Rosetta 3.4
Public Member Functions | Protected Member Functions
protocols::relax::FastRelax Class Reference

#include <FastRelax.hh>

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List of all members.

Public Member Functions

 FastRelax (core::Size standard_repeats=0)
 Initialize FastRelax with a specific script file, which encodes the script of steps the is to be applied.
 FastRelax (core::scoring::ScoreFunctionOP scorefxn_in, core::Size standard_repeats=0)
 Initialize FastRelax using the default script with a varying number of rounds, defined by the standard_repeats repeats paramter. By default, 5.
 FastRelax (core::scoring::ScoreFunctionOP scorefxn_in, std::string const &script_file)
 Initialize FastRelax with a specific script file, which encodes the script of steps the is to be applied.
 FastRelax (core::scoring::ScoreFunctionOP scorefxn_in, core::Size standard_repeats, const std::string &script_file)
 Initialize FastRelax with a specific script file, and allows fastrelax to only use a subset of the number of stages in the scriptfile.
void set_script_to_batchrelax_default (core::Size standard_repeats=0)
 Override the stored script with the default script for batchrelax Ignores '-default_repeat' value.
void set_force_nonideal (bool val)
 Force us to batchrelax with nonideal geometry (using additional memory)
virtual ~FastRelax ()
 virtual constructor to allow derivation
void parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &data, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
 Parses the FastRelaxTags.
void set_to_default ()
 Initializes class using option system. This is called by the constructors.
virtual std::string get_name () const
 Return the name of this mover.
virtual protocols::moves::MoverOP clone () const
 return a fresh instance of this class in an owning pointer
virtual void apply (core::pose::Pose &pose)
 Apply the FastRelax. Overloaded apply function from mover base class.
void makeDnaRigid (core::pose::Pose &pose, core::kinematics::MoveMapOP mm)
 sets the movemap to not allow DNA to move during relax.
void batch_apply (std::vector< core::io::silent::SilentStructOP > &input_structs, core::scoring::constraints::ConstraintSetOP input_csts=NULL)
 Batch Relax, a new even faster way to relax entire batches of structures.

Protected Member Functions

void cmd_accept_to_best (const core::scoring::ScoreFunctionOP local_scorefxn, core::pose::Pose &pose, core::pose::Pose &best_pose, const core::pose::Pose &start_pose, core::Real &best_score, core::Size &accept_count)
void do_minimize (core::pose::Pose &pose, core::Real tolerance, core::kinematics::MoveMapOP local_movemap, core::scoring::ScoreFunctionOP local_scorefxn)

Constructor & Destructor Documentation

protocols::relax::FastRelax::FastRelax ( core::Size  standard_repeats = 0)

Initialize FastRelax with a specific script file, which encodes the script of steps the is to be applied.

--------------------------------------------------------------------------------- FastRelax main code: ---------------------------------------------------------------------------------

References protocols::relax::RelaxProtocolBase::explicit_ramp_constraints(), protocols::relax::RelaxProtocolBase::ramp_down_constraints(), and set_to_default().

Referenced by clone().

protocols::relax::FastRelax::FastRelax ( core::scoring::ScoreFunctionOP  scorefxn_in,
core::Size  standard_repeats = 0 
)

Initialize FastRelax using the default script with a varying number of rounds, defined by the standard_repeats repeats paramter. By default, 5.

References protocols::relax::RelaxProtocolBase::explicit_ramp_constraints(), protocols::relax::RelaxProtocolBase::ramp_down_constraints(), and set_to_default().

protocols::relax::FastRelax::FastRelax ( core::scoring::ScoreFunctionOP  scorefxn_in,
std::string const &  script_file 
)

Initialize FastRelax with a specific script file, which encodes the script of steps the is to be applied.

References set_to_default().

protocols::relax::FastRelax::FastRelax ( core::scoring::ScoreFunctionOP  scorefxn_in,
core::Size  standard_repeats,
const std::string &  script_file 
)

Initialize FastRelax with a specific script file, and allows fastrelax to only use a subset of the number of stages in the scriptfile.

References set_to_default().

protocols::relax::FastRelax::~FastRelax ( ) [virtual]

virtual constructor to allow derivation

destructor - this class has no dynamic allocation, so / nothing needs to be cleaned. C++ will take care of that for us.


Member Function Documentation

void protocols::relax::FastRelax::apply ( core::pose::Pose pose) [virtual]

Apply the FastRelax. Overloaded apply function from mover base class.

Implements protocols::moves::Mover.

References protocols::viewer::add_conformation_viewer(), protocols::toolbox::task_operations::LimitAromaChi2Operation::apply(), protocols::relax::RelaxProtocolBase::apply_disulfides(), core::scoring::CA_rmsd_symmetric(), clone(), protocols::relax::RelaxScriptCommand::command, core::pose::Pose::conformation(), protocols::relax::RelaxProtocolBase::constrain_coords(), core::pose::Pose::constraint_set(), core::scoring::coordinate_constraint, core::pack::interaction_graph::debug, do_minimize(), protocols::relax::RelaxProtocolBase::dry_run(), core::pose::Pose::dump_pdb(), core::scoring::fa_rep, core::chemical::FA_STANDARD, protocols::relax::fix_worst_bad_ramas(), core::pose::Pose::fold_tree(), protocols::moves::Mover::get_current_tag(), protocols::relax::RelaxProtocolBase::get_movemap(), protocols::moves::Mover::get_native_pose(), protocols::relax::RelaxProtocolBase::get_scorefxn(), protocols::relax::RelaxProtocolBase::get_task_factory(), protocols::relax::RelaxProtocolBase::initialize_movemap(), core::pose::Pose::is_fullatom(), core::pose::symmetry::is_symmetric(), protocols::relax::RelaxProtocolBase::limit_aroma_chi2(), core::pose::symmetry::make_symmetric_movemap(), makeDnaRigid(), core::scoring::native_CA_rmsd(), protocols::relax::RelaxScriptCommand::nparams, protocols::relax::RelaxScriptCommand::param1, protocols::relax::RelaxScriptCommand::param2, protocols::relax::RelaxScriptCommand::param3, protocols::rosetta_scripts::parse_movemap(), core::scoring::rms, core::scoring::score_type_from_name(), protocols::relax::RelaxProtocolBase::set_movemap(), protocols::moves::Mover::set_native_pose(), protocols::relax::RelaxProtocolBase::set_up_constraints(), core::pose::setPoseExtraScores(), core::kinematics::simple_visualize_fold_tree_and_movemap_bb_chi(), core::util::switch_to_residue_type_set(), core::pose::Pose::total_residue(), and protocols::relax::TR().

Referenced by protocols::relax::MiniRelax::apply(), protocols::rbsegment_relax::AutoRBMover::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::comparative_modeling::hybridize::HybridizeProtocol::apply(), protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::fascore(), protocols::abinitio::AbrelaxApplication::relax(), and protocols::relax::WorkUnit_BatchRelax_and_PostRescore::rescore_all_decoys().

void protocols::relax::FastRelax::batch_apply ( std::vector< core::io::silent::SilentStructOP > &  input_structs,
core::scoring::constraints::ConstraintSetOP  input_csts = NULL 
)

Batch Relax, a new even faster way to relax entire batches of structures.

References protocols::relax::SRelaxPose::active, protocols::relax::SRelaxPose::best_score, protocols::relax::SRelaxPose::best_struct, core::scoring::CA_rmsd_symmetric(), clone(), protocols::relax::RelaxScriptCommand::command, core::pose::Pose::constraint_set(), protocols::relax::SRelaxPose::current_score, protocols::relax::SRelaxPose::current_struct, core::pack::interaction_graph::debug, do_minimize(), protocols::relax::RelaxProtocolBase::dry_run(), core::scoring::fa_rep, core::chemical::FA_STANDARD, protocols::relax::fix_worst_bad_ramas(), core::io::silent::SilentStructFactory::get_instance(), protocols::relax::RelaxProtocolBase::get_movemap(), protocols::moves::Mover::get_native_pose(), protocols::relax::RelaxProtocolBase::get_scorefxn(), core::io::silent::SilentStructFactory::get_silent_struct(), core::io::silent::SilentStructFactory::get_silent_struct_out(), protocols::relax::RelaxProtocolBase::get_task_factory(), protocols::relax::SRelaxPose::initial_rms, protocols::relax::SRelaxPose::initial_score, protocols::relax::RelaxProtocolBase::initialize_movemap(), core::pose::symmetry::is_symmetric(), core::pose::symmetry::make_symmetric_movemap(), protocols::relax::SRelaxPose::mem_footprint(), core::scoring::native_CA_gdtmm(), core::scoring::native_CA_rmsd(), protocols::relax::RelaxScriptCommand::nparams, protocols::relax::RelaxScriptCommand::param1, protocols::relax::RelaxScriptCommand::param2, core::scoring::rms, core::scoring::score_type_from_name(), core::pose::setPoseExtraScores(), core::kinematics::simple_visualize_fold_tree_and_movemap_bb_chi(), protocols::relax::SRelaxPose::start_struct, core::util::switch_to_residue_type_set(), and protocols::relax::TR().

Referenced by protocols::loophash::Mover_LoopHashRefine::apply(), protocols::loophash::LoopHashLibrary::apply(), protocols::comparative_modeling::hybridize::HybridizeProtocol::apply(), and protocols::relax::WorkUnit_BatchRelax::run().

protocols::moves::MoverOP protocols::relax::FastRelax::clone ( ) const [virtual]

return a fresh instance of this class in an owning pointer

Return a copy of ourselves.

Reimplemented from protocols::moves::Mover.

References FastRelax().

Referenced by apply(), and batch_apply().

void protocols::relax::FastRelax::cmd_accept_to_best ( const core::scoring::ScoreFunctionOP  local_scorefxn,
core::pose::Pose pose,
core::pose::Pose best_pose,
const core::pose::Pose start_pose,
core::Real best_score,
core::Size accept_count 
) [protected]
void protocols::relax::FastRelax::do_minimize ( core::pose::Pose pose,
core::Real  tolerance,
core::kinematics::MoveMapOP  local_movemap,
core::scoring::ScoreFunctionOP  local_scorefxn 
) [protected]
std::string protocols::relax::FastRelax::get_name ( ) const [virtual]

Return the name of this mover.

Implements protocols::moves::Mover.

void protocols::relax::FastRelax::makeDnaRigid ( core::pose::Pose pose,
core::kinematics::MoveMapOP  mm 
)

sets the movemap to not allow DNA to move during relax.

References core::conformation::Residue::is_DNA(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and protocols::relax::TR().

Referenced by apply().

void protocols::relax::FastRelax::parse_my_tag ( utility::tag::TagPtr const  tag,
protocols::moves::DataMap data,
protocols::filters::Filters_map const &  ,
protocols::moves::Movers_map const &  ,
core::pose::Pose const &  pose 
) [virtual]
void protocols::relax::FastRelax::set_force_nonideal ( bool  val) [inline]

Force us to batchrelax with nonideal geometry (using additional memory)

Referenced by protocols::comparative_modeling::hybridize::HybridizeProtocol::apply().

void protocols::relax::FastRelax::set_script_to_batchrelax_default ( core::Size  standard_repeats = 0)
void protocols::relax::FastRelax::set_to_default ( )

Initializes class using option system. This is called by the constructors.

Referenced by FastRelax().


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