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Functions | Variables
demo.D010_Pose_structure Namespace Reference

Functions

def pose_structure
 

Variables

tuple parser = optparse.OptionParser()
 INTERPRETING RESULTS. More...
 
string default = '../test/data/test_in.pdb'
 
string help = 'the PDB file containing the loop to remodel'
 
 pdb_filename = options.pdb_filename
 
tuple pose = Pose()
 
 residues = options.residues
 

Function Documentation

def demo.D010_Pose_structure.pose_structure (   pose,
  display_residues = [] 
)
Extracts and displays various structural properties of the input  <pose>
    and its  <display_residues>  including:
        -PDB numbering
        -chain identification
        -sequence
        -secondary structure

References ObjexxFCL.len(), fmt.print(), basic::options::OptionKeys::run::PyMOLMover.PyMOLMover, basic::options::OptionKeys::relax::range.range, and ObjexxFCL.strip().

Variable Documentation

string demo.D010_Pose_structure.default = '../test/data/test_in.pdb'
string demo.D010_Pose_structure.help = 'the PDB file containing the loop to remodel'
tuple demo.D010_Pose_structure.parser = optparse.OptionParser()

INTERPRETING RESULTS.

COMMANDLINE COMPATIBILITY

demo.D010_Pose_structure.pdb_filename = options.pdb_filename

Referenced by run_pep_prep(), and RunPepSpec().

tuple demo.D010_Pose_structure.pose = Pose()

Referenced by RNA_DeNovoJobQueen.add_chem_shift_info(), HDdesignMover.ala_interface(), RNA_DeNovoJobQueen.align_and_output_to_silent_file(), align_pdbs(), analyze_base_pair_test(), analyze_poses_for_convergence(), PackingAngle.apply(), IAMover.apply(), Minimize.apply(), LigandRepackMinimizeProtocol.apply(), ExtractATD.apply(), MetalSiteFinderMover.apply(), MyScoreMover.apply(), NCMinimize.apply(), ExposedStrandMover.apply(), FitMover.apply(), HDdesignMover.apply(), HDmakerMover.apply(), BacksideHbondFinderMover.apply(), DockGlycansProtocol.apply(), DougsDockDesignMinimizeMagicMover.apply(), HBondReporter.apply(), RNA_ScoreMover.apply(), PhProtocol.apply(), UBQ_GTPase_disulfide_Mover.apply(), UBQ_E2Mover.apply(), calc_rama_scores(), calc_rms_test(), calc_rmsf_and_avrg(), calculate_binding_energy(), calculate_pairwise_RMSD(), calculate_sasa(), BacksideHbondFinderMover.check_for_hbonds(), StepWiseJobQueen.complete_larval_job_maturation(), RNA_DeNovoJobQueen.complete_larval_job_maturation(), compute_chem_shift_RMSD(), correct_dunbrack(), create_base_pair_step_database_test(), create_bp_jump_database_test(), create_rna_vall_torsions_test(), create_theozyme_pdb(), cs_rosetta_rna_pdb(), densityTools(), drrafter_error_estimation(), extract_pdbs_test(), fill_designable_set(), filter_combine_long_loop(), find_close_motifs(), find_neighbors_directional(), gen_pep_bb_sequential(), get_binding_score(), get_clash_pairs(), get_complex_score(), get_elec_score(), get_hbond_score(), get_n_mer_maltose(), get_n_mer_polyalanine(), get_packing_score(), get_pose_and_numbering(), get_unbound_protein_score(), graft_pdb(), harvest_motifs(), harvest_motifs_one(), has_clash(), helix_from_sequence(), import_and_dump_pdb(), initialize_native_pose(), initialize_peptide(), main(), apps::pilot::frankdt.main(), make_fragments(), match_main(), MC_run(), mg_modeler_test(), minimize_test(), mutate_residue(), mutate_residues_wrapper(), my_main(), myMC.myMC(), nucleobase_probe_score_test(), o2prime_packer(), output_single_motif(), packmin_unbound_pep(), pdb_to_silent_file(), perturb_pep_bb(), poses_from_cmd_line(), post_rebuild_bulge_assembly(), predict_chem_map_test(), PhProtocol.prepack_pose(), Prepare(), prepare_threaded_model(), print_pep_analysis(), MPDomainAssembly.print_score(), quick_score_test(), read_library_w_simpose(), read_native_sequence_for_entity_elements(), read_pose(), rebuild_test(), PhProtocol.relax_pose(), repack_test(), resample_full_model_test(), rhiju_pdbstats(), rna_build_helix_test(), rna_denovo(), rna_denovo_legacy(), rna_design_test(), rna_fullatom_minimize_test(), rna_motif_test(), rna_sample_virtual_sugar(), rna_sequence_recovery_metrics(), rna_suitename(), rna_thread_test(), myMC.roll(), DatabaseIOBenchmark.run(), DockingBenchmark< dock, TScale >.run(), MinimizerBenchmark< sft, TScale >.run(), run(), run_pep_prep(), RunPepSpec(), sequence_tolerance_main(), NBuriedUnsatsCalcultor.setup(), slice_ellipsoid_envelope(), slice_sample_res_and_surrounding(), spanfile_from_pdb(), stepwise_monte_carlo_legacy(), superimpose_pdb(), swa_rna_sample(), HDdesignMover.sym_repack_minimize(), thermal_sampler(), and PhProtocol.titrate_pH().

list demo.D010_Pose_structure.residues = options.residues