Rosetta 3.4
Public Member Functions | Static Public Member Functions
protocols::abinitio::AbrelaxApplication Class Reference

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

#include <AbrelaxApplication.hh>

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List of all members.

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.
 AbrelaxApplication (AbrelaxApplication const &)
 Explicit copy constructor since AbrelaxApplication contains OPs.
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... )
void add_constraints (core::pose::Pose &pose)
 read constraint set (self-initializing) and connect it to pose
void setup ()
 initialization of application: read some pdb files, set evaluator_
void run ()
 run application code: calls do_rerun() or fold() depending on cmd-options
void do_rerun ()
 run process_decoy on all poses in silent-in file
void do_distributed_rerun ()
 run process_decoy on all poses in silent-in file -- use of JobDistributor
void setup_fold (core::pose::Pose &extended_pose, ProtocolOP &prot_ptr)
 setup everything needed for fold() --- calls helper functions below
void fold (core::pose::Pose &extended_pose, ProtocolOP prot_ptr)
 run abrelax-type protocols
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
void relax (core::pose::Pose &pose, core::scoring::ScoreFunctionOP, std::string const &tag)
 relax structure ( fast / classic as controlled by cmd-options )
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
void add_evaluation (evaluation::PoseEvaluatorOP)
 little helper: minimize structure to have lower chainbreak score ( seems particularly necessary after reading from silent-file )
bool check_filters (core::pose::Pose &pose)
 check if the given pose passes the set of abinitio filters.

Static Public Member Functions

static void register_options ()

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)
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

add a PoseEvaluator derived instance for decoy-processing

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

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

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

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 
)
void protocols::abinitio::AbrelaxApplication::do_distributed_rerun ( )
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(), core::io::silent::SilentFileData::begin(), make_table_of_pilot_apps::begin, core::chemical::CENTROID, check_filters(), close_loops(), core::sequence::end, core::io::silent::SilentFileData::end(), core::chemical::FA_STANDARD, core::pose::Pose::is_fullatom(), core::scoring::linear_chainbreak, core::pose::Pose::metric(), core::scoring::overlap_chainbreak, protocols::ligand_docking::passes_filters(), process_decoy(), core::io::silent::SilentFileData::read_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 )

References add_evaluation(), core::io::silent::SilentFileData::add_structure(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::idealize::IdealizeMover::apply(), protocols::abinitio::ResolutionSwitcher::apply(), protocols::abinitio::Protocol::apply(), core::scoring::methods::ContactOrderEnergy::calculate_contact_order(), check_filters(), protocols::loops::Loop::choose_cutpoint(), protocols::checkpoint::CheckPointer::clear_checkpoints(), close_loops(), core::pose::Pose::constraint_set(), core::kinematics::FoldTree::cutpoint(), core::pose::Pose::data(), core::pack::interaction_graph::debug, core::pose::Pose::dump_pdb(), protocols::idealize::IdealizeMover::fast(), core::pose::Pose::fold_tree(), protocols::forge::methods::fold_tree_from_loops(), 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(), core::scoring::constraints::ConstraintIO::get_instance(), protocols::moves::Mover::get_last_move_status(), core::pose::Pose::is_fullatom(), protocols::moves::MS_SUCCESS, multi_fast_relax(), core::kinematics::FoldTree::num_cutpoint(), core::pose::Pose::omega(), protocols::ligand_docking::passes_filters(), core::pose::Pose::phi(), process_decoy(), core::pose::Pose::psi(), core::scoring::constraints::ConstraintIO::read_constraints(), relax(), protocols::abinitio::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(), core::pose::setPoseExtraScores(), protocols::relax::ClassicRelax::setPoseExtraScores(), core::scoring::SS_Killhairpins_Info::setup_killhairpins(), core::kinematics::FoldTree::simple_tree(), core::pose::datacache::CacheableDataType::SS_KILLHAIRPINS_INFO, protocols::loops::Loop::start(), core::io::silent::SilentFileData::strict_column_mode(), core::pose::Pose::total_residue(), tr(), and core::io::silent::SilentFileData::write_silent_struct().

Referenced by run().

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(), core::pose::Pose::data(), core::io::silent::SilentStruct::fill_struct(), core::pose::Pose::fold_tree(), 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

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

void protocols::abinitio::AbrelaxApplication::setup ( )
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(), core::chemical::CENTROID, core::pose::Pose::conformation(), core::pose::Pose::constraint_set(), core::pack::interaction_graph::debug, core::io::raw_data::DisulfideFile::disulfides(), core::sequence::end, core::chemical::FA_STANDARD, core::conformation::Conformation::fix_disulfides(), core::pose::Pose::fold_tree(), core::chemical::ChemicalManager::get_instance(), protocols::abinitio::Protocol::init(), core::pose::Pose::is_fullatom(), make_table_of_pilot_apps::name, core::import_pose::pose_from_pdb(), relax(), core::chemical::ChemicalManager::residue_type_set(), protocols::abinitio::Protocol::return_centroid(), protocols::abinitio::Protocol::set_evaluation(), protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::set_fullatom_pose(), protocols::moves::Mover::set_native_pose(), protocols::abinitio::FoldConstraints::set_show_viol_level(), core::kinematics::simple_visualize_fold_tree(), protocols::jumping::MembraneJump::template_size(), core::pose::Pose::total_residue(), tr(), and protocols::loops::Loops::verify_against().

Referenced by run().


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