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protocols::relax::FastRelax Class Reference

#include <FastRelax.hh>

Inheritance diagram for protocols::relax::FastRelax:
Inheritance graph
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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_script_from_lines (std::vector< std::string > const &filelines)
 replace schedule by providing lines of commands explicitly More...
 
void set_force_nonideal (bool val)
 Force us to batchrelax with nonideal geometry (using additional memory) More...
 
void dualspace (bool val)
 Use the dualspace (Dihedral + Cartesian) relax protocol (Default false) More...
 
bool dualspace ()
 
core::Size default_repeats () const
 Return the number of repeats. More...
 
void set_movemap_disables_packing_of_fixed_chi_positions (bool const setting)
 Set whether the MoveMap can automatically disable packing of positions where sidechain minimization is prohibited. Default false. More...
 
bool movemap_disables_packing_of_fixed_chi_positions () const
 Get whether the MoveMap can automatically disable packing of positions where sidechain minimization is prohibited. Default false. More...
 
 ~FastRelax () override
 virtual constructor to allow derivation More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 Parses the FastRelaxTags. More...
 
void set_to_default ()
 Initializes class using option system. This is called by the constructors. More...
 
protocols::moves::MoverOP clone () const override
 return a fresh instance of this class in an owning pointer More...
 
void apply (core::pose::Pose &pose) override
 Apply the FastRelax. Overloaded apply function from mover base class. More...
 
void batch_apply (std::vector< core::io::silent::SilentStructOP > &input_structs, core::scoring::constraints::ConstraintSetOP input_csts=nullptr, core::Real decay_rate=0.5)
 Batch Relax, a new even faster way to relax entire batches of structures. More...
 
void set_enable_design (bool const val)
 sets the enable_design option. Note - (Only used by ParseMyTag! Class will respect the passed TF otherwise, as it should.) More...
 
std::string get_name () const override
 Return the name of this mover. More...
 
bool mover_provides_citation_info () const override
 Does this mover provide information about how to cite it? More...
 
utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const override
 Provide the citation. 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 () override
 
protocols::moves::MoverOP fresh_instance () const override
 Generates a new Mover object freshly created with the default ctor. More...
 
void apply_disulfides (core::pose::Pose &pose)
 
void set_defaults ()
 
void set_default_minimization_settings ()
 
void set_default_coordinate_settings ()
 
void set_default_movemap ()
 
core::kinematics::MoveMapCOP get_movemap () const
 
core::kinematics::MoveMapOP get_movemap ()
 
const
core::scoring::ScoreFunctionCOP 
get_scorefxn () const
 
core::pack::task::TaskFactoryOP
const & 
get_task_factory () const
 
bool cartesian () const
 
std::string min_type () const
 
core::Size max_iter () const
 
bool dry_run () const
 
bool constrain_relax_to_native_coords () const
 
bool constrain_relax_to_start_coords () const
 
bool constrain_coords () const
 
bool coord_constrain_sidechains () const
 
bool ramp_down_constraints () const
 
bool constrain_relax_segments () const
 
bool minimize_bond_lengths () const
 
bool minimize_bond_angles () const
 
void set_movemap (core::kinematics::MoveMapOP movemap)
 
void set_movemap_factory (core::select::movemap::MoveMapFactoryOP mm_factory)
 
void set_scorefxn (core::scoring::ScoreFunctionOP scorefxn)
 
void set_task_factory (core::pack::task::TaskFactoryOP task_factory)
 
void cartesian (bool newval)
 Use cartesian (minimization step) More...
 
void min_type (std::string min_type)
 
void max_iter (core::Size max_iter)
 
void dry_run (bool setting)
 
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 coord_constrain_sidechains (bool coord_constrain_sidechains)
 
void constrain_relax_segments (bool constrain_relax_segments)
 
void ramp_down_constraints (bool ramp_down_constraints)
 
void minimize_bond_lengths (bool minimize_bond_lengths)
 
void minimize_bond_angles (bool minimize_bond_angles)
 
bool mover_provides_citation_info () const override
 Does this mover provide information about how to cite it? More...
 
utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const override
 Provide the citation. More...
 
bool mover_is_unpublished () const override
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const override
 Provide a list of authors and their e-mail addresses, as strings. More...
 
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
 
virtual MoverOP create ()
 
MoverCOP get_self_ptr () const
 
MoverOP get_self_ptr ()
 
MoverCAP get_self_weak_ptr () const
 
MoverAP get_self_weak_ptr ()
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
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...
 
virtual bool reinitialize_for_each_job () const
 Inform 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
 Inform 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...
 
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...
 
void set_type (std::string const &setting)
 Set the 'type' string. More...
 
std::string get_type () const
 
void type (const std::string &type_in)
 Set the 'type' string. More...
 
std::string const & type () const
 Get the set 'type' string. More...
 
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
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 
virtual void set_current_tag (std::string const &new_tag)
 
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...
 
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...
 
virtual core::Real last_proposal_density_ratio ()
 
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...
 

Static Public Member Functions

static std::string mover_name ()
 Return the name of this mover. More...
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
static
utility::tag::XMLSchemaComplexTypeGeneratorOP 
complex_type_generator_for_fast_relax (utility::tag::XMLSchemaDefinition &)
 
- Static Public Member Functions inherited from protocols::relax::RelaxProtocolBase
static void register_options ()
 
- Static Public Member Functions inherited from protocols::moves::Mover
static std::string name ()
 
static void register_options ()
 Overload this static method if you access options within the mover. More...
 

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)
 
virtual void set_constraint_weight (core::scoring::ScoreFunctionOP local_scorefxn, core::scoring::EnergyMap const &full_weights, core::Real const weight, core::pose::Pose &pose) const
 Use for constraint scaling – sets the coordinate constraint weight given a scorefxn, energy map, and weight. TL - Derived classes which may want to scale more than coordinate constraints can override this without forking apply() More...
 
void do_md (core::pose::Pose &pose, core::Real nstep, core::Real temp0, core::kinematics::MoveMapOP local_movemap, core::scoring::ScoreFunctionOP local_scorefxn)
 
std::string determine_default_relax_script ()
 default is currently MonomerDesign2019 or MonomerRelax2019, depending on the state of enable_design_ More...
 
core::pack::task::TaskFactoryOP setup_local_tf (core::pose::Pose const &pose, core::kinematics::MoveMapOP const &local_movemap)
 helper function for apply(). Helps setup the task factory More...
 
- Protected Member Functions inherited from protocols::relax::RelaxProtocolBase
core::scoring::ScoreFunctionOP get_scorefxn ()
 
bool fix_omega () const
 
int minimize_bondlength_subset () const
 
int minimize_bondangle_subset () const
 
bool limit_aroma_chi2 () const
 
std::string cst_files (core::Size const i) const
 
void fix_omega (bool fix_omega)
 
void minimize_bondangle_subset (int minimize_bondangle_subset)
 
void minimize_bondlength_subset (int minimize_bondlength_subset)
 
void initialize_movemap (core::pose::Pose const &pose, core::kinematics::MoveMap &movemap)
 
void set_up_constraints (core::pose::Pose &pose, core::kinematics::MoveMap &local_movemap)
 
void output_debug_structure (core::pose::Pose &pose, std::string prefix)
 
void add_cst_files (std::string const &cstfile)
 
- 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

utility::vector1< std::string > get_possible_relax_script_names (std::string const &prefix) const
 
void read_script_file (std::string script_file, core::Size standard_repeats=5)
 
void check_nonideal_mintype ()
 Make sure correct mintype for cartesian or dualspace during apply. More...
 
void inner_loop_repack_command (core::Size const chk_counter, core::pose::Pose &pose, core::scoring::ScoreFunctionOP const &local_scorefxn, minimization_packing::PackRotamersMoverOP const &pack_full_repack, int &dump_counter)
 
void inner_loop_min_command (RelaxScriptCommand const &cmd, core::pose::Pose &pose, core::kinematics::MoveMapOP const &local_movemap, core::scoring::ScoreFunctionOP const &local_scorefxn, core::Size &chk_counter, int &dump_counter)
 
void inner_loop_ramp_repack_min_command (RelaxScriptCommand const &cmd, int const total_repeat_count, bool const do_rama_repair, core::scoring::EnergyMap &full_weights, core::pose::Pose &pose, minimization_packing::PackRotamersMoverOP const &pack_full_repack, int const repeat_count, int const total_count, core::kinematics::MoveMapOP const &local_movemap, core::scoring::ScoreFunctionOP const &local_scorefxn, core::Size &chk_counter, int &dump_counter)
 
void inner_loop_dumpall_command (RelaxScriptCommand const &cmd)
 
void inner_loop_md_command (RelaxScriptCommand const &cmd, core::Size &chk_counter, core::pose::Pose &pose, core::kinematics::MoveMapOP const &local_movemap, core::scoring::ScoreFunctionOP const &local_scorefxn)
 
void inner_loop_reset_reference_command (core::scoring::ScoreFunctionOP const &local_scorefxn) const
 
void inner_loop_reference_command (RelaxScriptCommand const &cmd, core::scoring::ScoreFunctionOP const &local_scorefxn) const
 
void inner_loop_accept_to_best_command (core::scoring::ScoreFunctionOP const &local_scorefxn, core::pose::Pose &pose, core::Real &best_score, core::Size &accept_count, core::pose::Pose &best_pose, core::pose::Pose const &start_pose, std::vector< core::Real > &best_score_log, std::vector< core::Real > &curr_score_log, int const )
 

Private Attributes

core::Size default_repeats_
 Number of repeats if using default script. More...
 
bool movemap_disables_packing_of_fixed_chi_positions_ = false
 Option to have the MoveMap disable packing at positions where sidechain minimization is disabled. More...
 
bool delete_virtual_residues_after_FastRelax_
 If true, delete virtual residues at the end of FastRelax for smooth rmsd calculation later. 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 dna_move_
 Allow DNA to move? default is False. If True will setup DNA-specific relax settings. 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...
 
bool dualspace_
 Use dualspace (Dihedral + Cartesian) Relax? More...
 
bool enable_design_
 Enable design – if false, a RestrictToRepacking task will be added to the TaskFactory. 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_
 

Friends

class ::FastRelaxTests
 

Additional Inherited Members

- Public Types inherited from protocols::relax::RelaxProtocolBase
typedef moves::Mover parent
 
- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP TagCOP
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef std::list< std::string > Strings
 

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_, read_script_file(), and set_to_default().

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_, 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 ( )
overridedefault

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)
overridevirtual

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

Implements protocols::moves::Mover.

References protocols::viewer::add_conformation_viewer(), protocols::relax::RelaxProtocolBase::apply_disulfides(), core::scoring::CA_rmsd_symmetric(), protocols::relax::RelaxProtocolBase::cartesian(), check_nonideal_mintype(), 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::pack::interaction_graph::debug, protocols::relax::delete_virtual_residues(), delete_virtual_residues_after_FastRelax_, dna_move_, protocols::relax::RelaxProtocolBase::dry_run(), core::pose::Pose::dump_pdb(), core::scoring::fa_rep, core::pose::Pose::fold_tree(), core::chemical::FULL_ATOM_t, protocols::relax::RelaxProtocolBase::get_movemap(), protocols::moves::Mover::get_native_pose(), protocols::relax::RelaxProtocolBase::get_scorefxn(), protocols::relax::RelaxProtocolBase::initialize_movemap(), inner_loop_accept_to_best_command(), inner_loop_dumpall_command(), inner_loop_md_command(), inner_loop_min_command(), inner_loop_ramp_repack_min_command(), inner_loop_reference_command(), inner_loop_repack_command(), inner_loop_reset_reference_command(), core::pose::Pose::is_fullatom(), core::pose::symmetry::is_symmetric(), protocols::relax::make_dna_rigid(), core::pose::symmetry::make_symmetric_movemap(), core::scoring::native_CA_rmsd(), protocols::relax::RelaxScriptCommand::nparams, protocols::relax::RelaxScriptCommand::param1, protocols::relax::RelaxScriptCommand::param2, ramady_, ramady_force_, protocols::relax::RelaxProtocolBase::ramp_down_constraints(), core::scoring::rms, core::scoring::score_type_from_name(), script_, script_max_accept_, set_constraint_weight(), protocols::moves::Mover::set_native_pose(), protocols::relax::RelaxProtocolBase::set_up_constraints(), core::pose::setPoseExtraScore(), protocols::relax::setup_for_dna(), setup_local_tf(), core::kinematics::simple_visualize_fold_tree_and_movemap_bb_chi(), core::pose::Pose::size(), core::util::switch_to_residue_type_set(), symmetric_rmsd_, test_cycles_, and protocols::relax::TR().

Referenced by protocols::relax::MiniRelax::apply(), protocols::rbsegment_relax::AutoRBMover::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::symmetric_docking::SymDockingHiRes::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::calculate_free_receptor_score(), protocols::evolution::NucleotideMutation::compute_folding_energies(), protocols::forge::remodel::RemodelMover::design_refine_seq_relax(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::do_initial_import_and_scoring(), protocols::forge::remodel::RemodelLoopMover::fa_relax_stage(), protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::fascore(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_cartmin(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_scmin(), protocols::residue_optimization::MetapatchEnumeration::final_sampling(), protocols::residue_optimization::MetapatchEnumeration::initial_sampling(), protocols::cyclic_peptide::CrosslinkerMover::pack_and_minimize_linker_and_sidechains(), protocols::abinitio::AbrelaxApplication::relax(), protocols::relax::RepeatProteinRelax::relax_pose(), protocols::relax::WorkUnit_BatchRelax_and_PostRescore::rescore_all_decoys(), and protocols::mpi_refinement::WorkUnit_Relax::run().

void protocols::relax::FastRelax::batch_apply ( std::vector< core::io::silent::SilentStructOP > &  input_structs,
core::scoring::constraints::ConstraintSetOP  input_csts = nullptr,
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(), check_nonideal_mintype(), 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, protocols::relax::fix_worst_bad_ramas(), force_nonideal_, core::chemical::FULL_ATOM_t, protocols::relax::RelaxProtocolBase::get_movemap(), protocols::moves::Mover::get_native_pose(), protocols::relax::RelaxProtocolBase::get_scorefxn(), 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_, protocols::antibody::design::repack, core::scoring::rms, protocols::hybridization::score, core::scoring::score_type_from_name(), script_, core::pose::setPoseExtraScore(), 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().

void protocols::relax::FastRelax::check_nonideal_mintype ( )
private
protocols::moves::MoverOP protocols::relax::FastRelax::clone ( ) const
overridevirtual

return a fresh instance of this class in an owning pointer

Return a copy of ourselves.

Reimplemented from protocols::moves::Mover.

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

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
utility::tag::XMLSchemaComplexTypeGeneratorOP protocols::relax::FastRelax::complex_type_generator_for_fast_relax ( utility::tag::XMLSchemaDefinition &  xsd)
static
core::Size protocols::relax::FastRelax::default_repeats ( ) const
inline

Return the number of repeats.

References default_repeats_.

std::string protocols::relax::FastRelax::determine_default_relax_script ( )
protected

default is currently MonomerDesign2019 or MonomerRelax2019, depending on the state of enable_design_

Author
Jack Maguire, jackm.nosp@m.agui.nosp@m.re144.nosp@m.4@gm.nosp@m.ail.c.nosp@m.om

References enable_design_.

Referenced by read_script_file().

void protocols::relax::FastRelax::do_md ( core::pose::Pose pose,
core::Real  nstep,
core::Real  temp0,
core::kinematics::MoveMapOP  local_movemap,
core::scoring::ScoreFunctionOP  local_scorefxn 
)
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
void protocols::relax::FastRelax::dualspace ( bool  val)

Use the dualspace (Dihedral + Cartesian) relax protocol (Default false)

Sets to use the lbfgs_armijo_nonmonotone if true or FR default if false Recommended to set max_iter to 200. Recommended to set minimize_bond_angles to true as well. Requires scorefunction setup for non-ideal minimization.

References dualspace_, and protocols::hybridization::val.

bool protocols::relax::FastRelax::dualspace ( )

References dualspace_.

Referenced by check_nonideal_mintype(), and parse_my_tag().

std::string protocols::relax::FastRelax::get_name ( ) const
overridevirtual

Return the name of this mover.

Implements protocols::moves::Mover.

References mover_name().

Referenced by provide_citation_info().

utility::vector1< std::string > protocols::relax::FastRelax::get_possible_relax_script_names ( std::string const &  prefix) const
private
void protocols::relax::FastRelax::inner_loop_accept_to_best_command ( core::scoring::ScoreFunctionOP const &  local_scorefxn,
core::pose::Pose pose,
core::Real best_score,
core::Size accept_count,
core::pose::Pose best_pose,
core::pose::Pose const &  start_pose,
std::vector< core::Real > &  best_score_log,
std::vector< core::Real > &  curr_score_log,
int const   
)
private
void protocols::relax::FastRelax::inner_loop_dumpall_command ( RelaxScriptCommand const &  cmd)
private
void protocols::relax::FastRelax::inner_loop_md_command ( RelaxScriptCommand const &  cmd,
core::Size chk_counter,
core::pose::Pose pose,
core::kinematics::MoveMapOP const &  local_movemap,
core::scoring::ScoreFunctionOP const &  local_scorefxn 
)
private
void protocols::relax::FastRelax::inner_loop_min_command ( RelaxScriptCommand const &  cmd,
core::pose::Pose pose,
core::kinematics::MoveMapOP const &  local_movemap,
core::scoring::ScoreFunctionOP const &  local_scorefxn,
core::Size chk_counter,
int &  dump_counter 
)
private
void protocols::relax::FastRelax::inner_loop_ramp_repack_min_command ( RelaxScriptCommand const &  cmd,
int const  total_repeat_count,
bool const  do_rama_repair,
core::scoring::EnergyMap full_weights,
core::pose::Pose pose,
minimization_packing::PackRotamersMoverOP const &  pack_full_repack,
int const  repeat_count,
int const  total_count,
core::kinematics::MoveMapOP const &  local_movemap,
core::scoring::ScoreFunctionOP const &  local_scorefxn,
core::Size chk_counter,
int &  dump_counter 
)
private
void protocols::relax::FastRelax::inner_loop_reference_command ( RelaxScriptCommand const &  cmd,
core::scoring::ScoreFunctionOP const &  local_scorefxn 
) const
private
void protocols::relax::FastRelax::inner_loop_repack_command ( core::Size const  chk_counter,
core::pose::Pose pose,
core::scoring::ScoreFunctionOP const &  local_scorefxn,
minimization_packing::PackRotamersMoverOP const &  pack_full_repack,
int &  dump_counter 
)
private
void protocols::relax::FastRelax::inner_loop_reset_reference_command ( core::scoring::ScoreFunctionOP const &  local_scorefxn) const
private
bool protocols::relax::FastRelax::movemap_disables_packing_of_fixed_chi_positions ( ) const
inline

Get whether the MoveMap can automatically disable packing of positions where sidechain minimization is prohibited. Default false.

References movemap_disables_packing_of_fixed_chi_positions_.

std::string protocols::relax::FastRelax::mover_name ( )
static

Return the name of this mover.

Referenced by get_name(), protocols::relax::FastRelaxCreator::keyname(), and provide_xml_schema().

bool protocols::relax::FastRelax::mover_provides_citation_info ( ) const
overridevirtual

Does this mover provide information about how to cite it?

Returns true.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)

Reimplemented from protocols::moves::Mover.

void protocols::relax::FastRelax::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
utility::vector1< basic::citation_manager::CitationCollectionCOP > protocols::relax::FastRelax::provide_citation_info ( ) const
overridevirtual

Provide the citation.

Returns
A vector of citation collections. This allows the mover to provide citations for itself and for any modules that it invokes.

This function provides citations for the task operations in the task factory and for FastRelax.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)

Reimplemented from protocols::moves::Mover.

References get_name(), and protocols::relax::RelaxProtocolBase::provide_citation_info().

void protocols::relax::FastRelax::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::relax::FastRelax::read_script_file ( std::string  script_file,
core::Size  standard_repeats = 5 
)
private
void protocols::relax::FastRelax::set_constraint_weight ( core::scoring::ScoreFunctionOP  local_scorefxn,
core::scoring::EnergyMap const &  full_weights,
core::Real const  weight,
core::pose::Pose pose 
) const
protectedvirtual

Use for constraint scaling – sets the coordinate constraint weight given a scorefxn, energy map, and weight. TL - Derived classes which may want to scale more than coordinate constraints can override this without forking apply()

Reimplemented in protocols::denovo_design::movers::FastDesign.

References core::scoring::coordinate_constraint.

Referenced by apply(), and inner_loop_ramp_repack_min_command().

void protocols::relax::FastRelax::set_enable_design ( bool const  val)
inline

sets the enable_design option. Note - (Only used by ParseMyTag! Class will respect the passed TF otherwise, as it should.)

References enable_design_, and protocols::hybridization::val.

Referenced by protocols::denovo_design::movers::FastDesign::FastDesign(), and parse_my_tag().

void protocols::relax::FastRelax::set_force_nonideal ( bool  val)
inline

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

References force_nonideal_, and protocols::hybridization::val.

Referenced by protocols::hybridization::HybridizeProtocol::apply().

void protocols::relax::FastRelax::set_movemap_disables_packing_of_fixed_chi_positions ( bool const  setting)
void protocols::relax::FastRelax::set_script_from_lines ( std::vector< std::string > const &  filelines)
void protocols::relax::FastRelax::set_script_to_batchrelax_default ( core::Size  standard_repeats = 0)

Override the stored script with the default script for batchrelax Ignores '-default_repeat' value.

References default_repeats_, script_, and set_script_from_lines().

Referenced by protocols::hybridization::HybridizeProtocol::apply(), and parse_my_tag().

void protocols::relax::FastRelax::set_to_default ( )
core::pack::task::TaskFactoryOP protocols::relax::FastRelax::setup_local_tf ( core::pose::Pose const &  pose,
core::kinematics::MoveMapOP const &  local_movemap 
)
protected

Friends And Related Function Documentation

friend class ::FastRelaxTests
friend

Member Data Documentation

protocols::checkpoint::CheckPointer protocols::relax::FastRelax::checkpoints_
private
core::Size protocols::relax::FastRelax::default_repeats_
private

Number of repeats if using default script.

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

bool protocols::relax::FastRelax::delete_virtual_residues_after_FastRelax_
private

If true, delete virtual residues at the end of FastRelax for smooth rmsd calculation later.

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

bool protocols::relax::FastRelax::dna_move_
private

Allow DNA to move? default is False. If True will setup DNA-specific relax settings.

Referenced by apply(), and set_to_default().

bool protocols::relax::FastRelax::dualspace_
private

Use dualspace (Dihedral + Cartesian) Relax?

Referenced by dualspace(), get_possible_relax_script_names(), read_script_file(), and set_to_default().

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

Enable design – if false, a RestrictToRepacking task will be added to the TaskFactory.

Referenced by determine_default_relax_script(), parse_my_tag(), set_enable_design(), 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().

bool protocols::relax::FastRelax::movemap_disables_packing_of_fixed_chi_positions_ = false
private

Option to have the MoveMap disable packing at positions where sidechain minimization is disabled.

Defaults to false.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)

Referenced by movemap_disables_packing_of_fixed_chi_positions(), parse_my_tag(), set_movemap_disables_packing_of_fixed_chi_positions(), set_to_default(), and setup_local_tf().

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 batch_apply(), inner_loop_ramp_repack_min_command(), 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 batch_apply(), inner_loop_ramp_repack_min_command(), and set_to_default().

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

Reject ramady changes perturbing structure more than this amount.

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

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

Allow Chi angles to move ?

Referenced by 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(), inner_loop_accept_to_best_command(), 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: