erraser_analysis Namespace Reference

Functions
def	find_chi_angle_std_pdb (input_pdb)
def	syn_anti_check (chi)

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

Function Documentation

find_chi_angle_std_pdb()

def erraser_analysis.find_chi_angle_std_pdb

(

input_pdb

)

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

syn_anti_check()

def erraser_analysis.syn_anti_check

(

chi

)

Variable Documentation

angle1

list erraser_analysis.angle1 = START_rna_validate_data['angle']

Referenced by find_neighbors_directional(), get_interface_residues(), CrystDesign.get_interface_residues(), get_neighbor_residues(), CrystDesign.get_neighbor_residues(), and make_bonded_rna_move().

angle2

list erraser_analysis.angle2 = ERRASER_rna_validate_data['angle']

Referenced by find_neighbors_directional(), get_interface_residues(), CrystDesign.get_interface_residues(), get_neighbor_residues(), CrystDesign.get_neighbor_residues(), and make_bonded_rna_move().

atoms

string erraser_analysis.atoms = line_split [3] + '-' + line_split[4]

bond1

list erraser_analysis.bond1 = START_rna_validate_data['bond']

Referenced by add_constraints(), make_bonded_rna_move(), and RerootEdgeSorter.operator()().

bond2

list erraser_analysis.bond2 = ERRASER_rna_validate_data['bond']

Referenced by add_constraints(), and RerootEdgeSorter.operator()().

chi_list1

def erraser_analysis.chi_list1 = find_chi_angle_std_pdb( pdb1 )

chi_list2

def erraser_analysis.chi_list2 = find_chi_angle_std_pdb( pdb2 )

clash1

erraser_analysis.clash1 = 0

Referenced by run().

clash2

erraser_analysis.clash2 = 0

Referenced by run().

delta1

erraser_analysis.delta1 = float(line1[3])

Referenced by ZF_PatchupMover.apply(), get_backbone_rotamers(), and numeric::interpolation::spline::CubicSpline.train().

delta2

erraser_analysis.delta2 = float(line2[3])

Referenced by ZF_PatchupMover.apply(), get_backbone_rotamers(), and numeric::interpolation::spline::CubicSpline.train().

diff

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

Referenced by backbone_sampling(), cal_distance(), calc_SID_score(), calculate_percent_hydrophobic_stats(), numeric::expression_parser::DivideExpression.differentiate(), elementdiff(), protocols::jd2::RECONMPIJobDistributor.find_consensus_sequence(), detail.get_milliseconds(), InstantiateModulesBenchmark.instantiate_filters(), InstantiateModulesBenchmark.instantiate_movers(), InstantiateModulesBenchmark.instantiate_packer_palettes(), InstantiateModulesBenchmark.instantiate_res_selectors(), InstantiateModulesBenchmark.instantiate_reslvl_taskops(), InstantiateModulesBenchmark.instantiate_simple_metrics(), InstantiateModulesBenchmark.instantiate_taskops(), main(), multiclass_probability(), nearlyEqual(), nosuper_CA_rmsd(), nucleoside_sampling(), sd(), numeric::VoxelGrid< T >.SetupGrid(), Solver.Solve(), ui::task::TaskSyncer_TaskStrategy.subscribe(), numeric::linear_algebra.sum_of_square_differences(), and test().

ERRASER_rna_validate_data

erraser_analysis.ERRASER_rna_validate_data = phenix_rna_validate( pdb2 )

file_path

erraser_analysis.file_path = os.path.split( os.path.abspath(__file__) ) [0]

info1

string erraser_analysis.info1 = '%8.1f/!!' % delta1

info2

string erraser_analysis.info2 = ' OK'

line_split

erraser_analysis.line_split = i

lines

list erraser_analysis.lines = []

pdb1

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

Referenced by fname2pdbcode().

pdb2

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

pucker1

erraser_analysis.pucker1 = START_rna_validate_data['pucker']

Referenced by apply_backbone_rotamer(), and get_backbone_rotamers().

pucker2

erraser_analysis.pucker2 = ERRASER_rna_validate_data['pucker']

Referenced by apply_backbone_rotamer(), and get_backbone_rotamers().

res

string erraser_analysis.res = '%4s%2s%4s ' % tuple(i[:3])

res1

string erraser_analysis.res1 = '%4s%2s%4s ' % tuple(line1[:3])

Referenced by add_symm_sf4(), add_symm_zns(), HemeBindingMover.apply(), PhProtocol.apply(), MikeLinkerMover.apply(), AnchorFinderMover.apply(), calc_dist(), check_jump(), cl_score(), create_schema(), do_color_by_score(), find_next_repeat_inflection_point(), get_base_pair_coordinate_system(), get_contact_list(), get_inflection_points(), get_jump(), main(), make_move_map(), makesplitwork(), parse_nonstandard_angles(), parse_nonstandard_bondlengths(), read_covalent_connections_file(), read_RDC_file(), reorient_to_base_pair_coordinate_system(), report_and_dump(), DisulfEpos.rms(), DisulfEposDatabase.rms(), setup_rna_minimizer(), and PhProtocol.titrate_pH().

res2

string erraser_analysis.res2 = '%4s%2s%4s ' % tuple(line2[:3])

Referenced by add_symm_sf4(), add_symm_zns(), HemeBindingMover.apply(), PhProtocol.apply(), MikeLinkerMover.apply(), AnchorFinderMover.apply(), calc_dist(), check_jump(), cl_score(), create_schema(), do_color_by_score(), fast_clash_check(), find_next_repeat_inflection_point(), get_base_pair_coordinate_system(), get_contact_list(), get_inflection_points(), get_jump(), main(), make_move_map(), makesplitwork(), parse_nonstandard_angles(), parse_nonstandard_bondlengths(), read_covalent_connections_file(), read_RDC_file(), reorient_to_base_pair_coordinate_system(), report_and_dump(), rescore_test(), DisulfEpos.rms(), DisulfEposDatabase.rms(), setup_rna_minimizer(), sweep_params_from_match_constraint_file(), and PhProtocol.titrate_pH().

sigma

erraser_analysis.sigma = float(line_split[5])

START_rna_validate_data

erraser_analysis.START_rna_validate_data = phenix_rna_validate( pdb1 )

suite1

erraser_analysis.suite1 = START_rna_validate_data['suite']

suite2

erraser_analysis.suite2 = ERRASER_rna_validate_data['suite']

suite_outlier1

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

suite_outlier2

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

temp

list erraser_analysis.temp = []

Referenced by utility::graph::Graph.add_edge(), utility::graph::LowMemGraph< _LMNode, _LMEdge >.add_edge(), xtal_water_bunsat.apply(), ColorByLipidType.apply(), FindOptimalHydrophobicThk.apply(), FloatScMonteCarlo.apply(), CrystRelax.apply(), BBG8T3A_sample(), HubDenovo.cen_fold(), cen_fold(), compare_gpu_result_against_cpu(), design(), do_event_prediction(), CrystDesign.do_reversion(), doit(), utility::Inline_File_Provider.file_exists(), CrystDesign.filter_and_report(), fixbb_design(), forward_in_time(), gen_pep_bb_frag(), get_temp(), numeric::nls.lm_enorm(), numeric::nls.lm_lmdif(), numeric::nls.lm_lmpar(), numeric::nls.lm_qrfac(), numeric::nls.lm_qrsolv(), utility::options::OptionCollection.load(), main(), my_main(), myMC.myMC(), obtain_secstruct_segments(), opt_bicelle_params(), opt_double_vesicle_params(), opt_vesicle_params(), numeric::random.random_permutation(), numeric::random::RandomGenerator.random_range(), refine(), FragMonteCarlo.report_score(), myMC.roll(), numeric::model_quality.rsym_rotation(), FragmentAssemblyMover.run(), FragMonteCarlo.run(), run_parallel_docking(), basic::svd::SVD_Solver.run_score_svd_on_matrix(), basic::svd::SVD_Solver.run_score_svd_without_solving(), utility::graph::Edge.same_edge(), utility::graph::LowMemEdge.same_edge(), numeric::HomogeneousTransform< T >.set_xaxis_rotation_deg(), numeric::HomogeneousTransform< T >.set_xaxis_rotation_rad(), numeric::HomogeneousTransform< T >.set_yaxis_rotation_deg(), numeric::HomogeneousTransform< T >.set_yaxis_rotation_rad(), numeric::HomogeneousTransform< T >.set_zaxis_rotation_deg(), numeric::HomogeneousTransform< T >.set_zaxis_rotation_rad(), setup_transform_mover(), strip_comment_and_whitespace(), HemeBindingMover.temperature(), and numeric::xyzMatrix< T >.transpose().