def test_full_itp_vsites(self):
"""Test full operation to output of .itp file for molecule with vsites."""
options = DummyOptions()
options.generate_angles = False
measure = BondSet(self.data_dir.joinpath("martini3/naphthalene.bnd"),
options)
frame = Frame(self.data_dir.joinpath("martini3/naphthalene.gro"))
mapping = Mapping(self.data_dir.joinpath("martini3/naphthalene.map"),
options)
cg_frame = mapping.apply(frame)
measure.apply(cg_frame)
measure.boltzmann_invert()
with tempfile.TemporaryDirectory() as tmpdir:
tmp_path = pathlib.Path(tmpdir)
measure.write_itp(tmp_path.joinpath("naphthalene_out.itp"),
mapping)
self.assertTrue(
cmp_file_whitespace_float(
tmp_path.joinpath("naphthalene_out.itp"),
self.data_dir.joinpath("martini3/naphthalene_out.itp"),
rtol=0.005,
verbose=True,
))
def test_full_itp_sugar(self):
measure = BondSet("test/data/sugar.bnd", DummyOptions)
frame = Frame("test/data/sugar.gro", xtc="test/data/sugar.xtc")
mapping = Mapping("test/data/sugar.map", DummyOptions)
cgframe = mapping.apply(frame)
while frame.next_frame():
cgframe = mapping.apply(frame, cgframe=cgframe)
measure.apply(cgframe)
measure.boltzmann_invert()
logging.disable(logging.WARNING)
measure.write_itp("sugar_out.itp", mapping)
logging.disable(logging.NOTSET)
self.assertTrue(cmp_whitespace_float("sugar_out.itp", "test/data/sugar_out.itp", float_rel_error=0.001))
def test_full_itp_sugar(self):
measure = BondSet("test/data/sugar.bnd", DummyOptions)
frame = Frame("test/data/sugar.gro", xtc="test/data/sugar.xtc")
mapping = Mapping("test/data/sugar.map", DummyOptions)
cgframe = mapping.apply(frame)
while frame.next_frame():
cgframe = mapping.apply(frame, cgframe=cgframe)
measure.apply(cgframe)
measure.boltzmann_invert()
logging.disable(logging.WARNING)
measure.write_itp("sugar_out.itp", mapping)
logging.disable(logging.NOTSET)
self.assertTrue(
cmp_whitespace_float("sugar_out.itp",
"test/data/sugar_out.itp",
float_rel_error=0.001))
def test_full_itp_sugar(self):
measure = BondSet(self.data_dir.joinpath("sugar.bnd"), DummyOptions)
frame = Frame(self.data_dir.joinpath("sugar.gro"),
self.data_dir.joinpath("sugar.xtc"))
mapping = Mapping(self.data_dir.joinpath("sugar.map"), DummyOptions)
cg_frame = mapping.apply(frame)
measure.apply(cg_frame)
measure.boltzmann_invert()
with tempfile.TemporaryDirectory() as tmpdir:
tmp_path = pathlib.Path(tmpdir)
measure.write_itp(tmp_path.joinpath("sugar_out.itp"), mapping)
self.assertTrue(
cmp_file_whitespace_float(
tmp_path.joinpath("sugar_out.itp"),
self.data_dir.joinpath("sugar_out.itp"),
rtol=0.005,
verbose=True,
))
class PyCGTOOL:
def __init__(self, config):
self.config = config
self.in_frame = Frame(
topology_file=self.config.topology,
trajectory_file=self.config.trajectory, # May be None
frame_start=self.config.begin,
frame_end=self.config.end,
)
self.mapping = None
self.out_frame = self.in_frame
if self.config.mapping:
self.mapping, self.out_frame = self.apply_mapping(self.in_frame)
if self.out_frame.natoms == 0:
# The following steps won't work with frames containing no atoms
logger.warning(
"Mapped trajectory contains no atoms - check your mapping file is correct!"
)
return
self.bondset = None
if self.config.bondset:
self.bondset = BondSet(self.config.bondset, self.config)
self.measure_bonds()
if self.config.output_xtc:
self.out_frame.save(self.get_output_filepath("xtc"))
def get_output_filepath(self, ext: PathLike) -> pathlib.Path:
"""Get file path for an output file by extension.
Creates the output directory if missing.
"""
out_dir = pathlib.Path(self.config.out_dir)
out_dir.mkdir(parents=True, exist_ok=True)
return out_dir.joinpath(self.config.output_name + "." + ext)
def apply_mapping(self, in_frame: Frame) -> typing.Tuple[Mapping, Frame]:
"""Map input frame to output using requested mapping file."""
mapping = Mapping(self.config.mapping,
self.config,
itp_filename=self.config.itp)
out_frame = mapping.apply(in_frame)
out_frame.save(self.get_output_filepath("gro"), frame_number=0)
if self.config.backmapper_resname and self.out_frame.n_frames > 1:
try:
self.train_backmapper(self.config.resname)
except ImportError:
logger.error("MDPlus must be installed to perform backmapping")
return mapping, out_frame
def measure_bonds(self) -> None:
"""Measure bonds at the end of a run."""
self.bondset.apply(self.out_frame)
if self.mapping is not None and self.out_frame.n_frames > 1:
# Only perform Boltzmann Inversion if we have a mapping and a trajectory.
# Otherwise we get infinite force constants.
logger.info("Starting Boltzmann Inversion")
self.bondset.boltzmann_invert()
logger.info("Finished Boltzmann Inversion")
if self.config.output_forcefield:
logger.info("Writing GROMACS forcefield directory")
out_dir = pathlib.Path(self.config.out_dir)
forcefield = ForceField(self.config.output_name,
dir_path=out_dir)
forcefield.write(self.config.output_name, self.mapping,
self.bondset)
logger.info("Finished writing GROMACS forcefield directory")
else:
self.bondset.write_itp(self.get_output_filepath("itp"),
mapping=self.mapping)
if self.config.dump_measurements:
logger.info("Writing bond measurements to file")
self.bondset.dump_values(self.config.dump_n_values,
self.config.out_dir)
logger.info("Finished writing bond measurements to file")
def train_backmapper(self, resname: str):
from mdplus.multiscale import GLIMPS
sel = f"resname {resname}"
aa_subset_traj = self.in_frame._trajectory.atom_slice(
self.in_frame._trajectory.topology.select(sel))
cg_subset_traj = self.out_frame._trajectory.atom_slice(
self.out_frame._trajectory.topology.select(sel))
logger.info("Training backmapper")
# Param x_valence is approximate number of bonds per CG bead
# Values greater than 2 fail for small molecules e.g. sugar test case
backmapper = GLIMPS(x_valence=2)
backmapper.fit(cg_subset_traj.xyz, aa_subset_traj.xyz)
logger.info("Finished training backmapper")
backmapper.save(self.get_output_filepath("backmapper.pkl"))
