besmarts.core.geometry module

besmarts.core.geometry

Functions to process the geometry of a molecular graph.

besmarts.core.geometry.angle(x)

besmarts.core.geometry.array_add(a, b)

besmarts.core.geometry.array_basis(a, b)

unit vector from a to b and its projection (magnitude)

besmarts.core.geometry.array_cross(a, b)

besmarts.core.geometry.array_difference(a, b)

besmarts.core.geometry.array_distance(a, b) → float

besmarts.core.geometry.array_inner_product(a, b)

besmarts.core.geometry.array_magnitude(a) → float

besmarts.core.geometry.array_multiply(a, b)

besmarts.core.geometry.array_outer_product(a, b)

besmarts.core.geometry.array_round(a, b)

besmarts.core.geometry.array_scale(a, s)

besmarts.core.geometry.array_unit(a, b)

unit vector from a to b

besmarts.core.geometry.bond(x)

besmarts.core.geometry.is_dihedral(combo, edges) → bool

besmarts.core.geometry.is_outofplane(combo, edges) → bool

besmarts.core.geometry.is_torsion(combo, edges) → bool

besmarts.core.geometry.jacobian2_angle(xyz1, xyz2, xyz3)

gives 3x3 1x9 arrays

besmarts.core.geometry.jacobian2_angle_term_reduce(coef, terms, cs, dq1, dq2)

besmarts.core.geometry.jacobian2_angle_terms(uu, uv, vv, lu, lv, cosq, sinq)

besmarts.core.geometry.jacobian2_distance(xyz1, xyz2)

from Bakken & Helgaker 2012 10.1063/1.1515483 gives 2x2 1x9 arrays per position, (4 3x3)

besmarts.core.geometry.jacobian2_distance_terms(u, lu)

besmarts.core.geometry.jacobian2_outofplane(xyz1, xyz2, xyz3, xyz4)

besmarts.core.geometry.jacobian2_reshape_to_matrix(b2)

Give the canonical 3Nx3N form

besmarts.core.geometry.jacobian2_torsion(xyz1, xyz2, xyz3, xyz4)

Returns 4x4 1x9s

besmarts.core.geometry.jacobian2_torsion_term_reduce(coef, terms)

besmarts.core.geometry.jacobian2_torsion_terms(u, v, w, lu, lv, lw, cosu, cosv)

besmarts.core.geometry.jacobian_angle(xyz1, xyz2, xyz3)

besmarts.core.geometry.jacobian_distance(xyz1, xyz2)

besmarts.core.geometry.jacobian_outofplane(xyz1, xyz2, xyz3, xyz4)

besmarts.core.geometry.jacobian_outofplane_v2(xyz1, xyz2, xyz3, xyz4)

besmarts.core.geometry.jacobian_torsion(xyz1, xyz2, xyz3, xyz4)

besmarts.core.geometry.jacobian_torsion_v2(xyz1, xyz2, xyz3, xyz4)

besmarts.core.geometry.measure_angle(xyz1, xyz2, xyz3)

besmarts.core.geometry.measure_dihedral(xyz1, xyz2, xyz3, xyz4)

besmarts.core.geometry.measure_distance(xyz1, xyz2)

besmarts.core.geometry.outofplane(x)

besmarts.core.geometry.pair(x)

besmarts.core.geometry.torsion(x)