measure_params Namespace Reference

Functions
def	norm (a)
def	cross (a, b)
def	dot (a, b)
def	vec_diff (a, b)
def	normalize (a)
def	compute_squared_dist (coord1, coord2)
def	compute_dist (coord1, coord2)
def	compute_angle (v1, v2)
def	compute_torsion (v1, v2, v3, v4)

Function Documentation

compute_angle()

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().

compute_dist()

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().

compute_squared_dist()

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().

compute_torsion()

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_analysis.find_chi_angle_std_pdb(), and erraser_single_res_analysis.find_chi_angle_std_pdb().

cross()

def measure_params.cross	(		a,
			b
	)

Cross product.

Referenced by pyrosetta.tests.numeric.test_alignment.TestAlignment._rotation_matrix(), align_carboxyl_m8(), Tet4HMatchAligner.align_info(), HDmakerMover.apply(), ch_o_pdbstats_from_pose(), change_floating_sc_geometry(), compute_torsion(), dock(), get_base_coordinate_system(), get_base_pair_coordinate_system(), get_base_pucker(), get_coordinate_system(), get_phosphate_stub(), ik_his_clamp(), isctfast(), zinc_stats::ZincStatisticGenerator.recursively_model_rotamer_chis(), erraser_util.regularize_OP1_OP2(), run(), run_m8(), run_tyr_his(), sicfast(), slice_ellipsoid_envelope(), make_comparison.torsion(), and internal_coordinates.torsion().

dot()

def measure_params.dot	(		a,
			b
	)

Dot product.

Referenced by make_comparison.angle(), internal_coordinates.angle(), assign_stack_faces(), calculate_theoretical_RNA_length_with_bond_angle_dependence(), ch_o_pdbstats_from_pose(), check_contact_and_output(), check_filter_base_stack(), compute_angle(), compute_torsion(), dock(), generate_from_fiber(), get_base_pucker(), hbond_stats(), isctfast(), kono_sarai_stats(), kono_sarai_zscore(), main(), norm(), pointGroupHit.pointGroupHit(), erraser_util.regularize_OP1_OP2(), rna_stack_pdbstats_from_pose(), run_diiron_glu(), run_m8(), run_tyr_his(), sicfast(), make_comparison.torsion(), and internal_coordinates.torsion().

norm()

def measure_params.norm

(

a

)

Norm of vector.

References dot().

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

normalize()

def measure_params.normalize

(

a

)

Normalize a vector.

References norm().

Referenced by compute_torsion().

vec_diff()

def measure_params.vec_diff	(		a,
			b
	)

Return difference vector.

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