measure_params Namespace Reference

Functions
def	norm
def	cross
def	dot
def	vec_diff
def	normalize
def	compute_squared_dist
def	compute_dist
def	compute_angle
def	compute_torsion

Function Documentation

def measure_params.compute_angle	(		v1,
			v2
	)

calculates the angle between two vectors.
v1 and v2 are array objects.
returns a float containing the angle in radians.

References numeric::conversions.degrees(), dot(), and norm().

Referenced by compute_torsion().

def measure_params.compute_dist	(		coord1,
			coord2
	)

compute the distance between two xyz vector (3D).

References compute_squared_dist().

Referenced by erraser_util.find_nearby_res(), and erraser_util.pdb2rosetta().

def measure_params.compute_squared_dist	(		coord1,
			coord2
	)

compute the squared distance between two xyz vector (3D).

Referenced by compute_dist(), and erraser_util.res_wise_rmsd().

def measure_params.compute_torsion	(		v1,
			v2,
			v3,
			v4
	)

Returns a float value for the dihedral angle between
the four vectors. They define the bond for which the
torsion is calculated (~) as:
V1 - V2 ~ V3 - V4

References compute_angle(), cross(), dot(), erraser_util.error_exit(), norm(), normalize(), and vec_diff().

Referenced by erraser_util.find_chi_angle(), erraser_single_res_analysis.find_chi_angle_std_pdb(), and erraser_analysis.find_chi_angle_std_pdb().

def measure_params.cross	(		a,
			b
	)

Cross product.

Referenced by pyrosetta.tests.numeric.test_alignment.TestAlignment._rotation_matrix(), HDmakerMover.apply(), compute_torsion(), zinc_stats::ZincStatisticGenerator.recursively_model_rotamer_chis(), erraser_util.regularize_OP1_OP2(), and slice_ellipsoid_envelope().

def measure_params.dot	(		a,
			b
	)

Dot product.

Referenced by compute_angle(), compute_torsion(), norm(), and erraser_util.regularize_OP1_OP2().

def measure_params.norm

(

a

)

Norm of vector.

References dot().

Referenced by pyrosetta.tests.numeric.test_alignment.TestAlignment._rotation_matrix(), pyrosetta.toolbox.numpy_utils.calc_dihedral(), compute_angle(), compute_torsion(), numeric.distance(), numeric::model_quality.fixEigenvector(), normalize(), numeric::model_quality.rsym_eigenval(), and numeric::model_quality.rsym_rotation().

def measure_params.normalize

(

a

)

Normalize a vector.

References norm().

Referenced by compute_torsion().

def measure_params.vec_diff	(		a,
			b
	)

Return difference vector.

Referenced by compute_torsion(), and erraser_util.regularize_OP1_OP2().