erraser_analysis Namespace Reference

Functions
def	find_chi_angle_std_pdb
def	syn_anti_check

Variables
tuple	file_path = os.path.split( os.path.abspath(__file__) )
tuple	pdb1 = abspath( sys.argv[1] )
tuple	pdb2 = abspath( sys.argv[2] )
int	clash1 = 0
int	clash2 = 0
tuple	START_rna_validate_data = phenix_rna_validate( pdb1 )
list	pucker1 = START_rna_validate_data['pucker']
list	bond1 = START_rna_validate_data['bond']
list	angle1 = START_rna_validate_data['angle']
list	suite1 = START_rna_validate_data['suite']
tuple	ERRASER_rna_validate_data = phenix_rna_validate( pdb2 )
list	pucker2 = ERRASER_rna_validate_data['pucker']
list	bond2 = ERRASER_rna_validate_data['bond']
list	angle2 = ERRASER_rna_validate_data['angle']
list	suite2 = ERRASER_rna_validate_data['suite']
tuple	suite_outlier1 = sum( ['!!' in suite[3] for suite in suite1] )
tuple	suite_outlier2 = sum( ['!!' in suite[3] for suite in suite2] )
list	lines = []
string	res = '%4s%2s%4s '
string	res1 = '%4s%2s%4s '
tuple	delta1 = float(line1[3])
string	info1 = '%8.1f/!!'
string	info2 = ' OK'
string	res2 = '%4s%2s%4s '
tuple	delta2 = float(line2[3])
list	temp = []
	line_split = i
list	atoms = line_split[3]
tuple	sigma = float(line_split[5])
tuple	chi_list1 = find_chi_angle_std_pdb( pdb1 )
tuple	chi_list2 = find_chi_angle_std_pdb( pdb2 )
tuple	diff = abs(i[1] - j[1])

Function Documentation

def erraser_analysis.find_chi_angle_std_pdb

(

input_pdb

)

References measure_params.compute_torsion(), ObjexxFCL.len(), basic::database.open(), and binder.replace().

def erraser_analysis.syn_anti_check

(

chi

)

Variable Documentation

list erraser_analysis.angle1 = START_rna_validate_data['angle']

Referenced by find_neighbors_directional().

list erraser_analysis.angle2 = ERRASER_rna_validate_data['angle']

Referenced by find_neighbors_directional().

tuple erraser_analysis.atoms = line_split[3]

Referenced by numeric::kinematic_closure::radians.bridge_objects(), numeric::kinematic_closure.bridgeObjects(), numeric::kinematic_closure.bridgeObjects_nonredundant(), numeric::kinematic_closure.chainParams(), numeric::kinematic_closure::radians.chainParams(), numeric::kinematic_closure.chainTORS(), numeric::kinematic_closure::radians.chainTORS(), numeric::kinematic_closure.chainXYZ(), numeric::kinematic_closure::radians.chainXYZ(), numeric::geometry::hashing::xyzStripeHashWithMeta< float >.init(), numeric::kinematic_closure.test_bridgeObjects(), numeric::kinematic_closure.test_chainParams(), numeric::kinematic_closure.test_chainTORS(), numeric::kinematic_closure.test_chainXYZ(), and numeric::geometry::hashing::xyzStripeHashWithMeta< float >.xyzStripeHashWithMeta().

list erraser_analysis.bond1 = START_rna_validate_data['bond']

list erraser_analysis.bond2 = ERRASER_rna_validate_data['bond']

tuple erraser_analysis.chi_list1 = find_chi_angle_std_pdb( pdb1 )

tuple erraser_analysis.chi_list2 = find_chi_angle_std_pdb( pdb2 )

tuple erraser_analysis.clash1 = 0

tuple erraser_analysis.clash2 = 0

tuple erraser_analysis.delta1 = float(line1[3])

Referenced by numeric::interpolation::spline::CubicSpline.train().

tuple erraser_analysis.delta2 = float(line2[3])

Referenced by numeric::interpolation::spline::CubicSpline.train().

int erraser_analysis.diff = abs(i[1] - j[1])

Referenced by numeric::expression_parser::DivideExpression.differentiate(), multiclass_probability(), numeric::VoxelGrid< typename >.SetupGrid(), and Solver.Solve().

tuple erraser_analysis.ERRASER_rna_validate_data = phenix_rna_validate( pdb2 )

tuple erraser_analysis.file_path = os.path.split( os.path.abspath(__file__) )

string erraser_analysis.info1 = '%8.1f/!!'

string erraser_analysis.info2 = ' OK'

erraser_analysis.line_split = i

list erraser_analysis.lines = []

Referenced by utility::io.get_lines_from_file_data(), binder.indent(), and binder.split().

tuple erraser_analysis.pdb1 = abspath( sys.argv[1] )

Referenced by add_rosetta_options_5().

tuple erraser_analysis.pdb2 = abspath( sys.argv[2] )

Referenced by add_rosetta_options_5(), and add_rosetta_options_6().

list erraser_analysis.pucker1 = START_rna_validate_data['pucker']

list erraser_analysis.pucker2 = ERRASER_rna_validate_data['pucker']

string erraser_analysis.res = '%4s%2s%4s '

string erraser_analysis.res1 = '%4s%2s%4s '

Referenced by AnchorFinderMover.apply(), do_color_by_score(), get_contact_list(), report_and_dump(), setup_rna_minimizer(), and PhProtocol.titrate_pH().

string erraser_analysis.res2 = '%4s%2s%4s '

Referenced by AnchorFinderMover.apply(), do_color_by_score(), get_contact_list(), main(), report_and_dump(), and PhProtocol.titrate_pH().

tuple erraser_analysis.sigma = float(line_split[5])

Referenced by main(), basic::sampling::orientations.pind(), and sigmoid_train().

tuple erraser_analysis.START_rna_validate_data = phenix_rna_validate( pdb1 )

list erraser_analysis.suite1 = START_rna_validate_data['suite']

list erraser_analysis.suite2 = ERRASER_rna_validate_data['suite']

tuple erraser_analysis.suite_outlier1 = sum( ['!!' in suite[3] for suite in suite1] )

tuple erraser_analysis.suite_outlier2 = sum( ['!!' in suite[3] for suite in suite2] )

list erraser_analysis.temp = []

Referenced by utility::graph::LowMemGraph< _Node, _Edge >.add_edge(), utility::graph::Graph.add_edge(), utility::Inline_File_Provider.file_exists(), numeric::nls.lm_enorm(), numeric::nls.lm_lmdif(), numeric::nls.lm_lmpar(), numeric::nls.lm_qrfac(), numeric::nls.lm_qrsolv(), utility::options::OptionCollection.load(), numeric::random.random_permutation(), numeric::random::RandomGenerator.random_range(), numeric::model_quality.rsym_rotation(), FragmentAssemblyMover.run(), basic::svd::SVD_Solver.run_score_svd_on_matrix(), basic::svd::SVD_Solver.run_score_svd_without_solving(), utility::graph::LowMemEdge.same_edge(), utility::graph::Edge.same_edge(), numeric::HomogeneousTransform< double >.set_xaxis_rotation_deg(), numeric::HomogeneousTransform< double >.set_xaxis_rotation_rad(), numeric::HomogeneousTransform< double >.set_yaxis_rotation_deg(), numeric::HomogeneousTransform< double >.set_yaxis_rotation_rad(), numeric::HomogeneousTransform< double >.set_zaxis_rotation_deg(), numeric::HomogeneousTransform< double >.set_zaxis_rotation_rad(), and numeric::xyzMatrix< T >.transpose().