internal_coordinates Namespace Reference

Functions
def	length (model, index)
def	angle (model, index)
def	torsion (model, index)

Variables
	parser = argparse.ArgumentParser()
	nargs
	arguments = parser.parse_args()
list	backbones = []
	loop = pdb.Model(path)
	backbone = loop.select_atoms('N', 'CA', 'C')
	wrap = len(backbones[0].coordinates)
list	indices = backbones[0].indices()
list	lengths = [length(backbone, index) for backbone in backbones]
list	readout = lengths[0], lengths[1], lengths[0] - lengths[1]
list	angles = [angle(backbone, index) for backbone in backbones]
list	torsions = [torsion(backbone, index) for backbone in backbones]

Function Documentation

angle()

def internal_coordinates.angle	(		model,
			index
	)

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

length()

def internal_coordinates.length	(		model,
			index
	)

References measure_params.norm().

torsion()

def internal_coordinates.torsion	(		model,
			index
	)

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

Referenced by apply_torsion_set(), compare_frags(), compute_intrinsic_deviation(), get_torsion_set(), main(), reroot_restype(), myspace::Scheduler.Scheduler(), torsion2bin(), and torsion2decoy().

Variable Documentation

angles

list internal_coordinates.angles = [angle(backbone, index) for backbone in backbones]

arguments

internal_coordinates.arguments = parser.parse_args()

backbone

internal_coordinates.backbone = loop.select_atoms('N', 'CA', 'C')

Referenced by apply_backbone(), backbone_sampling(), get_backbone(), and torsion2pdb().

backbones

list internal_coordinates.backbones = []

Referenced by apply_all(), get_all(), get_all_tor_id(), get_torsion_list(), hessian_estimate(), MC_run(), torsion2pdb(), and update_backbone().

indices

list internal_coordinates.indices = backbones[0].indices()

Referenced by CovalentPeptidomimeticCreator.apply(), numeric::MultiDimensionalHistogram.bin_index(), numeric::linear_algebra::GeneralizedEigenSolver< _MatrixType >.extract_real_indices(), numeric::interpolation::spline::PolycubicSpline< N >.get_all_derivs(), numeric::VoxelArray< _Float, _Value >.operator()(), numeric::interpolation::InterpolatedPotential< N >.operator()(), numeric::interpolation.polycubic_interpolation(), numeric::MathNTensor< T, N >.replace_layer(), numeric::VoxelArray< _Float, _Value >.resize(), pyrosetta.bindings.utility.slice_1base_indicies(), svm_get_sv_indices(), and numeric::interpolation::spline::PolycubicSpline< N >.train().

lengths

list internal_coordinates.lengths = [length(backbone, index) for backbone in backbones]

Referenced by detail.code_point_length().

loop

internal_coordinates.loop = pdb.Model(path)

Referenced by numeric::kinematic_closure::radians.bridge_objects(), numeric::kinematic_closure.bridgeObjects(), ccd_close_loop(), ccd_loop_close(), ccd_test(), copy_each_residue(), copy_using_constructor(), download_url(), id_from_index(), KIC_loop_close(), apps::pilot::KicSandbox.KicSandbox(), loop_closure_test(), main(), modeler_closure_test(), modelSSLoop(), print_internal_coordinates(), randomly_open_pose_loop(), register_options(), NativeEnsemble.set_loop(), and setup_pose_with_loop().

nargs

internal_coordinates.nargs

parser

internal_coordinates.parser = argparse.ArgumentParser()

readout

list internal_coordinates.readout = lengths[0], lengths[1], lengths[0] - lengths[1]

torsions

list internal_coordinates.torsions = [torsion(backbone, index) for backbone in backbones]

Referenced by create_starting_template(), get_all_tor_id(), hessian_estimate(), main(), UniformPerturber.perturb_chain(), and UniformPerturber.set_pose_after_closure().

wrap

internal_coordinates.wrap = len(backbones[0].coordinates)

Referenced by pyrosetta.distributed.packed_pose.core.pack_result().