def test_double_conversion(self):
# Pick some OPLS parameters at random
params = { 'k0' : 1.38 * u.Unit('kJ/mol'),
'k1' : -0.51 * u.Unit('kJ/mol'),
'k2' : 2.2 * u.Unit('kJ/mol'),
'k3' : -0.25 * u.Unit('kJ/mol'),
'k4' : 1.44 * u.Unit('kJ/mol')
}
name = OPLSTorsionPotential().name
expression = OPLSTorsionPotential().expression
variables = OPLSTorsionPotential().independent_variables
opls_connection_type = DihedralType(
name=name,
expression=expression,
independent_variables=variables,
parameters=params)
# Convert connection to RB
ryckaert_connection_type = convert_opls_to_ryckaert(
opls_connection_type)
# Convert connection back to OPLS
final_connection_type = convert_ryckaert_to_opls(
ryckaert_connection_type)
assert np.allclose([*opls_connection_type.parameters.values()],
[*final_connection_type.parameters.values()])
def test_double_conversion(self, templates):
# Pick some OPLS parameters at random
params = {
'k0': 1.38 * u.Unit('kJ/mol'),
'k1': -0.51 * u.Unit('kJ/mol'),
'k2': 2.2 * u.Unit('kJ/mol'),
'k3': -0.25 * u.Unit('kJ/mol'),
'k4': 1.44 * u.Unit('kJ/mol')
}
opls_torsion_potential = templates['OPLSTorsionPotential']
name = opls_torsion_potential.name
expression = opls_torsion_potential.expression
variables = opls_torsion_potential.independent_variables
opls_connection_type = DihedralType(name=name,
expression=expression,
independent_variables=variables,
parameters=params)
# Convert connection to RB
ryckaert_connection_type = convert_opls_to_ryckaert(
opls_connection_type)
# Convert connection back to OPLS
final_connection_type = convert_ryckaert_to_opls(
ryckaert_connection_type)
assert_allclose_units([*opls_connection_type.parameters.values()],
[*final_connection_type.parameters.values()],
rtol=1e-5,
atol=1e-8)
def test_ryckaert_to_opls(self, templates):
# Pick some RB parameters at random
params = {
"c0": 1.53 * u.Unit("kJ/mol"),
"c1": 0.76 * u.Unit("kJ/mol"),
"c2": -0.22 * u.Unit("kJ/mol"),
"c3": 3.55 * u.Unit("kJ/mol"),
"c4": 0.94 * u.Unit("kJ/mol"),
"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 = DihedralType(
name=name,
expression=expression,
independent_variables=variables,
parameters=params,
)
# Convert connection to OPLS
opls_connection_type = convert_ryckaert_to_opls(
ryckaert_connection_type)
# Pick some angles to check
angles = [-2.38, -1.31, -0.44, 0.0, 0.26, 0.92, 1.84, 3.10]
for angle in angles:
assert np.isclose(
float(
ryckaert_connection_type.expression.subs([
(param, val) for param, val in {
**ryckaert_connection_type.parameters,
"phi":
angle - np.pi,
}.items()
])),
float(
opls_connection_type.expression.subs([
(param, val) for param, val in {
**opls_connection_type.parameters,
"phi": angle,
}.items()
])),
)
def test_ryckaert_to_opls(self, templates):
# Pick some RB parameters at random
params = {
'c0': 1.53 * u.Unit('kJ/mol'),
'c1': 0.76 * u.Unit('kJ/mol'),
'c2': -0.22 * u.Unit('kJ/mol'),
'c3': 3.55 * u.Unit('kJ/mol'),
'c4': 0.94 * u.Unit('kJ/mol'),
'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 = DihedralType(
name=name,
expression=expression,
independent_variables=variables,
parameters=params)
# Convert connection to OPLS
opls_connection_type = convert_ryckaert_to_opls(
ryckaert_connection_type)
# Pick some angles to check
angles = [-2.38, -1.31, -0.44, 0.0, 0.26, 0.92, 1.84, 3.10]
for angle in angles:
assert np.isclose(
float(
ryckaert_connection_type.expression.subs([
(param, val) for param, val in {
**ryckaert_connection_type.parameters, 'phi':
angle - np.pi
}.items()
])),
float(
opls_connection_type.expression.subs([
(param, val) for param, val in {
**opls_connection_type.parameters, 'phi': angle
}.items()
])),
)
def test_invalid_connection_type(self, templates):
params = {
'c0': 1.53 * u.Unit('kJ/mol'),
'c1': 0.76 * u.Unit('kJ/mol'),
'c2': -0.22 * u.Unit('kJ/mol'),
'c3': 3.55 * u.Unit('kJ/mol'),
'c4': 0.94 * u.Unit('kJ/mol'),
'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 = ['phi', 'psi']
ryckaert_connection_type = DihedralType(
name=name,
expression=expression,
independent_variables=variables,
parameters=params)
with pytest.raises(GMSOError, match='Cannot use'):
opls_connection_type = convert_ryckaert_to_opls(
ryckaert_connection_type)
expression = 'c0+c1+c2+c3+c4+c5+phi'
variables = ryckaert_bellemans_torsion_potential.independent_variables
ryckaert_connection_type = DihedralType(
name=name,
expression=expression,
independent_variables=variables,
parameters=params)
with pytest.raises(GMSOError, match='Cannot use'):
opls_connection_type = convert_ryckaert_to_opls(
ryckaert_connection_type)
# Pick some OPLS parameters at random
params = {
'k0': 1.38 * u.Unit('kJ/mol'),
'k1': -0.51 * u.Unit('kJ/mol'),
'k2': 2.2 * u.Unit('kJ/mol'),
'k3': -0.25 * u.Unit('kJ/mol'),
'k4': 1.44 * u.Unit('kJ/mol')
}
opls_torsion_potential = templates['OPLSTorsionPotential']
name = opls_torsion_potential.name
expression = opls_torsion_potential.expression
variables = ['phi', 'psi']
opls_connection_type = DihedralType(name=name,
expression=expression,
independent_variables=variables,
parameters=params)
with pytest.raises(GMSOError, match=''):
ryckaert_connection_type = convert_opls_to_ryckaert(
opls_connection_type)
variables = opls_torsion_potential.independent_variables
expression = 'k0+k1+k2+k3+k4+phi'
opls_connection_type = DihedralType(name=name,
expression=expression,
independent_variables=variables,
parameters=params)
with pytest.raises(GMSOError, match=''):
ryckaert_connection_type = convert_opls_to_ryckaert(
opls_connection_type)
def test_invalid_connection_type(self, templates):
params = {
"c0": 1.53 * u.Unit("kJ/mol"),
"c1": 0.76 * u.Unit("kJ/mol"),
"c2": -0.22 * u.Unit("kJ/mol"),
"c3": 3.55 * u.Unit("kJ/mol"),
"c4": 0.94 * u.Unit("kJ/mol"),
"c5": 0.0 * u.Unit("kJ/mol"),
}
ryckaert_bellemans_torsion_potential = templates[
"RyckaertBellemansTorsionPotential"]
name = ryckaert_bellemans_torsion_potential.name
expression = (str(ryckaert_bellemans_torsion_potential.expression) +
" + 3 * psi")
variables = ["phi", "psi"]
ryckaert_connection_type = DihedralType(
name=name,
expression=expression,
independent_variables=variables,
parameters=params,
)
with pytest.raises(GMSOError, match="Cannot use"):
opls_connection_type = convert_ryckaert_to_opls(
ryckaert_connection_type)
expression = "c0+c1+c2+c3+c4+c5+phi"
variables = ryckaert_bellemans_torsion_potential.independent_variables
ryckaert_connection_type = DihedralType(
name=name,
expression=expression,
independent_variables=variables,
parameters=params,
)
with pytest.raises(GMSOError, match="Cannot use"):
opls_connection_type = convert_ryckaert_to_opls(
ryckaert_connection_type)
# Pick some OPLS parameters at random
params = {
"k0": 1.38 * u.Unit("kJ/mol"),
"k1": -0.51 * u.Unit("kJ/mol"),
"k2": 2.2 * u.Unit("kJ/mol"),
"k3": -0.25 * u.Unit("kJ/mol"),
"k4": 1.44 * u.Unit("kJ/mol"),
}
opls_torsion_potential = templates["OPLSTorsionPotential"]
name = opls_torsion_potential.name
expression = (str(opls_torsion_potential.expression) +
" + 0.5 * k1 * (1 + cos(psi))")
variables = ["phi", "psi"]
opls_connection_type = DihedralType(
name=name,
expression=expression,
independent_variables=variables,
parameters=params,
)
with pytest.raises(GMSOError, match=""):
ryckaert_connection_type = convert_opls_to_ryckaert(
opls_connection_type)
variables = opls_torsion_potential.independent_variables
expression = "k0+k1+k2+k3+k4+phi"
opls_connection_type = DihedralType(
name=name,
expression=expression,
independent_variables=variables,
parameters=params,
)
with pytest.raises(GMSOError, match=""):
ryckaert_connection_type = convert_opls_to_ryckaert(
opls_connection_type)
def _write_dihedral_information(mcf, top):
"""Write the dihedrals in the system.
Parameters
----------
mcf : file object
The file object of the Cassandra mcf being written
top : Topology
Topology object
dihedral_style : string
Dihedral style for Cassandra to use
"""
# Dihedral info
header = ("\n!Dihedral Format\n"
"!index i j k l type parameters\n"
'!type="none"\n'
'!type="CHARMM", parms=a0 a1 delta\n'
'!type="OPLS", parms=c0 c1 c2 c3\n'
'!type="harmonic", parms=force_constant equilibrium_dihedral\n'
"\n# Dihedral_Info\n")
mcf.write(header)
# TODO: Are impropers buried in dihedrals?
mcf.write("{:d}\n".format(len(top.dihedrals)))
for (idx, dihedral) in enumerate(top.dihedrals):
mcf.write("{:<4d} "
"{:<4d} "
"{:<4d} "
"{:<4d} "
"{:<4d} ".format(
idx + 1,
dihedral.connection_members[0].idx + 1,
dihedral.connection_members[1].idx + 1,
dihedral.connection_members[2].idx + 1,
dihedral.connection_members[3].idx + 1,
))
dihedral_style = _get_dihedral_style(dihedral)
# If ryckaert, convert to opls
if dihedral_style == "ryckaert":
dihedral.connection_type = convert_ryckaert_to_opls(
dihedral.connection_type)
dihedral_style = "opls"
if dihedral_style == "opls":
mcf.write(
"{:s} "
"{:10.5f} "
"{:10.5f} "
"{:10.5f} "
"{:10.5f}\n".format(
dihedral_style,
0.5 * dihedral.connection_type.parameters["k0"].in_units(
"kJ/mol").value,
0.5 * dihedral.connection_type.parameters["k1"].in_units(
"kJ/mol").value,
0.5 * dihedral.connection_type.parameters["k2"].in_units(
"kJ/mol").value,
0.5 * dihedral.connection_type.parameters["k3"].in_units(
"kJ/mol").value,
))
elif dihedral_style == "charmm":
mcf.write(
"{:s} "
"{:10.5f} "
"{:10.5f} "
"{:10.5f}\n".format(
dihedral_style,
dihedral.connection_type.parameters["k"].in_units(
"kJ/mol").value,
dihedral.connection_type.parameters["n"],
dihedral.connection_type.parameters["phi_eq"].in_units(
u.degrees).value,
))
elif dihedral_style == "harmonic":
mcf.write(
"{:s} "
"{:10.5f} "
"{:10.5f}\n".format(
dihedral_style,
0.5 * dihedral.connection_type.parameters["k"].in_units(
"kJ/mol").value,
dihedral.connection_type.parameters["phi_eq"].in_units(
u.degrees).value,
))
else:
raise GMSOError(
"Unsupported dihedral style for Cassandra MCF writer")
def write_lammpsdata(topology, filename, atom_style="full"):
"""Output a LAMMPS data file.
Outputs a LAMMPS data file in the 'full' atom style format.
Assumes use of 'real' units.
See http://lammps.sandia.gov/doc/atom_style.html for more information on atom styles.
Parameters
----------
Topology : `Topology`
A Topology Object
filename : str
Path of the output file
atom_style : str, optional, default='full'
Defines the style of atoms to be saved in a LAMMPS data file.
The following atom styles are currently supported: 'full', 'atomic', 'charge', 'molecular'
see http://lammps.sandia.gov/doc/atom_style.html for more information on atom styles.
Notes
-----
See http://lammps.sandia.gov/doc/2001/data_format.html for a full description of the LAMMPS data format.
This is a work in progress, as only atoms, masses, and atom_type information can be written out.
Some of this function has been adopted from `mdtraj`'s support of the LAMMPSTRJ trajectory format.
See https://github.com/mdtraj/mdtraj/blob/master/mdtraj/formats/lammpstrj.py for details.
"""
if atom_style not in ["atomic", "charge", "molecular", "full"]:
raise ValueError(
'Atom style "{}" is invalid or is not currently supported'.format(
atom_style))
# TODO: Support various unit styles
box = topology.box
with open(filename, "w") as data:
data.write("{} written by topology at {}\n\n".format(
topology.name if topology.name is not None else "",
str(datetime.datetime.now()),
))
data.write("{:d} atoms\n".format(topology.n_sites))
if atom_style in ["full", "molecular"]:
if topology.n_bonds != 0:
data.write("{:d} bonds\n".format(topology.n_bonds))
else:
data.write("0 bonds\n")
if topology.n_angles != 0:
data.write("{:d} angles\n".format(topology.n_angles))
else:
data.write("0 angles\n")
if topology.n_dihedrals != 0:
data.write("{:d} dihedrals\n\n".format(topology.n_dihedrals))
else:
data.write("0 dihedrals\n\n")
data.write("\n{:d} atom types\n".format(len(topology.atom_types)))
data.write("{:d} bond types\n".format(len(topology.bond_types)))
data.write("{:d} angle types\n".format(len(topology.angle_types)))
data.write("{:d} dihedral types\n".format(len(
topology.dihedral_types)))
data.write("\n")
# Box data
if allclose_units(
box.angles,
u.unyt_array([90, 90, 90], "degree"),
rtol=1e-5,
atol=1e-8,
):
warnings.warn("Orthorhombic box detected")
box.lengths.convert_to_units(u.angstrom)
for i, dim in enumerate(["x", "y", "z"]):
data.write("{0:.6f} {1:.6f} {2}lo {2}hi\n".format(
0, box.lengths.value[i], dim))
else:
warnings.warn("Non-orthorhombic box detected")
box.lengths.convert_to_units(u.angstrom)
box.angles.convert_to_units(u.radian)
vectors = box.get_vectors()
a, b, c = box.lengths
alpha, beta, gamma = box.angles
lx = a
xy = b * np.cos(gamma)
xz = c * np.cos(beta)
ly = np.sqrt(b**2 - xy**2)
yz = (b * c * np.cos(alpha) - xy * xz) / ly
lz = np.sqrt(c**2 - xz**2 - yz**2)
xhi = vectors[0][0]
yhi = vectors[1][1]
zhi = vectors[2][2]
xy = vectors[1][0]
xz = vectors[2][0]
yz = vectors[2][1]
xlo = u.unyt_array(0, xy.units)
ylo = u.unyt_array(0, xy.units)
zlo = u.unyt_array(0, xy.units)
xlo_bound = xlo + u.unyt_array(np.min([0.0, xy, xz, xy + xz]),
xy.units)
xhi_bound = xhi + u.unyt_array(np.max([0.0, xy, xz, xy + xz]),
xy.units)
ylo_bound = ylo + u.unyt_array(np.min([0.0, yz]), xy.units)
yhi_bound = yhi + u.unyt_array(np.max([0.0, yz]), xy.units)
zlo_bound = zlo
zhi_bound = zhi
data.write("{0:.6f} {1:.6f} xlo xhi\n".format(
xlo_bound.value, xhi_bound.value))
data.write("{0:.6f} {1:.6f} ylo yhi\n".format(
ylo_bound.value, yhi_bound.value))
data.write("{0:.6f} {1:.6f} zlo zhi\n".format(
zlo_bound.value, zhi_bound.value))
data.write("{0:.6f} {1:.6f} {2:.6f} xy xz yz\n".format(
xy.value, xz.value, yz.value))
# TODO: Get a dictionary of indices and atom types
if topology.is_typed():
# Write out mass data
data.write("\nMasses\n\n")
for atom_type in topology.atom_types:
data.write("{:d}\t{:.6f}\t# {}\n".format(
topology.atom_types.index(atom_type) + 1,
atom_type.mass.in_units(u.g / u.mol).value,
atom_type.name,
))
# TODO: Modified cross-interactions
# Pair coefficients
data.write("\nPair Coeffs # lj\n\n")
for idx, param in enumerate(topology.atom_types):
data.write("{}\t{:.5f}\t{:.5f}\n".format(
idx + 1,
param.parameters["epsilon"].in_units(
u.Unit("kcal/mol")).value,
param.parameters["sigma"].in_units(u.angstrom).value,
))
if topology.bonds:
data.write("\nBond Coeffs\n\n")
for idx, bond_type in enumerate(topology.bond_types):
data.write("{}\t{:.5f}\t{:.5f}\n".format(
idx + 1,
bond_type.parameters["k"].in_units(
u.Unit("kcal/mol/angstrom**2")).value / 2,
bond_type.parameters["r_eq"].in_units(
u.Unit("angstrom")).value,
))
if topology.angles:
data.write("\nAngle Coeffs\n\n")
for idx, angle_type in enumerate(topology.angle_types):
data.write("{}\t{:.5f}\t{:.5f}\n".format(
idx + 1,
angle_type.parameters["k"].in_units(
u.Unit("kcal/mol/radian**2")).value / 2,
angle_type.parameters["theta_eq"].in_units(
u.Unit("degree")).value,
))
# TODO: Write out multiple dihedral styles
if topology.dihedrals:
data.write("\nDihedral Coeffs\n\n")
for idx, dihedral_type in enumerate(topology.dihedral_types):
rbtorsion = PotentialTemplateLibrary(
)["RyckaertBellemansTorsionPotential"]
if (dihedral_type.expression == sympify(
rbtorsion.expression)
or dihedral_type.name == rbtorsion.name):
dihedral_type = convert_ryckaert_to_opls(dihedral_type)
data.write("{}\t{:.5f}\t{:5f}\t{:5f}\t{:.5f}\n".format(
idx + 1,
dihedral_type.parameters["k1"].in_units(
u.Unit("kcal/mol")).value,
dihedral_type.parameters["k2"].in_units(
u.Unit("kcal/mol")).value,
dihedral_type.parameters["k3"].in_units(
u.Unit("kcal/mol")).value,
dihedral_type.parameters["k4"].in_units(
u.Unit("kcal/mol")).value,
))
# Atom data
data.write("\nAtoms\n\n")
if atom_style == "atomic":
atom_line = "{index:d}\t{type_index:d}\t{x:.6f}\t{y:.6f}\t{z:.6f}\n"
elif atom_style == "charge":
atom_line = "{index:d}\t{type_index:d}\t{charge:.6f}\t{x:.6f}\t{y:.6f}\t{z:.6f}\n"
elif atom_style == "molecular":
atom_line = "{index:d}\t{zero:d}\t{type_index:d}\t{x:.6f}\t{y:.6f}\t{z:.6f}\n"
elif atom_style == "full":
atom_line = "{index:d}\t{zero:d}\t{type_index:d}\t{charge:.6f}\t{x:.6f}\t{y:.6f}\t{z:.6f}\n"
for i, site in enumerate(topology.sites):
data.write(
atom_line.format(
index=topology.sites.index(site) + 1,
type_index=topology.atom_types.index(site.atom_type) + 1,
zero=0,
charge=site.charge.to(u.elementary_charge).value,
x=site.position[0].in_units(u.angstrom).value,
y=site.position[1].in_units(u.angstrom).value,
z=site.position[2].in_units(u.angstrom).value,
))
if topology.bonds:
data.write("\nBonds\n\n")
for i, bond in enumerate(topology.bonds):
data.write("{:d}\t{:d}\t{:d}\t{:d}\n".format(
i + 1,
topology.bond_types.index(bond.connection_type) + 1,
topology.sites.index(bond.connection_members[0]) + 1,
topology.sites.index(bond.connection_members[1]) + 1,
))
if topology.angles:
data.write("\nAngles\n\n")
for i, angle in enumerate(topology.angles):
data.write("{:d}\t{:d}\t{:d}\t{:d}\t{:d}\n".format(
i + 1,
topology.angle_types.index(angle.connection_type) + 1,
topology.sites.index(angle.connection_members[0]) + 1,
topology.sites.index(angle.connection_members[1]) + 1,
topology.sites.index(angle.connection_members[2]) + 1,
))
if topology.dihedrals:
data.write("\nDihedrals\n\n")
for i, dihedral in enumerate(topology.dihedrals):
data.write("{:d}\t{:d}\t{:d}\t{:d}\t{:d}\t{:d}\n".format(
i + 1,
topology.dihedral_types.index(dihedral.connection_type) +
1,
topology.sites.index(dihedral.connection_members[0]) + 1,
topology.sites.index(dihedral.connection_members[1]) + 1,
topology.sites.index(dihedral.connection_members[2]) + 1,
topology.sites.index(dihedral.connection_members[3]) + 1,
))