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protocols::relax::FastRelax Class Reference

#include <FastRelax.hh>

Inheritance diagram for protocols::relax::FastRelax:
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Collaboration diagram for protocols::relax::FastRelax:
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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. More...
 
 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. More...
 
 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. More...
 
 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. More...
 
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. More...
 
void set_force_nonideal (bool val)
 Force us to batchrelax with nonideal geometry (using additional memory) More...
 
virtual ~FastRelax ()
 virtual constructor to allow derivation More...
 
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. More...
 
virtual void parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, protocols::moves::MoverCacheSP cache)
 
void set_to_default ()
 Initializes class using option system. This is called by the constructors. More...
 
virtual std::string get_name () const
 Return the name of this mover. More...
 
virtual protocols::moves::MoverOP clone () const
 return a fresh instance of this class in an owning pointer More...
 
virtual void apply (core::pose::Pose &pose)
 Apply the FastRelax. Overloaded apply function from mover base class. More...
 
void makeDnaRigid (core::pose::Pose &pose, core::kinematics::MoveMapOP mm)
 sets the movemap to not allow DNA to move during relax. More...
 
void batch_apply (std::vector< core::io::silent::SilentStructOP > &input_structs, core::scoring::constraints::ConstraintSetOP input_csts=NULL, core::Real decay_rate=0.5)
 Batch Relax, a new even faster way to relax entire batches of structures. More...
 
- Public Member Functions inherited from protocols::relax::RelaxProtocolBase
 RelaxProtocolBase (core::scoring::ScoreFunctionOP)
 
 RelaxProtocolBase (std::string const &movername="RelaxProtocol")
 
 RelaxProtocolBase (std::string const &movername, core::scoring::ScoreFunctionOP)
 
 ~RelaxProtocolBase ()
 
virtual protocols::moves::MoverOP fresh_instance () const
 this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...
 
void set_defaults ()
 
void set_default_minimization_settings ()
 
void set_default_coordinate_settings ()
 
void set_default_movemap ()
 
void minimize_bond_lengths (bool setting)
 
void minimize_bond_angles (bool setting)
 
void minimize_bondlength_subset (int setting)
 
void minimize_bondangle_subset (int setting)
 
bool minimize_bond_lengths () const
 
bool minimize_bond_angles () const
 
int minimize_bondlength_subset () const
 
int minimize_bondangle_subset () const
 
bool constrain_relax_to_native_coords () const
 
bool constrain_relax_to_start_coords () const
 
bool constrain_coords () const
 
bool explicit_ramp_constraints () const
 
bool ramp_down_constraints () const
 
bool constrain_relax_segments () const
 
bool limit_aroma_chi2 () const
 
void constrain_relax_to_native_coords (bool constrain_relax_to_native_coords)
 
void constrain_relax_to_start_coords (bool constrain_relax_to_start_coords)
 
void constrain_coords (bool constrain_coords)
 
void ramp_down_constraints (bool ramp_down_constraints)
 
void constrain_relax_segments (bool constrain_relax_segments)
 
void cartesian (bool newval)
 
bool cartesian () const
 
core::kinematics::MoveMapOP get_movemap ()
 
void set_movemap (core::kinematics::MoveMapOP movemap)
 
void set_min_type (std::string min_type)
 
void set_scorefxn (core::scoring::ScoreFunctionOP score)
 
const
core::scoring::ScoreFunctionCOP 
get_scorefxn () const
 
void set_task_factory (core::pack::task::TaskFactoryOP taskf)
 
core::pack::task::TaskFactoryOP
const & 
get_task_factory () const
 
void set_dry_run (bool setting)
 
bool dry_run () const
 
void apply_disulfides (core::pose::Pose &pose)
 
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
 
virtual ~Mover ()
 
virtual MoverSP create ()
 
virtual void apply (core::io::serialization::PipeMap &pmap)
 
virtual void parse_state (SerializableState const &state)
 
virtual void save_state (SerializableState &state)
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
 Mover (Mover const &other)
 
Moveroperator= (Mover const &other)
 assignment operator More...
 
virtual core::Real last_proposal_density_ratio ()
 
std::string const & type () const
 
std::string get_current_tag () const
 A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...
 
void set_current_tag (std::string const &new_tag)
 
virtual void set_input_pose (PoseCOP pose)
 setter for poses contained for rms More...
 
virtual void set_native_pose (PoseCOP pose)
 setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...
 
PoseCOP get_input_pose () const
 
PoseCOP get_native_pose () const
 
virtual void test_move (Pose &pose)
 : Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...
 
void type (const std::string &type_in)
 
std::string get_type () const
 
MoverStatus get_last_move_status () const
 end parser interface, start Job Distributor interface///////////// More...
 
void reset_status ()
 resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...
 
virtual core::pose::PoseOP get_additional_output ()
 Mechanism by which a mover may return multiple output poses from a single input pose. More...
 
virtual void clear_info ()
 Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...
 
virtual Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 
virtual bool reinitialize_for_each_job () const
 this function informs the job distributor (august 08 vintage) whether this object needs to be freshly regenerated on each use. More...
 
virtual bool reinitialize_for_new_input () const
 this function informs the job distributor (august 08 vintage) whether this object needs to be regenerated when the input pose is about to change (for example, if the mover has special code on the first apply() that is only valid for that one input pose). More...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 

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)
 
- Protected Member Functions inherited from protocols::relax::RelaxProtocolBase
void initialize_movemap (core::pose::Pose const &pose, core::kinematics::MoveMap &movemap)
 
core::scoring::ScoreFunctionOP get_scorefxn ()
 
void set_up_constraints (core::pose::Pose &pose, core::kinematics::MoveMap &local_movemap)
 
void output_debug_structure (core::pose::Pose &pose, std::string prefix)
 
- Protected Member Functions inherited from protocols::moves::Mover
void set_last_move_status (MoverStatus status)
 nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...
 

Private Member Functions

void read_script_file (const std::string &script_file, core::Size standard_repeats=5)
 

Private Attributes

core::Size default_repeats_
 Number of repeats if using default script. More...
 
bool ramady_
 Apply Ramady(tm) fix to residues with bad rama scores ? More...
 
core::Size ramady_num_rebuild_
 Number of bad ramas to fix per call to 'fix_worst_bad_ramas'. More...
 
core::Real ramady_rms_limit_
 Reject ramady changes perturbing structure more than this amount. More...
 
core::Real ramady_cutoff_
 Cutoff for calling a rama 'bad'. More...
 
bool ramady_force_
 Force ramady to be run (normally skip rate of 10%) More...
 
bool repack_
 Allow Chi angles to move ? More...
 
bool test_cycles_
 Do only a few test_cycles ? More...
 
bool force_nonideal_
 [batch mode only] force structures to be nonideal? Default uses -out:silent_struct_type to decide More...
 
bool dumpall_
 Dump pdb after repack, min, or ramp_repack_min? More...
 
core::Size script_max_accept_
 Quit after this many accepts ?// limits themaximum number of accepts, default is 1000000. More...
 
bool symmetric_rmsd_
 Do a symmetric RMSD calculation rather then a monomeric one. More...
 
protocols::checkpoint::CheckPointer checkpoints_
 
std::vector< RelaxScriptCommandscript_
 
utility::tag::TagPtr movemap_tag_
 

Additional Inherited Members

- Public Types inherited from protocols::relax::RelaxProtocolBase
typedef moves::Mover parent
 
- Static Public Member Functions inherited from protocols::relax::RelaxProtocolBase
static void register_options ()
 
- Protected Attributes inherited from protocols::relax::RelaxProtocolBase
bool constrain_relax_to_native_coords_
 
bool constrain_relax_to_start_coords_
 
bool constrain_coords_
 
bool coord_constrain_sidechains_
 
bool explicit_ramp_constraints_
 
bool ramp_down_constraints_
 
bool constrain_relax_segments_
 
std::string min_type_
 
bool cartesian_
 Do cartesian-space minimization? More...
 
bool limit_aroma_chi2_
 

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 default_repeats_, protocols::relax::RelaxProtocolBase::explicit_ramp_constraints(), protocols::relax::RelaxProtocolBase::ramp_down_constraints(), read_script_file(), 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 default_repeats_, protocols::relax::RelaxProtocolBase::explicit_ramp_constraints(), protocols::relax::RelaxProtocolBase::ramp_down_constraints(), read_script_file(), 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 read_script_file(), and 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 default_repeats_, read_script_file(), and 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(), protocols::relax::RelaxProtocolBase::cartesian(), protocols::checkpoint::CheckPointer::checkpoint(), checkpoints_, protocols::checkpoint::CheckPointer::clear_checkpoints(), 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::task::TaskFactory::create_packer_task(), core::pack::interaction_graph::debug, do_minimize(), protocols::relax::RelaxProtocolBase::dry_run(), core::pose::Pose::dump_pdb(), dumpall_, 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(), protocols::relax::make_dna_rigid(), core::pose::symmetry::make_symmetric_movemap(), movemap_tag_, 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(), ramady_, ramady_cutoff_, ramady_force_, ramady_num_rebuild_, ramady_rms_limit_, protocols::checkpoint::CheckPointer::recover_checkpoint(), repack_, core::scoring::rms, core::scoring::score_type_from_name(), script_, script_max_accept_, 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(), symmetric_rmsd_, test_cycles_, core::pose::Pose::total_residue(), and protocols::relax::TR().

Referenced by protocols::rbsegment_relax::AutoRBMover::apply(), protocols::relax::MiniRelax::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::forge::remodel::RemodelMover::design_refine_seq_relax(), 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,
core::Real  decay_rate = 0.5 
)

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(), protocols::relax::RelaxProtocolBase::cartesian(), clone(), protocols::relax::RelaxScriptCommand::command, core::pose::Pose::constraint_set(), core::pack::task::TaskFactory::create_packer_task(), 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(), force_nonideal_, 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, ramady_, ramady_cutoff_, ramady_force_, ramady_num_rebuild_, ramady_rms_limit_, core::scoring::rms, core::scoring::score_type_from_name(), script_, 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::hybridization::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(), batch_apply(), and parse_def().

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().

void protocols::relax::FastRelax::parse_def ( utility::lua::LuaObject const &  def,
utility::lua::LuaObject const &  score_fxns,
utility::lua::LuaObject const &  tasks,
protocols::moves::MoverCacheSP  cache 
)
virtual
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::read_script_file ( const std::string &  script_file,
core::Size  standard_repeats = 5 
)
private
void protocols::relax::FastRelax::set_force_nonideal ( bool  val)
inline

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

References force_nonideal_.

Referenced by protocols::hybridization::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.

References default_repeats_, dumpall_, force_nonideal_, ramady_, ramady_cutoff_, ramady_force_, ramady_num_rebuild_, ramady_rms_limit_, repack_, script_max_accept_, symmetric_rmsd_, and test_cycles_.

Referenced by FastRelax().

Member Data Documentation

protocols::checkpoint::CheckPointer protocols::relax::FastRelax::checkpoints_
private

Referenced by apply().

core::Size protocols::relax::FastRelax::default_repeats_
private

Number of repeats if using default script.

Referenced by FastRelax(), parse_def(), parse_my_tag(), set_script_to_batchrelax_default(), and set_to_default().

bool protocols::relax::FastRelax::dumpall_
private

Dump pdb after repack, min, or ramp_repack_min?

Referenced by apply(), and set_to_default().

bool protocols::relax::FastRelax::force_nonideal_
private

[batch mode only] force structures to be nonideal? Default uses -out:silent_struct_type to decide

Referenced by batch_apply(), set_force_nonideal(), and set_to_default().

utility::tag::TagPtr protocols::relax::FastRelax::movemap_tag_
private

Referenced by apply().

bool protocols::relax::FastRelax::ramady_
private

Apply Ramady(tm) fix to residues with bad rama scores ?

Referenced by apply(), batch_apply(), and set_to_default().

core::Real protocols::relax::FastRelax::ramady_cutoff_
private

Cutoff for calling a rama 'bad'.

Referenced by apply(), batch_apply(), and set_to_default().

bool protocols::relax::FastRelax::ramady_force_
private

Force ramady to be run (normally skip rate of 10%)

Referenced by apply(), batch_apply(), and set_to_default().

core::Size protocols::relax::FastRelax::ramady_num_rebuild_
private

Number of bad ramas to fix per call to 'fix_worst_bad_ramas'.

Referenced by apply(), batch_apply(), and set_to_default().

core::Real protocols::relax::FastRelax::ramady_rms_limit_
private

Reject ramady changes perturbing structure more than this amount.

Referenced by apply(), batch_apply(), and set_to_default().

bool protocols::relax::FastRelax::repack_
private

Allow Chi angles to move ?

Referenced by apply(), and set_to_default().

std::vector<RelaxScriptCommand> protocols::relax::FastRelax::script_
private
core::Size protocols::relax::FastRelax::script_max_accept_
private

Quit after this many accepts ?// limits themaximum number of accepts, default is 1000000.

Referenced by apply(), and set_to_default().

bool protocols::relax::FastRelax::symmetric_rmsd_
private

Do a symmetric RMSD calculation rather then a monomeric one.

Referenced by apply(), cmd_accept_to_best(), and set_to_default().

bool protocols::relax::FastRelax::test_cycles_
private

Do only a few test_cycles ?

Referenced by apply(), and set_to_default().


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