lactamize Namespace Reference

Functions
def	find_lactams (pose)

Variables
	residue_set_cap
	ii
	other_res
	dist
	lys_id = ii
	glu_id = other_res
	cs
	i
	other_cst
	nr
	new_name
	nr2
	score_fxn
	filename
	outfile

Function Documentation

find_lactams()

def lactamize.find_lactams

(

pose

)

References atoms, CB, CD, CG, utility.contains(), data, build_jacobian.distance, vancomycin.harm, ObjexxFCL.len(), beta_sc_scan.name3, and basic::options::OptionKeys::in::file.xyz.

Variable Documentation

cs

lactamize.cs

Referenced by PoseWrap.add_floating_sc_csts(), PoseWrap.get_closest_res_for_sc_attach(), numeric::geometry::hashing::MinimalClashHash.init(), main(), PoseWrap.replace_scattach_res(), report(), run_mc(), numeric::interpolation::spline::BicubicSpline.train(), numeric::interpolation::spline::TricubicSpline.train(), numeric::interpolation::spline::PolycubicSpline< N >.train(), and numeric::VoxelArray< _Float, _Value >.VoxelArray().

dist

lactamize.dist

filename

lactamize.filename

Referenced by BuriedUnsatPolarsFinder.apply(), InverseRotlibDumpMover.apply(), khSandbox.apply(), KHSandbox.apply(), xtal_water_bunsat.apply(), IAMover.apply(), XMLprinterMover.apply(), InterfaceStrandFinderMover.apply(), FindOptimalHydrophobicThk.apply(), assure(), buffered_file.buffered_file(), bzip_test(), calculate_hASA_by_type_and_attractiveE(), calculate_hASA_by_type_and_exposure(), calculate_hASA_by_type_and_nbcount(), calculate_hydrophobic_accessible_surface_area(), calculate_total_hASA_within_distance_avgresiduevalues_allnbs_conditionalonnumnbs(), calculate_total_hASA_within_distance_miniSASAvalues_allnbs_exposedornot_conditionalonnumnbs(), capri_t033_loop_test(), cendnapose_from_file(), cenpose_from_file(), collect_residue_types(), define_states_test(), design_test(), diversify_sam_loop_test(), dna_specificity_test(), protocols::abinitio::JumpSpecificAbrelax.do_distributed_rerun(), dump_clash_pdb(), dump_efactor_pdb(), dump_hbond_pdb(), dump_rotamerset_pdb(), dump_table(), endo_test(), ZincSiteEvaluator.evaluate_mutations_native(), extract_replica(), basic::resource_manager::locator::FileStream.FileStream(), fillPoseAndDataList(), basic::database.find_database_path(), Foldptn.Foldptn(), generateRankedAlignments(), get_pair_keys_from_list(), get_sequence_and_secstruct_from_dssp(), initialize_from_pdb(), lk_ball_wtd_deriv_test(), load_as_fullatom(), load_checkpoint(), load_loops_from_file(), basic::citation_manager::CitationManager.load_rosetta_citations_from_database(), LocalRmsd.LocalRmsd(), luxr_test(), main(), mismatch_test(), motif_scan(), MSA_design(), MSA_design_main(), my_main(), not1_loop_test(), MainWindow.on_importPDB_button_clicked(), MainWindow.on_pushButton_clicked(), ui::ui_protocols::helical_bundle::HelicalBundleDialogueWidget.on_radioButton_custom_helix_clicked(), basic::resource_manager::locator::FileStream.open(), myspace::DataClass.open_trgfile(), opt_bicelle_params(), opt_double_vesicle_params(), opt_vesicle_params(), optimize_weights(), output_constraints(), output_constraints_for_full_length(), output_PCA(), PairDistance.PairDistance(), pep_energies_analysis(), PickBAB.PickBAB(), CalcsTestMover.pretty_print(), print_cst_file(), ExposedStrandMover.print_sheets(), ExposedStrandMover.print_sheets_extras(), printScoreTermsPose(), process_file_list(), processChildren(), processChildrenIntensification(), rb_entropy_test(), RBSegmentRelax_test(), read_equivalent_position_file(), read_in_extension(), APDBCMover.read_in_insert_loop_info(), read_in_mutations(), myspace.read_input(), read_list_file(), read_list_pose_range(), read_master_pose_range(), read_NACCESS_asa_file(), read_PCAfile(), numeric.read_probabilities_or_die(), read_rama_map_file(), read_RDC_file(), basic::resource_manager::ResourceManager.read_resource_locators_tags(), basic::resource_manager::ResourceManager.read_resources_from_xml(), basic::resource_manager::ResourceManager.read_resources_tags(), numeric.read_tensor_from_file(), read_tensor_test(), readPDBcoords(), readPoseAndData_PDB(), readPoseAndData_SILENT(), rebuild_test(), report_and_dump(), myspace::DataClass.report_by_aa(), nacl_rosetta::RosettaURLFileHandler.request_file(), rotamerize(), run_parallel_docking(), RunPepSpec(), sample_rna_dofs_new(), Sasa.Sasa(), scan_neutral(), score12_plot_test(), sequence_tolerance_mf_main(), set_basic_dock_options(), PoseAndData.set_file_name(), DockGlycansProtocol.set_ref_pose_from_filename(), set_secstruct_from_psipred_ss2(), protocols::abinitio::JumpSpecificAbrelax.setup_fold(), setup_hotspot_filter(), show(), simple_opte_test(), simple_rotamer_recovery(), numeric::interpolation.spline_from_file(), statistics(), tar_motif_test(), test_cofactor(), test_sugar(), tf_specificity_test(), protocols::moves::FragCaptureMover.write(), XMLprinterMover.write_output_file(), numeric.write_tensor_to_file(), numeric.write_tensor_to_file_without_json(), writeScores(), zf_test(), and zif268_test().

glu_id

lactamize.glu_id = other_res

i

lactamize.i

ii

lactamize.ii

lys_id

lactamize.lys_id = ii

new_name

lactamize.new_name

Referenced by utility::json_spirit::Json_grammer< Value_type, Iter_type >::definition< ScannerT >.definition(), and main().

nr

lactamize.nr

Referenced by TCDock.dump_pdb(), jitterloop(), numeric::model_quality.maxsub(), numeric::kinematic_closure.modp(), my_main(), protocols::abinitio::JumpSpecificAbrelax.setup_fragments(), and write_cluster_frags().

nr2

lactamize.nr2

Referenced by protocols::abinitio::JumpSpecificAbrelax.setup_fragments().

other_cst

lactamize.other_cst

other_res

lactamize.other_res

outfile

lactamize.outfile

Referenced by CrystCluster.apply(), assign_rigid_body_settings_to_clusters_test(), calculate_theoretical_RNA_length_with_bond_angle_dependence(), chi_stats_test(), cluster_rigid_body_settings_test(), coarse_to_full_test(), color_by_geom_sol_RNA_test(), color_by_lj_base_RNA_test(), connectivity_test(), correct_dunbrack(), correct_rama(), create_bp_jump_database_test(), create_rna_vall_torsions_test(), delta_chi_correction_test(), design_cluster(), dist_matrix_test(), dna_test(), do_event_prediction(), double_helix_test(), each_aa_test(), entropy_calculate_test(), filter_combine_long_loop(), frag_extract_test(), get_info_test(), graft_pdb(), harvest_motifs(), helix_ST(), hermann_phase_two(), homolog_finder(), ligand_dock_main_jd1(), main(), make_fragments(), mg_modeler_test(), mg_pdbstats_test(), one_chain_MC_sampling(), one_chain_ST_MC(), output_results(), output_strand1_strand2_info(), output_stuff(), output_superimposed_pdb(), output_torsion_list(), output_torsion_M_v_lists(), pack_polar_hydrogens(), polar_pdbstats_test(), Prepare(), print_verbose_ddgs(), RBSegmentRelax_test(), register_options(), repack_cluster(), reverse_rbs_test(), rhiju_pdbstats(), rna_build_helix_test(), rna_build_helix_test_precompute(), rna_design_gap_test(), rna_design_test(), rna_fullatom_minimize_silent_test(), rna_lores_score_silent_test(), rna_protein_pdbstats_test(), rna_thread_test(), FragmentAssemblyMover.run(), sicdock_thread_num(), swa_rna_cluster(), tar_motif_test(), and two_base_pairs_via_loop_closure_test().

residue_set_cap

lactamize.residue_set_cap

Referenced by A3BPeptideBuilder.apply(), CovalentPeptidomimeticDockDesign.apply(), CovalentPeptidomimeticCreator.apply(), TriazoleCreator.apply(), and main().

score_fxn

lactamize.score_fxn