protocols::abinitio::AbrelaxApplication Class Reference

application level code for Abrelax, Foldconstraints and JumpingFoldconstraints WARNING WARNING WARNING. THREAD UNSAFE. INVOKES ConstraintFactory::replace_creator. CODE THAT ABUSES SINGLETONS LIKE THIS OUGHT TO BE SHOT. More...

#include <AbrelaxApplication.hh>

Public Member Functions
	AbrelaxApplication ()
	@detail c'stor - nothing special More...
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 VirtualBase, 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...
void	set_use_trRosetta_constraints (bool const setting)
	Set whether we're using trRosetta. More...
void	provide_citation_info (basic::citation_manager::CitationCollectionList &citation_list) const
	Get citation information for the AbinitioRelaxApplication. 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)

Private Attributes
core::io::silent::SilentFileOptionsOP	silent_options_
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_
bool	use_trRosetta_constraints_ = false
	Are we adding trRosetta constraints? More...

Detailed Description

application level code for Abrelax, Foldconstraints and JumpingFoldconstraints WARNING WARNING WARNING. THREAD UNSAFE. INVOKES ConstraintFactory::replace_creator. CODE THAT ABUSES SINGLETONS LIKE THIS OUGHT TO BE SHOT.

Constructor & Destructor Documentation

AbrelaxApplication() [1/2]

protocols::abinitio::AbrelaxApplication::AbrelaxApplication

(

)

@detail c'stor - nothing special

~AbrelaxApplication()

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

virtualdefault

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 VirtualBase, then it will inherit a virtual destructor If it does not, as AbrelaxApplication does not, then you must declare the destructor virtual.

AbrelaxApplication() [2/2]

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

add_constraints()

void protocols::abinitio::AbrelaxApplication::add_constraints

(

core::pose::Pose &

pose

)

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

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

References core::pose::Pose::add_constraints(), add_evaluation(), core::scoring::atom_pair_constraint, protocols::abinitio::StrandConstraints::build_constraints(), core::pose::Pose::constraint_set(), cstset_, core::scoring::constraints::cull_violators(), core::scoring::constraints::get_cst_file_option(), native_pose_, core::scoring::ScoreFunction::set_weight(), core::scoring::ScoreFunction::show(), templates_, core::id::to_string(), and tr().

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

add_evaluation()

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 )

@detail add a PoseEvaluator derived instance for decoy-processing

add a PoseEvaluator derived instance for decoy-processing

References core::energy_methods::eval(), and evaluator_.

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

check_filters()

bool protocols::abinitio::AbrelaxApplication::check_filters

(

core::pose::Pose &

pose

)

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

References protocols::simple_filters::COFilter::apply(), protocols::simple_filters::RGFilter::apply(), protocols::simple_filters::SheetFilter::apply(), core::energy_methods::ref_spectrum, core::pose::setPoseExtraScore(), and tr().

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

close_loops()

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(), core::pack::interaction_graph::debug, protocols::checkpoint::CheckPointer::debug(), core::pose::Pose::dump_pdb(), evaluator_, protocols::idealize::IdealizeMover::fast(), fragset_small_, core::pose::Pose::is_fullatom(), native_pose_, protocols::checkpoint::CheckPointer::recover_checkpoint(), and setup_fragments().

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

copy_native_structure()

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.

@detail 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().

copy_structure()

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::fragment::FragData::apply(), core::conformation::Residue::is_protein(), protocols::mean_field::min(), core::pose::Pose::residue(), core::pose::Pose::size(), core::fragment::FragData::steal(), and tr().

Referenced by copy_native_structure(), and setup_fold().

do_distributed_rerun()

void protocols::abinitio::AbrelaxApplication::do_distributed_rerun

(

)

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

@detail 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(), bRelax_, check_filters(), close_loops(), core::pose::Pose::conformation(), core::pose::Pose::constraint_set(), core::pack::interaction_graph::debug, core::io::raw_data::DisulfideFile::disulfides(), evaluator_, core::io::silent::SilentStruct::fill_pose(), core::conformation::Conformation::fix_disulfides(), protocols::loops::fix_with_coord_cst(), core::chemical::FULL_ATOM_t, generate_scorefxn(), core::io::silent::SilentFileData::get_structure(), protocols::loops::Loops::grow_all_loops(), protocols::loops::Loops::invert(), core::pose::Pose::is_fullatom(), core::scoring::linear_chainbreak, loops_in_, protocols::mean_field::max(), core::scoring::overlap_chainbreak, protocols::ligand_docking::passes_filters(), process_decoy(), core::io::silent::SilentFileData::read_file(), relax(), protocols::antibody::design::relax, core::pose::set_ss_from_phipsi(), protocols::relax::ClassicRelax::setPoseExtraScore(), silent_options_, silent_score_file_, core::pose::Pose::size(), protocols::loops::Loops::size(), core::util::switch_to_residue_type_set(), core::io::silent::SilentFileData::tags(), tr(), protocols::loops::Loops::verify_against(), and core::io::silent::SilentFileData::write_silent_struct().

Referenced by run().

do_rerun()

void protocols::abinitio::AbrelaxApplication::do_rerun

(

)

run process_decoy on all poses in silent-in file

@detail 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(), core::io::silent::SilentFileData::begin(), core::chemical::CENTROID, check_filters(), close_loops(), core::io::silent::SilentFileData::end(), core::sequence::end, evaluator_, core::chemical::FA_STANDARD, generate_scorefxn(), core::pose::Pose::is_fullatom(), core::scoring::linear_chainbreak, core::pose::Pose::metric(), native_pose_, core::scoring::overlap_chainbreak, protocols::ligand_docking::passes_filters(), process_decoy(), core::io::silent::SilentFileData::read_file(), silent_options_, silent_score_file_, core::io::silent::SilentFileData::size(), and tr().

Referenced by run().

fold()

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

run abrelax-type protocols

@detail 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::Protocol::apply(), protocols::abinitio::ResolutionSwitcher::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::idealize::IdealizeMover::apply(), bRelax_, core::energy_methods::ContactOrderEnergy::calculate_contact_order(), check_filters(), protocols::checkpoint::CheckPointer::checkpoint(), protocols::loops::Loop::choose_cutpoint(), protocols::checkpoint::CheckPointer::clear_checkpoints(), core::kinematics::FoldTree::clone(), close_loops(), core::pose::Pose::conformation(), core::pose::Pose::constraint_set(), core::scoring::ScoreFunctionFactory::create_score_function(), cstset_, core::kinematics::FoldTree::cutpoint(), core::pose::Pose::data(), core::pack::interaction_graph::debug, protocols::checkpoint::CheckPointer::debug(), core::conformation::Conformation::detect_disulfides(), core::pose::Pose::dump_pdb(), evaluator_, protocols::idealize::IdealizeMover::fast(), core::pose::Pose::fold_tree(), protocols::loops::fold_tree_from_loops(), generate_scorefxn(), protocols::checkpoint::CheckPointer::get_checkpoint_recoveries(), protocols::abinitio::Protocol::get_checkpoints(), core::scoring::constraints::get_cst_fa_file_option(), protocols::moves::Mover::get_current_tag(), protocols::moves::Mover::get_last_move_status(), core::pose::Pose::is_centroid(), core::pose::Pose::is_fullatom(), protocols::mean_field::max(), membrane_jumps_, protocols::mean_field::min(), protocols::moves::MS_SUCCESS, multi_fast_relax(), core::kinematics::FoldTree::num_cutpoint(), core::pose::Pose::omega(), protocols::ligand_docking::passes_filters(), protocols::hybridization::path, core::pose::Pose::phi(), process_decoy(), core::pose::Pose::psi(), protocols::checkpoint::CheckPointer::recover_checkpoint(), relax(), core::scoring::rg, 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(), protocols::relax::ClassicRelax::setPoseExtraScore(), core::pose::setPoseExtraScore(), core::scoring::SS_Killhairpins_Info::setup_killhairpins(), silent_options_, silent_score_file_, core::kinematics::FoldTree::simple_tree(), core::pose::Pose::size(), core::pose::datacache::CacheableDataType::SS_KILLHAIRPINS_INFO, protocols::loops::Loop::start(), core::io::silent::SilentFileData::strict_column_mode(), tr(), and core::io::silent::SilentFileData::write_silent_struct().

Referenced by run().

generate_extended_pose()

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"

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

References core::chemical::CENTROID, core::pose::Pose::conformation(), core::io::raw_data::DisulfideFile::disulfides(), core::conformation::Conformation::fix_disulfides(), core::conformation::Residue::is_protein(), core::pose::make_pose_from_sequence(), core::pose::Pose::residue(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), and core::pose::Pose::size().

Referenced by setup_fold().

generate_scorefxn()

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(), jump_def_, core::scoring::linear_chainbreak, and core::scoring::overlap_chainbreak.

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

initialize_constraint_forest()

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

private

References tr().

Referenced by setup_fold().

insert_template_frags()

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 core::sequence::end, core::conformation::membrane::out, core::fragment::FragmentIO::read_frames_from_file(), and core::scoring::rg.

multi_fast_relax()

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

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

Referenced by fold().

process_decoy()

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... )

@detail 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(), core::pose::Pose::data(), evaluator_, core::io::silent::SilentStruct::fill_struct(), core::pose::Pose::fold_tree(), native_pose_, core::pose::Pose::num_jump(), and tr().

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

provide_citation_info()

void protocols::abinitio::AbrelaxApplication::provide_citation_info

(

basic::citation_manager::CitationCollectionList &

citation_list

)

const

Get citation information for the AbinitioRelaxApplication.

Includes trRosetta information if this is set.

Author

Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

References protocols::trRosetta_protocols::constraint_generators::trRosettaConstraintGenerator::provide_citation_info_static(), and use_trRosetta_constraints_.

register_options()

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

static

registering of options that are relevant for AbrelaxApplication

References protocols::abinitio::register_common_options(), and protocols::evaluation::register_options().

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

relax()

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 )

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

References abrelax_checkpoints_, core::pose::Pose::add_constraints(), core::scoring::constraints::add_fa_constraints_from_cmdline(), core::scoring::angle_constraint, protocols::relax::FastRelax::apply(), core::scoring::atom_pair_constraint, protocols::checkpoint::CheckPointer::checkpoint(), core::pose::Pose::constraint_set(), protocols::relax::cyclize_pose(), protocols::checkpoint::CheckPointer::debug(), core::scoring::dihedral_constraint, protocols::checkpoint::CheckPointer::recover_checkpoint(), protocols::antibody::design::relax, protocols::relax::relax_pose(), core::pose::Pose::remove_constraints(), protocols::moves::Mover::set_current_tag(), tr(), and use_trRosetta_constraints_.

Referenced by do_distributed_rerun(), and fold().

run()

void protocols::abinitio::AbrelaxApplication::run

(

)

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

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

References do_distributed_rerun(), do_rerun(), fold(), setup(), and setup_fold().

set_use_trRosetta_constraints()

void protocols::abinitio::AbrelaxApplication::set_use_trRosetta_constraints

(

bool const

setting

)

Set whether we're using trRosetta.

Author

Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

References use_trRosetta_constraints_.

Referenced by setup().

setup()

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 add_evaluation(), core::scoring::func::FuncFactory::add_type(), core::chemical::CENTROID_t, evaluator_, core::scoring::constraints::ConstraintIO::get_func_factory(), core::pose::metrics::CalculatorFactory::Instance(), native_pose_, pca_, core::import_pose::PDB_file, core::import_pose::pose_from_file(), core::sequence::read_fasta_file(), core::pose::metrics::CalculatorFactory::register_calculator(), sequence_, core::pose::set_ss_from_phipsi(), set_use_trRosetta_constraints(), setup_templates(), silent_options_, silent_score_file_, core::util::switch_to_residue_type_set(), and tr().

Referenced by run().

setup_fold()

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

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

@detail 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(), core::fragment::FragData::apply(), bRelax_, core::chemical::CENTROID, core::pose::Pose::conformation(), core::pose::Pose::constraint_set(), copy_native_structure(), copy_structure(), protocols::relax::cyclize_pose(), core::pack::interaction_graph::debug, core::io::raw_data::DisulfideFile::disulfides(), core::sequence::end, evaluator_, core::chemical::FA_STANDARD, protocols::abinitio::filename(), core::conformation::Conformation::fix_disulfides(), core::pose::Pose::fold_tree(), fragset_large_, fragset_small_, fragset_small_top25_, generate_extended_pose(), protocols::loops::Loops::grow_all_loops(), protocols::abinitio::Protocol::init(), initialize_constraint_forest(), protocols::loops::Loops::invert(), core::pose::Pose::is_fullatom(), jump_def_, loops_in_, membrane_jumps_, native_pose_, core::import_pose::PDB_file, core::import_pose::pose_from_file(), protocols::antibody::design::relax, protocols::abinitio::Protocol::return_centroid(), sequence_, protocols::abinitio::Protocol::set_evaluation(), protocols::abinitio::Protocol::set_use_trRosetta_constraints(), setup_fragments(), setup_jumps(), setup_membrane_topology(), core::kinematics::simple_visualize_fold_tree(), core::pose::Pose::size(), ss_def_, protocols::loops::start, protocols::abinitio::ResolutionSwitcher::start_pose(), core::fragment::FragData::steal(), tr(), use_trRosetta_constraints_, and protocols::loops::Loops::verify_against().

Referenced by run().

setup_fragments()

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

private

read fragment data

@detail 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 fragset_large_, fragset_small_, fragset_small_top25_, fragset_templates_, core::fragment::merge_frags(), native_pose_, core::fragment::FragmentIO::read_data(), core::fragment::steal_frag_set_from_pose(), templates_, and tr().

Referenced by close_loops(), and setup_fold().

setup_jumps()

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

private

read jump definitions and set jump_def_

@detail 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(), fragset_small_, protocols::jumping::JumpSample::has_orientation_and_pleating(), jump_def_, native_pose_, core::fragment::FragmentIO::read_data(), core::scoring::dssp::read_pairing_list(), core::pose::Pose::size(), ss_def_, protocols::jumping::JumpSample::steal_orientation_and_pleating(), templates_, and tr().

Referenced by setup_fold().

setup_membrane_topology()

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(), core::scoring::MembraneTopology::initialize(), and core::pose::datacache::CacheableDataType::MEMBRANE_TOPOLOGY.

Referenced by setup_fold().

setup_templates()

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

private

initialize template_

@detail called by setup_fold(). Read template definitions

References fragset_large_, native_pose_, sequence_, templates_, and tr().

Referenced by setup().

Member Data Documentation

abrelax_checkpoints_

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

private

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

bRelax_

bool protocols::abinitio::AbrelaxApplication::bRelax_

private

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

cstset_

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

private

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

evaluator_

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().

fragset_large_

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

private

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

fragset_small_

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

private

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

fragset_small_top25_

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

private

Referenced by setup_fold(), and setup_fragments().

fragset_templates_

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

private

Referenced by setup_fragments().

init_pose_obj_

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

private

jump_def_

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

private

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

loops_in_

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

private

Referenced by do_distributed_rerun(), and setup_fold().

membrane_jumps_

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

private

Referenced by fold(), and setup_fold().

native_pose_

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().

pca_

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

private

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

sequence_

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

private

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

silent_options_

core::io::silent::SilentFileOptionsOP protocols::abinitio::AbrelaxApplication::silent_options_

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().

silent_score_file_

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

private

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

ss_def_

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

private

Referenced by setup_fold(), and setup_jumps().

templates_

TemplatesOP protocols::abinitio::AbrelaxApplication::templates_

private

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

use_trRosetta_constraints_

bool protocols::abinitio::AbrelaxApplication::use_trRosetta_constraints_ = false

private

Are we adding trRosetta constraints?

Referenced by provide_citation_info(), relax(), set_use_trRosetta_constraints(), and setup_fold().

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

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