geomm.superimpose module

geomm.superimpose.superimpose(ref_coords, coords, idxs=None, weights=None)

Superimpose a set of coordinates to reference coordinates using the Theobald-QCP method.

Assumes coordinates are centered appropriately.

Parameters

• ref_coords (arraylike) – The template coordinates that coords will be aligned to.

• coords (arraylike) – The coordinates which will be aligned to the template coordinates and have the rotation matrix applied to them and returned.

• idxs (arraylike, optional) –

  If given will superimpose the coordinates based only on the

  alignment on this subset of atoms to the reference.

  (Default = None)

• weights (arraylike, optional) –

  Give weights to the coordinates for a weighted centroid

  (‘center of mass’) used in translations to the origin and to the centroid of the reference structure.

  (Default = None)

Returns

• superimposed_coords (arraylike of float) – The transformed coordinates.

• rotation_matrix (arraylike) – The rotation matrix from Theobald-QCP that minimized the RMSD

• qcp_rmsd (float) – The RMSD calculated from Theobald-QCP.

Warning

Assumes that the coordinates are both centered.

geomm.superimpose.alt_superimpose(ref_coords, coords)

Returns the translation and rotation mapping mobile onto target.

Parameters

• mobile (ndarray, shape = (n_atoms, 3)) – xyz coordinates of a single frame, to be aligned onto target.

• target (ndarray, shape = (n_atoms, 3)) – xyz coordinates of a single frame

Returns

• translation (ndarray, shape=(3,)) – Difference between the centroids of the two conformations

• rotation (ndarray, shape=(3,3)) – Rotation matrix to apply to mobile to carry out the transformation.