application level code for Abrelax, Foldconstraints and JumpingFoldconstraints More...

#include <AbrelaxApplication.hh>

Public Member Functions
	AbrelaxApplication ()

virtual	~AbrelaxApplication ()
	Explicit virtual destructor since AbrelaxApplication contains OPs NOTE: any time you define a class that is derived from by other classes and which contains polymorphic functions, it needs to have a virtual destructor. If your class derives from ReferenceCount, then it will inherit a virtual destructor If it does not, as AbrelaxApplication does not, then you must declare the destructor virtual. More...

	AbrelaxApplication (AbrelaxApplication const &)
	Explicit copy constructor since AbrelaxApplication contains OPs. More...

void	process_decoy (core::pose::Pose &pose, core::scoring::ScoreFunction const &, std::string tag, core::io::silent::SilentStruct &) const
	diagnostic stuff, i.e., computing numbers like an RMSD for each decoy and storing in silent-score-file put everything in here. — actually it mainly calls the evaluator_->apply method. add diagnostic stuff either here as explicit code or in form of a PoseEvaluator to evaluator_ ( see setup () ) the latter has the advantage that the specific evaluation can be carried out during the run of the protocol e.g., for abinitio:debug ( output to stage1_outfile stage2_outfile... ) More...

void	add_constraints (core::pose::Pose &pose)
	read constraint set (self-initializing) and connect it to pose More...

void	setup ()
	initialization of application: read some pdb files, set evaluator_ More...

void	run ()
	run application code: calls do_rerun() or fold() depending on cmd-options More...

void	do_rerun ()
	run process_decoy on all poses in silent-in file More...

void	do_distributed_rerun ()
	run process_decoy on all poses in silent-in file – use of JobDistributor More...

void	setup_fold (core::pose::Pose &extended_pose, ProtocolOP &prot_ptr)
	setup everything needed for fold() — calls helper functions below More...

void	fold (core::pose::Pose &extended_pose, ProtocolOP prot_ptr)
	run abrelax-type protocols More...

bool	close_loops (core::pose::Pose &pose, core::scoring::ScoreFunctionOP scorefxn, std::string const &tag)
	return pose with simple fold-tree that has small <0.1 RMSD to input pose More...

void	relax (core::pose::Pose &pose, core::scoring::ScoreFunctionOP, std::string const &tag)
	relax structure ( fast / classic as controlled by cmd-options ) More...

bool	multi_fast_relax (Protocol &abinitio_protocol, core::scoring::ScoreFunctionOP, jobdist::PlainSilentFileJobDistributor jobdist, int &curr_nstruct, jobdist::BasicJobOP &curr_job)
	relax multiple structures that are stored in abinitio_protocol.structure_store More...

void	add_evaluation (evaluation::PoseEvaluatorOP)
	little helper: minimize structure to have lower chainbreak score ( seems particularly necessary after reading from silent-file ) More...

bool	check_filters (core::pose::Pose &pose)
	check if the given pose passes the set of abinitio filters. More...

Static Public Member Functions
static void	register_options ()

Private Member Functions
core::scoring::ScoreFunctionOP	generate_scorefxn (bool fullatom=false)
	create score-functions for centroid and fullatom level More...

void	copy_native_structure (core::pose::Pose &extended_pose) const
	-— Helper functions for setup_fold More...

void	copy_structure (core::pose::Pose &extended_pose, core::pose::Pose &desired_pose) const
	copy torsions from the desired_pose, copy them into the extended_pose. More...

void	generate_extended_pose (core::pose::Pose &extended_pose, std::string const &sequence) const
	steal native torsions from native_pose_ and apply to the "extended_pose" More...

void	setup_fragments ()
	read fragment data More...

void	setup_jumps (core::pose::Pose const &extended_pose)
	read jump definitions and set jump_def_ More...

void	setup_membrane_topology (core::pose::Pose &pose, std::string spanfile) const
	read in membrane topology More...

void	setup_templates ()
	initialize template_ More...

void	insert_template_frags (core::pose::Pose &, core::kinematics::MoveMapOP movemap, std::string tag) const
	insert fragments from aligned regions More...

void	initialize_constraint_forest (core::pose::Pose &pose)

Detailed Description

application level code for Abrelax, Foldconstraints and JumpingFoldconstraints

Constructor & Destructor Documentation

protocols::abinitio::AbrelaxApplication::AbrelaxApplication ( )

c'stor - nothing special

protocols::abinitio::AbrelaxApplication::~AbrelaxApplication ( )

virtual

Explicit virtual destructor since AbrelaxApplication contains OPs NOTE: any time you define a class that is derived from by other classes and which contains polymorphic functions, it needs to have a virtual destructor. If your class derives from ReferenceCount, then it will inherit a virtual destructor If it does not, as AbrelaxApplication does not, then you must declare the destructor virtual.

protocols::abinitio::AbrelaxApplication::AbrelaxApplication ( AbrelaxApplication const & src )

Explicit copy constructor since AbrelaxApplication contains OPs.

Shallow copy to mimic the pre 9/8/09 compiler-generated version of this method. If you add new

Member Function Documentation

void protocols::abinitio::AbrelaxApplication::add_constraints ( core::pose::Pose & pose )

read constraint set (self-initializing) and connect it to pose

read constraints file (once) and constraints_set to the pose (each call)

References core::scoring::constraints::ConstraintSet::add_constraints(), core::pose::Pose::add_constraints(), add_evaluation(), core::scoring::atom_pair_constraint, protocols::abinitio::StrandConstraints::build_constraints(), core::pose::Pose::constraint_set(), constraints::cst_file, cstset_, core::scoring::constraints::cull_violators(), constraints::cull_with_native, constraints::dump_cst_set, constraints::evaluate_max_seq_sep, core::scoring::constraints::ConstraintSet::get_all_constraints(), core::scoring::constraints::get_cst_file_option(), core::scoring::constraints::ConstraintIO::get_instance(), utility::io::izstream::good(), native_pose_, option, core::scoring::constraints::ConstraintIO::read_constraints(), core::scoring::constraints::ConstraintSet::show_definition(), size(), templates::strand_constraint, templates_, utility::to_string(), jumps::topology_file, tr, user, and utility_exit_with_message.

Referenced by do_distributed_rerun(), do_rerun(), and setup_fold().

void protocols::abinitio::AbrelaxApplication::add_evaluation ( evaluation::PoseEvaluatorOP eval )

little helper: minimize structure to have lower chainbreak score ( seems particularly necessary after reading from silent-file )

add a PoseEvaluator derived instance for decoy-processing

References evaluator_.

Referenced by add_constraints(), do_distributed_rerun(), do_rerun(), fold(), setup(), and setup_jumps().

bool protocols::abinitio::AbrelaxApplication::check_filters ( core::pose::Pose & pose )

check if the given pose passes the set of abinitio filters.

Referenced by protocols::abinitio::DomainAssembly::apply(), do_distributed_rerun(), do_rerun(), and fold().

bool protocols::abinitio::AbrelaxApplication::close_loops	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunctionOP	scorefxn,
		std::string const &	tag
	)

return pose with simple fold-tree that has small <0.1 RMSD to input pose

References abrelax_checkpoints_, protocols::idealize::IdealizeMover::apply(), protocols::checkpoint::CheckPointer::checkpoint(), protocols::jumping::close_chainbreaks(), core::pose::Pose::constraint_set(), protocols::checkpoint::CheckPointer::debug(), debug_output, core::pose::Pose::dump_pdb(), evaluator_, protocols::idealize::IdealizeMover::fast(), fragset_small_, core::pose::Pose::is_fullatom(), movemap, native_pose_, option, protocols::checkpoint::CheckPointer::recover_checkpoint(), runtime_assert, setup_fragments(), and basic::options::OptionKeys::out::file::silent_struct_type.

Referenced by do_distributed_rerun(), do_rerun(), and fold().

void protocols::abinitio::AbrelaxApplication::copy_native_structure ( core::pose::Pose & extended_pose ) const

private

-— Helper functions for setup_fold

steal native torsions from native_pose_ and apply to the extended_pose.

called by setup_fold() if option[ start_native ] is active the routine defines a fragment of the length of the structure steals the fragment from the native and applies it to the decoy native needs to be idealized!

References copy_structure(), native_pose_, and tr.

Referenced by setup_fold().

void protocols::abinitio::AbrelaxApplication::copy_structure	(	core::pose::Pose &	extended_pose,
		core::pose::Pose &	desired_pose
	)		const

private

copy torsions from the desired_pose, copy them into the extended_pose.

References core::conformation::Residue::is_protein(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and tr.

Referenced by copy_native_structure(), and setup_fold().

void protocols::abinitio::AbrelaxApplication::do_distributed_rerun ( )

run process_decoy on all poses in silent-in file – use of JobDistributor

loop over structures in silent-input file small trick is used to also have native structure in the set of analysis: it is added to the collection of silent_file-structures manually TODO we need to do something about difference between fullatom and centroid input!

References add_constraints(), add_evaluation(), begin, bRelax_, check_filters(), close_loops(), run::condor, core::pose::Pose::conformation(), core::pose::Pose::constraint_set(), loopfcst::coord_cst_all_atom, core::io::raw_data::DisulfideFile::disulfides(), evaluator_, basic::options::OptionKeys::abinitio::fastrelax, basic::options::OptionKeys::in::fix_disulf, core::conformation::Conformation::fix_disulfides(), protocols::loops::fix_with_coord_cst(), generate_scorefxn(), protocols::loops::Loops::grow_all_loops(), protocols::loops::Loops::invert(), core::pose::Pose::is_fullatom(), core::scoring::linear_chainbreak, loops_in_, jumps::no_chainbreak_in_relax, run::nproc, out::nstruct, nstruct, option, basic::options::option, output_tag, core::scoring::overlap_chainbreak, protocols::ligand_docking::passes_filters(), run::proc_id, process_decoy(), protocols::antibody::design::relax, relax(), rigid, set_ss_from_phipsi(), protocols::relax::ClassicRelax::setPoseExtraScore(), basic::options::OptionKeys::out::file::silent, in::file::silent, silent_score_file_, protocols::loops::Loops::size(), core::util::switch_to_residue_type_set(), tag, core::pose::Pose::total_residue(), tr, user, utility_exit_with_message, protocols::loops::Loops::verify_against(), and core::io::silent::SilentFileData::write_silent_struct().

Referenced by run().

void protocols::abinitio::AbrelaxApplication::do_rerun ( )

run process_decoy on all poses in silent-in file

loop over structures in silent-input file small trick is used to also have native structure in the set of analysis: it is added to the collection of silent_file-structures manually TODO we need to do something about difference between fullatom and centroid input!

References add_constraints(), add_evaluation(), begin, core::io::silent::SilentFileData::begin(), check_filters(), close_loops(), core::io::silent::SilentFileData::end(), end, evaluator_, in::file::fullatom, generate_scorefxn(), core::pose::Pose::is_fullatom(), core::scoring::linear_chainbreak, core::pose::Pose::metric(), native_pose_, option, core::scoring::overlap_chainbreak, protocols::ligand_docking::passes_filters(), process_decoy(), core::io::silent::SilentFileData::read_file(), residue_type_set, in::file::silent, out::file::silent, silent_score_file_, core::io::silent::SilentFileData::size(), ss, tag, in::file::tags, tr, user, basic::MetricValue< T >::value(), and constraints::viol.

Referenced by run().

void protocols::abinitio::AbrelaxApplication::fold	(	core::pose::Pose &	init_pose,
		ProtocolOP	prot_ptr
	)

run abrelax-type protocols

everything happens in fold()! setup of stuff that is not needed for rerun() read fragments [ optional ] steal fragments ( take fragments from native pose )

References abrelax_checkpoints_, add_evaluation(), core::io::silent::SilentFileData::add_structure(), protocols::moves::AddPyMolObserver(), protocols::abinitio::ResolutionSwitcher::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::abinitio::Protocol::apply(), protocols::idealize::IdealizeMover::apply(), bRelax_, core::scoring::methods::ContactOrderEnergy::calculate_contact_order(), check_filters(), run::checkpoint, protocols::checkpoint::CheckPointer::checkpoint(), protocols::loops::Loop::choose_cutpoint(), protocols::checkpoint::CheckPointer::clear_checkpoints(), close_loops(), basic::options::OptionKeys::abinitio::close_loops_by_idealizing, core::pose::Pose::conformation(), core::pose::Pose::constraint_set(), core::scoring::ScoreFunctionFactory::create_score_function(), cstset_, core::kinematics::FoldTree::cutpoint(), core::pose::Pose::data(), protocols::checkpoint::CheckPointer::debug(), core::conformation::Conformation::detect_disulfides(), core::pose::Pose::dump_pdb(), evaluator_, protocols::idealize::IdealizeMover::fast(), basic::options::OptionKeys::abinitio::fastrelax, core::pose::Pose::fold_tree(), protocols::loops::fold_tree_from_loops(), numeric::random::gaussian(), generate_scorefxn(), protocols::checkpoint::CheckPointer::get_checkpoint_recoveries(), protocols::abinitio::Protocol::get_checkpoints(), get_cst_fa_file_option(), protocols::moves::Mover::get_current_tag(), core::scoring::constraints::ConstraintIO::get_instance(), protocols::moves::Mover::get_last_move_status(), basic::datacache::BasicDataCache::get_ptr(), basic::datacache::BasicDataCache::has(), core::pose::Pose::is_centroid(), core::pose::Pose::is_fullatom(), membrane_jumps_, protocols::moves::MS_SUCCESS, multi_fast_relax(), basic::options::OptionKeys::abinitio::multifastrelax, jumps::njumps, njumps, nstruct, out::nstruct, core::kinematics::FoldTree::num_cutpoint(), core::pose::Pose::omega(), basic::options::OptionKeys::abinitio::optimize_cutpoints_using_kic, option, output_tag, protocols::ligand_docking::passes_filters(), core::pose::Pose::phi(), process_decoy(), core::pose::Pose::psi(), core::scoring::constraints::ConstraintIO::read_constraints(), protocols::checkpoint::CheckPointer::recover_checkpoint(), relax(), basic::options::OptionKeys::abinitio::relax_failures, protocols::abinitio::RG, runtime_assert, basic::datacache::BasicDataCache::set(), protocols::abinitio::Protocol::set_centroid_scorefxn(), protocols::moves::Mover::set_current_job(), protocols::moves::Mover::set_current_tag(), protocols::abinitio::Protocol::set_evaluation(), protocols::abinitio::Protocol::set_fullatom_scorefxn(), protocols::abinitio::ResolutionSwitcher::set_map_cst_from_centroid_to_fa(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), protocols::loops::Loop::set_start(), core::pose::setPoseExtraScore(), protocols::relax::ClassicRelax::setPoseExtraScore(), core::scoring::SS_Killhairpins_Info::setup_killhairpins(), basic::options::OptionKeys::out::file::silent, silent_score_file_, core::kinematics::FoldTree::simple_tree(), core::pose::datacache::CacheableDataType::SS_KILLHAIRPINS_INFO, protocols::loops::Loop::start(), core::io::silent::SilentFileData::strict_column_mode(), in::file::tagfile, in::file::tags, core::pose::Pose::total_residue(), tr, numeric::random::RandomGenerator::uniform(), user, and core::io::silent::SilentFileData::write_silent_struct().

Referenced by run().

void protocols::abinitio::AbrelaxApplication::generate_extended_pose	(	core::pose::Pose &	extended_pose,
		std::string const &	sequence
	)		const

private

steal native torsions from native_pose_ and apply to the "extended_pose"

called by setup_fold(): setup the decoy pose with correct target sequence and extended structure

References core::pose::Pose::conformation(), core::io::raw_data::DisulfideFile::disulfides(), basic::options::OptionKeys::in::fix_disulf, core::conformation::Conformation::fix_disulfides(), core::conformation::Residue::is_protein(), core::pose::make_pose_from_sequence(), basic::options::option, core::pose::Pose::residue(), residue_type_set, core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), core::pose::Pose::total_residue(), and user.

Referenced by setup_fold().

core::scoring::ScoreFunctionOP protocols::abinitio::AbrelaxApplication::generate_scorefxn ( bool fullatom = false )

private

create score-functions for centroid and fullatom level

References core::scoring::angle_constraint, core::scoring::atom_pair_constraint, core::scoring::coordinate_constraint, core::scoring::ScoreFunctionFactory::create_score_function(), cstset_, core::scoring::dihedral_constraint, core::scoring::get_score_function(), core::scoring::constraints::ConstraintSet::has_residue_pair_constraints(), jump_def_, core::scoring::linear_chainbreak, basic::options::OptionKeys::abinitio::membrane, option, core::scoring::overlap_chainbreak, and user.

Referenced by do_distributed_rerun(), do_rerun(), and fold().

void protocols::abinitio::AbrelaxApplication::initialize_constraint_forest ( core::pose::Pose & pose )

private

References constraints::forest_file, option, tr, user, and utility_exit_with_message.

Referenced by setup_fold().

void protocols::abinitio::AbrelaxApplication::insert_template_frags	(	core::pose::Pose &	pose,
		core::kinematics::MoveMapOP	movemap,
		std::string	tag
	)		const

private

insert fragments from aligned regions

References templates::fix_frag_file, frame(), option, out, core::fragment::FragmentIO::read_data(), protocols::abinitio::RG, numeric::random::RandomGenerator::uniform(), and user.

bool protocols::abinitio::AbrelaxApplication::multi_fast_relax	(	Protocol &	abinitio_protocol,
		core::scoring::ScoreFunctionOP	,
		jobdist::PlainSilentFileJobDistributor	jobdist,
		int &	curr_nstruct,
		jobdist::BasicJobOP &	curr_job
	)

relax multiple structures that are stored in abinitio_protocol.structure_store

do fast relax on multiple structures that have been visited during abinitio-protocol. MIKE: please give more documentation to this

Referenced by fold().

void protocols::abinitio::AbrelaxApplication::process_decoy	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunction const &	scorefxn,
		std::string	tag,
		core::io::silent::SilentStruct &	pss
	)		const

diagnostic stuff, i.e., computing numbers like an RMSD for each decoy and storing in silent-score-file put everything in here. — actually it mainly calls the evaluator_->apply method. add diagnostic stuff either here as explicit code or in form of a PoseEvaluator to evaluator_ ( see setup () ) the latter has the advantage that the specific evaluation can be carried out during the run of the protocol e.g., for abinitio:debug ( output to stage1_outfile stage2_outfile... )

run all evaluations on the decoy from this function if you want these evaluations also available during internal stages of the protocols –> put them into a PoseEvaluator and use add_evaluation in setup() otherwise you can also use "manual" code right here in process_decoy –> this will only appear in final silent_out and silent_score - files.

References protocols::evaluation::MetaPoseEvaluator::add_evaluation(), protocols::evaluation::MetaPoseEvaluator::apply(), basic::datacache::BasicDataCache::clear(), core::pose::Pose::data(), jumps::evaluate, evaluator_, core::io::silent::SilentStruct::fill_struct(), core::pose::Pose::fold_tree(), native_pose_, core::pose::Pose::num_jump(), option, tr, and utility_exit_with_message.

Referenced by do_distributed_rerun(), do_rerun(), and fold().

void protocols::abinitio::AbrelaxApplication::register_options ( )

static

registering of options that are relevant for AbrelaxApplication

References utility::options::OptionCollection::add_relevant(), frags::annotate, constraints::compute_total_dist_cst, run::condor, templates::config, loopfcst::coord_cst_all_atom, loopfcst::coord_cst_weight, loopfcst::coord_cst_weight_array, constraints::cst_file, constraints::cull_with_native, loopfcst::dump_coord_cst_weight_array, constraints::dump_cst_set, constraints::epr_distance, jumps::evaluate, constraints::evaluate_max_seq_sep, jumps::extra_frags_for_ss, in::file::fasta, templates::fix_aligned_residues, jumps::fix_chainbreak, templates::fix_frag_file, jumps::fix_jumps, templates::fix_margin, constraints::forest_file, in::file::frag3, in::file::frag9, jumps::jump_lib, jumps::loop_definition_from_file, templates::min_nr_large_frags, templates::min_nr_small_frags, constraints::named, in::file::native, in::file::native_exclude_res, jumps::no_chainbreak_in_relax, constraints::no_cst_in_relax, constraints::no_linearize_bounded, templates::no_pick_fragments, run::nproc, templates::nr_large_copies, frags::nr_large_copies, templates::nr_small_copies, out::nstruct, option, jumps::pairing_file, templates::pairings, templates::pick_multiple_sizes, run::proc_id, jumps::random_sheets, protocols::evaluation::register_options(), protocols::antibody::design::relax, jumps::residue_pair_jump_file, jumps::sheets, out::file::silent, in::file::silent, templates::strand_constraint, in::file::tags, jumps::topology_file, loopfcst::use_general_protocol, templates::vary_frag_size, constraints::viol, constraints::viol_level, and constraints::viol_type.

Referenced by protocols::protein_interface_design::movers::TopologyBrokerMover::apply().

void protocols::abinitio::AbrelaxApplication::relax	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunctionOP	scorefxn,
		std::string const &	tag
	)

relax structure ( fast / classic as controlled by cmd-options )

full-atom relax of decoys uses either ClassicRelax or FastRelax protocols.

References abrelax_checkpoints_, add_fa_constraints_from_cmdline(), protocols::relax::FastRelax::apply(), protocols::checkpoint::CheckPointer::checkpoint(), core::pose::Pose::constraint_set(), protocols::checkpoint::CheckPointer::debug(), basic::options::OptionKeys::relax::fast, basic::options::OptionKeys::abinitio::fastrelax, constraints::no_cst_in_relax, option, protocols::checkpoint::CheckPointer::recover_checkpoint(), basic::options::OptionKeys::abinitio::relax, protocols::antibody::design::relax, protocols::relax::relax_pose(), protocols::moves::Mover::set_current_tag(), and tr.

Referenced by do_distributed_rerun(), and fold().

void protocols::abinitio::AbrelaxApplication::run ( )

run application code: calls do_rerun() or fold() depending on cmd-options

after setup() run either fold() or rerun()

References basic::options::OptionKeys::in::path::database, do_distributed_rerun(), do_rerun(), fold(), basic::options::option, option, setup(), setup_fold(), and user.

void protocols::abinitio::AbrelaxApplication::setup ( )

initialization of application: read some pdb files, set evaluator_

setup of Application data that is used for both, fold() and run() this is mainly stuff for scoring and evaluation ( process_decoys(), evaluator_ )

References protocols::evaluation::EvaluatorFactory::add_all_evaluators(), add_evaluation(), core::scoring::func::FuncFactory::add_type(), constraints::compute_total_dist_cst, evaluator_, in::file::fasta, core::scoring::constraints::ConstraintIO::get_func_factory(), core::scoring::constraints::ConstraintFactory::get_instance(), protocols::evaluation::EvaluatorFactory::get_instance(), core::pose::metrics::CalculatorFactory::Instance(), constraints::named, in::file::native, native_pose_, constraints::no_linearize_bounded, option, pca_, core::import_pose::pose_from_pdb(), core::sequence::read_fasta_file(), core::pose::metrics::CalculatorFactory::register_calculator(), core::scoring::constraints::ConstraintFactory::replace_creator(), core::pose::Pose::sequence(), sequence_, setup_templates(), out::sf, silent_score_file_, core::util::switch_to_residue_type_set(), tr, user, utility_exit_with_message, and constraints::viol.

Referenced by run().

void protocols::abinitio::AbrelaxApplication::setup_fold	(	core::pose::Pose &	extended_pose,
		ProtocolOP &	prot_ptr
	)

setup everything needed for fold() — calls helper functions below

setup_fold() all initialization that is necessary to run abinitio production loop in fold() read fragments, make pose from sequence, get constraints, set jumps, movemap .etc the two parameters are OUTPUT: extended_pose to run A) with ( might actually contain native starting structure (option!) ) prot_ptr: an initialized instance of ClassicAbinitio, FoldConstraints or JumpingFoldConstraints depending on user settings.

References add_constraints(), protocols::simple_moves::RepulsiveOnlyMover::apply(), bRelax_, core::chemical::CENTROID, core::pose::Pose::conformation(), core::pose::Pose::constraint_set(), loopfcst::coord_cst_all_atom, loopfcst::coord_cst_weight, loopfcst::coord_cst_weight_array, copy_native_structure(), copy_structure(), core::io::raw_data::DisulfideFile::disulfides(), loopfcst::dump_coord_cst_weight_array, end, evaluator_, core::chemical::FA_STANDARD, file, protocols::abinitio::filename(), basic::options::OptionKeys::in::fix_disulf, core::conformation::Conformation::fix_disulfides(), core::pose::Pose::fold_tree(), fragset_large_, fragset_small_, fragset_small_top25_, in::file::fullatom, generate_extended_pose(), core::chemical::ChemicalManager::get_instance(), utility::io::izstream::good(), protocols::loops::Loops::grow_all_loops(), protocols::abinitio::Protocol::init(), initialize_constraint_forest(), protocols::loops::Loops::invert(), core::pose::Pose::is_fullatom(), jump_def_, jumps::jump_lib, loops_in_, basic::options::OptionKeys::abinitio::membrane, membrane_jumps_, movemap, native_pose_, option, jumps::pairing_file, core::import_pose::pose_from_pdb(), read_vector(), protocols::antibody::design::relax, core::chemical::ChemicalManager::residue_type_set(), protocols::abinitio::Protocol::return_centroid(), runtime_assert, in::file::s, sequence_, protocols::abinitio::Protocol::set_evaluation(), protocols::moves::Mover::set_native_pose(), setup_fragments(), setup_jumps(), setup_membrane_topology(), basic::options::OptionKeys::out::file::silent_struct_type, core::kinematics::simple_visualize_fold_tree(), in::file::spanfile, spanfile, ss_def_, protocols::loops::start, core::pose::Pose::total_residue(), tr, user, utility_exit_with_message, protocols::loops::Loops::verify_against(), constraints::viol_level, and weights.

Referenced by run().

void protocols::abinitio::AbrelaxApplication::setup_fragments ( )

private

read fragment data

called by setup_fold(): read fragment libraries, I strongly suggest to use different options than A and B if option[ steal ] fragments from the native structure are added to the set. native structure needs to be idealized for this!

References in::file::frag3, in::file::frag9, in::file::fragA, in::file::fragB, fragset_large_, fragset_small_, fragset_small_top25_, fragset_templates_, merge_frags(), templates::min_nr_large_frags, templates::min_nr_small_frags, native_pose_, templates::no_pick_fragments, nr_large_copies, templates::nr_large_copies, nr_small_copies, templates::nr_small_copies, option, templates::pick_multiple_sizes, steal_frag_set_from_pose(), templates_, tr, user, and templates::vary_frag_size.

Referenced by close_loops(), and setup_fold().

void protocols::abinitio::AbrelaxApplication::setup_jumps ( core::pose::Pose const & extended_pose )

private

read jump definitions and set jump_def_

called by setup_fold(). Read jump definitions / barcodes (not yet) etc. if jump_def_ points to an object we will use JumpFoldConstraint-protocol in fold()

References add_evaluation(), jumps::extra_frags_for_ss, utility::io::izstream::fail(), jumps::fix_jumps, constraints::forest_file, fragset_small_, utility::io::izstream::good(), helix_pairings, jump_def_, jumps::jump_lib, jumps::loop_definition_from_file, native_pose_, option, jumps::pairing_file, pairings, templates::pairings, jumps::random_sheets, protocols::jumping::read_pairing_list(), jumps::residue_pair_jump_file, runtime_assert, core::pose::Pose::secstruct(), jumps::sheets, sheets, ss_def_, templates_, jumps::topology_file, core::pose::Pose::total_residue(), tr, user, and utility_exit_with_message.

Referenced by setup_fold().

void protocols::abinitio::AbrelaxApplication::setup_membrane_topology	(	core::pose::Pose &	pose,
		std::string	spanfile
	)		const

private

read in membrane topology

References core::pose::Pose::data(), basic::datacache::BasicDataCache::get_ptr(), core::scoring::MembraneTopology::initialize(), core::pose::datacache::CacheableDataType::MEMBRANE_TOPOLOGY, and basic::datacache::BasicDataCache::set().

Referenced by setup_fold().

void protocols::abinitio::AbrelaxApplication::setup_templates ( )

private

initialize template_

called by setup_fold(). Read template definitions

References templates::config, fragset_large_, native_pose_, option, templates::pairings, runtime_assert, sequence_, templates_, tr, user, and utility_exit_with_message.

Referenced by setup().

Member Data Documentation

checkpoint::CheckPointer protocols::abinitio::AbrelaxApplication::abrelax_checkpoints_

private

Referenced by close_loops(), fold(), and relax().

bool protocols::abinitio::AbrelaxApplication::bRelax_

private

Referenced by do_distributed_rerun(), fold(), and setup_fold().

core::scoring::constraints::ConstraintSetOP protocols::abinitio::AbrelaxApplication::cstset_

private

Referenced by add_constraints(), fold(), and generate_scorefxn().

evaluation::MetaPoseEvaluatorOP protocols::abinitio::AbrelaxApplication::evaluator_

private

Referenced by add_evaluation(), close_loops(), do_distributed_rerun(), do_rerun(), fold(), process_decoy(), setup(), and setup_fold().

core::fragment::FragSetOP protocols::abinitio::AbrelaxApplication::fragset_large_

private

Referenced by setup_fold(), setup_fragments(), and setup_templates().

core::fragment::FragSetOP protocols::abinitio::AbrelaxApplication::fragset_small_

private

Referenced by close_loops(), setup_fold(), setup_fragments(), and setup_jumps().

core::fragment::FragSetOP protocols::abinitio::AbrelaxApplication::fragset_small_top25_

private

Referenced by setup_fold(), and setup_fragments().

core::fragment::FragSetOP protocols::abinitio::AbrelaxApplication::fragset_templates_

private

Referenced by setup_fragments().

core::pose::PoseOP protocols::abinitio::AbrelaxApplication::init_pose_obj_

private

jumping::BaseJumpSetupOP protocols::abinitio::AbrelaxApplication::jump_def_

private

Referenced by generate_scorefxn(), setup_fold(), and setup_jumps().

loops::Loops protocols::abinitio::AbrelaxApplication::loops_in_

private

Referenced by do_distributed_rerun(), and setup_fold().

jumping::MembraneJumpOP protocols::abinitio::AbrelaxApplication::membrane_jumps_

private

Referenced by fold(), and setup_fold().

core::pose::PoseOP protocols::abinitio::AbrelaxApplication::native_pose_

private

Referenced by add_constraints(), close_loops(), copy_native_structure(), do_rerun(), process_decoy(), setup(), setup_fold(), setup_fragments(), setup_jumps(), and setup_templates().

evaluation::PCA_OP protocols::abinitio::AbrelaxApplication::pca_

private

Referenced by protocols::abinitio::PcaEvaluator::apply(), and setup().

std::string protocols::abinitio::AbrelaxApplication::sequence_

private

Referenced by setup(), setup_fold(), and setup_templates().

core::io::silent::SilentFileDataOP protocols::abinitio::AbrelaxApplication::silent_score_file_

private

----------— Data ----------------------------— -----— When you add new data to this class, -— -----— you must update the copy constructor -—

Referenced by do_distributed_rerun(), do_rerun(), fold(), and setup().

core::fragment::SecondaryStructureOP protocols::abinitio::AbrelaxApplication::ss_def_

private

Referenced by setup_fold(), and setup_jumps().

TemplatesOP protocols::abinitio::AbrelaxApplication::templates_

private

Referenced by add_constraints(), setup_fragments(), setup_jumps(), and setup_templates().

The documentation for this class was generated from the following files:

src/protocols/abinitio/AbrelaxApplication.hh
src/protocols/abinitio/AbrelaxApplication.cc

Private Attributes
core::io::silent::SilentFileDataOP	silent_score_file_

core::pose::PoseOP	native_pose_

core::pose::PoseOP	init_pose_obj_

loops::Loops	loops_in_

evaluation::PCA_OP	pca_

bool	bRelax_

std::string	sequence_

core::scoring::constraints::ConstraintSetOP	cstset_

jumping::MembraneJumpOP	membrane_jumps_

jumping::BaseJumpSetupOP	jump_def_

core::fragment::SecondaryStructureOP	ss_def_

TemplatesOP	templates_

core::fragment::FragSetOP	fragset_large_

core::fragment::FragSetOP	fragset_small_top25_

core::fragment::FragSetOP	fragset_small_

core::fragment::FragSetOP	fragset_templates_

evaluation::MetaPoseEvaluatorOP	evaluator_

checkpoint::CheckPointer	abrelax_checkpoints_

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation