Internal coordinates

Zmat

The Zmat class which is used to represent a molecule in non redundant, internal coordinates.

Zmat(frame[, metadata, _metadata])

The main class for dealing with internal Coordinates.

zmat_functions

A collection of functions operating on instances of Zmat.

Functions

apply_grad_cartesian_tensor(grad_X, zmat_dist)

Apply the gradient for transformation to cartesian space onto zmat_dist.

Contextmanagers

DummyManipulation(dummy_manipulation_allowed)	Contextmanager that controls the behaviour of safe_loc() and safe_iloc().
TestOperators(test_operators[, cls])	Switch the validity testing of zmatrices resulting from operators.
PureInternalMovement(pure_internal_mov[, cls])	Remove the translational and rotational degrees of freedom.
CleanDihedralOrientation(...[, cls])	Clean the orientation of dihedral references.

Redundant Internal Coordinates (RICs)

The RedundantInternalCoordinates class which is used to represent a molecule in redundant internal coordinates, along with the related methods. And the DeltaRedundantInternalCoordinates class which is used to represent differences of RICs.

RedundantInternalCoordinates(q, ...)
DeltaRedundantInternalCoordinates(delta_q, ...)

RIC functions

A collection of functions operating on instances of RedundantInternalCoordinates or DeltaRedundantInternalCoordinates.

RIC_interpolate(start, end, N, *[, opt_alg, ...])	Generates an N-image interpolation between start and end.
get_primitives_idx(start, end[, bonds, ...])	Returns the set of primitive internal coordinates for a pair of start and end structures.
DefaultWeights([bond, angle, dihedral, bending])	Default weights for the cost function in the weighted least-squares.