app.surface_docking.surface_docking Namespace Reference

Functions
def	input_checker
def	run
def	append_data

Variables
tuple	parser = argparse.ArgumentParser(description='Surface Docking Script',fromfile_prefix_chars='@')
tuple	args = parser.parse_args(['@flags'])
	input = args.s
	path = args.database
	constraints = args.constraints
tuple	decoy_num = int(args.n)
	frag3 = args.f3
	frag9 = args.f9
	disulf_file = args.d
	nosmallshear_ref = args.nosmallshear
tuple	newpath = os.path.expandvars(path)
list	opts
tuple	Rargs = rosetta.utility.vector1_string()
tuple	sol_cycles = randint(1,5)
int	sol_outer_cycles = 5
int	sol_inner_cycles = 5
int	ads_cycles = 5
int	ads_outer_cycles = 5
int	ads_inner_cycles = 5
tuple	start_pose = Pose()
list	PDB = input[:-4]
float	elec = 1.0
tuple	score_high = create_score_function("score12")
tuple	score_pack = create_score_function("score12")
tuple	std_scorefxn = create_score_function("score12")
tuple	switch_low = SwitchResidueTypeSetMover('centroid')
tuple	switch_high = SwitchResidueTypeSetMover('fa_standard')
tuple	cwd1 = os.getcwd()
tuple	cwd2 = cwd1.split('/')
tuple	cwdn = len(cwd2)
list	dir = cwd2[cwdn - 1]
tuple	jd = PyJobDistributor("AdsState_" + PDB + "_" + dir, decoy_num, score_high)
tuple	jd1 = PyJobDistributor("SolState_" + PDB + "_" + dir, decoy_num, score_high)
	x = jd1.current_name
	y = jd.current_name
tuple	time_start = datetime.datetime.now()
tuple	pose = Pose()
tuple	combined_pose = Pose()
tuple	abinitio = Abinitio(PDB, frag3, frag9)
tuple	cen_relax = CentroidRelax()
tuple	fa_relax = FullAtomRelax(score_high, score_pack, std_scorefxn, nosmallshear_ref)
tuple	sol_pose = Pose()
tuple	curr_sol = str(x)
tuple	curr_ads = str(y)
string	append_surf_sol = "grep SURFA "
string	append_surf_ads = "grep SURFA "
tuple	time_end = datetime.datetime.now()
	time_diff = time_end-time_start

Function Documentation

def app.surface_docking.surface_docking.append_data	(		name,
			pose,
			scorefxn,
			PDB,
			state
	)

References app.surface_docking.append_data.append_constraints(), app.surface_docking.append_data.append_hbonds(), app.surface_docking.append_data.append_scores(), app.surface_docking.constraints.apply_constraints(), and app.surface_docking.constraints.load_constraints().

def app.surface_docking.surface_docking.input_checker	(		input,
			constraints,
			frag3,
			frag9,
			disulf_file
	)

def app.surface_docking.surface_docking.run

(

state

)

References basic::options::OptionKeys::relax::range.range.

Variable Documentation

tuple app.surface_docking.surface_docking.abinitio = Abinitio(PDB, frag3, frag9)

Referenced by add_rosetta_options_4().

int app.surface_docking.surface_docking.ads_cycles = 5

int app.surface_docking.surface_docking.ads_inner_cycles = 5

int app.surface_docking.surface_docking.ads_outer_cycles = 5

string app.surface_docking.surface_docking.append_surf_ads = "grep SURFA "

string app.surface_docking.surface_docking.append_surf_sol = "grep SURFA "

tuple app.surface_docking.surface_docking.args = parser.parse_args(['@flags'])

tuple app.surface_docking.surface_docking.cen_relax = CentroidRelax()

tuple app.surface_docking.surface_docking.combined_pose = Pose()

Referenced by ExposedStrandMover.apply().

app.surface_docking.surface_docking.constraints = args.constraints

Referenced by add_bond_angle_constraint(), add_bond_constraint(), add_rosetta_options_2(), add_rosetta_options_3(), ca_to_allatom_main(), main(), minimize_test(), mutate_residues_wrapper(), pdb_minimizer(), rebuild_test(), repack_test(), rna_denovo_test(), rna_fullatom_minimize_test(), run_mc(), set_pep_cst(), set_pep_csts(), zinc1_homodimer_design.setup_metalsite_constraints(), zinc2_homodimer_design.setup_taskfactory_scorefunction_movers(), HDdesignMover.task_constraint_setup(), and vary_bond_geometry().

tuple app.surface_docking.surface_docking.curr_ads = str(y)

tuple app.surface_docking.surface_docking.curr_sol = str(x)

tuple app.surface_docking.surface_docking.cwd1 = os.getcwd()

tuple app.surface_docking.surface_docking.cwd2 = cwd1.split('/')

tuple app.surface_docking.surface_docking.cwdn = len(cwd2)

tuple app.surface_docking.surface_docking.decoy_num = int(args.n)

list app.surface_docking.surface_docking.dir = cwd2[cwdn - 1]

Referenced by tools.CppParser.CD.__repr__(), BuildBindings.__repr__(), src.CD.__repr__(), tools.CppParser.CLANG_XML(), and utility::file.create_temp_filename().

app.surface_docking.surface_docking.disulf_file = args.d

float app.surface_docking.surface_docking.elec = 1.0

tuple app.surface_docking.surface_docking.fa_relax = FullAtomRelax(score_high, score_pack, std_scorefxn, nosmallshear_ref)

app.surface_docking.surface_docking.frag3 = args.f3

Referenced by add_rosetta_options_0().

app.surface_docking.surface_docking.frag9 = args.f9

Referenced by add_rosetta_options_0().

app.surface_docking.surface_docking.input = args.s

Referenced by calc_rms_test(), numeric.FArray_to_vector_of_xyzvectors(), numeric.FArray_to_xyzmatrix(), get_refine_pose_list(), main(), utility.replace_environment_variables(), rna_fullatom_minimize_test(), rna_score_test(), rna_suitename(), and numeric.vector_of_xyzvectors_to_FArray().

tuple app.surface_docking.surface_docking.jd = PyJobDistributor("AdsState_" + PDB + "_" + dir, decoy_num, score_high)

Referenced by main().

tuple app.surface_docking.surface_docking.jd1 = PyJobDistributor("SolState_" + PDB + "_" + dir, decoy_num, score_high)

tuple app.surface_docking.surface_docking.newpath = os.path.expandvars(path)

Referenced by utility::file::PathName.parent().

app.surface_docking.surface_docking.nosmallshear_ref = args.nosmallshear

list app.surface_docking.surface_docking.opts

Initial value:

= ['app','-database',newpath,'-ex1','-ex2aro','-multiple_processes_writing_to_one_directory',\
        '-mute','core','-mute','protocols','-mute','basic']

Referenced by main(), output_packstat(), output_packstat_pdb(), and ScoreEachBenchmark.setUp().

tuple app.surface_docking.surface_docking.parser = argparse.ArgumentParser(description='Surface Docking Script',fromfile_prefix_chars='@')

app.surface_docking.surface_docking.path = args.database

Referenced by add_rosetta_options_0(), add_rosetta_options_1(), add_rosetta_options_10(), supercharge.apply(), utility::graph::RingEdgeAnnotationVisitor< Graph, EdgeMap, PathMap >.back_edge(), basic::database.find_database_path(), basic::database.full_cache_name(), main(), basic::database.parse_database_connection(), basic::options.process(), stepwise_monte_carlo(), and utility::graph::RingEdgeAnnotationVisitor< Graph, EdgeMap, PathMap >.tree_edge().

list app.surface_docking.surface_docking.PDB = input[:-4]

tuple app.surface_docking.surface_docking.pose = Pose()

Referenced by align_pdbs(), IAMover.apply(), LigandRepackMinimizeProtocol.apply(), Minimize.apply(), ExtractATD.apply(), MyScoreMover.apply(), NCMinimize.apply(), ExposedStrandMover.apply(), FitMover.apply(), HDmakerMover.apply(), HDdesignMover.apply(), DougsDockDesignMinimizeMagicMover.apply(), UBQ_GTPaseMover.apply(), UBQ_GTPase_disulfide_Mover.apply(), UBQ_E2Mover.apply(), calc_rms_test(), calculate_pairwise_RMSD(), compute_chem_shift_RMSD(), create_base_pair_step_database_test(), create_bp_jump_database_test(), create_rna_vall_torsions_test(), create_theozyme_pdb(), cs_rosetta_rna_pdb(), densityTools(), extract_pdbs_test(), fill_designable_set(), filter_combine_long_loop(), find_close_motifs(), gen_pep_bb_sequential(), get_binding_score(), get_clash_pairs(), get_elec_score(), get_hbond_score(), get_n_mer_maltose(), get_n_mer_polyalanine(), get_packing_score(), get_pose_and_numbering(), graft_pdb(), has_clash(), import_and_dump_pdb(), initialize_native_pose(), initialize_peptide(), main(), match_main(), MC_run(), mg_modeler_test(), minimize_test(), mutate_residue(), mutate_residues_wrapper(), myMC.myMC(), nucleobase_probe_score_test(), o2prime_packer(), output_single_motif(), packmin_unbound_pep(), pdb_minimizer(), pdb_to_silent_file(), perturb_pep_bb(), pose_setup(), PosePyObserverTesterFunction(), poses_from_cmd_line(), post_rebuild_bulge_assembly(), predict_chem_map_test(), prepare_threaded_model(), print_pep_analysis(), pyrimidine_flip_trial(), quick_score_test(), read_native_sequence_for_entity_elements(), read_pose(), rebuild_test(), repack_test(), rhiju_pdbstats(), rna_build_helix_test(), rna_denovo_test(), rna_design_test(), rna_fullatom_minimize_test(), rna_sample_virtual_sugar(), rna_score_test(), rna_sequence_recovery_metrics(), rna_suitename(), rna_thread_test(), myMC.roll(), DatabaseIOBenchmark.run(), PDB_IOBenchmark.run(), DockingBenchmark< dock, TScale >.run(), SmallMoverBenchmark.run(), MinimizerBenchmark< sft, TScale >.run(), ShearMoverBenchmark.run(), ScoreBenchmark.run(), run(), run_pep_prep(), RunPepSpec(), sequence_tolerance_main(), SmallMoverBenchmark.setUp(), ShearMoverBenchmark.setUp(), ScoreBenchmark.setUp(), slice_ellipsoid_envelope(), slice_sample_res_and_surrounding(), spanfile_from_pdb(), stepwise_monte_carlo(), superimpose_pdb(), swa_rna_sample(), HDdesignMover.sym_repack_minimize(), SmallMoverBenchmark.tearDown(), and ShearMoverBenchmark.tearDown().

tuple app.surface_docking.surface_docking.Rargs = rosetta.utility.vector1_string()

tuple app.surface_docking.surface_docking.score_high = create_score_function("score12")

tuple app.surface_docking.surface_docking.score_pack = create_score_function("score12")

tuple app.surface_docking.surface_docking.sol_cycles = randint(1,5)

int app.surface_docking.surface_docking.sol_inner_cycles = 5

int app.surface_docking.surface_docking.sol_outer_cycles = 5

tuple app.surface_docking.surface_docking.sol_pose = Pose()

tuple app.surface_docking.surface_docking.start_pose = Pose()

Referenced by initialize_peptide(), main(), minimize_test(), mutate_residue(), pdb_minimizer(), post_rebuild_bulge_assembly(), repack_test(), rna_fullatom_minimize_test(), rna_score_test(), MinimizerBenchmark< sft, TScale >.run(), run_pep_prep(), RunPepSpec(), MinimizerBenchmark< sft, TScale >.setUp(), and swa_rna_sample().

tuple app.surface_docking.surface_docking.std_scorefxn = create_score_function("score12")

tuple app.surface_docking.surface_docking.switch_high = SwitchResidueTypeSetMover('fa_standard')

tuple app.surface_docking.surface_docking.switch_low = SwitchResidueTypeSetMover('centroid')

app.surface_docking.surface_docking.time_diff = time_end-time_start

tuple app.surface_docking.surface_docking.time_end = datetime.datetime.now()

tuple app.surface_docking.surface_docking.time_start = datetime.datetime.now()

Referenced by main(), MC_run(), slice_ellipsoid_envelope(), and slice_sample_res_and_surrounding().

app.surface_docking.surface_docking.x = jd1.current_name

app.surface_docking.surface_docking.y = jd.current_name