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

#include <JumpSpecificAbrelax.hh>

Public Member Functions
	JumpSpecificAbrelax ()
	@detail c'stor - nothing special More...

void	process_decoy (core::pose::Pose &pose, core::scoring::ScoreFunction const &, std::string tag, core::io::silent::ProteinSilentStruct &) 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	fold ()
	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	setup_fold (core::pose::Pose &extended_pose, ProtocolOP &prot_ptr)
	setup everything needed for fold() — calls helper functions below 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_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::SilentFileDataOP	silent_score_file_
	----------— Data ---------------------------— More...

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_

core::scoring::constraints::ConstraintForestOP	constraint_forest_

jumping::BaseJumpSetupOP	jump_def_

jumping::SecondaryStructureOP	ss_def_

TemplatesOP	templates_

core::fragment::FragSetOP	fragset_large_

core::fragment::FragSetOP	fragset_small_

core::fragment::FragSetOP	fragset_templates_

evaluation::MetaPoseEvaluatorOP	evaluator_

checkpoint::CheckPointer	abrelax_checkpoints_

Detailed Description

application level code for Abrelax, Foldconstraints and JumpingFoldconstraints

Constructor & Destructor Documentation

◆ JumpSpecificAbrelax()

protocols::abinitio::JumpSpecificAbrelax::JumpSpecificAbrelax ( )

@detail c'stor - nothing special

Member Function Documentation

◆ add_constraints()

void protocols::abinitio::JumpSpecificAbrelax::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 add_evaluation(), constraint_forest_, basic::options::OptionKeys::constraints::constraints, constraints::cst_file(), cstset_, constraints::cull_with_native(), constraints::dump_cst_set(), constraints::evaluate_max_seq_sep(), utility::io::izstream::good(), create_a3b_hbs::i, basic::Tracer::Info, native_pose_, option, beta_nonlocal::pose, subloop_histogram::size, templates::strand_constraint(), templates_, create_a3b_hbs::test_pose, utility::to_string(), jumps::topology_file(), protocols::abinitio::tr, basic::options::OptionKeys::inout::dbms::user, utility_exit_with_message, and basic::Tracer::Warning.

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

◆ add_evaluation()

void protocols::abinitio::JumpSpecificAbrelax::add_evaluation ( evaluation::PoseEvaluatorOP )

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 evaluator_.

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

◆ check_filters()

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

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

References basic::options::OptionKeys::filters::disable_all_filters, basic::options::OptionKeys::filters::disable_co_filter, basic::options::OptionKeys::filters::disable_rg_filter, basic::options::OptionKeys::filters::disable_sheet_filter, basic::options::OptionKeys::AnchoredDesign::filters::filters, basic::Tracer::Info, basic::options::option, option, beta_nonlocal::pose, protocols::abinitio::tr, and basic::options::OptionKeys::abinitio::use_filters.

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

◆ close_loops()

bool protocols::abinitio::JumpSpecificAbrelax::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_, basic::options::OptionKeys::loops::debug_loop_closure, fragset_small_, basic::options::OptionKeys::in::file::movemap, option, beta_nonlocal::pose, basic::options::OptionKeys::loops::scored_frag_cycles, oop_conformations::scorefxn, setup_fragments(), basic::options::OptionKeys::loops::short_frag_cycles, loops_kic::success, tag, protocols::abinitio::tr, and basic::Tracer::Warning.

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

◆ copy_native_structure()

void protocols::abinitio::JumpSpecificAbrelax::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(), basic::options::OptionKeys::in::file::extended_pose, basic::Tracer::Info, native_pose_, and protocols::abinitio::tr.

Referenced by setup_fold().

◆ copy_structure()

void protocols::abinitio::JumpSpecificAbrelax::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 basic::options::OptionKeys::in::file::extended_pose, create_a3b_hbs::i, basic::Tracer::Info, min(), and protocols::abinitio::tr.

Referenced by copy_native_structure(), and setup_fold().

◆ do_distributed_rerun()

void protocols::abinitio::JumpSpecificAbrelax::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!

Referenced by run().

◆ do_rerun()

void protocols::abinitio::JumpSpecificAbrelax::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(), begin, basic::options::OptionKeys::abinitio::bGDT, check_filters(), close_loops(), close_loops(), utility::io::oc::cout, end, evaluator_, detail::find(), utility::io::ocstream::flush(), in::file::fullatom(), generate_scorefxn(), basic::Tracer::Info, subloop_histogram::iterator, native_pose_, option, basic::options::OptionKeys::jumps::overlap_chainbreak, beta_nonlocal::pose, process_decoy(), basic::options::OptionKeys::in::file::residue_type_set, oop_conformations::scorefxn, sfd, basic::options::OptionKeys::in::file::silent, in::file::silent(), out::file::silent(), silent_score_file_, challenge::ss, tag, protocols::abinitio::tr, basic::options::OptionKeys::inout::dbms::user, and basic::MetricValue< T >::value().

Referenced by run().

◆ fold()

void protocols::abinitio::JumpSpecificAbrelax::fold ( )

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 )

Referenced by run().

◆ generate_extended_pose()

void protocols::abinitio::JumpSpecificAbrelax::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 basic::Tracer::Debug, basic::options::OptionKeys::in::file::extended_pose, make_symmdef_file_denovo::pos, basic::options::OptionKeys::in::file::residue_type_set, basic::options::OptionKeys::relax::sequence, and protocols::abinitio::tr.

Referenced by setup_fold().

◆ generate_scorefxn()

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

private

create score-functions for centroid and fullatom level

References basic::options::OptionKeys::loopfcst::coord_cst_weight, pyrosetta::create_score_function, basic::options::OptionKeys::constraints::cst_weight, cstset_, basic::options::OptionKeys::in::file::fullatom, jump_def_, basic::options::OptionKeys::jumps::no_chainbreak_in_relax, option, basic::options::OptionKeys::jumps::overlap_chainbreak, oop_conformations::scorefxn, and basic::options::OptionKeys::inout::dbms::user.

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

◆ initialize_constraint_forest()

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

private

References constraint_forest_, constraints::forest_file(), basic::Tracer::Info, option, beta_nonlocal::pose, protocols::abinitio::tr, and basic::options::OptionKeys::inout::dbms::user.

Referenced by setup_fold().

◆ insert_template_frags()

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

private

insert fragments from aligned regions

References job_manager::app, end, templates::fix_frag_file(), basic::options::OptionKeys::templates::fix_margin, numeric::kinematic_closure::frame(), basic::options::OptionKeys::in::file::movemap, option, erraser_single_res_analysis::out, make_symmdef_file_denovo::pos, beta_nonlocal::pose, numeric::random::rg(), ObjexxFCL::format::RJ(), tag, numeric::random::uniform(), and basic::options::OptionKeys::inout::dbms::user.

◆ multi_fast_relax()

bool protocols::abinitio::JumpSpecificAbrelax::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

References create_a3b_hbs::i, min(), process_decoy(), ObjexxFCL::right_string_of(), oop_conformations::scorefxn, silent_score_file_, subloop_histogram::size, protocols::abinitio::sort_PoseWithScore(), and ObjexxFCL::string_of().

Referenced by fold().

◆ process_decoy()

void protocols::abinitio::JumpSpecificAbrelax::process_decoy	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunction const &	,
		std::string	tag,
		core::io::silent::ProteinSilentStruct &
	)		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 jumps::evaluate(), evaluator_, native_pose_, option, beta_nonlocal::pose, oop_conformations::scorefxn, tag, and utility_exit_with_message.

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

◆ register_options()

void protocols::abinitio::JumpSpecificAbrelax::register_options ( )

static

registering of options that are relevant for JumpSpecificAbrelax

◆ relax()

void protocols::abinitio::JumpSpecificAbrelax::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_, basic::options::OptionKeys::abinitio::detect_disulfide_before_relax, basic::options::OptionKeys::abinitio::fastrelax, constraints::no_cst_in_relax(), option, beta_nonlocal::pose, basic::options::OptionKeys::abinitio::relax, oop_conformations::scorefxn, and tag.

Referenced by do_distributed_rerun(), and fold().

◆ run()

void protocols::abinitio::JumpSpecificAbrelax::run ( )

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

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

References basic::options::OptionKeys::in::path::database, do_distributed_rerun(), do_rerun(), fold(), basic::options::OptionKeys::abinitio::jdist_rerun, basic::options::option, option, basic::options::OptionKeys::abinitio::rerun, setup(), and basic::options::OptionKeys::inout::dbms::user.

◆ setup()

void protocols::abinitio::JumpSpecificAbrelax::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_ )

Referenced by pyrosetta.distributed.tasks.taskbase.TaskBase::maybe_setup(), and run().

◆ setup_fold()

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

private

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.

Referenced by fold().

◆ setup_fragments()

void protocols::abinitio::JumpSpecificAbrelax::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!

Referenced by close_loops(), and setup_fold().

◆ setup_jumps()

void protocols::abinitio::JumpSpecificAbrelax::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 constraint_forest_, utility::io::oc::cout, basic::options::OptionKeys::in::file::extended_pose, jumps::extra_frags_for_ss(), jumps::fix_jumps(), constraints::forest_file(), fragset_small_, utility::io::izstream::good(), basic::options::OptionKeys::templates::helix_pairings, create_a3b_hbs::i, basic::Tracer::Info, enumerate_junctions::int, jump_def_, jumps::jump_lib(), jumps::loop_definition_from_file(), native_pose_, basic::options::OptionKeys::out::file::o, option, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, jumps::pairing_file(), templates::pairings(), basic::options::OptionKeys::templates::pairings, ptr(), jumps::residue_pair_jump_file(), basic::options::OptionKeys::jumps::sheets, jumps::sheets(), ss_def_, templates_, jumps::topology_file(), protocols::abinitio::tr, basic::Tracer::Trace, basic::options::OptionKeys::inout::dbms::user, utility_exit_with_message, and basic::Tracer::Warning.

Referenced by setup_fold().

◆ setup_templates()

void protocols::abinitio::JumpSpecificAbrelax::setup_templates ( )

private

initialize template_

@detail called by setup_fold(). Read template definitions

References templates::config(), fragset_large_, basic::Tracer::Info, native_pose_, option, templates::pairings(), sequence_, templates_, protocols::abinitio::tr, basic::options::OptionKeys::inout::dbms::user, utility_exit_with_message, and basic::Tracer::Warning.

Referenced by setup().

Member Data Documentation

◆ abrelax_checkpoints_

checkpoint::CheckPointer protocols::abinitio::JumpSpecificAbrelax::abrelax_checkpoints_

private

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

◆ bRelax_

bool protocols::abinitio::JumpSpecificAbrelax::bRelax_

private

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

◆ constraint_forest_

core::scoring::constraints::ConstraintForestOP protocols::abinitio::JumpSpecificAbrelax::constraint_forest_

private

Referenced by add_constraints(), initialize_constraint_forest(), and setup_jumps().

◆ cstset_

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

private

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

◆ evaluator_

evaluation::MetaPoseEvaluatorOP protocols::abinitio::JumpSpecificAbrelax::evaluator_

private

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

◆ fragset_large_

core::fragment::FragSetOP protocols::abinitio::JumpSpecificAbrelax::fragset_large_

private

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

◆ fragset_small_

core::fragment::FragSetOP protocols::abinitio::JumpSpecificAbrelax::fragset_small_

private

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

◆ fragset_templates_

core::fragment::FragSetOP protocols::abinitio::JumpSpecificAbrelax::fragset_templates_

private

Referenced by setup_fragments().

◆ init_pose_obj_

core::pose::PoseOP protocols::abinitio::JumpSpecificAbrelax::init_pose_obj_

private

◆ jump_def_

jumping::BaseJumpSetupOP protocols::abinitio::JumpSpecificAbrelax::jump_def_

private

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

◆ loops_in_

loops::Loops protocols::abinitio::JumpSpecificAbrelax::loops_in_

private

Referenced by do_distributed_rerun(), and setup_fold().

◆ native_pose_

core::pose::PoseOP protocols::abinitio::JumpSpecificAbrelax::native_pose_

private

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

◆ pca_

evaluation::PCA_OP protocols::abinitio::JumpSpecificAbrelax::pca_

private

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

◆ sequence_

std::string protocols::abinitio::JumpSpecificAbrelax::sequence_

private

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

◆ silent_score_file_

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

private

----------— Data ---------------------------—

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

◆ ss_def_

jumping::SecondaryStructureOP protocols::abinitio::JumpSpecificAbrelax::ss_def_

private

Referenced by setup_fold(), and setup_jumps().

◆ templates_

TemplatesOP protocols::abinitio::JumpSpecificAbrelax::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/apps/pilot/dgront/JumpSpecificAbrelax.hh
src/apps/pilot/dgront/JumpSpecificAbrelax.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ JumpSpecificAbrelax()

Member Function Documentation

◆ add_constraints()

◆ add_evaluation()

◆ check_filters()

◆ close_loops()

◆ copy_native_structure()

◆ copy_structure()

◆ do_distributed_rerun()

◆ do_rerun()

◆ fold()

◆ generate_extended_pose()

◆ generate_scorefxn()

◆ initialize_constraint_forest()

◆ insert_template_frags()

◆ multi_fast_relax()

◆ process_decoy()

◆ register_options()

◆ relax()

◆ run()

◆ setup()

◆ setup_fold()

◆ setup_fragments()

◆ setup_jumps()

◆ setup_templates()

Member Data Documentation

◆ abrelax_checkpoints_

◆ bRelax_

◆ constraint_forest_

◆ cstset_

◆ evaluator_

◆ fragset_large_

◆ fragset_small_

◆ fragset_templates_

◆ init_pose_obj_

◆ jump_def_

◆ loops_in_

◆ native_pose_

◆ pca_

◆ sequence_

◆ silent_score_file_

◆ ss_def_

◆ templates_