build_jacobian Namespace Reference

Functions
def	normalize (array)

Variables
	r_n
	r_ca
	r_c
	jacobian = zeros((4, 4))
	r_1 = array([r_n[0], r_ca[0], r_n[1], r_ca[1], r_n[2], r_ca[2]])
	r_2 = array([r_ca[0], r_c[0], r_ca[1], r_c[1], r_ca[2], r_c[2]])
def	axis = normalize(r_2 - r_1)
	cross_56 = cross(axis[4], axis[5])
	distance = r_1[5] - r_1[i]
def	direction = axis[i]
int	result = 1 / abs(det(jacobian))

Function Documentation

normalize()

def build_jacobian.normalize

(

array

)

References sum().

Variable Documentation

axis

def build_jacobian.axis = normalize(r_2 - r_1)

cross_56

build_jacobian.cross_56 = cross(axis[4], axis[5])

direction

def build_jacobian.direction = axis[i]

Referenced by calculate_helical_parameters(), and protocols::hotspot_hashing.tryParseLSMSpec().

distance

build_jacobian.distance = r_1[5] - r_1[i]

Referenced by SuperDeviationMover.apply(), SpartaSuperDeviationMover.apply(), apps::pilot::HelixMover.apply(), JDmover.apply(), HotspotPlacementMover.apply(), assign_models(), average_degree(), Tet4HMatchAligner.bondedN(), calc_contacts(), calculate_theoretical_RNA_length(), HbondZincBackbone.carbonyl_hbond_search(), change_floating_sc_geometry(), check_coords_match(), choose_centroids(), compute_chi(), HECTMover.create_extra_output(), distance_from_line2D(), dock(), find_clusters(), lactamize.find_lactams(), find_residues_around_mutation(), fit_helix_in_map(), get_atom_vdw(), get_contacts(), get_distance_around_rna_base(), get_distances(), get_distances_around_rna_backbone(), get_interface_type(), get_num_nbrs(), get_RNA_binding_residues(), utility::vector1< bool, A >.index(), utility::vector1< T, A >.index(), interface_between_chains(), utility::graph::RingDetection< Graph >.LengthOfSmallestCycleWithVertex(), main(), mg_hires_pdbstats_from_pose(), mg_pdbstats_from_pose(), neighbor_count(), ui::task::Node.node_index(), place_water_acceptor(), place_water_donor(), DisulfideBondEnergy.probability(), DisulfideBondEnergy.rebuildAndDetectDisulfideBond(), apps::pilot::momeara::HBondConformation.relax_pose_around_hbond(), FragmentAssemblyMover.run(), run_tyr_his(), run_zn2his(), search_other_atoms(), apps::pilot::HelixMover.slide_non_ideal_helix(), utility::keys::ClassKeyVector< K, T, C >.sort(), sphere_cen_nc_calculator(), sphere_FA_nc_anyatom_calculator(), sphere_FA_nc_calculator(), PhProtocol.titrate_pH(), utility::graph::RingSizeVisitor< Graph, DistanceMap, LabelMap >.tree_edge(), apps::public1::scenarios::chemically_conjugated_docking.ubq_ras_distance(), and update_double_vesicle().

jacobian

build_jacobian.jacobian = zeros((4, 4))

r_1

build_jacobian.r_1 = array([r_n[0], r_ca[0], r_n[1], r_ca[1], r_n[2], r_ca[2]])

r_2

build_jacobian.r_2 = array([r_ca[0], r_c[0], r_ca[1], r_c[1], r_ca[2], r_c[2]])

r_c

build_jacobian.r_c

Initial value:

=  array([
    [  99.429, 40.636, 55.791 ],
    [ 101.057, 42.540, 58.216 ],
    [  99.665, 42.264, 61.706 ]])

r_ca

build_jacobian.r_ca

Initial value:

=  array([
    [  98.448, 39.501, 55.622 ],
    [ 100.335, 42.688, 56.897 ],
    [ 100.816, 42.188, 60.731 ]])

r_n

build_jacobian.r_n

Initial value:

=  array([
    [  97.259, 39.712, 56.443 ],
    [  99.345, 41.629, 56.722 ],
    [ 100.357, 42.410, 59.363 ]])

result

int build_jacobian.result = 1 / abs(det(jacobian))