def test_shorten_atomname(self, ethane):
import foyer
from mbuild.formats.cassandramcf import write_mcf
typed_ethane = foyer.forcefields.load_OPLSAA().apply(ethane)
typed_ethane[0].type = "C_very_very_very_extended"
write_mcf(
typed_ethane,
"ethane-opls.mcf",
angle_style="harmonic",
dihedral_style="opls",
)
mcf_data = []
with open("ethane-opls.mcf") as f:
for line in f:
mcf_data.append(line.strip().split())
for idx, line in enumerate(mcf_data):
if len(line) > 1:
if line[1] == "Atom_Info":
atom_section_start = idx
assert mcf_data[atom_section_start + 2][1] == "y_very_very_extended"
def write_mcfs(system):
if not isinstance(system, mosdef_cassandra.System):
raise TypeError('"system" must be of type ' "mosdef_cassandra.System")
for species_count, species in enumerate(system.species_topologies):
if not isinstance(species, parmed.Structure):
raise TypeError('Your "system" object appears to have '
"been corrupted. Species {} is not a parmed"
".Structure object".format(species))
if len(species.dihedrals) > 0 and len(species.rb_torsions) > 0:
raise ValueError(
"Your species has both CHARMM style "
"dihedrals and Ryckaert-Bellemans style dihedrals. "
"Only a single dihedral style per species is "
"currently supported")
elif len(species.dihedrals) > 0:
dihedral_style = "charmm"
elif len(species.rb_torsions) > 0:
dihedral_style = "opls"
else:
dihedral_style = "none"
mcf_name = "species{}.mcf".format(species_count + 1)
write_mcf(
species,
mcf_name,
angle_style="harmonic",
dihedral_style=dihedral_style,
)
def test_infer_14_scaling_zero_eps(self):
import mbuild
import foyer
from mbuild.formats.cassandramcf import write_mcf
mol = mbuild.load("CO", smiles=True)
mol_ff = foyer.forcefields.load_OPLSAA().apply(mol)
with pytest.warns(UserWarning):
write_mcf(mol_ff, "test.mcf", angle_style="harmonic", dihedral_style="opls")
def test_fused_rings(self):
import foyer
import mbuild
from mbuild.formats.cassandramcf import write_mcf
naph = mbuild.load("C1=CC=C2C=CC=CC2=C1", smiles=True)
# Note the atomtyping is wrong -- doesn't matter for test though
naph_ff = foyer.forcefields.load_OPLSAA().apply(naph)
write_mcf(naph_ff,
"naph.mcf",
angle_style="harmonic",
dihedral_style="opls")
mcf_data = []
with open("naph.mcf") as f:
for line in f:
mcf_data.append(line.strip().split())
for idx, line in enumerate(mcf_data):
if len(line) > 1:
if line[1] == "Fragment_Info":
frag_section_start = idx
assert int(mcf_data[frag_section_start + 1][0]) == 1
assert int(mcf_data[frag_section_start + 2][1]) == 18
tmada = mbuild.load("C[C](C)(C)C12CC3CC(C1)CC(C3)C2", smiles=True)
tmada_ff = foyer.forcefields.load_OPLSAA().apply(tmada)
write_mcf(tmada_ff,
"tmada.mcf",
angle_style="harmonic",
dihedral_style="opls")
mcf_data = []
with open("tmada.mcf") as f:
for line in f:
mcf_data.append(line.strip().split())
for idx, line in enumerate(mcf_data):
if len(line) > 1:
if line[1] == "Fragment_Info":
frag_section_start = idx
assert int(mcf_data[frag_section_start + 1][0]) == 5
assert int(mcf_data[frag_section_start + 2][1]) == 26
assert int(mcf_data[frag_section_start + 3][1]) == 5
assert int(mcf_data[frag_section_start + 4][1]) == 5
assert int(mcf_data[frag_section_start + 5][1]) == 5
assert int(mcf_data[frag_section_start + 6][1]) == 5
def write_mcfs(system, angle_style="harmonic"):
"""Write a MCF file for a given mosdef_cassandra.System
Parameters
----------
system : mosdef_cassandra.System
System to simulate in Cassandra
angle_style : str, default="harmonic"
Angle style for the system, valid arguments: "harmonic", "fixed"
"""
if type(angle_style) == str:
angle_style = [angle_style] * len(system.species_topologies)
for astyle in angle_style:
if astyle not in ["harmonic", "fixed"]:
raise ValueError(
'Invalid "angle_style" {} given.'.format(angle_style)
)
if not isinstance(system, mosdef_cassandra.System):
raise TypeError('"system" must be of type ' "mosdef_cassandra.System")
for species_count, species in enumerate(system.species_topologies):
if not isinstance(species, parmed.Structure):
raise TypeError(
'Your "system" object appears to have '
"been corrupted. Species {} is not a parmed"
".Structure object".format(species)
)
if len(species.dihedrals) > 0 and len(species.rb_torsions) > 0:
raise ValueError(
"Your species has both CHARMM style "
"dihedrals and Ryckaert-Bellemans style dihedrals. "
"Only a single dihedral style per species is "
"currently supported"
)
elif len(species.dihedrals) > 0:
dihedral_style = "charmm"
elif len(species.rb_torsions) > 0:
dihedral_style = "opls"
else:
dihedral_style = "none"
mcf_name = "species{}.mcf".format(species_count + 1)
write_mcf(
species,
mcf_name,
angle_style=angle_style[species_count],
dihedral_style=dihedral_style,
)
def build_run_measure_cassandra(structure):
py2, fraglib_setup, cassandra = detect_cassandra_binaries()
workdir = os.getcwd()
mcf_file = 'structure.mcf'
xyz_file = 'structure.xyz'
pdb_file = 'structure.pdb'
with temporary_directory() as tmp_dir:
with temporary_cd(tmp_dir):
# Guess dihedral type...from contents of structure
if len(structure.dihedrals) > 0:
dihedral_style = 'charmm'
else:
dihedral_style = 'opls'
write_mcf(structure,
mcf_file,
angle_style='harmonic',
dihedral_style=dihedral_style)
mb.load(structure).save(xyz_file)
mb.load(structure).to_trajectory().save_pdb(pdb_file)
inp_file, output = write_cassandra_inp()
successful_fraglib = run_fraglib_setup(py2, fraglib_setup,
cassandra, inp_file,
mcf_file, pdb_file, workdir)
if successful_fraglib:
run_cassandra(cassandra, inp_file, workdir)
energies = get_cassandra_energy(output + '.log')
else:
print(
"Cassandra failed due to unsuccessful fragment generation")
df = pd.DataFrame.from_dict(energies, orient='index')
return df