__all__ = [
"align",
"create_quaternion",
"get_alignment",
"EnergyTrajectory",
"kabasch",
"kabasch_fit",
"Matrix",
"pi",
"rotate",
"RanGenerator",
"Sphere",
"Torsion",
"Transform",
"Triangle",
"Vector",
]
from ..legacy import Maths as _Maths
from ..legacy.Maths import (
Matrix,
Quaternion,
RanGenerator,
Triangle,
Transform,
Torsion,
pi,
EnergyTrajectory,
)
from ._vector import Vector
from ._sphere import Sphere
from .. import use_new_api as _use_new_api
_use_new_api()
try:
kabasch_fit = _Maths.kabaschFit
get_alignment = _Maths.getAlignment
except AttributeError:
kabasch_fit = _Maths.kabasch_fit
get_alignment = _Maths.get_alignment
kabasch = _Maths.kabasch
align = _Maths.align
[docs]
def rotate(point, angle=None, axis=None, matrix=None, quaternion=None, center=None):
"""
Rotate the passed point by the passed angle and axis, or the
passed matrix, or the passed quaternion, optionally centering
the rotation about the passed center.
point: sire.maths.Vector
The vector to be rotated
angle: (float or angle)
The angle to rotate by - this is interpreted as
degrees if you pass in a float. Otherwise use
sire.units.degrees or sire.units.radians to specify
the angle unit. This is superseded by the
matrix and quaternion arguments.
axis: sire.maths.Vector (or anything that can convert to a Vector)
The vector about which to rotate. If this is not
specified, and no other rotation specification is
used, then the rotation is about the z axis.
This is superseded by the matrix and
quaternion arguments.
quaternion: sire.maths.Quaternion
The Quaternion description of the rotation. Note that,
if you pass this, then the angle, axis and matrix
arguments will be ignored.
matrix: sire.maths.Matrix
The 3x3 rotation matrix that describes the rotation.
Note that, if you pass this, then the angle and axis
arguments will be ignored. This is superseded by
the quaternion argument.
center: sire.maths.Vector
The center of rotation. Defaults to (0,0,0) if not set.
Returns: sire.maths.Vector
The rotated vector
"""
q = create_quaternion(angle=angle, axis=axis, matrix=matrix, quaternion=quaternion)
if center is None:
center = Vector(0, 0, 0)
return _Maths.rotate(point, q.to_matrix(), center)
[docs]
def create_quaternion(angle=None, axis=None, matrix=None, quaternion=None):
"""Create a quaternion from the passed angle and axis
of the passed rotation matrix. If a rotation
matrix is passed then this will ignore the
passed angle and axis. If a quaternion is passed
then this will ignore the matrix, angle and axis
arguments.
angle: (float or angle)
The angle to rotate by - this is interpreted as
degrees if you pass in a float. Otherwise use
sire.units.degrees or sire.units.radians to specify
the angle unit. This is superseded by the
matrix and quaternion arguments.
axis: sire.maths.Vector (or anything that can convert to a Vector)
The vector about which to rotate. If this is not
specified, and no other rotation specification is
used, then the rotation is about the z axis.
This is superseded by the matrix and
quaternion arguments.
quaternion: sire.maths.Quaternion
The Quaternion description of the rotation. Note that,
if you pass this, then the angle, axis and matrix
arguments will be ignored.
matrix: sire.maths.Matrix
The 3x3 rotation matrix that describes the rotation.
Note that, if you pass this, then the angle and axis
arguments will be ignored. This is superseded by
the quaternion argument.
Returns: sire.maths.Quaternion
The quaternion that represents the rotation
"""
if quaternion is None:
if type(angle) is Quaternion:
# the user has passed in a quaternion as the first argument
return angle
if type(angle) is Matrix and matrix is None:
# the user has passed in a rotation matrix as the first argument
matrix = angle
angle = None
axis = None
if matrix is None:
if angle is None:
raise ValueError(
"You must specify either the angle, rotation matrix "
"or quaternion used to rotate the molecule."
)
from ..units import degrees
try:
valid_angle = angle.has_same_units(degrees)
except Exception:
try:
angle = float(angle) * degrees
valid_angle = True
except Exception:
valid_angle = False
if not valid_angle:
raise TypeError(
f"The passed angle of rotation ({angle}) has the wrong "
f"type ({type(angle)}). It should be an angle or a float."
)
if axis is None:
axis = Vector(0, 0, 1)
# construct from the passed angle and vector
return Quaternion(angle, Vector(axis))
else:
if angle is not None or axis is not None:
from ..utils import Console
Console.warning(
"The angle and/or axis of rotation will be ignored "
"because you have passed in a rotation matrix."
)
if type(matrix) is not Matrix:
raise TypeError(
f"The rotation matrix ({matrix}) must be of type "
f"sire.maths.Matrix. Type {type(matrix)} is not "
"supported."
)
return Quaternion(matrix)
else:
if matrix is not None:
from ..utils import Console
Console.warning(
"The rotation matrix will be ignored "
"because you have passed in a quaternion."
)
if angle is not None or axis is not None:
from ..utils import Console
Console.warning(
"The angle and/or axis of rotation will be ignored "
"because you have passed in a quaternion."
)
if type(quaternion) is not Quaternion:
raise TypeError(
f"The quaternion ({quaternion}) must be of type "
f"sire.maths.Quaternion. Type {type(quaternion)} is not "
"supported."
)
return quaternion
if not hasattr(EnergyTrajectory, "to_pandas"):
def _to_pandas(
obj, temperature=None, to_alchemlyb: bool = False, energy_unit: str = None
):
"""
Return the energy trajectory as a pandas DataFrame
Parameters
----------
temperature: temperature
The temperature of the simulation. If this is
not set then the temperature from this table's
`ensemble` or `temperature` property will be
used. Note that you only need a temperature
if you are converting to alchemlyb format.
to_alchemlyb: bool
This will format the DataFrame in a way that is
compatible with alchemlyb. This will allow the
DataFrame to be used as part of an alchemlyb
free energy calculation.
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 set to True.
"""
import pandas as pd
from ..units import picosecond, kcal_per_mol, kJ_per_mol
data = {}
convert_to_kt = False
if to_alchemlyb:
time_unit = picosecond
time_unit_string = "ps"
if energy_unit == "kT":
energy_unit = kcal_per_mol
energy_unit_string = "kT"
convert_to_kt = True
elif energy_unit == "kJ/mol":
energy_unit = kJ_per_mol
energy_unit_string = "kJ/mol"
else:
energy_unit = kcal_per_mol
energy_unit_string = "kcal/mol"
if temperature is None:
# look for the temperature in the ensemble property
if obj.has_property("ensemble"):
temperature = obj.property("ensemble").temperature()
# ok, try the temperature property
if temperature is None and obj.has_property("temperature"):
temperature = obj.property("temperature")
if temperature is None:
raise ValueError(
"You must specify the temperature of the simulation "
"when converting to alchemlyb format, or ensure that "
"the trajectory has an ensemble or temperature "
"property."
)
else:
time_unit = picosecond.get_default()
time_unit_string = time_unit.unit_string()
energy_unit = kcal_per_mol.get_default()
energy_unit_string = energy_unit.unit_string()
data["time"] = obj.times(time_unit)
keys = obj.label_keys()
keys.sort()
if convert_to_kt:
from ..units import k_boltz
kT = (k_boltz * temperature).to(kcal_per_mol)
for key in keys:
if to_alchemlyb and key == "lambda":
data["fep-lambda"] = obj.labels_as_numbers(key)
else:
# use float keys if possible
try:
column_header = float(key)
except Exception:
column_header = key
try:
data[column_header] = obj.labels_as_numbers(key)
except Exception:
data[column_header] = obj.labels(key)
keys = obj.keys()
keys.sort()
if to_alchemlyb:
keys.remove("kinetic")
keys.remove("potential")
for key in keys:
# use float keys if possible
try:
column_header = float(key)
except Exception:
column_header = key
nrgs = obj.energies(key, energy_unit)
if convert_to_kt:
nrgs = [x / kT for x in nrgs]
data[column_header] = nrgs
if to_alchemlyb:
df = pd.DataFrame(data).set_index(["time", "fep-lambda"])
else:
df = pd.DataFrame(data).set_index("time")
if temperature is not None:
from .. import u
from ..units import kelvin
df.attrs["temperature"] = u(temperature).to(kelvin)
df.attrs["energy_unit"] = energy_unit_string
df.attrs["time_unit"] = time_unit_string
return df
def _to_alchemlyb(obj, temperature=None, energy_unit: str = "kcal/mol"):
"""
Return the energy trajectory as an alchemlyb-formatted pandas DataFrame
Parameters
----------
temperature: temperature
The temperature of the simulation. If this is
not set then the temperature from this table's
`ensemble` or `temperature` property will be
used.
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`
Returns
-------
pandas.DataFrame
A pandas DataFrame that is compatible with alchemlyb.
"""
return obj.to_pandas(
temperature=temperature, to_alchemlyb=True, energy_unit=energy_unit
)
EnergyTrajectory.to_pandas = _to_pandas
EnergyTrajectory.to_alchemlyb = _to_alchemlyb