API documentation
API documentation for the distopia python layer
distopia.calc_bonds_no_box(coords0, coords1, results=None)calc_bonds_no_box(signatures, args, kwargs, defaults, _fused_sigindex={}) Calculate 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.calc_bonds_ortho(coords0, coords1, box, results=None)calc_bonds_ortho(signatures, args, kwargs, defaults, _fused_sigindex={}) Calculate 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.calc_bonds_triclinic(coords0, coords1, box, results=None)calc_bonds_triclinic(signatures, args, kwargs, defaults, _fused_sigindex={}) Calculate 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.calc_angles_no_box(coords0, coords1, coords2, results=None)calc_angles_no_box(signatures, args, kwargs, defaults, _fused_sigindex={}) Calculate 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.calc_angles_ortho(coords0, coords1, coords2, box, results=None)calc_angles_ortho(signatures, args, kwargs, defaults, _fused_sigindex={}) Calculate 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.calc_angles_triclinic(coords0, coords1, coords2, box, results=None)calc_angles_triclinic(signatures, args, kwargs, defaults, _fused_sigindex={}) Calculate 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.calc_dihedrals_no_box(coords0, coords1, coords2, coords3, results=None)calc_dihedrals_no_box(signatures, args, kwargs, defaults, _fused_sigindex={}) Calculate 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.calc_dihedrals_ortho(coords0, coords1, coords2, coords3, box, results=None)calc_dihedrals_ortho(signatures, args, kwargs, defaults, _fused_sigindex={}) Calculate 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.calc_dihedrals_triclinic(coords0, coords1, coords2, coords3, box, results=None)calc_dihedrals_triclinic(signatures, args, kwargs, defaults, _fused_sigindex={}) Calculate 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.calc_distance_array_no_box(coords0, coords1, results=None)calc_distance_array_no_box(signatures, args, kwargs, defaults, _fused_sigindex={}) Calculate 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.calc_distance_array_ortho(coords0, coords1, box, results=None)calc_distance_array_ortho(signatures, args, kwargs, defaults, _fused_sigindex={}) Calculate 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.calc_distance_array_triclinic(coords0, coords1, box, results=None)calc_distance_array_triclinic(signatures, args, kwargs, defaults, _fused_sigindex={}) Calculate 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.calc_self_distance_array_no_box(coords0, results=None)calc_self_distance_array_no_box(signatures, args, kwargs, defaults, _fused_sigindex={}) Calculate 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.calc_self_distance_array_ortho(coords0, box, results=None)calc_self_distance_array_ortho(signatures, args, kwargs, defaults, _fused_sigindex={}) Calculate 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.calc_self_distance_array_triclinic(coords0, box, results=None)calc_self_distance_array_triclinic(signatures, args, kwargs, defaults, _fused_sigindex={}) Calculate 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