__all__ = ["System"]
[docs]
class System:
"""
This class holds a complete system of molecules. This is normally
created by reading in molecules from an input file.
This provides a "MoleculeView"-style interface to the molecules,
acting very similarly to a sire.mol.SelectorMol object.
You can convert this to a sire.mol.SelectorMol object by
calling the System.molecules() function.
"""
def __init__(self, system=None):
from ..legacy.System import System as _System
if system is None:
from ..vol import Cartesian
from ..units import picosecond
from ..base import wrap
from ..legacy.Mol import MoleculeGroup
self._system = _System()
self._system.add_shared_property("space", Cartesian())
self._system.add_shared_property("time", wrap(0 * picosecond))
self._system.add(MoleculeGroup("all"))
else:
if _System not in type(system).mro():
raise TypeError(
"You can only construct from a sire.legacy.System.System, "
f"not a {type(system)}"
)
if isinstance(system, System):
self._system == system._system
else:
self._system = system
self._molecules = None
[docs]
@staticmethod
def is_system(obj):
"""
Return whether the passed object is a System class
(either a new or legacy System)
"""
from ..legacy.System import System as _System
return isinstance(obj, System) or isinstance(obj, _System)
def _to_legacy_system(self):
"""
Internal function used to convert this back to a legacy system
"""
return self._system
def __copy__(self):
other = System()
other._system = self._system.clone()
other._molecules = None
return other
def __deepcopy__(self, memo):
return self.__copy__()
def __str__(self):
return str(self._system)
def __repr__(self):
return self.__str__()
def __getitem__(self, key):
return self.molecules()[key]
def __iadd__(self, molecules):
self.add(molecules)
return self
def __add__(self, molecules):
ret = self.__copy__()
ret.add(molecules)
return ret
def __radd__(self, molecules):
return self.__add__(molecules)
def __isub__(self, molecules):
self.remove(molecules)
return self
def __sub__(self, molecules):
ret = self.__copy__()
ret.remove(molecules)
return ret
[docs]
def clone(self):
"""Return a copy (clone) of this System"""
s = System()
s._system = self._system.clone()
s._molecules = None
return s
[docs]
def count(self):
"""Return the number of items in this System"""
return self.__len__()
[docs]
def size(self):
"""Return the number of items in this System"""
return self.__len__()
def __len__(self):
return len(self.molecules())
[docs]
def num_atoms(self):
"""Return the number of atoms in this System"""
return self._system.num_atoms()
[docs]
def num_residues(self):
"""Return the number of residues in this System"""
return self._system.num_residues()
[docs]
def num_chains(self):
"""Return the number of chains in this System"""
return self._system.num_chains()
[docs]
def num_segments(self):
"""Return the number of segments in this System"""
return self._system.num_segments()
[docs]
def num_molecules(self):
"""Return the number of molecules in this System"""
return self._system.num_molecules()
[docs]
def find(self, views):
"""Return the index(es) of the molecule(s) that are in `views`"""
return self.molecules().find(views)
[docs]
def names(self):
"""Return the names of all of the molecules in this System"""
return self.molecules().names()
[docs]
def numbers(self):
"""Return the numbers of all of the molecules in this System"""
return self.molecules().numbers()
[docs]
def make_whole(self, center=None, map=None):
"""
Make all of the molecules in this system whole. This
maps each molecule into the current space, such that no
molecule is broken across a periodic box boundary
"""
if center is None:
if map is None:
self._system.make_whole()
else:
from ..base import create_map
self._system.make_whole(map=create_map(map))
else:
from ..maths import Vector
center = Vector(center)
if map is None:
self._system.make_whole(center=center)
else:
from ..base import create_map
self._system.make_whole(center=center, map=create_map(map))
self._molecules = None
[docs]
def num_frames(self, map=None):
"""Return the number of trajectory frames for this System"""
from ..base import create_map
return self._system.num_frames(map=create_map(map))
[docs]
def load_frame(self, i, map=None):
"""Load the ith frame into this System"""
from ..base import create_map
self._system.load_frame(i, map=create_map(map))
self._molecules = None
[docs]
def save_frame(self, i=None, map=None):
"""Save the current coordinates to the ith frame of this System.
If i is not specfied then this adds the frame onto the
end of the trajectory
"""
from ..base import create_map
map = create_map(map)
if i is None:
self._system.save_frame(map=map)
else:
self._system.save_frame(i, map=map)
self._molecules = None
[docs]
def delete_frame(self, i, map=None):
"""Delete the ith frame from the trajectory"""
from ..base import create_map
self._system.delete_frame(i, map=create_map(map))
self._molecules = None
[docs]
def delete_all_frames(self, map=None):
"""Delete all the frames from the trajectory"""
from ..base import create_map
self._system.delete_all_frames(map=create_map(map))
self._molecules = None
[docs]
def to_molecule_group(self):
"""Return this System converted to a sire.mol.MoleculeGroup"""
return self.molecules().to_molecule_group()
[docs]
def molecules(self, *args, **kwargs):
"""Return this System converted to a sire.mol.SelectorMol.
You can pass in arguments to search or index so that you
limit the number of molecules returned.
"""
if self._molecules is not None:
return self._molecules.molecules(*args, **kwargs)
import sire.mol
self._molecules = sire.mol.SelectorMol(self._system)
if self._molecules.num_atoms() != self._system.num_atoms():
# oh dear - this is an edge case where the System does
# not contain complete molecules. We need to extract
# the molecules and re-add them
raise NotImplementedError(
"sire.system.System does not yet support Systems that hold "
"partial molecules!. Let us know that you have hit this "
"bug and we will add support."
)
return self.molecules(*args, **kwargs)
[docs]
def segments(self, *args, **kwargs):
"""Return all segments in this System (or those that match
the passed index, if supplied)
"""
return self.molecules().segments(*args, **kwargs)
[docs]
def chains(self, *args, **kwargs):
"""Return all chains in this System (or those that match
the passed index, if supplied)
"""
return self.molecules().chains(*args, **kwargs)
[docs]
def residues(self, *args, **kwargs):
"""Return all residues in this System (or those that match
the passed index, if supplied)
"""
return self.molecules().residues(*args, **kwargs)
[docs]
def atoms(self, *args, **kwargs):
"""Return all atoms in this System (or those that match
the passed index, if supplied)
"""
return self.molecules().atoms(*args, **kwargs)
[docs]
def bonds(self, *args, **kwargs):
"""Return all bonds in this System (or those that match
the passed index, if supplied)
"""
return self.molecules().bonds(*args, **kwargs)
[docs]
def angles(self, *args, **kwargs):
"""Return all angles in this System (or those that match
the passed index, if supplied)
"""
return self.molecules().angles(*args, **kwargs)
[docs]
def dihedrals(self, *args, **kwargs):
"""Return all dihedrals in this System (or those that match
the passed index, if supplied)
"""
return self.molecules().dihedrals(*args, **kwargs)
[docs]
def impropers(self, *args, **kwargs):
"""Return all impropers in this System (or those that match
the passed index, if supplied)
"""
return self.molecules().impropers(*args, **kwargs)
[docs]
def molecule(self, *args, **kwargs):
"""Return the molecule that matches the passed index/search"""
return self.molecules().molecule(*args, **kwargs)
[docs]
def segment(self, *args, **kwargs):
"""Return the segment that matches the passed index/search"""
return self.molecules().segment(*args, **kwargs)
[docs]
def chain(self, *args, **kwargs):
"""Return the chain that matches the passed index/search"""
return self.molecules().chain(*args, **kwargs)
[docs]
def residue(self, *args, **kwargs):
"""Return the residue that matches the passed index/search"""
return self.molecules().residue(*args, **kwargs)
[docs]
def atom(self, *args, **kwargs):
"""Return the atom that matches the passed index/search"""
return self.molecules().atom(*args, **kwargs)
[docs]
def bond(self, *args, **kwargs):
"""Return the bond that matches the passed index/search"""
return self.molecules().bond(*args, **kwargs)
[docs]
def angle(self, *args, **kwargs):
"""Return the angle that matches the passed index/search"""
return self.molecules().angle(*args, **kwargs)
[docs]
def dihedral(self, *args, **kwargs):
"""Return the dihedral that matches the passed index/search"""
return self.molecules().dihedral(*args, **kwargs)
[docs]
def improper(self, *args, **kwargs):
"""Return the improper that matches the passed index/search"""
return self.molecules().improper(*args, **kwargs)
[docs]
def trajectory(self, *args, **kwargs):
"""
Return an iterator over the trajectory of frames of this view.
align:
Pass in a selection string to select atoms against which
every frame will be aligned. These atoms will be moved
to the center of the periodic box (if a periodic box
is used). If "True" is passed, then this will attempt
to align *ALL* of the coordinates in the view.
You can also choose to pass in a molecular container,
and it will align against the atoms in that container,
assuming they are contained in this view. If not, then
you need to supply a mapping that maps from the
atoms in the align container, to the atoms in this view.
frame:
The frame of the trajectory against which the alignment
should be based. For example, `frame=3` would align based
on the coordinates of the aligned atoms in frame 3 of
the trajectory. If this is `None` (the default) then the
first frame will be used.
mapping: AtomMapping
An AtomMapping object that maps from atoms in the alignment
container to atoms in this view. You only need to supply
this if all of the alignment atoms are not contained
in this view.
smooth:
Pass in the number of frames to smooth (average) the view
over. If 'True' is passed, then the recommended number
of frames will be averaged over
wrap: bool
Whether or not to wrap the coordinates into the periodic box
"""
from ..mol._trajectory import TrajectoryIterator
return TrajectoryIterator(self, *args, **kwargs)
[docs]
def minimisation(self, *args, **kwargs):
"""
Return a Minimisation object that can be used to perform
minimisation of the molecule(s) in this System
cutoff: Length
The size of the non-bonded cutoff
cutoff_type: str
The type of cutoff to use, e.g. "PME", "RF" etc.
See https://sire.openbiosim.org/cheatsheet/openmm.html#choosing-options
for the full list of options
constraint: str
The type of constraint to use for bonds and/or angles, e.g.
`h-bonds`, `bonds` etc.
See https://sire.openbiosim.org/cheatsheet/openmm.html#choosing-options
for the full list of options. This will be `none` if it hasn't
been set.
perturbable_constraint: str
The type of constraint to use for perturbable bonds and/or angles,
e.g. `h-bonds`, `bonds` etc.
See https://sire.openbiosim.org/cheatsheet/openmm.html#choosing-options
for the full list of options. This equal the value of `constraint`
if it isn't set.
include_constrained_energies: bool
Whether or not to include the energies of the perturbable bonds
and angles. If this is False, then the internal bond or angle
energy of the perturbable degrees of freedom are not included
in the total energy, and their forces are not evaluated.
schedule: sire.cas.LambdaSchedule
The schedule used to control how perturbable forcefield parameters
should be morphed as a function of lambda. If this is not set
then a sire.cas.LambdaSchedule.standard_morph() is used.
lambda_value: float
The value of lambda at which to run minimisation. This only impacts
perturbable molecules, whose forcefield parameters will be
scaled according to the lambda schedule for the specified
value of lambda.
swap_end_states: bool
Whether or not to swap the end states. If this is True, then
the perturbation will run from the perturbed back to the
reference molecule (the perturbed molecule will be at lambda=0,
while the reference molecule will be at lambda=1). This will
use the coordinates of the perturbed molecule as the
starting point.
ignore_perturbations: bool
Whether or not to ignore perturbations. If this is True, then
the perturbation will be ignored, and the simulation will
be run using the properties of the reference molecule
(or the perturbed molecule if swap_end_states is True). This
is useful if you just want to run standard molecular dynamics
of the reference or perturbed states.
shift_coulomb: length
The shift_coulomb parameter that controls the electrostatic
softening potential that smooths the creation and deletion
of ghost atoms during a potential. This defaults to 1.0 A.
shift_delta: length
The shift_delta parameter that controls the electrostatic
and van der Waals softening potential that smooths the
creation and deletion of ghost atoms during a potential.
This defaults to 2.0 A.
coulomb_power: int
The coulomb power parmeter that controls the electrostatic
softening potential that smooths the creation and deletion
of ghost atoms during a potential. This defaults to 0.
vacuum: bool
Whether or not to run the simulation in vacuum. If this is
set to `True`, then the simulation space automatically be
replaced by a `sire.vol.Cartesian` space, and the
simulation run in vacuum.
restraints: sire.mm.Restraints or list[sire.mm.Restraints]
A single set of restraints, or a list of sets of
restraints that will be applied to the atoms during
the simulation.
fixed: molecule(s) view, search string, int, list[int] etc
Anything that can be used to identify the atom or atoms
that should be fixed in place during the simulation. These
atoms will not be moved by minimisation.
platform: str
The name of the OpenMM platform on which to run the dynamics,
e.g. "CUDA", "OpenCL", "Metal" etc.
device: str or int
The ID of the GPU (or accelerator) used to accelerate
minimisation. This would be CUDA_DEVICE_ID or similar
if CUDA was used. This can be any valid OpenMM device string
dynamic_constraints: bool
Whether or not to update the length of constraints of
perturbable bonds with lambda. This defaults to True,
meaning that changing lambda will change any constraint
on a perturbable bond to equal to the value of r0 at
that lambda value. If this is false, then the constraint
is set based on the current length.
map: dict
A dictionary of additional options. Note that any options
set in this dictionary that are also specified via one of
the arguments above will be overridden by the argument
value
""" # noqa: E501
from ..mol import _minimisation
return _minimisation(self, *args, **kwargs)
[docs]
def dynamics(self, *args, **kwargs):
"""
Return a Dynamics object that can be used to perform
dynamics on the molecule(s) in this System
cutoff: Length
The size of the non-bonded cutoff
cutoff_type: str
The type of cutoff to use, e.g. "PME", "RF" etc.
See https://sire.openbiosim.org/cheatsheet/openmm.html#choosing-options
for the full list of options
timestep: time
The size of the dynamics timestep
save_frequency: time
The amount of simulation time between saving energies and frames.
This can be overridden using `energy_frequency` or `frame_frequency`,
or by these options in individual dynamics runs. Set this
to zero if you don't want any saves.
energy_frequency: time
The amount of time between saving energies. This overrides the
value in `save_frequency`. Set this to zero if you don't want
to save energies during the trajectory. This can be overridden
by setting energy_frequency during an individual run.
frame_frequency: time
The amount of time between saving frames. This overrides the
value in `save_frequency`. Set this to zero if you don't want
to save frames during the trajectory. This can be overridden
by setting frame_frequency during an individual run.
save_velocities: bool
Whether or not to save velocities when saving trajectory frames
during the simulation. This defaults to False, as velocity
trajectories aren't often needed, and they double the amount
of space that is required for a trajectory.
constraint: str
The type of constraint to use for bonds and/or angles, e.g.
`h-bonds`, `bonds` etc.
See https://sire.openbiosim.org/cheatsheet/openmm.html#choosing-options
for the full list of options. This will be automatically
guessed from the timestep if it isn't set.
perturbable_constraint: str
The type of constraint to use for perturbable bonds and/or angles,
e.g. `h-bonds`, `bonds` etc.
See https://sire.openbiosim.org/cheatsheet/openmm.html#choosing-options
for the full list of options. This equal the value of `constraint`
if it isn't set.
include_constrained_energies: bool
Whether or not to include the energies of the perturbable bonds
and angles. If this is False, then the internal bond or angle
energy of the perturbable degrees of freedom are not included
in the total energy, and their forces are not evaluated.
schedule: sire.cas.LambdaSchedule
The schedule used to control how perturbable forcefield parameters
should be morphed as a function of lambda. If this is not set
then a sire.cas.LambdaSchedule.standard_morph() is used.
lambda_value: float
The value of lambda at which to run dynamics. This only impacts
perturbable molecules, whose forcefield parameters will be
scaled according to the lambda schedule for the specified
value of lambda.
swap_end_states: bool
Whether or not to swap the end states. If this is True, then
the perturbation will run from the perturbed back to the
reference molecule (the perturbed molecule will be at lambda=0,
while the reference molecule will be at lambda=1). This will
use the coordinates of the perturbed molecule as the
starting point.
ignore_perturbations: bool
Whether or not to ignore perturbations. If this is True, then
the perturbation will be ignored, and the simulation will
be run using the properties of the reference molecule
(or the perturbed molecule if swap_end_states is True). This
is useful if you just want to run standard molecular dynamics
of the reference or perturbed states.
integrator: str
The type of integrator to use, e.g. `langevin`, `verlet` etc.
See https://sire.openbiosim.org/cheatsheet/openmm.html#choosing-options
for the full list of options. This will be automatically
set to `langevin_middle` (NVT/NPT) or `verlet` (NVE) depending
on the ensemble if this is not set (or is set to `auto`)
temperature: temperature
The temperature at which to run the simulation. A
microcanonical (NVE) simulation will be run if you don't
specify the temperature.
pressure: pressure
The pressure at which to run the simulation. A
microcanonical (NVE) or canonical (NVT) simulation will be
run if the pressure is not set.
rest2_scale: float
The scaling factor to apply when running a REST2 simulation
(Replica Exchange with Solute Tempering). This defaults to 1.0.
This specifies the ratio of the temperature of the REST2 region
to the temperature of the rest of the system.
rest2_selection: str
A selection string for atoms to include in the REST2 region
in addition to any perturbable molecules. For example,
"molidx 0 and residx 0,1,2" would select atoms from the first
three residues of the first molecule. If None, then all atoms
within perturbable molecules will be included in the REST2
region. When atoms within a perturbable molecule are also
included in the selection, then only those atoms will be
considered as part of the REST2 region. This allows REST2 to
be applied to protein mutations.
vacuum: bool
Whether or not to run the simulation in vacuum. If this is
set to `True`, then the simulation space automatically be
replaced by a `sire.vol.Cartesian` space, and the
simulation run in vacuum.
shift_coulomb: length
The shift_coulomb parameter that controls the electrostatic
softening potential that smooths the creation and deletion
of ghost atoms during a potential. This defaults to 1.0 A.
shift_delta: length
The shift_delta parameter that controls the electrostatic
and van der Waals softening potential that smooths the
creation and deletion of ghost atoms during a potential.
This defaults to 2.0 A.
coulomb_power: int
The coulomb power parmeter that controls the electrostatic
softening potential that smooths the creation and deletion
of ghost atoms during a potential. This defaults to 0.
restraints: sire.mm.Restraints or list[sire.mm.Restraints]
A single set of restraints, or a list of sets of
restraints that will be applied to the atoms during
the simulation.
fixed: molecule(s) view, search string, int, list[int] etc
Anything that can be used to identify the atom or atoms
that should be fixed in place during the simulation. These
atoms will not be moved by dynamics.
qm_engine:
A sire.qm.QMMMEngine object to used to compute QM/MM forces
and energies on a subset of the atoms in the system.
lambda_interpolate: float
The lambda value at which to interpolate the QM/MM forces and
energies, which can be used to perform end-state correction
simulations. A value of 1.0 is full QM, whereas a value of 0.0 is
full MM. If two values are specified, then lambda will be linearly
interpolated between the two values over the course of the
simulation, which lambda updated at the energy_frequency.
platform: str
The name of the OpenMM platform on which to run the dynamics,
e.g. "CUDA", "OpenCL", "Metal" etc.
device: str or int
The ID of the GPU (or accelerator) used to accelerate
the simulation. This would be CUDA_DEVICE_ID or similar
if CUDA was used. This can be any valid OpenMM device string
precision: str
The desired precision for the simulation (e.g. `single`,
`mixed` or `double`)
com_reset_frequency:
Either the number of steps between center-of-mass resets,
or the time between resets. If this is unset, then
the center-of-mass is not reset during the simulation.
barostat_frequency:
Either the number of steps between MC moves to apply the
barostat, of the time between moves. If this is unset,
then the default of every 25 steps is used.
dynamic_constraints: bool
Whether or not to update the length of constraints of
perturbable bonds with lambda. This defaults to True,
meaning that changing lambda will change any constraint
on a perturbable bond to equal to the value of r0 at
that lambda value. If this is false, then the constraint
is set based on the current length.
map: dict
A dictionary of additional options. Note that any options
set in this dictionary that are also specified via one of
the arguments above will be overridden by the argument
value
""" # noqa: E501
from ..mol import _dynamics
return _dynamics(self, *args, **kwargs)
[docs]
def ensemble(self, map=None):
"""
Return the last ensemble that was used to simulate this system.
This returns a microcanonical ensemble if None was used
"""
from ..base import create_map
map = create_map(map)
try:
return self._system.property(map["ensemble"])
except Exception:
from ..move import Ensemble
return Ensemble.microcanonical()
[docs]
def set_ensemble(self, ensemble, map=None):
"""
Set the ensemble that was last used to simulate this system.
This is copied into the map["ensemble"] property
"""
from ..base import create_map
map = create_map(map)
self._system.set_property(map["ensemble"].source(), ensemble)
[docs]
def energy(self, *args, **kwargs):
"""Calculate and return the energy of this System
(or of the matching index/search subset of this System)
"""
return self.molecules().energy(*args, **kwargs)
[docs]
def energies(self, *args, **kwargs):
"""Calculate and return the individual energies of the
contents of this System (or of the matching index/search
subset of this System)
"""
return self.molecules().energies(*args, **kwargs)
[docs]
def charge(self, *args, **kwargs):
"""Return the total charge of this System (or of the matching
index/search subset of this System)
"""
return self.molecules().charge(*args, **kwargs)
[docs]
def mass(self, *args, **kwargs):
"""Return the total mass of this System (or of the matching
index/search subset of this System)
"""
return self.molecules().mass(*args, **kwargs)
[docs]
def coordinates(self, *args, **kwargs):
"""Return the center of geometry of this System (or of the matching
index/search subset of this System)
"""
return self.molecules().coordinates(*args, **kwargs)
[docs]
def space(self, map=None):
"""
Return the space used for this system
"""
try:
if map is None:
return self._system.property("space")
else:
from ..base import create_map
map = create_map(map)
return self._system.property(map["space"])
except Exception:
from ..vol import Cartesian
return Cartesian()
[docs]
def time(self, map=None):
"""
Return the current system time
"""
try:
if map is None:
return self._system.property("time")
else:
from ..base import create_map
map = create_map(map)
return self._system.property(map["time"])
except Exception:
from ..units import picosecond
return 0 * picosecond
[docs]
def set_space(self, space, map=None):
"""
Set the space to be used to hold all of the molecules
in this system
"""
from ..legacy.Vol import Space
if not issubclass(type(space), Space):
raise TypeError(
"You can only set the space to a type derived from "
"sire.vol.Space, e.g. sire.vol.PeriodicBox, "
"sire.vol.TriclinicBox or sire.vol.Cartesian. "
f"You cannot use a {type(space)}."
)
if map is None:
self._system.set_property("space", space)
else:
from ..base import create_map
map = create_map(map)
space_property = map["space"]
if space_property.has_source():
self._system.set_property(space_property.source(), space)
self._molecules = None
[docs]
def set_time(self, time, map=None):
"""
Set the current time for the system
"""
from ..units import picosecond
from ..base import wrap
if time == 0:
time = wrap(0 * picosecond)
else:
if not hasattr(time, "has_same_units"):
raise TypeError(
"You can only set the time to a value with units 'time', "
"e.g. 5 * sire.units.picosecond. "
f"You cannot use a {type(time)}."
)
if not time.has_same_units(picosecond):
raise TypeError(
"You can only set the time to a value of units time. You "
f"cannot use {time}."
)
time = wrap(time)
if map is None:
self._system.set_property("time", time)
else:
from ..base import create_map
map = create_map(map)
time_property = map["time"]
if time_property.has_source():
self._system.set_property(time_property.source(), time)
self._molecules = None
[docs]
def energy_trajectory(
self,
to_pandas: bool = False,
to_alchemlyb: bool = False,
energy_unit: str = "kcal/mol",
map=None,
):
"""
Return the energy trajectory for this System. This is the history
of energies evaluate during any dynamics runs. It could include
energies calculated at different values of lambda.
Parameters
----------
to_pandas: bool
Whether or not to return the energy trajectory as a
pandas DataFrame.
to_alchemlyb: bool
Whether or not to return the energy trajectory as a
pandas DataFrame that is formatted to usable in alchemlyb
energy_unit: str
Whichever of the alchemlyb energy units you want the output
DataFrame to use. This is in alchemlyb format, e.g.
`kcal/mol`, `kJ/mol`, or `kT`. This is only used if
`to_alchemlyb` is True.
"""
from ..base import create_map
map = create_map(map)
traj_propname = map["energy_trajectory"]
try:
traj = self._system.property(traj_propname)
except Exception:
traj = None
if traj is not None:
if traj.what() != "SireMaths::EnergyTrajectory":
if traj_propname.has_value():
raise TypeError(
f"You cannot force the use of a {type(traj)} "
"as an EnergyTrajectory"
)
traj = None
if traj is None:
# we need to create this trajectory
from ..maths import EnergyTrajectory
self._system.set_property(traj_propname.source(), EnergyTrajectory())
traj = self._system.property(traj_propname)
if to_pandas or to_alchemlyb:
try:
return traj.to_pandas(
to_alchemlyb=to_alchemlyb, energy_unit=energy_unit
)
except Exception:
ensemble = self.ensemble()
if ensemble.is_constant_temperature():
temperature = ensemble.temperature()
else:
temperature = None
return traj.to_pandas(
to_alchemlyb=to_alchemlyb,
temperature=temperature,
energy_unit=energy_unit,
)
else:
return traj
[docs]
def set_energy_trajectory(self, trajectory, map=None):
"""
Set the energy trajectory to the passed value
"""
from ..base import create_map
map = create_map(map)
traj_propname = map["energy_trajectory"]
if traj_propname.has_value():
return
if trajectory.what() != "SireMaths::EnergyTrajectory":
raise TypeError(
f"You cannot set a {type(trajectory)} as an " "energy trajectory!"
)
self._system.set_property(traj_propname.source(), trajectory)
[docs]
def clear_energy_trajectory(self, map=None):
"""
Completely clear any existing energy trajectory
"""
from ..base import create_map
map = create_map(map)
traj_propname = map["energy_trajectory"]
if traj_propname.has_value():
return
from ..maths import EnergyTrajectory
self._system.set_property(traj_propname.source(), EnergyTrajectory())
[docs]
def evaluate(self, *args, **kwargs):
"""Return an evaluator for this Systme (or of the matching
index/search subset of this System)"""
return self.molecules().evaluate(*args, **kwargs)
[docs]
def has_property(self, *args, **kwargs):
"""Return whether or not this system has the passed property"""
return self._system.contains_property(*args, **kwargs)
[docs]
def property(self, *args, **kwargs):
"""Return the System property that matches the passed key/arguments"""
return self._system.property(*args, **kwargs)
[docs]
def set_property(self, *args, **kwargs):
"""Set the System property according to the passed arguments"""
self._system.set_property(*args, **kwargs)
self._molecules = None
[docs]
def set_shared_property(self, name, value):
"""Set the shared System property according to the passed arguments"""
from ..base import wrap
self._system.set_shared_property(name, wrap(value))
self._molecules = None
[docs]
def add_shared_property(self, name, value=None):
"""
Add the shared System property called 'name' to this system.
If 'value' is supplied, then this also sets the property too.
"""
if value is None:
self._system.add_shared_property(name)
else:
from ..base import wrap
self._system.add_shared_property(name, wrap(value))
self._molecules = None
[docs]
def remove_shared_property(self, *args, **kwargs):
"""
Completely remove the specified shared property, and set this
as a non-shared property for the future
"""
self._system.remove_shared_property(*args, **kwargs)
self._molecules = None
[docs]
def remove_all_shared_properties(self, *args, **kwargs):
"""
Completely remove all shared properties, and set no properties
as being shared from this system
"""
self._system.remove_all_shared_properties(*args, **kwargs)
self._molecules = None
[docs]
def properties(self):
"""Return all of the System-level properties of this System"""
return self._system.properties()
[docs]
def property_keys(self):
"""Return the keys (IDs) of all of the System-level properties
of this System
"""
return self._system.property_keys()
[docs]
def shared_properties(self):
"""
Return all of the System properties that are being shared
(copied) to all contained molecules
"""
return self._system.shared_properties()
[docs]
def cursor(self):
"""
Return a sire.mol.Cursor that can be used to edit
the molecules in this System
"""
from ..mol._cursor import CursorsM
return CursorsM(self)
[docs]
def smiles(self, *args, **kwargs):
"""
Return the molecule views in this container as smiles strings. Include
hydrogens in 'include_hydrogens' is True. This returns a list
of smiles strings, in the same order as the views in the container
"""
return self.molecules().smiles(*args, **kwargs)
[docs]
def smarts(self, *args, **kwargs):
"""
Return the molecule views in this container as smarts strings. Include
hydrogens in 'include_hydrogens' is True. This returns a list
of smarts strings, in the same order as the views in the container
"""
return self.molecules().smarts(*args, **kwargs)
[docs]
def view(self, *args, **kwargs):
"""
View this System (or the matching index/search subset)
via a nglview viewer. Only works in an interactive
notebook session, e.g. in a Jupyter notebook
"""
return self.molecules().view(*args, **kwargs)
[docs]
def view2d(self, *args, **kwargs):
"""
Create a 2D representation of the molecules in this system.
If 'filename' is set then this will be written to that file. Otherwise
this will be returned for visualisation in a jupyter notebook.
"""
return self.molecules().view2d(*args, **kwargs)
[docs]
def add(self, molecules):
"""
Add the passed molecules to this system. This will only
add molecules that don't already exist in this system.
"""
if type(molecules) is list:
for molecule in molecules:
self.add(molecule)
return
from ..legacy.Mol import MGName
mgid = MGName("all")
if hasattr(molecules, "molecules"):
# rather convoluted way to get a 'Molecules' object...
mols = molecules.molecules().to_molecule_group().molecules()
self._system.add_if_unique(mols, mgid)
else:
self._system.add_if_unique(molecules, mgid)
self._molecules = None
[docs]
def remove(self, molecules):
"""
Remove the passed molecules from this system.
"""
if type(molecules) is list:
for molecule in molecules:
self.remove(molecule)
return
molnums = None
if hasattr(molecules, "molecules"):
molnums = molecules.molecules().mol_nums()
else:
molnums = [molecule.molecule().number()]
for molnum in molnums:
self._system.remove(molnum)
self._molecules = None
[docs]
def update(self, molecules):
"""
Update the molecules in this system so that they have
the same versions and data as the new molecules contained
in 'value'
"""
if type(molecules) is list:
for molecule in molecules:
self.update(molecule)
return
if hasattr(molecules, "molecules"):
self._system.update(molecules.molecules())
else:
self._system.update(molecules)
self._molecules = None
[docs]
def apply(self, *args, **kwargs):
"""
Apply (perform / map) the passed function (with associated arguments)
on all of the molecules in this System
"""
return self.molecules().apply(*args, **kwargs)
[docs]
def apply_reduce(self, *args, **kwargs):
"""
Apply (perform / map) the passed function (with associated arguments)
on all of the molecules in this System, reducing the result
using the passed reduction function
"""
return self.molecules().apply_reduce(*args, **kwargs)