def compare(self, other, t_threshold=1e-3, r_threshold=1e-3):
"""Compare two transformations
The RMSD values of the rotation matrices and the translation vectors
are computed. The return value is True when the RMSD values are below
the thresholds, i.e. when the two transformations are almost
identical.
"""
return compute_rmsd(self.t, other.t) < t_threshold and compute_rmsd(self.r, other.r) < r_threshold
def compare(self, other, t_threshold=1e-3, r_threshold=1e-3):
"""Compare two transformations
The RMSD values of the rotation matrices and the translation vectors
are computed. The return value is True when the RMSD values are below
the thresholds, i.e. when the two transformations are almost
identical.
"""
return compute_rmsd(self.t, other.t) < t_threshold and compute_rmsd(
self.r, other.r) < r_threshold
def fit_rmsd(ras, rbs, weights=None):
"""Fit geometry rbs onto ras, returns more info than superpose
Arguments:
| ``ras`` -- a numpy array with 3D coordinates of geometry A,
shape=(N,3)
| ``rbs`` -- a numpy array with 3D coordinates of geometry B,
shape=(N,3)
Optional arguments:
| ``weights`` -- a numpy array with fitting weights for each
coordinate, shape=(N,)
Return values:
| ``transformation`` -- the transformation that brings geometry A into
overlap with geometry B
| ``rbs_trans`` -- the transformed coordinates of geometry B
| ``rmsd`` -- the rmsd of the distances between corresponding atoms in
geometry A and B
This is a utility routine based on the function superpose. It just
computes rbs_trans and rmsd after calling superpose with the same
arguments
"""
transformation = superpose(ras, rbs, weights)
rbs_trans = transformation * rbs
rmsd = compute_rmsd(ras, rbs_trans)
return transformation, rbs_trans, rmsd
def fit_rmsd(ras, rbs, weights=None):
"""Fit geometry rbs onto ras, returns more info than superpose
Arguments:
| ``ras`` -- a numpy array with 3D coordinates of geometry A,
shape=(N,3)
| ``rbs`` -- a numpy array with 3D coordinates of geometry B,
shape=(N,3)
Optional arguments:
| ``weights`` -- a numpy array with fitting weights for each
coordinate, shape=(N,)
Return values:
| ``transformation`` -- the transformation that brings geometry A into
overlap with geometry B
| ``rbs_trans`` -- the transformed coordinates of geometry B
| ``rmsd`` -- the rmsd of the distances between corresponding atoms in
geometry A and B
This is a utility routine based on the function superpose. It just
computes rbs_trans and rmsd after calling superpose with the same
arguments
"""
transformation = superpose(ras, rbs, weights)
rbs_trans = transformation * rbs
rmsd = compute_rmsd(ras, rbs_trans)
return transformation, rbs_trans, rmsd
def compare(self, other, r_threshold=1e-3):
"""Compare two rotations
The RMSD of the rotation matrices is computed. The return value
is True when the RMSD is below the threshold, i.e. when the two
rotations are almost identical.
"""
return compute_rmsd(self.r, other.r) < r_threshold
def compare(self, other, t_threshold=1e-3):
"""Compare two translations
The RMSD of the translation vectors is computed. The return value
is True when the RMSD is below the threshold, i.e. when the two
translations are almost identical.
"""
return compute_rmsd(self.t, other.t) < t_threshold
def compare(self, other, r_threshold=1e-3):
"""Compare two rotations
The RMSD of the rotation matrices is computed. The return value
is True when the RMSD is below the threshold, i.e. when the two
rotations are almost identical.
"""
return compute_rmsd(self.r, other.r) < r_threshold
def compare(self, other, t_threshold=1e-3):
"""Compare two translations
The RMSD of the translation vectors is computed. The return value
is True when the RMSD is below the threshold, i.e. when the two
translations are almost identical.
"""
return compute_rmsd(self.t, other.t) < t_threshold
