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

#include <AbrelaxApplication.hh>

Collaboration diagram for protocols::abinitio::AbrelaxApplication:

Public Member Functions
	AbrelaxApplication ()
	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 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

Definition at line 79 of file AbrelaxApplication.hh.

Constructor & Destructor Documentation

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

c'stor - nothing special

Definition at line 398 of file AbrelaxApplication.cc.

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.

Definition at line 413 of file AbrelaxApplication.cc.

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

Definition at line 417 of file AbrelaxApplication.cc.

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)

Definition at line 647 of file AbrelaxApplication.cc.

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(), core::scoring::constraints::ConstraintIO::get_instance(), native_pose_, core::scoring::constraints::ConstraintIO::read_constraints(), core::scoring::ScoreFunction::set_weight(), core::scoring::ScoreFunction::show(), core::io::serialization::size(), templates_, and tr().

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

Definition at line 439 of file AbrelaxApplication.cc.

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.

Definition at line 1667 of file AbrelaxApplication.cc.

References core::scoring::saxs::ref_spectrum, core::pose::setPoseExtraScores(), and tr().

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

Definition at line 516 of file AbrelaxApplication.cc.

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().

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!

Definition at line 1071 of file AbrelaxApplication.cc.

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.

Definition at line 1078 of file AbrelaxApplication.cc.

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!

Definition at line 885 of file AbrelaxApplication.cc.

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::chemical::FA_STANDARD, 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_, core::scoring::overlap_chainbreak, protocols::ligand_docking::passes_filters(), process_decoy(), relax(), core::pose::set_ss_from_phipsi(), protocols::relax::ClassicRelax::setPoseExtraScores(), silent_score_file_, protocols::loops::Loops::size(), core::util::switch_to_residue_type_set(), core::pose::Pose::total_residue(), tr(), 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!

Definition at line 776 of file AbrelaxApplication.cc.

References add_constraints(), add_evaluation(), core::io::silent::SilentFileData::begin(), core::chemical::CENTROID, check_filters(), close_loops(), core::sequence::end, core::io::silent::SilentFileData::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_score_file_, core::io::silent::SilentFileData::size(), and tr().

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 )

Definition at line 1739 of file AbrelaxApplication.cc.

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

Definition at line 1106 of file AbrelaxApplication.cc.

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::total_residue().

Referenced by setup_fold().

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

private

create score-functions for centroid and fullatom level

Definition at line 1706 of file AbrelaxApplication.cc.

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

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

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

private

Definition at line 638 of file AbrelaxApplication.cc.

References tr().

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

Definition at line 750 of file AbrelaxApplication.cc.

References core::fragment::FragmentIO::read_data(), and protocols::abinitio::RG().

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

Definition at line 2050 of file AbrelaxApplication.cc.

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.

Definition at line 604 of file AbrelaxApplication.cc.

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().

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

static

registering of options that are relevant for AbrelaxApplication

Definition at line 212 of file AbrelaxApplication.cc.

References core::pack::interaction_graph::debug, and protocols::evaluation::register_options().

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.

Definition at line 2065 of file AbrelaxApplication.cc.

References abrelax_checkpoints_, core::scoring::constraints::add_fa_constraints_from_cmdline(), protocols::relax::FastRelax::apply(), protocols::checkpoint::CheckPointer::checkpoint(), core::pose::Pose::conformation(), core::pose::Pose::constraint_set(), protocols::checkpoint::CheckPointer::debug(), core::conformation::Conformation::detect_disulfides(), protocols::checkpoint::CheckPointer::recover_checkpoint(), 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()

Definition at line 2117 of file AbrelaxApplication.cc.

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

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_ )

Definition at line 445 of file AbrelaxApplication.cc.

References protocols::evaluation::EvaluatorFactory::add_all_evaluators(), add_evaluation(), core::scoring::constraints::FuncFactory::add_type(), core::chemical::CENTROID, evaluator_, core::scoring::constraints::ConstraintIO::get_func_factory(), core::scoring::constraints::ConstraintFactory::get_instance(), protocols::evaluation::EvaluatorFactory::get_instance(), core::pose::metrics::CalculatorFactory::Instance(), native_pose_, pca_, core::import_pose::pose_from_pdb(), core::sequence::read_fasta_file(), core::pose::metrics::CalculatorFactory::register_calculator(), core::scoring::constraints::ConstraintFactory::replace_creator(), sequence_, core::pose::set_ss_from_phipsi(), setup_templates(), silent_score_file_, core::util::switch_to_residue_type_set(), and tr().

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.

Definition at line 1400 of file AbrelaxApplication.cc.

References add_constraints(), protocols::simple_moves::RepulsiveOnlyMover::apply(), bRelax_, core::chemical::CENTROID, core::pose::Pose::conformation(), core::pose::Pose::constraint_set(), copy_native_structure(), copy_structure(), 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(), core::chemical::ChemicalManager::get_instance(), 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::pose_from_pdb(), core::chemical::ChemicalManager::residue_type_set(), protocols::abinitio::Protocol::return_centroid(), sequence_, core::kinematics::MoveMap::set_bb(), protocols::abinitio::Protocol::set_evaluation(), protocols::moves::Mover::set_native_pose(), setup_fragments(), setup_jumps(), setup_membrane_topology(), core::kinematics::simple_visualize_fold_tree(), ss_def_, protocols::loops::start, core::pose::Pose::total_residue(), tr(), and protocols::loops::Loops::verify_against().

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!

Definition at line 1139 of file AbrelaxApplication.cc.

References fragset_large_, fragset_small_, fragset_small_top25_, fragset_templates_, core::fragment::merge_frags(), native_pose_, core::fragment::steal_frag_set_from_pose(), templates_, and tr().

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()

Definition at line 1279 of file AbrelaxApplication.cc.

References add_evaluation(), fragset_small_, jump_def_, native_pose_, core::scoring::dssp::read_pairing_list(), ss_def_, templates_, core::pose::Pose::total_residue(), and tr().

Referenced by setup_fold().

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

private

read in membrane topology

Definition at line 1384 of file AbrelaxApplication.cc.

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

Referenced by setup_fold().

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

private

initialize template_

called by setup_fold(). Read template definitions

Definition at line 1254 of file AbrelaxApplication.cc.

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

Referenced by setup().

Member Data Documentation

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

private

Definition at line 248 of file AbrelaxApplication.hh.

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

bool protocols::abinitio::AbrelaxApplication::bRelax_

private

Definition at line 210 of file AbrelaxApplication.hh.

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

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

private

Definition at line 216 of file AbrelaxApplication.hh.

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

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

private

Definition at line 245 of file AbrelaxApplication.hh.

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

Definition at line 233 of file AbrelaxApplication.hh.

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

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

private

Definition at line 239 of file AbrelaxApplication.hh.

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

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

private

Definition at line 236 of file AbrelaxApplication.hh.

Referenced by setup_fold(), and setup_fragments().

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

private

Definition at line 242 of file AbrelaxApplication.hh.

Referenced by setup_fragments().

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

private

Definition at line 201 of file AbrelaxApplication.hh.

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

private

Definition at line 224 of file AbrelaxApplication.hh.

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

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

private

Definition at line 204 of file AbrelaxApplication.hh.

Referenced by do_distributed_rerun(), and setup_fold().

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

private

Definition at line 221 of file AbrelaxApplication.hh.

Referenced by fold(), and setup_fold().

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

private

Definition at line 198 of file AbrelaxApplication.hh.

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

Definition at line 207 of file AbrelaxApplication.hh.

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

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

private

Definition at line 213 of file AbrelaxApplication.hh.

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 -—

Definition at line 195 of file AbrelaxApplication.hh.

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

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

private

Definition at line 227 of file AbrelaxApplication.hh.

Referenced by setup_fold(), and setup_jumps().

TemplatesOP protocols::abinitio::AbrelaxApplication::templates_

private

Definition at line 230 of file AbrelaxApplication.hh.

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