API Periodic Boundary Conditions#

get_angles_from_box(box[, skip_digestion])

Extracting box angles from a box matrix.

get_box_from_lengths_and_angles(box_lengths, ...)

Building a box matrix from lengths and angles.

get_box_with_shape([shape, length, ...])

Constructing a box matrix for a given shape.

get_lengths_and_angles_from_box(box[, ...])

Return box lengths and angles from a 3x3 box matrix or an array of boxes.

get_lengths_from_box(box[, skip_digestion])

Extracting box edge lengths from a box matrix.

get_shape_from_angles(box_angles[, ...])

Determining box shape from its angles.

get_shape_from_box(box[, skip_digestion])

Inferring the box shape from its matrix.

get_volume_from_box(box)

Computing box volume from a box matrix.

get_volume_from_lengths_and_angles(...)

Computing box volume from lengths and angles.

has_pbc(molecular_system[, skip_digestion])

Check whether a molecular system has periodic boundary conditions (box).

unwrap(molecular_system[, selection, ...])

Unwrapping coordinates across periodic boundaries to produce continuous trajectories.

wrap_to_mic(molecular_system[, selection, ...])

Wrap coordinates into the minimum image convention (MIC) box.

wrap_to_pbc(molecular_system[, selection, ...])

Wrap coordinates into the primary periodic box.