API documentation

API documentation for the distopia python layer

distopia.distances_no_box(coords0, coords1, results=None)

distances_no_box(signatures, args, kwargs, defaults, _fused_sigindex={}) ulate pairwise distances between coords0 and coords1 with no periodic boundary conditions

Parameters
----------
coords0, coords1 : float32 or float64 array
  must be same length and same dtype
results: float32 of float 64 array (optional)
  array to store results in, must be same size and dtype as coords0/coords1

Returns
-------
distances : np.array
  same length and dtype as coords0/coords1

distopia.distances_ortho(coords0, coords1, box, results=None)

distances_ortho(signatures, args, kwargs, defaults, _fused_sigindex={}) ulate pairwise distances between coords0 and coords1 under orthorhombic boundary conditions

Parameters
----------
coords0, coords1 : float32 or float64 array
  must be same length and dtype
box : float32 or float64 array
  orthorhombic periodic boundary dimensions in [L, L, L] format
results: float32 or float64 array (optional)
  array to store results in, must be same length and dtype as coords0/coords1

Returns
-------
distances : np.array
  same length and dtype as coords0/coords1

distopia.distances_triclinic(coords0, coords1, box, results=None)

distances_triclinic(signatures, args, kwargs, defaults, _fused_sigindex={}) ulate pairwise distances between coords0 and coords1 under triclinic boundary conditions

Parameters
----------
coords0, coords1 : float32 or float64 array
  must be same length and dtype
box : float32 or float64 array
  periodic boundary dimensions, in 3x3 format
results: float32 or float64 array (optional)
  array to store results in, must be same length and dtype as coords0/coords1

Returns
-------
distances : np.array
  same length and dtype as coords0/coords1

distopia.angles_no_box(coords0, coords1, coords2, results=None)

angles_no_box(signatures, args, kwargs, defaults, _fused_sigindex={}) ulate angles between sets of coordinates with no periodic boundary conditions

Parameters
----------
coords0, coords1, coords2 : float32 or float64 array
  must be same length and dtype
results: float32 or float64 array (optional)
    array to store results in, must be same length and dtype as coords0/coords1/coords2

Returns
-------
angles : np.array
  same length and dtype as coords0/coords1/coords2

distopia.angles_ortho(coords0, coords1, coords2, box, results=None)

angles_ortho(signatures, args, kwargs, defaults, _fused_sigindex={}) ulate angles between sets of coordinates under orthorhombic boundary conditions

Parameters
----------
coords0, coords1, coords2 : float32 or float64 array
  must be same length and dtype
box : float32 or float64 array
    orthorhombic periodic boundary dimensions in [L, L, L] format
results: float32 or float64 array (optional)
    array to store results in, must be same length and dtype as coords0/coords1/coords2

Returns
-------
angles : np.array
  same length and dtype as coords0/coords1/coords2

distopia.angles_triclinic(coords0, coords1, coords2, box, results=None)

angles_triclinic(signatures, args, kwargs, defaults, _fused_sigindex={}) ulate angles between sets of coordinates under triclinic boundary conditions

Parameters
----------
coords0, coords1, coords2 : float32 or float64 array
    must be same length and dtype
box : float32 or float64 array
    periodic boundary dimensions, in 3x3 format
results: float32 or float64 array (optional)
    array to store results in, must be same length and dtype as coords0/coords1/coords2

Returns
-------
angles : np.array
    same length and dtype as coords0/coords1/coords2

distopia.dihedrals_no_box(coords0, coords1, coords2, coords3, results=None)

dihedrals_no_box(signatures, args, kwargs, defaults, _fused_sigindex={}) ulate dihedral angles between sets of coordinates with no periodic boundary conditions

Parameters
----------
coords0, coords1, coords2, coords3 : float32 or float64 array
  must be same length and dtype
results: float32 or float64 array (optional)
    array to store results in, must be same length and dtype as coords0/coords1/coords2/coords3

Returns
-------
dihedrals : np.array
  same length and dtype as coords0/coords1/coords2/coords3

distopia.dihedrals_ortho(coords0, coords1, coords2, coords3, box, results=None)

dihedrals_ortho(signatures, args, kwargs, defaults, _fused_sigindex={}) ulate dihedral angles between sets of coordinates under orthorhombic boundary conditions

Parameters
----------
coords0, coords1, coords2, coords3 : float32 or float64 array
  must be same length and dtype
box : float32 or float64 array
    orthorhombic periodic boundary dimensions in [L, L, L] format
results: float32 or float64 array (optional)
    array to store results in, must be same length and dtype as coords0/coords1/coords2/coords3

Returns
-------
dihedrals : np.array
  same length and dtype as coords0/coords1/coords2/coords3

distopia.dihedrals_triclinic(coords0, coords1, coords2, coords3, box, results=None)

dihedrals_triclinic(signatures, args, kwargs, defaults, _fused_sigindex={}) ulate dihedral angles between sets of coordinates under triclinic boundary conditions

Parameters
----------
coords0, coords1, coords2, coords3 : float32 or float64 array
  must be same length and dtype
box : float32 or float64 array
    periodic boundary dimensions, in 3x3 format
results: float32 or float64 array (optional)
    array to store results in, must be same length and dtype as coords0/coords1/coords2/coords3

Returns
-------
dihedrals : np.array
  same length and dtype as coords0/coords1/coords2/coords3

distopia.distance_array_no_box(coords0, coords1, results=None)

distance_array_no_box(signatures, args, kwargs, defaults, _fused_sigindex={}) ulate pairwise distance matrix between coordinates with no periodic boundary conditions

Parameters
----------
coords0, coords1 : float32 or float64 array
  must be same length and dtype
results: float32 or float64 array (optional)
    array to store results in, must be of length MxN where M is the length of coords0 and N is the length of coords1

Returns
-------
distances : np.array
  MxN array of distances

distopia.distance_array_ortho(coords0, coords1, box, results=None)

distance_array_ortho(signatures, args, kwargs, defaults, _fused_sigindex={}) ulate pairwise distance matrix between coordinates under orthorhombic boundary conditions

Parameters
----------
coords0, coords1 : float32 or float64 array
  must be same length and dtype
box : float32 or float64 array
    orthorhombic periodic boundary dimensions in [L, L, L] format
results: float32 or float64 array (optional)
    array to store results in, must be  of length MxN where M is the length of coords0 and N is the length of coords1

Returns
-------
distances : np.array
  MxN array of distances

distopia.distance_array_triclinic(coords0, coords1, box, results=None)

distance_array_triclinic(signatures, args, kwargs, defaults, _fused_sigindex={}) ulate pairwise distance matrix between coordinates under triclinic boundary conditions

Parameters
----------
coords0, coords1 : float32 or float64 array
  must be same length and dtype
box : float32 or float64 array
    periodic boundary dimensions, in 3x3 format
results: float32 or float64 array (optional)
    array to store results in, must be of length MxN where M is the length of coords0 and N is the length of coords1

Returns
-------
distances : np.array
  MxN array of distances

distopia.self_distance_array_no_box(coords0, results=None)

self_distance_array_no_box(signatures, args, kwargs, defaults, _fused_sigindex={}) ulate self-pairwise distance matrix between coordinates with no periodic boundary conditions

Parameters
----------
coords0, float32 or float64 array
  must be same length and dtype
results: float32 or float64 array (optional)
    array to store results in, must be a single dimension of length N(N-1)/2 where N is the length of coords0

Returns
-------
distances : np.array
  N(N-1)/2 array of distances, a flattened upper triangle of the full NxN matrix with the diagonal removed

distopia.self_distance_array_ortho(coords0, box, results=None)

self_distance_array_ortho(signatures, args, kwargs, defaults, _fused_sigindex={}) ulate self-pairwise distance matrix between coordinates under orthorhombic periodic boundary conditions

Parameters
----------
coords0: float32 or float64 array
  must be same length and dtype
box : float32 or float64 array
    periodic boundary dimensions, in 3x3 format
results: float32 or float64 array (optional)
    array to store results in, must be a single dimension of length N(N-1)/2 where N is the length of coords0

Returns
-------
distances : np.array
  N(N-1)/2 array of distances, a flattened upper triangle of the full NxN matrix with the diagonal removed

distopia.self_distance_array_triclinic(coords0, box, results=None)

self_distance_array_triclinic(signatures, args, kwargs, defaults, _fused_sigindex={}) ulate self-pairwise distance matrix between coordinates under triclinic boundary conditions

Parameters
----------
coords0, coords1 : float32 or float64 array
  must be same length and dtype
box : float32 or float64 array
    periodic boundary dimensions, in 3x3 format
results: float32 or float64 array (optional)
    array to store results in, must be a single dimension of length NxN where M is the length of coords0

Returns
-------
distances : np.array
  N*(N-1)/2 array of distances, a flattened upper triangle of the full NxN matrix with the diagonal removed