Source code for BioSimSpace.Box._box

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# BioSimSpace: Making biomolecular simulation a breeze!
#
# Copyright: 2017-2023
#
# Authors: Lester Hedges <lester.hedges@gmail.com>
#
# BioSimSpace is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# BioSimSpace is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with BioSimSpace. If not, see <http://www.gnu.org/licenses/>.
#####################################################################

"""Functionality for generating box parameters."""

__author__ = "Lester Hedges"
__email__ = "lester.hedges@gmail.com"

__all__ = [
    "boxTypes",
    "generateBoxParameters",
    "cubic",
    "rhombicDodecahedronSquare",
    "rhombicDodecahedronHexagon",
    "truncatedOctahedron",
]

from sire.legacy.Maths import Vector as _Vector
from sire.legacy.Vol import TriclinicBox as _TriclinicBox

from ..Types import Angle as _Angle
from ..Types import Length as _Length


[docs] def generateBoxParameters(box_type, image_distance): """ Generate parameters for the named box type with specified image distance. Parameters ---------- box_type : str The name of the box type. Run BioSimSpace.Box.boxTypes() to get a list of the supported boxes. image_distance : :class:`Length <BioSimSpace.Types.Length>` The image distance. Returns ------- box : [:class:`Length <BioSimSpace.Types.Length>`] The box vector magnitudes. angles : [:class:`Angle <BioSimSpace.Types.Angle>`] The box vector angles: yz, xz, and xy. """ if not isinstance(box_type, str): raise TypeError("'box_type' must be of type 'str'") else: # Strip whitespace and convert to lower case. box_type = box_type.replace(" ", "").lower() if box_type not in _box_types_lower: raise ValueError("Supported box types are: %s" % boxTypes()) return _box_types_dict[box_type](image_distance)
[docs] def cubic(image_distance): """ Generate parameters for a cubic box. Parameters ---------- image_distance : :class:`Length <BioSimSpace.Types.Length>` The image distance. Returns ------- box : [:class:`Length <BioSimSpace.Types.Length>`] The box vector magnitudes. angles : [:class:`Angle <BioSimSpace.Types.Angle>`] The box vector angles: yz, xz, and xy. """ # Validate arguments. if not isinstance(image_distance, _Length): raise TypeError("'image_distance' must be of type 'BioSimSpace.Types.Length'.") if image_distance.value() <= 0: raise ValueError("'image_distance' must be greater than zero.") box = 3 * [image_distance] angles = 3 * [_Angle(90, "degrees")] return box, angles
[docs] def rhombicDodecahedronSquare(image_distance): """ Generate parameters for a square rhombic dodecahedron. Parameters ---------- image_distance : :class:`Length <BioSimSpace.Types.Length>` The image distance. Returns ------- box : [:class:`Length <BioSimSpace.Types.Length>`] The box vector magnitudes. angles : [:class:`Angle <BioSimSpace.Types.Angle>`] The box vector angles: yz, xz, and xy. """ # Validate arguments. if not isinstance(image_distance, _Length): raise TypeError("'image_distance' must be of type 'BioSimSpace.Types.Length'.") if image_distance.value() <= 0: raise ValueError("'image_distance' must be greater than zero.") # Create the triclinic box. triclinic_box = _TriclinicBox.rhombicDodecahedronSquare( image_distance.angstroms().value() ) return _get_box_parameters(triclinic_box)
[docs] def rhombicDodecahedronHexagon(image_distance): """ Generate parameters for a hexagonal rhombic dodecahedron. Parameters ---------- image_distance : :class:`Length <BioSimSpace.Types.Length>` The image distance. Returns ------- box : [:class:`Length <BioSimSpace.Types.Length>`] The box vector magnitudes. angles : [:class:`Angle <BioSimSpace.Types.Angle>`] The box vector angles: yz, xz, and xy. """ # Validate arguments. if not isinstance(image_distance, _Length): raise TypeError("'image_distance' must be of type 'BioSimSpace.Types.Length'.") if image_distance.value() <= 0: raise ValueError("'image_distance' must be greater than zero.") # Create the triclinic box. triclinic_box = _TriclinicBox.rhombicDodecahedronHexagon( image_distance.angstroms().value() ) return _get_box_parameters(triclinic_box)
[docs] def truncatedOctahedron(image_distance): """ Generate parameters for a truncated octahedron. Parameters ---------- image_distance : :class:`Length <BioSimSpace.Types.Length>` The image distance. Returns ------- box : [:class:`Length <BioSimSpace.Types.Length>`] The box vector magnitudes. angles : [:class:`Angle <BioSimSpace.Types.Angle>`] The box vector angles: yz, xz, and xy. """ # Validate arguments. if not isinstance(image_distance, _Length): raise TypeError("'image_distance' must be of type 'BioSimSpace.Types.Length'.") if image_distance.value() <= 0: raise ValueError("'image_distance' must be greater than zero.") # Create the triclinic box. triclinic_box = _TriclinicBox.truncatedOctahedron( image_distance.angstroms().value() ) return _get_box_parameters(triclinic_box)
def _get_box_parameters(triclinic_box): """ Internal helper function to get parameters for the passed triclinic box. Parameters ---------- triclinic_box : :class `TriclinicBox <Sire.Vol.TriclinicBox>` Returns ------- box : [:class:`Length <BioSimSpace.Types.Length>`] The box vector magnitudes. """ box = [ _Length(triclinic_box.vector0().magnitude(), "angstrom"), _Length(triclinic_box.vector1().magnitude(), "angstrom"), _Length(triclinic_box.vector2().magnitude(), "angstrom"), ] angles = [ _Angle( _Vector.angle(triclinic_box.vector1(), triclinic_box.vector2()).value(), "radians", ).degrees(), _Angle( _Vector.angle(triclinic_box.vector0(), triclinic_box.vector2()).value(), "radians", ).degrees(), _Angle( _Vector.angle(triclinic_box.vector0(), triclinic_box.vector1()).value(), "radians", ).degrees(), ] return box, angles # Create a list of the box type names. # This needs to come after all of the box functions. _box_types = [] # List of box types (actual names). _box_types_lower = [] # List of lower case names. _box_types_dict = {} # Mapping between lower case names and functions. import sys as _sys _namespace = _sys.modules[__name__] for _var in dir(): if _var[0] != "_" and _var[0].upper() != "G": _box_types.append(_var) _box_types_lower.append(_var.lower()) _box_types_dict[_var.lower()] = getattr(_namespace, _var) del _namespace del _sys del _var
[docs] def boxTypes(): """ Return a list of the supported box types. Returns ------- box_types_fields : [str] A list of the supported box types. """ return _box_types