vancomycin Namespace Reference

Functions
def	add_constraints (vancomycin)

Variables
	scorefxn = get_score_function()
	chm = rosetta.core.chemical.ChemicalManager.get_instance()
	restype_set_cap = chm.residue_type_set('fa_standard').get_self_ptr()
	dleu_type = residue_set_cap.name_map("DLEU:NtermProteinMethylated")
	V01_type = residue_set_cap.name_map("DV01:aryl-O-conjugated")
	asn_type = residue_set_cap.name_map("ASN")
	V02_type = residue_set_cap.name_map("DV02:aryl-O-conjugated:phg_cd1_conjugation:phg_cd2_conjugation")
	V02_type2 = residue_set_cap.name_map("DV02:phg_cd1_conjugation")
	V04_type = residue_set_cap.name_map("V04:aryl-O-conjugated")
	V03_type = residue_set_cap.name_map("V03:CtermProteinFull:aryl-C-conjugated")
	dleu = Residue(dleu_type, True)
	V01 = Residue(V01_type, True)
	asn = Residue(asn_type, True)
	V02 = Residue(V02_type, True)
	V022 = Residue(V02_type2, True)
	V04 = Residue(V04_type, True)
	V03 = Residue(V03_type, True)
	vancomycin = Pose()
	translate = protocols.rigid.RigidBodyTransMover(vancomycin, 1)
int	ii = i + 1
	pert_mm = kinematics.MoveMap()
	min_mover = minimization_packing.MinMover(pert_mm, scorefxn, "lbfgs_armijo_nonmonotone", 0.0001, True)
	f = vancomycin.fold_tree()
	task = TaskFactory.create_packer_task(vancomycin)
int	i = ii + 1
	pack = PackRotamersMover(scorefxn, task)
	vanc2 = Pose()
	trans2 = protocols.rigid.RigidBodyTransMover(vanc2, 1)
	dharm = core.scoring.func.CircularHarmonicFunc(-71.5 * 3.14159 / 180, 0.02)
	dharm2 = core.scoring.func.CircularHarmonicFunc(176.9 * 3.14159 / 180, 0.02)
	dharm3 = core.scoring.func.CircularHarmonicFunc(60 * 3.14159 / 180, 0.02)
	harm = core.scoring.func.HarmonicFunc(1.31, 0.02)
	aharm2 = core.scoring.func.CircularHarmonicFunc(120 * 3.14159 / 180, 0.02)
	OZ4 = core.id.AtomID(vanc2.residue(2).type().atom_index("OZ"), 2)
	C18 = core.id.AtomID(vanc2.residue(4).type().atom_index("C1"), 4)
	C28 = core.id.AtomID(vanc2.residue(4).type().atom_index("C2"), 4)
	O28 = core.id.AtomID(vanc2.residue(4).type().atom_index("O2"), 4)
	C19 = core.id.AtomID(vanc2.residue(5).type().atom_index("C1"), 5)
	O58 = core.id.AtomID(vanc2.residue(4).type().atom_index("O5"), 4)
	O59 = core.id.AtomID(vanc2.residue(5).type().atom_index("O5"), 5)
	C58 = core.id.AtomID(vanc2.residue(4).type().atom_index("C5"), 4)
	C59 = core.id.AtomID(vanc2.residue(5).type().atom_index("C5"), 5)
	CE = core.id.AtomID(vanc2.residue(2).type().atom_index("CE"), 2)
	pert_mm2 = kinematics.MoveMap()
	min_mover2 = minimization_packing.MinMover(pert_mm2, scorefxn, "lbfgs_armijo_nonmonotone", 0.0001, True)
	f2 = vanc2.fold_tree()
	task2 = TaskFactory.create_packer_task(vanc2)
	pack2 = PackRotamersMover(scorefxn, task2)

Function Documentation

add_constraints()

def vancomycin.add_constraints

(

vancomycin

)

References aharm2, CB, CD1, CD2, CE, and CG2.

Variable Documentation

aharm2

vancomycin.aharm2 = core.scoring.func.CircularHarmonicFunc(120 * 3.14159 / 180, 0.02)

Referenced by add_constraints(), add_constraints(), and main().

asn

vancomycin.asn = Residue(asn_type, True)

Referenced by main(), and BruteRotSel.place_n().

asn_type

vancomycin.asn_type = residue_set_cap.name_map("ASN")

Referenced by main().

C18

vancomycin.C18 = core.id.AtomID(vanc2.residue(4).type().atom_index("C1"), 4)

Referenced by add_constraints(), and main().

C19

vancomycin.C19 = core.id.AtomID(vanc2.residue(5).type().atom_index("C1"), 5)

Referenced by add_constraints(), and main().

C28

vancomycin.C28 = core.id.AtomID(vanc2.residue(4).type().atom_index("C2"), 4)

Referenced by add_constraints(), and main().

C58

vancomycin.C58 = core.id.AtomID(vanc2.residue(4).type().atom_index("C5"), 4)

Referenced by main().

C59

vancomycin.C59 = core.id.AtomID(vanc2.residue(5).type().atom_index("C5"), 5)

Referenced by main().

CE

vancomycin.CE = core.id.AtomID(vanc2.residue(2).type().atom_index("CE"), 2)

Referenced by add_constraints(), add_constraints(), capri_t033_trim_dock_test(), get_bonded_rna_dof_ids(), main(), and make_bonded_rna_move().

chm

vancomycin.chm = rosetta.core.chemical.ChemicalManager.get_instance()

dharm

vancomycin.dharm = core.scoring.func.CircularHarmonicFunc(-71.5 * 3.14159 / 180, 0.02)

Referenced by add_constraints(), and main().

dharm2

vancomycin.dharm2 = core.scoring.func.CircularHarmonicFunc(176.9 * 3.14159 / 180, 0.02)

Referenced by main().

dharm3

vancomycin.dharm3 = core.scoring.func.CircularHarmonicFunc(60 * 3.14159 / 180, 0.02)

Referenced by main().

dleu

vancomycin.dleu = Residue(dleu_type, True)

Referenced by main().

dleu_type

vancomycin.dleu_type = residue_set_cap.name_map("DLEU:NtermProteinMethylated")

Referenced by main().

f

vancomycin.f = vancomycin.fold_tree()

f2

vancomycin.f2 = vanc2.fold_tree()

Referenced by numeric::deriv.angle_p1_deriv(), numeric::deriv.angle_p2_deriv(), CustomMover.apply(), attach_simple_abego_pools(), compare_text_files(), numeric::deriv.dihedral_p1_cosine_deriv(), numeric::deriv.dihedral_p2_cosine_deriv(), distance(), numeric::deriv.distance_f1_f2_deriv(), numeric::deriv.helper(), numeric::interpolation.interpolated(), numeric::interpolation.interpolated_delta(), main(), utility::tools.make_map(), numeric::deriv.p1_theta_deriv(), rb_test(), numeric::model_quality.rsym_eigenval(), and run().

harm

vancomycin.harm = core.scoring.func.HarmonicFunc(1.31, 0.02)

Referenced by add_constraints(), pna.add_hbond_constraints(), CovalentPeptidomimeticCreator.apply(), lactamize.find_lactams(), and main().

i

int vancomycin.i = ii + 1

ii

int vancomycin.ii = i + 1

min_mover

vancomycin.min_mover = minimization_packing.MinMover(pert_mm, scorefxn, "lbfgs_armijo_nonmonotone", 0.0001, True)

Referenced by HECTMover.apply(), UBQ_E2Mover.apply(), PepMinMover.apply(), CovalentPeptidomimeticCreator.apply(), FindOptimalHydrophobicThk.apply(), MinPackMinMover.apply(), UBQ_GTPase_disulfide_Mover.apply(), MinPackMin.backbone_minimization(), benchmark_contacts(), bk_test(), capri15_relax(), FixbbJobQueen.complete_larval_job_maturation(), HbondZinc.constrain_zinc(), dna_deriv_test(), protocols::antibody::design::AntibodyDesignMoverGenerator.generate_minimizer(), HbondZinc.hbond_constraint(), if(), main(), minimize_all_sidechains(), minimize_sidechain(), mutate_random_residue(), packmin_unbound_pep(), pep_scan_analysis(), rebuild_test(), refine_fa_pep_bb(), apps::pilot::momeara::HBondConformation.relax_pose_around_hbond(), repack_cluster(), repack_step(), MinPackMin.rigid_body_minimization(), run_pep_prep(), run_test(), RunPepSpec(), ZincMinimize.set_min_mover(), protocols::antibody::design::AntibodyDesignMoverGenerator.setup_minimizer(), simple_hbond_test(), small_min_test(), myspace::GraftTester.test_rb_min_graft(), and zf_relax_test().

min_mover2

vancomycin.min_mover2 = minimization_packing.MinMover(pert_mm2, scorefxn, "lbfgs_armijo_nonmonotone", 0.0001, True)

Referenced by main().

O28

vancomycin.O28 = core.id.AtomID(vanc2.residue(4).type().atom_index("O2"), 4)

Referenced by add_constraints(), and main().

O58

vancomycin.O58 = core.id.AtomID(vanc2.residue(4).type().atom_index("O5"), 4)

Referenced by add_constraints(), and main().

O59

vancomycin.O59 = core.id.AtomID(vanc2.residue(5).type().atom_index("O5"), 5)

Referenced by add_constraints(), and main().

OZ4

vancomycin.OZ4 = core.id.AtomID(vanc2.residue(2).type().atom_index("OZ"), 2)

Referenced by add_constraints(), and main().

pack

vancomycin.pack = PackRotamersMover(scorefxn, task)

Referenced by MinTestMover.apply(), design(), design_using_resfile(), dinucleotide_test(), double_helix_test(), get_rsrpl(), helix_ST(), initialize_o2prime_pack(), main(), minimize_and_score(), one_chain_MC_sampling(), one_chain_ST_MC(), packmin_unbound_pep(), pep_scan_analysis(), repack(), repack_test(), scan_hbond_jumps(), myspace.setup_packer(), HubDenovo.stupid_ddg(), and test_suck_res().

pack2

vancomycin.pack2 = PackRotamersMover(scorefxn, task2)

Referenced by main().

pert_mm

vancomycin.pert_mm = kinematics.MoveMap()

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

pert_mm2

vancomycin.pert_mm2 = kinematics.MoveMap()

Referenced by main().

restype_set_cap

vancomycin.restype_set_cap = chm.residue_type_set('fa_standard').get_self_ptr()

scorefxn

vancomycin.scorefxn = get_score_function()

task

vancomycin.task = TaskFactory.create_packer_task(vancomycin)

Referenced by adesign(), MirrorSymmTest.apply(), PhProtocol.apply(), UBQ_E2Mover.apply(), SilentProlineFixMover.apply(), A3BPeptideBuilder.apply(), CovalentPeptidomimeticDockDesign.apply(), CovalentPeptidomimeticCreator.apply(), TriazoleCreator.apply(), Packing_energies.apply(), SSM_energies.apply(), MinTestMover.apply(), FindOptimalHydrophobicThk.apply(), LigandRepackMinimizeProtocol.apply(), DockGlycansProtocol.apply(), RepackCenrotMover.apply(), RepackMinCenrotMover.apply(), MembraneViewMover.apply(), MyProtocol.apply(), TestQuickRelaxMover.apply(), MPDomainAssembly.apply(), aramid_main(), backrub_protocol(), build_bb_independent_rotamers(), build_helix_test(), HbondZinc.build_rotamers(), cen_design(), CenRotCanonicalMover.CenRotCanonicalMover(), ui::task::Task.clone(), ddg(), define_interface(), HubDenovo.design(), design(), design_1comp(), design_AFILV(), design_AFILVEK(), design_AL(), design_all(), design_dyad(), design_FILV(), design_FILVEK(), design_homodimer(), design_pose_motifs_only(), design_target(), design_test(), protocols::jd2::RECONMPIJobDistributor.design_this_nodes_pose(), design_using_resfile(), designloop(), dinucleotide_test(), dna_coupled_rotamer_design_test(), double_helix_test(), exclude_loop_residues(), fixbb_design(), full_protein_repack(), SetupHotspotMover.generate_csts(), generate_factory(), protocols::antibody::design::AntibodyDesignMoverGenerator.get_movemap_from_task(), get_opte_data(), get_rotset(), helix_ST(), DesignGlycansProtocol.init(), GlycomutagenesisProtocol.init(), DockGlycansProtocol.init(), UBQ_E2Mover.init_on_new_input(), UBQ_GTPase_disulfide_Mover.init_on_new_input(), FloppyTailMover.init_on_new_input(), initialize_o2prime_pack(), interface_repack_test(), JDtestmover.JDtestmover(), juke_sam_test(), lk_ball_wtd_deriv_test(), main(), make_motif_task(), minimize_and_score(), motif_scan(), MoveThenFixHMin.MoveThenFixHMin(), InterfaceDDGMover.mutate_and_relax(), my_main(), MembraneViewMover.new_fastrelax_cycle(), not1_test(), MainWindow.on_button_run_packer_clicked(), ui::task::ProjectView.on_cancel_task_clicked(), ui::task::ProjectView.on_clone_task_clicked(), ui::task::JobSubmit.on_delete_job_clicked(), ui::task::ProjectView.on_new_task_clicked(), ui::task::JobSubmit.on_rename_job_clicked(), ui::task::ProjectView.on_tasks_doubleClicked(), one_chain_MC_sampling(), one_chain_ST_MC(), ui::task.open_file_viewer(), pack_interface(), pack_it(), pack_o2prime(), pack_rotamers_test(), MinPackMin.pack_sidechains(), pack_sidechains(), packmin_unbound_pep(), packRotamers(), protocols::jd2::RECONMPIJobDistributor.pick_consensus_AA(), place_waters_and_minimize(), InteractionGraphPerformanceBenchmark.prepare_rotamer_sets(), prepare_start_model(), process_the_pose(), rebuild_test(), InteractionGraphPerformanceBenchmark.redesign_20(), refine(), relax_cenrot_pose(), HbondZinc.repack(), HbondZincBackbone.repack(), repack(), repack_all(), repack_iface(), repack_test(), repackmin(), rna_design_gap_test(), rna_design_test(), rna_protein_prepack_test(), rna_protein_repack_test(), rotamer_trials_test(), rotamerize_rna_test(), run(), ConsensusFragmentMover.run(), SolutionRescoreMover.run(), ui::task::TaskCancelDialog.run(), run_pep_prep(), sample_trp_test(), sample_trp_tyr_test(), saxs_energy(), scan_hbond_jumps(), HECTMover.set_up_taskfactory(), HPatchByChainNPDCalculator.setup(), NBuriedUnsatsCalcultor.setup(), myspace.setup_packer(), PhDocking.setup_pH_mode(), abbinding.setup_RepulsiveRampMover(), zinc1_homodimer_design.setup_taskfactory(), zinc2_homodimer_design.setup_taskfactory_scorefunction_movers(), show_allowed_residue_types(), simple_dna_test(), small_min_test(), spec_test(), stepwise_template_test(), test_gb(), test_suck_res(), NodeTest.test_task_serialization(), FunctorTest.test_task_upload(), NodeTest.test_task_upload_and_download(), PhProtocol.titrate_pH(), ui::task::FileTableModel.update_from_task(), water_test(), water_test_fixed_O(), and ZincMinimize.zn_min_pack().

task2

vancomycin.task2 = TaskFactory.create_packer_task(vanc2)

Referenced by main().

trans2

vancomycin.trans2 = protocols.rigid.RigidBodyTransMover(vanc2, 1)

Referenced by Tet4HMatchAligner.align_rot(), dostuff(), and main().

translate

vancomycin.translate = protocols.rigid.RigidBodyTransMover(vancomycin, 1)

V01

vancomycin.V01 = Residue(V01_type, True)

Referenced by main().

V01_type

vancomycin.V01_type = residue_set_cap.name_map("DV01:aryl-O-conjugated")

Referenced by main().

V02

vancomycin.V02 = Residue(V02_type, True)

Referenced by main().

V022

vancomycin.V022 = Residue(V02_type2, True)

Referenced by main().

V02_type

vancomycin.V02_type = residue_set_cap.name_map("DV02:aryl-O-conjugated:phg_cd1_conjugation:phg_cd2_conjugation")

Referenced by main().

V02_type2

vancomycin.V02_type2 = residue_set_cap.name_map("DV02:phg_cd1_conjugation")

Referenced by main().

V03

vancomycin.V03 = Residue(V03_type, True)

Referenced by main().

V03_type

vancomycin.V03_type = residue_set_cap.name_map("V03:CtermProteinFull:aryl-C-conjugated")

Referenced by main().

V04

vancomycin.V04 = Residue(V04_type, True)

Referenced by main().

V04_type

vancomycin.V04_type = residue_set_cap.name_map("V04:aryl-O-conjugated")

Referenced by main().

vanc2

vancomycin.vanc2 = Pose()

Referenced by main().

vancomycin

vancomycin.vancomycin = Pose()

Referenced by main().