box
- mdtools.check.box(box, with_angles=None, orthorhombic=False, allow_negative=False, allow_zero=False, dim=None, dtype=None)[source]
Check if the input array satisfies the conditions for a simulation box array in length-angle representation.
Arrays that contain the dimensions of simulation boxes in the length-angle representation must meet the following requirements:
Must be of an array_like type, i.e. a type that can be converted to a
numpy.ndarray
.Must have a data type equal to the supplied dtype.
If the array does not contain the box angles:
Must be of shape
(3,)
or(k, 3)
, wherek
is the number of frames.
If the array contains the box angles:
Must be of shape
(6,)
or(k, 6)
.The angles must be greater than 0 and less than 180°.
- Parameters:
box (
array_like
) – The array to check.with_angles (
None
orbool
, optional) – IfNone
(default), whether the box contains angles or not is inferred from the shape of the last dimension of box. If the last dimension has shape(3,)
, box is considered to not contain angles, if it has shape(6,)
, box is considered to contain angles. If with_angles isTrue
orFalse
the box must or must not contain angles, otherwise an exception is raised.orthorhombic (
bool
, optional) – IfTrue
and with_angles evaluates toTrue
, all angles of box must be 90°. Is ignored if with_angles isFalse
or if box does not contain angle information.allow_negative (
bool
, optional) – IfTrue
, allow negative box lengths (but not zero).allow_zero (
bool
, optional) – IfTrue
, allow box lengths to be zero.dim (
{None, 1, 2}
, optional) – The dimension expected for box. Default isNone
, which means that the dimension of box must be either 1 or 2. If box should contain the box parameters for only one frame, set dim to 1. If box should contain the box parameters for multiple frames, set dim to 2.dtype (
type
, optional) – The data type expected for box. Default isNone
, which means that the data type of box is not checked.
- Returns:
box (
numpy.ndarray
) – The input array asnumpy.ndarray
.- Raises:
ValueError – If box has an incorrect shape; incorrect dimensionality; an invalid angle; an invalid box length. Or if dim is not
None
and neither one or two. Seemdtools.check.array()
for further potentially raised exceptions.
See also
mdtools.check.box_mat()
Check if the input array satisfies the conditions for a simulation box matrix.
mdtools.check.array()
Check if an array meets given requirements
mdtools.check.pos_array()
Check if an array is a suitable position array