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[fmt] Format converters modules and tests (#4850)
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@RMeli
RMeli authored Dec 21, 2024
1 parent 4f143fd commit 9110a6e
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Showing 16 changed files with 1,072 additions and 709 deletions.
44 changes: 26 additions & 18 deletions package/MDAnalysis/converters/OpenMM.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -77,13 +77,17 @@ class OpenMMSimulationReader(base.SingleFrameReaderBase):
"""

format = "OPENMMSIMULATION"
units = {"time": "ps", "length": "nm", "velocity": "nm/ps",
"force": "kJ/(mol*nm)", "energy": "kJ/mol"}
units = {
"time": "ps",
"length": "nm",
"velocity": "nm/ps",
"force": "kJ/(mol*nm)",
"energy": "kJ/mol",
}

@staticmethod
def _format_hint(thing):
"""Can this reader read *thing*?
"""
"""Can this reader read *thing*?"""
try:
from openmm.app import Simulation
except ImportError:
Expand All @@ -104,34 +108,38 @@ def _read_first_frame(self):
self.ts.triclinic_dimensions = self.convert_pos_from_native(
self.ts.triclinic_dimensions, inplace=False
)
self.ts.dimensions[3:] = _sanitize_box_angles(self.ts.dimensions[3:])
self.ts.dimensions[3:] = _sanitize_box_angles(
self.ts.dimensions[3:]
)
self.convert_velocities_from_native(self.ts._velocities)
self.convert_forces_from_native(self.ts._forces)
self.convert_time_from_native(self.ts.dt)

def _mda_timestep_from_omm_context(self):
""" Construct Timestep object from OpenMM context """
"""Construct Timestep object from OpenMM context"""
try:
import openmm.unit as u
except ImportError: # pragma: no cover
import simtk.unit as u

state = self.filename.context.getState(-1, getVelocities=True,
getForces=True, getEnergy=True)
state = self.filename.context.getState(
-1, getVelocities=True, getForces=True, getEnergy=True
)

n_atoms = self.filename.context.getSystem().getNumParticles()

ts = self._Timestep(n_atoms, **self._ts_kwargs)
ts.frame = 0
ts.data["time"] = state.getTime()._value
ts.data["potential_energy"] = (
state.getPotentialEnergy().in_units_of(u.kilojoule/u.mole)._value
state.getPotentialEnergy().in_units_of(u.kilojoule / u.mole)._value
)
ts.data["kinetic_energy"] = (
state.getKineticEnergy().in_units_of(u.kilojoule/u.mole)._value
state.getKineticEnergy().in_units_of(u.kilojoule / u.mole)._value
)
ts.triclinic_dimensions = state.getPeriodicBoxVectors(
asNumpy=True)._value
asNumpy=True
)._value
ts.dimensions[3:] = _sanitize_box_angles(ts.dimensions[3:])
ts.positions = state.getPositions(asNumpy=True)._value
ts.velocities = state.getVelocities(asNumpy=True)._value
Expand All @@ -153,8 +161,7 @@ class OpenMMAppReader(base.SingleFrameReaderBase):

@staticmethod
def _format_hint(thing):
"""Can this reader read *thing*?
"""
"""Can this reader read *thing*?"""
try:
from openmm import app
except ImportError:
Expand All @@ -163,8 +170,7 @@ def _format_hint(thing):
except ImportError:
return False
else:
return isinstance(thing, (app.PDBFile, app.Modeller,
app.PDBxFile))
return isinstance(thing, (app.PDBFile, app.Modeller, app.PDBxFile))

def _read_first_frame(self):
self.n_atoms = self.filename.topology.getNumAtoms()
Expand All @@ -177,10 +183,12 @@ def _read_first_frame(self):
self.ts.triclinic_dimensions = self.convert_pos_from_native(
self.ts.triclinic_dimensions, inplace=False
)
self.ts.dimensions[3:] = _sanitize_box_angles(self.ts.dimensions[3:])
self.ts.dimensions[3:] = _sanitize_box_angles(
self.ts.dimensions[3:]
)

def _mda_timestep_from_omm_app(self):
""" Construct Timestep object from OpenMM Application object """
"""Construct Timestep object from OpenMM Application object"""

omm_object = self.filename
n_atoms = omm_object.topology.getNumAtoms()
Expand All @@ -198,7 +206,7 @@ def _mda_timestep_from_omm_app(self):


def _sanitize_box_angles(angles):
""" Ensure box angles correspond to first quadrant
"""Ensure box angles correspond to first quadrant
See `discussion on unitcell angles <https://github.com/MDAnalysis/mdanalysis/pull/2917/files#r620558575>`_
"""
Expand Down
48 changes: 24 additions & 24 deletions package/MDAnalysis/converters/OpenMMParser.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -84,9 +84,7 @@ class OpenMMTopologyParser(TopologyReaderBase):

@staticmethod
def _format_hint(thing):
"""Can this Parser read object *thing*?
"""
"""Can this Parser read object *thing*?"""
try:
from openmm import app
except ImportError:
Expand All @@ -98,7 +96,7 @@ def _format_hint(thing):
return isinstance(thing, app.Topology)

def _mda_topology_from_omm_topology(self, omm_topology):
""" Construct mda topology from omm topology
"""Construct mda topology from omm topology
Can be used for any openmm object that contains a topology object
Expand Down Expand Up @@ -130,9 +128,11 @@ def _mda_topology_from_omm_topology(self, omm_topology):
try:
from simtk.unit import daltons
except ImportError:
msg = ("OpenMM is required for the OpenMMParser but "
"it's not installed. Try installing it with \n"
"conda install -c conda-forge openmm")
msg = (
"OpenMM is required for the OpenMMParser but "
"it's not installed. Try installing it with \n"
"conda install -c conda-forge openmm"
)
raise ImportError(msg)

atom_resindex = [a.residue.index for a in omm_topology.atoms()]
Expand Down Expand Up @@ -168,19 +168,21 @@ def _mda_topology_from_omm_topology(self, omm_topology):
if elem.symbol.capitalize() in SYMB2Z:
validated_elements.append(elem.symbol)
else:
validated_elements.append('')
validated_elements.append("")
atomtypes.append(elem.symbol)
masses.append(elem.mass.value_in_unit(daltons))
else:
validated_elements.append('')
validated_elements.append("")
masses.append(0.0)
atomtypes.append('X')
atomtypes.append("X")

if not all(validated_elements):
if any(validated_elements):
warnings.warn("Element information missing for some atoms. "
"These have been given an empty element record ")
if any(i == 'X' for i in atomtypes):
warnings.warn(
"Element information missing for some atoms. "
"These have been given an empty element record "
)
if any(i == "X" for i in atomtypes):
warnings.warn(
"For absent elements, atomtype has been "
"set to 'X' and mass has been set to 0.0. "
Expand All @@ -189,10 +191,12 @@ def _mda_topology_from_omm_topology(self, omm_topology):
"to_guess=['masses', 'types']). "
"(for MDAnalysis version 2.x "
"this is done automatically,"
" but it will be removed in 3.0).")
" but it will be removed in 3.0)."
)

attrs.append(Elements(np.array(validated_elements,
dtype=object)))
attrs.append(
Elements(np.array(validated_elements, dtype=object))
)

else:
wmsg = (
Expand All @@ -205,7 +209,8 @@ def _mda_topology_from_omm_topology(self, omm_topology):
"These can be guessed using "
"universe.guess_TopologyAttrs("
"to_guess=['masses', 'types']) "
"See MDAnalysis.guessers.")
"See MDAnalysis.guessers."
)

warnings.warn(wmsg)
else:
Expand Down Expand Up @@ -239,9 +244,7 @@ class OpenMMAppTopologyParser(OpenMMTopologyParser):

@staticmethod
def _format_hint(thing):
"""Can this Parser read object *thing*?
"""
"""Can this Parser read object *thing*?"""
try:
from openmm import app
except ImportError:
Expand All @@ -252,10 +255,7 @@ def _format_hint(thing):
else:
return isinstance(
thing,
(
app.PDBFile, app.Modeller,
app.Simulation, app.PDBxFile
)
(app.PDBFile, app.Modeller, app.Simulation, app.PDBxFile),
)

def parse(self, **kwargs):
Expand Down
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