mdciao.utils.COM

Functions related to Center-Of-Mass (COM) computations

Functions

geom2COMdist(igeom, residue_pairs)

Returns the distances between center-of-mass (COM) :param igeom: :type igeom: mdtraj.Trajectory :param residue_pairs: pairs of residues by their zero-indexed serial indexes :type residue_pairs: iterable of integer pairs

geom2COMxyz(igeom[, residue_idxs])

Returns the time trace of per-residue center-of-masses (COMs) in cartesian coordinates

mdciao.utils.COM.geom2COMdist(igeom, residue_pairs)

Returns the distances between center-of-mass (COM) :param igeom: :type igeom: mdtraj.Trajectory :param residue_pairs: pairs of residues by their zero-indexed serial indexes :type residue_pairs: iterable of integer pairs

Returns

COMs_array – contains the time-traces of the residue COMs

Return type

np.ndarray of shape(igeom.n_frames, len(res_pairs))

mdciao.utils.COM.geom2COMxyz(igeom, residue_idxs=None)

Returns the time trace of per-residue center-of-masses (COMs) in cartesian coordinates

Parameters
  • igeom (mdtraj.Trajectory) –

  • residue_idxs (iterable, default is None) – Residues for which the center of mass will be computed. Default is to compute all residues. The excluded residues will appear as np.nans in the returned value, which has the same shape regardless of the input

Returns

COMs

Return type

numpy.ndarray of shape (igeom.n_frames, igeom.n_residues,3)