype = gmso.DihedralType(parameters=dihedral_params)
pmd_top_dihedraltypes[dihedraltype] = top_dihedraltype
for dihedraltype in structure.rb_torsion_types:
dihedral_params = {
'c0': (dihedraltype.c0 * u.Unit('kcal/mol')),
'c1': (dihedraltype.c1 * u.Unit('kcal/mol')),
'c2': (dihedraltype.c2 * u.Unit('kcal/mol')),
'c3': (dihedraltype.c3 * u.Unit('kcal/mol')),
'c4': (dihedraltype.c4 * u.Unit('kcal/mol')),
'c5': (dihedraltype.c5 * u.Unit('kcal/mol')),
}
top_dihedraltype = gmso.DihedralType(
parameters=dihedral_params,
expression='c0 * cos(phi)**0 + c1 * cos(phi)**1 + ' +
'c2 * cos(phi)**2 + c3 * cos(phi)**3 + c4 * cos(phi)**4 + ' +
'c5 * cos(phi)**5',
independent_variables='phi')
pmd_top_dihedraltypes[dihedraltype] = top_dihedraltype
return pmd_top_dihedraltypes
def convert_ryckaert_to_opls(ryckaert_connection_type):
"""Convert Ryckaert-Bellemans dihedral to OPLS.
NOTE: the conventions defining the dihedral angle are different
for OPLS and RB torsions. OPLS torsions are defined with
phi_cis = 0 while RB torsions are defined as phi_trans = 0.
"""
templates = PotentialTemplateLibrary()
ryckaert_bellemans_torsion_potential = templates[
"RyckaertBellemansTorsionPotential"]
opls_torsion_potential = templates["OPLSTorsionPotential"]
valid_connection_type = False
if (ryckaert_connection_type.independent_variables ==
ryckaert_bellemans_torsion_potential.independent_variables):
if (sympy.simplify(ryckaert_connection_type.expression -
ryckaert_bellemans_torsion_potential.expression) ==
0):
valid_connection_type = True
if not valid_connection_type:
raise GMSOError("Cannot use convert_ryckaert_to_opls "
"function to convert a ConnectionType that is not an "
"RyckaertBellemansTorsionPotential")
c0 = ryckaert_connection_type.parameters["c0"]
c1 = ryckaert_connection_type.parameters["c1"]
c2 = ryckaert_connection_type.parameters["c2"]
c3 = ryckaert_connection_type.parameters["c3"]
c4 = ryckaert_connection_type.parameters["c4"]
c5 = ryckaert_connection_type.parameters["c5"]
if c5 != 0.0:
raise GMSOError("Cannot convert Ryckaert-Bellemans dihedral "
"to OPLS dihedral if c5 is not equal to zero.")
converted_params = {
"k0": 2.0 * (c0 + c1 + c2 + c3 + c4),
"k1": (-2.0 * c1 - (3.0 / 2.0) * c3),
"k2": (-c2 - c4),
"k3": ((-1.0 / 2.0) * c3),
"k4": ((-1.0 / 4.0) * c4),
}
name = opls_torsion_potential.name
expression = opls_torsion_potential.expression
variables = opls_torsion_potential.independent_variables
opls_connection_type = gmso.DihedralType(
name=name,
expression=expression,
independent_variables=variables,
parameters=converted_params,
)
return opls_connection_type
def convert_ryckaert_to_opls(ryckaert_connection_type):
"""Convert Ryckaert-Bellemans dihedral to OPLS
NOTE: the conventions defining the dihedral angle are different
for OPLS and RB torsions. OPLS torsions are defined with
phi_cis = 0 while RB torsions are defined as phi_trans = 0.
"""
templates = PotentialTemplateLibrary()
ryckaert_bellemans_torsion_potential = templates[
'RyckaertBellemansTorsionPotential']
opls_torsion_potential = templates['OPLSTorsionPotential']
valid_connection_type = False
if (ryckaert_connection_type.independent_variables ==
ryckaert_bellemans_torsion_potential.independent_variables):
if sympy.simplify(
ryckaert_connection_type.expression -
ryckaert_bellemans_torsion_potential.expression) == 0:
valid_connection_type = True
if not valid_connection_type:
raise GMSOError('Cannot use convert_ryckaert_to_opls '
'function to convert a ConnectionType that is not an '
'RyckaertBellemansTorsionPotential')
c0 = ryckaert_connection_type.parameters['c0']
c1 = ryckaert_connection_type.parameters['c1']
c2 = ryckaert_connection_type.parameters['c2']
c3 = ryckaert_connection_type.parameters['c3']
c4 = ryckaert_connection_type.parameters['c4']
c5 = ryckaert_connection_type.parameters['c5']
if c5 != 0.0:
raise GMSOError('Cannot convert Ryckaert-Bellemans dihedral '
'to OPLS dihedral if c5 is not equal to zero.')
converted_params = {
'k0': 2. * (c0 + c1 + c2 + c3 + c4),
'k1': (-2. * c1 - (3. / 2.) * c3),
'k2': (-c2 - c4),
'k3': ((-1. / 2.) * c3),
'k4': ((-1. / 4.) * c4)
}
name = opls_torsion_potential.name
expression = opls_torsion_potential.expression
variables = opls_torsion_potential.independent_variables
opls_connection_type = gmso.DihedralType(name=name,
expression=expression,
independent_variables=variables,
parameters=converted_params)
return opls_connection_type
def convert_opls_to_ryckaert(opls_connection_type):
"""Convert an OPLS dihedral to Ryckaert-Bellemans dihedral.
Equations taken/modified from:
http://manual.gromacs.org/documentation/2019/
reference-manual/functions/bonded-interactions.html
NOTE: the conventions defining the dihedral angle are different
for OPLS and RB torsions. OPLS torsions are defined with
phi_cis = 0 while RB torsions are defined as phi_trans = 0.
"""
templates = PotentialTemplateLibrary()
opls_torsion_potential = templates["OPLSTorsionPotential"]
valid_connection_type = False
if (opls_connection_type.independent_variables ==
opls_torsion_potential.independent_variables):
if (sympy.simplify(opls_connection_type.expression -
opls_torsion_potential.expression) == 0):
valid_connection_type = True
if not valid_connection_type:
raise GMSOError("Cannot use convert_opls_to_ryckaert "
"function to convert a ConnectionType that is not an "
"OPLSTorsionPotential")
f0 = opls_connection_type.parameters["k0"]
f1 = opls_connection_type.parameters["k1"]
f2 = opls_connection_type.parameters["k2"]
f3 = opls_connection_type.parameters["k3"]
f4 = opls_connection_type.parameters["k4"]
converted_params = {
"c0": (f2 + 0.5 * (f0 + f1 + f3)),
"c1": (0.5 * (-f1 + 3.0 * f3)),
"c2": (-f2 + 4.0 * f4),
"c3": (-2.0 * f3),
"c4": (-4.0 * f4),
"c5": 0.0 * u.Unit("kJ/mol"),
}
ryckaert_bellemans_torsion_potential = templates[
"RyckaertBellemansTorsionPotential"]
name = ryckaert_bellemans_torsion_potential.name
expression = ryckaert_bellemans_torsion_potential.expression
variables = ryckaert_bellemans_torsion_potential.independent_variables
ryckaert_connection_type = gmso.DihedralType(
name=name,
expression=expression,
independent_variables=variables,
parameters=converted_params,
)
return ryckaert_connection_type
def convert_opls_to_ryckaert(opls_connection_type):
"""Convert an OPLS dihedral to Ryckaert-Bellemans dihedral
Equations taken/modified from:
http://manual.gromacs.org/documentation/2019/
reference-manual/functions/bonded-interactions.html
NOTE: the conventions defining the dihedral angle are different
for OPLS and RB torsions. OPLS torsions are defined with
phi_cis = 0 while RB torsions are defined as phi_trans = 0.
"""
templates = PotentialTemplateLibrary()
opls_torsion_potential = templates['OPLSTorsionPotential']
valid_connection_type = False
if (opls_connection_type.independent_variables ==
opls_torsion_potential.independent_variables):
if sympy.simplify(opls_connection_type.expression -
opls_torsion_potential.expression) == 0:
valid_connection_type = True
if not valid_connection_type:
raise GMSOError('Cannot use convert_opls_to_ryckaert '
'function to convert a ConnectionType that is not an '
'OPLSTorsionPotential')
f0 = opls_connection_type.parameters['k0']
f1 = opls_connection_type.parameters['k1']
f2 = opls_connection_type.parameters['k2']
f3 = opls_connection_type.parameters['k3']
f4 = opls_connection_type.parameters['k4']
converted_params = {
'c0': (f2 + 0.5 * (f0 + f1 + f3)),
'c1': (0.5 * (-f1 + 3. * f3)),
'c2': (-f2 + 4. * f4),
'c3': (-2. * f3),
'c4': (-4. * f4),
'c5': 0. * u.Unit('kJ/mol')
}
ryckaert_bellemans_torsion_potential = templates[
'RyckaertBellemansTorsionPotential']
name = ryckaert_bellemans_torsion_potential.name
expression = ryckaert_bellemans_torsion_potential.expression
variables = ryckaert_bellemans_torsion_potential.independent_variables
ryckaert_connection_type = gmso.DihedralType(
name=name,
expression=expression,
independent_variables=variables,
parameters=converted_params)
return ryckaert_connection_type