make_symmdef_file_denovo Namespace Reference

Variables
int	length = -1
	pos = argv.index('-symm_type')
	symm_type_name = argv[pos+1]
	nsub = argv[pos+1]
int	subsystem_size = 0
string	slide_type = ""
string	slide_criteria_type = ""
string	slide_order = ""
string	slide_criteria_val = ""
	subunits = int(nsub)
list	interfaces = []
int	num_interfaces = 0
string	E_string = "E = "+ nsub + "*VRT0001"
int	interface_num = 0
int	jump_num = sub+1
int	vrt_start_num = sub+1
int	vrt_stop_num = sub+2
string	jump_start = 'VRT' + str(vrt_start_num).zfill(4)
string	jump_stop = 'VRT' + str(vrt_stop_num).zfill(4)
	rotation_z = float(2*360.000/(float(subunits)))
int	z_jump = subunits/2
	z_random_rotation = float(360.000/float(subunits))
	rot_z1 = float(360.000/float(subunits))
float	rot_z2 = 360.000 -2*rot_z1
float	rotation_z2 = 360.000 - 2*rotation_z

Variable Documentation

E_string

string make_symmdef_file_denovo.E_string = "E = "+ nsub + "*VRT0001"

interface_num

int make_symmdef_file_denovo.interface_num = 0

interfaces

list make_symmdef_file_denovo.interfaces = []

Referenced by InterfaceFeaturesTests.test_interfaces(), and InterfaceFeaturesTests.test_reporter().

jump_num

int make_symmdef_file_denovo.jump_num = sub+1

Referenced by dostuff(), fold_tree_from_loops(), get_ddg(), ClosabilityScore.get_rt_over_leap(), main(), and output_interface_graphviz().

jump_start

string make_symmdef_file_denovo.jump_start = 'VRT' + str(vrt_start_num).zfill(4)

Referenced by fold_tree_from_loops().

jump_stop

string make_symmdef_file_denovo.jump_stop = 'VRT' + str(vrt_stop_num).zfill(4)

Referenced by fold_tree_from_loops().

length

int make_symmdef_file_denovo.length = -1

nsub

make_symmdef_file_denovo.nsub = argv[pos+1]

Referenced by ConstraintConfig.add_sym_cst(), count_int_CBs_clashes(), do_clustering(), numeric::UniformRotationSampler.generateIcosahedralSamples(), ConstraintConfig.hub_seq_sep(), main(), ConstraintConfig.parse_config_file(), ConstraintConfig.resi_to_primary(), and ConstraintConfig.show_cst_grids().

num_interfaces

int make_symmdef_file_denovo.num_interfaces = 0

pos

make_symmdef_file_denovo.pos = argv.index('-symm_type')

Referenced by add_dna_states(), add_protocols(), ObjexxFCL::bit.bit_clr(), ObjexxFCL::bit.bit_set(), ObjexxFCL::bit.bit_test(), CA_cst_generator(), FragMonteCarlo.cal_frag_score(), check_quality_of_cluster_frags(), checked_steal_fragment(), ClashCheck.clash_check(), myspace.collect_silent(), color_by_geom_sol_RNA_test(), color_by_lj_base_RNA_test(), apps::pilot::frankdt.compare_segment_to_motif(), compare_torsion_rmsd(), compute_intrinsic_deviation(), utility.contains(), protocols::abinitio::Application.copy_native_structure(), copying_side_chains(), copying_side_chains_swap_loop(), create_base_pair_step_database_test(), ui::task::TaskView.create_output_context_menu(), create_rna_benchmark_test(), define_movemap_extending_chain(), define_states_test(), design_cluster(), design_test(), detect_neighbors(), numeric::interpolation::spline::PolycubicSpline< N >.dFdxi(), dostuff(), utility::keys::SmallKeyVector< K, T >.erase(), utility::keys::ClassKeyVector< K, T, C >.erase(), utility::keys::KeyVector< K, T >.erase(), exclude_loop_residues(), extend_loop(), extending_chain(), extract_replica(), numeric::interpolation::spline::PolycubicSpline< N >.F(), filter_frags(), utility::fixedsizearray0< T, S >.fixedsizearray0(), utility::fixedsizearray1< T, S >.fixedsizearray1(), protocols::abinitio::JumpSpecificAbrelax.fold(), FragID.FragID(), ga_main(), gen_pep_bb_frag(), gen_pep_bb_frag_old(), gen_pep_bb_rama(), gen_pep_bb_sequential(), protocols::abinitio::JumpSpecificAbrelax.generate_extended_pose(), protocols::abinitio::ApplicationContext.generateExtendedPose(), FragMonteCarlo.get_candidate_frags(), MPInterfaceStatistics.get_charge(), get_file_name(), get_ncac(), get_opte_data(), get_pos_from_fragfn(), get_sequence_and_secstruct_from_dssp(), numeric::VoxelGrid< T >.GetIndex(), numeric::VoxelGrid< T >.GetNeighbors1D(), numeric::VoxelGrid< T >.GetNeighborsMultiDimensional(), numeric::VoxelGrid< T >.HasNeighbors1D(), numeric::VoxelGrid< T >.HasNeighborsMultiDimensional(), identify_targeted_positions(), FragMonteCarlo.initialize_frag_assignment(), utility::keys::SmallKeyVector< K, T >.insert(), utility::keys::ClassKeyVector< K, T, C >.insert(), utility::keys::KeyVector< K, T >.insert(), protocols::abinitio::JumpSpecificAbrelax.insert_template_frags(), loop_closure_test(), loop_modeling_test(), main(), make_helix(), mismatch_test(), modeler_map_test(), motif_scan(), obtain_secstruct_segments(), numeric::kdtree::KDPointList.operator[](), basic_string_view< Char >.operator[](), output_benchmark_stuff(), output_pdb(), output_superimposed_pdb(), ObjexxFCL::Fstring.overlay(), ObjexxFCL.overlay(), parse_pdb_pos(), passes_quality_check(), SwapElementsMover1.pick_fragments(), SwapElementsMover2.pick_fragments(), pick_fragments(), myspace.pose_from_scratch(), processRegions(), read_pdbs(), rebuild_centroid_test(), rebuild_test(), recover_clustered_frags(), numeric::VoxelGrid< T >.RemoveObject(), repack_cluster(), utility.replace_first_in(), utility.replace_in(), FragMonteCarlo.report_results(), rna_design_gap_test(), rna_design_test(), rna_fullatom_minimize_test(), DomainAssemblerNDocker.run(), protocols::abinitio::Application.run(), ThisApplication.run(), DockFragmentsMover.run(), FragmentAssemblyMover.run(), run(), RunPepSpec(), score_clustered_frags(), sequence_tolerance_main(), sequence_tolerance_mf_main(), set_secstruct_from_psipred_ss2(), DomainAssemblerNDocker.setup_cen_domains(), protocols::abinitio::JumpSpecificAbrelax.setup_fold(), numeric::VoxelGrid< T >.SetupGrid(), simple_loop_modeling_test(), spec_test(), ss_ds_ts_assign_test(), stepwise_template_test(), svm_load_model(), SymmAbRelaxTest(), tar_motif_test(), tf_specificity_test(), tokenize_string(), FragMonteCarlo.updated_covered_rsds(), and write_cluster_frags().

rot_z1

make_symmdef_file_denovo.rot_z1 = float(360.000/float(subunits))

rot_z2

float make_symmdef_file_denovo.rot_z2 = 360.000 -2*rot_z1

rotation_z

make_symmdef_file_denovo.rotation_z = float(2*360.000/(float(subunits)))

rotation_z2

float make_symmdef_file_denovo.rotation_z2 = 360.000 - 2*rotation_z

slide_criteria_type

make_symmdef_file_denovo.slide_criteria_type = ""

slide_criteria_val

make_symmdef_file_denovo.slide_criteria_val = ""

slide_order

string make_symmdef_file_denovo.slide_order = ""

slide_type

make_symmdef_file_denovo.slide_type = ""

subsystem_size

int make_symmdef_file_denovo.subsystem_size = 0

subunits

make_symmdef_file_denovo.subunits = int(nsub)

Referenced by main().

symm_type_name

make_symmdef_file_denovo.symm_type_name = argv[pos+1]

vrt_start_num

int make_symmdef_file_denovo.vrt_start_num = sub+1

vrt_stop_num

int make_symmdef_file_denovo.vrt_stop_num = sub+2

z_jump

int make_symmdef_file_denovo.z_jump = subunits/2

z_random_rotation

make_symmdef_file_denovo.z_random_rotation = float(360.000/float(subunits))