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protocols::forge::remodel::RemodelMover Class Reference

#include <RemodelMover.hh>

Inheritance diagram for protocols::forge::remodel::RemodelMover:
Inheritance graph
[legend]

Classes

struct  instruction_flags
 

Public Types

typedef std::string String
 
typedef core::Real Real
 
typedef core::Size Size
 
typedef
core::pack::task::TaskFactoryOP 
TaskFactoryOP
 
typedef core::pose::Pose Pose
 
typedef
core::scoring::ScoreFunction 
ScoreFunction
 
typedef
core::scoring::ScoreFunctionOP 
ScoreFunctionOP
 
typedef
protocols::forge::build::BuildInstructionOP 
BuildInstructionOP
 
typedef
protocols::forge::build::BuildManager 
BuildManager
 
typedef
protocols::forge::build::BuildManager::Original2Modified 
Original2Modified
 
typedef
protocols::forge::build::Interval 
Interval
 
typedef protocols::moves::MoverOP MoverOP
 
typedef
protocols::forge::components::VarLengthBuildOP 
VarLengthBuildOP
 
typedef
protocols::forge::components::VarLengthBuild 
VarLengthBuild
 
typedef
protocols::forge::remodel::RemodelData 
RemodelData
 
typedef
protocols::forge::remodel::RemodelWorkingSet 
RemodelWorkingSet
 
typedef std::pair< Interval,
String
OriginalInterval2DesignString
 A pair storing a instruction's original interval and a string denoting the sequence during design. More...
 
typedef utility::vector1
< OriginalInterval2DesignString
DesignInfo
 
typedef utility::tag::TagCOP TagCOP
 
typedef basic::datacache::DataMap DataMap
 
- 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
 

Public Member Functions

 RemodelMover ()
 default constructor More...
 
 RemodelMover (RemodelMover const &rval)
 copy constructor More...
 
 ~RemodelMover () override
 default destructor More...
 
MoverOP clone () const override
 clone this object, for parser More...
 
MoverOP fresh_instance () const override
 create this type of object, for parser More...
 
virtual MoverOP clone ()
 clone this object More...
 
virtual MoverOP fresh_instance ()
 create this type of object More...
 
ScoreFunction const & centroid_scorefunction () const
 the centroid level score function, default "remodel_cen" More...
 
ScoreFunction const & fullatom_scorefunction () const
 the full-atom level score function More...
 
void max_linear_chainbreak (Real const threshold)
 add instruction to the manager of this RemodelMover (no copy) More...
 
void centroid_loop_mover_str (String const &loop_mover_str)
 the loop mover string to use during centroid build More...
 
void redesign_loop_neighborhood (bool const flag)
 redesign the neighborhood around the loop? if false, then just repacks during the design phase More...
 
void dr_cycles (core::Size const cycles)
 set the number of design-refine cycles to perform More...
 
void centroid_scorefunction (ScoreFunction const &sfx)
 set the centroid level score function More...
 
void centroid_scorefunction (ScoreFunctionOP const &sfx)
 set the centroid level score function More...
 
void fullatom_scorefunction (ScoreFunction const &sfx)
 set the full-atom level score function More...
 
void fullatom_scorefunction (ScoreFunctionOP const &sfx)
 set the full-atom level score function More...
 
void apply (Pose &pose) override
 apply defined moves to given Pose More...
 
bool confirm_sequence (core::pose::Pose &pose)
 As best as I can tell, does some loop closure and calculates RMSD to native. Returns true. NOTE: CURRENTLY ALWAYS RETURNS TRUE regardless of rmsd value, because this stage is not being used as a filter Checks the value of -remodel::swap_refine_confirm_protocols. More...
 
void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data) override
 parse xml More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. 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...
 
virtual bool mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Static Public Member Functions

static String neighborhood_calc_name ()
 the name for the loops' neighborhood calculator More...
 
static String loops_buns_polar_calc_name ()
 the name for the loops' buried unsatisfied polars calculator More...
 
static String neighborhood_buns_polar_calc_name ()
 the name for the loops' neighborhood buried unsatisfied polars calculator More...
 
static std::string mover_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
- 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...
 

Private Types

typedef protocols::moves::Mover Super
 

Private Member Functions

RemodelMoveroperator= (RemodelMover const &rval)
 copy assignment More...
 
forge::remodel::RemodelData setup_remodel_data_for_loop_btw_parametric_components (core::pose::Pose &pose)
 sets up remodel data for combining blueprint with parametric mode More...
 
bool SamePose (Pose const &pose1, Pose const &pose2)
 Apply method for Mover. Checks the values of the following options -remodel::checkpoint -remodel::domainFusion::insert_segment_from_pdb -remodel::bypass_fragments, -remodel::num_trajectory, -remodel::repeat_structure -remodel::build_disulf -remodel::quick_and_dirty -remodel::use_pose_relax -remodel::run_confirmation -enzdes::cstfile -symmetry::symmetry_definition -run::show_simulation_in_pymol. More...
 
void register_user_options ()
 Checks for presence of any score term weight override options and calls set_weight on the centroid scorefunction. Note: options only get applied to centroid scorefunction - fullatom scorefunction left as is. More...
 
bool centroid_build (Pose &pose, protocols::forge::build::BuildManager &manager)
 get_name function for JobDistributor More...
 
bool centroid_build (Pose &pose)
 run the centroid level build stage More...
 
bool design_refine_seq_relax (Pose &pose, RemodelDesignMover &designMover)
 Sets up constraints and a modified scorefunction and run design/relax cycles. Checks the value of -remodel:repeat_structure. More...
 
bool design_refine_cart_relax (Pose &pose, RemodelDesignMover &designMover)
 
bool design_refine (Pose &pose, RemodelDesignMover &designMover)
 run the design-refine stage More...
 
TaskFactoryOP generic_taskfactory ()
 return a TaskFactory useable as a starting point for either design or refinement More...
 
void process_continuous_design_string (Interval const &original_interval, String const &design_str, Original2Modified const &original2modified_interval_endpoints, TaskFactoryOP design_tf)
 process a continuous design string, adding appropriate operations to the TaskFactory More...
 
void process_insert_design_string (Interval const &original_interval, String const &design_str, Original2Modified const &original2modified_interval_endpoints, TaskFactoryOP design_tf)
 process a design string containing an insert, adding appropriate operations to the TaskFactory More...
 
void set_param_from_options ()
 

Static Private Member Functions

static utility::vector1< bool >
const & 
allowed_surface_aa ()
 return a boolean vector specifying allowed a.a. when designing on the surface More...
 

Private Attributes

BuildManager manager_
 the BuildManager More...
 
Pose native_pose_
 
RemodelData remodel_data_
 holds all the blueprint info, contains build manager More...
 
RemodelWorkingSet working_model_
 working set holds all the modified index that is required for the remodeling task More...
 
DesignInfo design_info_
 Stores instructions' original interval and a string denoting the sequence during design. More...
 
Real max_linear_chainbreak_
 use sequence biased fragments when building the loop? (default false) bool use_sequence_bias_; More...
 
String centroid_loop_mover_str_
 the loop mover string to use during centroid build (default "RemodelLoopMover") More...
 
bool redesign_loop_neighborhood_
 redesign the neighborhood around the loop? if false, then just repacks during the design phase (default true) More...
 
core::Size dr_cycles_
 name of the resfile to use during design-refine; empty string implies no resfile String resfile_; More...
 
ScoreFunctionOP centroid_sfx_
 the centroid scorefunction to use, default "remodel_cen" More...
 
ScoreFunctionOP fullatom_sfx_
 the full-atom scorefunction to use More...
 
String blueprint_
 
bool rosetta_scripts_quick_and_dirty_
 
bool rosetta_scripts_build_disulfide_
 
bool rosetta_scripts_fast_disulfide_
 
bool rosetta_scripts_bypass_fragments_
 
core::Real rosetta_scripts_match_rt_limit_
 
core::Size rosetta_scripts_min_disulfides_
 
core::Size rosetta_scripts_max_disulfides_
 
bool rosetta_scripts_include_current_ds_
 
bool rosetta_scripts_keep_current_ds_
 
core::Size rosetta_scripts_min_loop_
 
bool rosetta_scripts_
 
core::pose::PoseOP last_input_pose_
 
forge::remodel::RemodelAccumulator accumulator_
 
bool relax_bb_for_disulf_
 
bool use_match_rt_
 
bool use_disulf_fa_score_
 
core::Real disulf_fa_max_
 
VarLengthBuildOP vlb_
 VLB for centroid_build. More...
 

Additional Inherited Members

- 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...
 

Member Typedef Documentation

typedef basic::datacache::DataMap protocols::forge::remodel::RemodelMover::DataMap

A pair storing a instruction's original interval and a string denoting the sequence during design.

Remarks
This is only for instructions such as SegmentRebuild or SegmentInsert. Non-applicable instructions will not have any data stored here.

Constructor & Destructor Documentation

protocols::forge::remodel::RemodelMover::RemodelMover ( )
protocols::forge::remodel::RemodelMover::RemodelMover ( RemodelMover const &  rval)

copy constructor

Copy constructor.

References vlb_.

protocols::forge::remodel::RemodelMover::~RemodelMover ( )
overridedefault

default destructor

Default destructor. Does this need to free the VarLengthBuild memory?

Member Function Documentation

utility::vector1< bool > const & protocols::forge::remodel::RemodelMover::allowed_surface_aa ( )
staticprivate

return a boolean vector specifying allowed a.a. when designing on the surface

References core::chemical::aa_from_oneletter_code().

Referenced by process_continuous_design_string(), and process_insert_design_string().

void protocols::forge::remodel::RemodelMover::apply ( Pose pose)
overridevirtual

apply defined moves to given Pose

Implements protocols::moves::Mover.

References core::chemical::aa_from_oneletter_code(), accumulator_, protocols::viewer::add_conformation_viewer(), protocols::symmetry::SetupNCSMover::add_group(), core::pose::add_lower_terminus_type_to_pose_residue(), core::pose::add_score_line_string(), protocols::forge::remodel::RemodelGlobalFrame::align_segment(), core::pose::Pose::append_residue_by_bond(), protocols::score_filters::ScoreTypeFilter::apply(), protocols::symmetry::SetupForSymmetryMover::apply(), protocols::forge::remodel::RemodelAccumulator::apply(), protocols::forge::remodel::RemodelGlobalFrame::apply(), protocols::forge::remodel::RemodelDesignMover::apply(), protocols::symmetry::SetupNCSMover::apply(), core::scoring::atom_pair_constraint, protocols::forge::remodel::RemodelData::blueprint, blueprint_, core::scoring::CA_rmsd(), core::scoring::cart_bonded_angle, core::scoring::cart_bonded_length, core::scoring::cart_bonded_torsion, core::scoring::cen_hb, centroid_build(), centroid_sfx_, core::chemical::CENTROID_t, protocols::forge::remodel::RemodelAccumulator::clear(), protocols::forge::remodel::RemodelAccumulator::cluster_switch(), protocols::forge::remodel::RemodelAccumulator::clustered_best_poses(), protocols::forge::remodel::RemodelData::collectInsertionPose(), protocols::score_filters::ScoreTypeFilter::compute(), confirm_sequence(), core::pose::Pose::conformation(), protocols::forge::remodel::RemodelAccumulator::contents_in_pose_store(), core::scoring::coordinate_constraint, core::conformation::ResidueFactory::create_residue(), core::id::D, core::pose::Pose::delete_residue_range_slow(), core::conformation::Conformation::delete_residue_slow(), design_refine(), design_refine_cart_relax(), design_refine_seq_relax(), core::scoring::dihedral_constraint, disulf_fa_max_, protocols::simple_filters::dssp(), core::scoring::dssp::Dssp::dssp_reduced(), protocols::forge::build::BuildManager::dummy_modify(), core::pose::Pose::dump_pdb(), core::sequence::end, core::pose::datacache::ENZDES_OBSERVER, protocols::moves::FAIL_DO_NOT_RETRY, protocols::moves::FAIL_RETRY, protocols::forge::remodel::RemodelDesignMover::find_disulfides_in_the_neighborhood(), core::pose::Pose::fold_tree(), core::chemical::FULL_ATOM_t, fullatom_sfx_, protocols::toolbox::match_enzdes_util::get_enzdes_observer(), core::pose::get_restype_for_pose(), core::scoring::get_score_function(), protocols::forge::remodel::RemodelData::getLoopsToBuildFromBlueprint(), protocols::forge::remodel::RemodelData::getLoopsToBuildFromFile(), core::scoring::hbond_lr_bb, core::scoring::hbond_sr_bb, core::conformation::Conformation::insert_ideal_geometry_at_polymer_bond(), core::scoring::dssp::Dssp::insert_ss_into_pose(), last_input_pose_, loops_buns_polar_calc_name(), protocols::forge::remodel::RemodelDesignMover::make_disulfide(), protocols::forge::remodel::RemodelDesignMover::make_disulfide_fast(), protocols::forge::remodel::RemodelWorkingSet::manager, manager_, core::pose::Pose::metric(), protocols::forge::remodel::RemodelLigandHandler::minimize(), protocols::forge::build::BuildManager::modify(), protocols::forge::build::BuildManager::movemap(), protocols::moves::MS_SUCCESS, core::chemical::name_from_aa(), native_pose_, protocols::forge::remodel::RemodelData::natro_movemap_, neighborhood_buns_polar_calc_name(), neighborhood_calc_name(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::observer_cache(), protocols::forge::remodel::RemodelGlobalFrame::omega(), core::scoring::omega, core::pose::Pose::omega(), core::pose::Pose::pdb_info(), core::pose::Pose::phi(), protocols::forge::remodel::RemodelAccumulator::pop(), core::pose::Pose::psi(), protocols::forge::remodel::RemodelGlobalFrame::radius(), protocols::forge::remodel::RemodelAccumulator::recover_checkpoint(), protocols::forge::remodel::recursive_multiple_disulfide_former(), relax_bb_for_disulf_, remodel_data_, core::pose::remove_lower_terminus_type_from_pose_residue(), core::pose::remove_upper_terminus_type_from_pose_residue(), core::pose::renumber_pdbinfo_based_on_conf_chains(), core::kinematics::FoldTree::reorder(), core::pose::replace_pose_residue_copying_existing_coordinates(), core::scoring::res_type_constraint, core::scoring::res_type_linking_constraint, core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::residue_type_set_for_pose(), protocols::forge::remodel::RemodelGlobalFrame::rise(), rosetta_scripts_, rosetta_scripts_build_disulfide_, rosetta_scripts_bypass_fragments_, rosetta_scripts_fast_disulfide_, rosetta_scripts_include_current_ds_, rosetta_scripts_keep_current_ds_, rosetta_scripts_match_rt_limit_, rosetta_scripts_max_disulfides_, rosetta_scripts_min_disulfides_, rosetta_scripts_min_loop_, rosetta_scripts_quick_and_dirty_, protocols::forge::remodel::RemodelWorkingSet::safe_root_, core::conformation::Conformation::safely_append_polymer_residue_after_seqpos(), SamePose(), protocols::hybridization::score, protocols::forge::remodel::RemodelDesignMover::scorefunction(), core::pose::Pose::secstruct(), protocols::forge::remodel::RemodelData::sequence, core::pose::datacache::ObserverCache::set(), protocols::moves::Mover::set_last_move_status(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), core::pose::Pose::set_secstruct(), protocols::forge::remodel::RemodelDesignMover::set_state(), setup_remodel_data_for_loop_btw_parametric_components(), protocols::forge::remodel::RemodelAccumulator::size(), protocols::forge::build::BuildManager::size(), core::pose::Pose::size(), core::pose::Pose::split_by_chain(), core::util::switch_to_residue_type_set(), core::id::THETA, core::id::to_string(), core::pose::Pose::total_residue(), core::scoring::total_score, protocols::forge::remodel::TR(), protocols::forge::build::BuildManager::union_of_intervals_containing_undefined_positions(), protocols::forge::remodel::RemodelData::updateWithDsspAssignment(), use_disulf_fa_score_, use_match_rt_, core::io::RemarkInfo::value, working_model_, protocols::forge::remodel::RemodelWorkingSet::workingSetGen(), and protocols::forge::remodel::RemodelAccumulator::write_checkpoint().

bool protocols::forge::remodel::RemodelMover::centroid_build ( Pose pose,
protocols::forge::build::BuildManager manager 
)
private
bool protocols::forge::remodel::RemodelMover::centroid_build ( Pose pose)
private
void protocols::forge::remodel::RemodelMover::centroid_loop_mover_str ( String const &  loop_mover_str)
inline

the loop mover string to use during centroid build

Remarks
set to either a string the create_loop_mover() LoopMoverFactory recognizes or the "RemodelLoopMover"

References centroid_loop_mover_str_.

ScoreFunction const & protocols::forge::remodel::RemodelMover::centroid_scorefunction ( ) const

the centroid level score function, default "remodel_cen"

References centroid_sfx_.

void protocols::forge::remodel::RemodelMover::centroid_scorefunction ( ScoreFunction const &  sfx)

set the centroid level score function

References centroid_sfx_, and core::scoring::ScoreFunction::clone().

void protocols::forge::remodel::RemodelMover::centroid_scorefunction ( ScoreFunctionOP const &  sfx)

set the centroid level score function

References centroid_sfx_.

RemodelMover::MoverOP protocols::forge::remodel::RemodelMover::clone ( ) const
overridevirtual

clone this object, for parser

clone for parser

Reimplemented from protocols::moves::Mover.

RemodelMover::MoverOP protocols::forge::remodel::RemodelMover::clone ( )
virtual

clone this object

bool protocols::forge::remodel::RemodelMover::confirm_sequence ( core::pose::Pose pose)
bool protocols::forge::remodel::RemodelMover::design_refine ( Pose pose,
RemodelDesignMover designMover 
)
private

run the design-refine stage

Run the design-refine stage. Checks the value of -remodel:repeat_structure and -remodel:swap_refine_confirm_protocols NOTE: CURRENTLY ALWAYS RETURNS TRUE regardless of if chain breaks test passes or fails.

Returns
currently always true

References protocols::forge::remodel::RemodelDesignMover::apply(), core::scoring::atom_pair_constraint, core::pack::dunbrack::c, core::scoring::Energies::clear(), core::scoring::coordinate_constraint, core::scoring::dihedral_constraint, dr_cycles_, core::pose::Pose::dump_pdb(), core::pose::Pose::energies(), core::pose::Pose::fold_tree(), protocols::loops::fold_tree_from_loops(), generic_taskfactory(), core::kinematics::MoveMap::get_chi(), core::scoring::get_score_function(), protocols::forge::build::BuildManager::intervals_containing_undefined_positions(), protocols::forge::methods::intervals_to_loops(), core::conformation::Residue::is_DNA(), protocols::loops::loop_mover::KIC(), protocols::forge::methods::linear_chainbreak(), manager_, max_linear_chainbreak_, protocols::forge::build::BuildManager::movemap(), protocols::forge::remodel::RemodelData::natro_movemap_, neighborhood_calc_name(), protocols::forge::build::BuildManager::original2modified_interval_endpoints(), remodel_data_, protocols::loops::remove_cutpoint_variants(), core::pose::Pose::residue(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), protocols::forge::remodel::RemodelDesignMover::set_state(), core::pose::Pose::size(), and protocols::forge::remodel::TR().

Referenced by apply().

bool protocols::forge::remodel::RemodelMover::design_refine_cart_relax ( Pose pose,
RemodelDesignMover designMover 
)
private
bool protocols::forge::remodel::RemodelMover::design_refine_seq_relax ( Pose pose,
RemodelDesignMover designMover 
)
private
void protocols::forge::remodel::RemodelMover::dr_cycles ( core::Size const  cycles)
inline

set the number of design-refine cycles to perform

Remarks
set this to 0 to skip design-refine

References dr_cycles_.

RemodelMover::MoverOP protocols::forge::remodel::RemodelMover::fresh_instance ( ) const
overridevirtual

create this type of object, for parser

fresh instance for parser

Reimplemented from protocols::moves::Mover.

RemodelMover::MoverOP protocols::forge::remodel::RemodelMover::fresh_instance ( )
virtual

create this type of object

ScoreFunction const & protocols::forge::remodel::RemodelMover::fullatom_scorefunction ( ) const

the full-atom level score function

References fullatom_sfx_.

void protocols::forge::remodel::RemodelMover::fullatom_scorefunction ( ScoreFunction const &  sfx)

set the full-atom level score function

References core::scoring::ScoreFunction::clone(), and fullatom_sfx_.

void protocols::forge::remodel::RemodelMover::fullatom_scorefunction ( ScoreFunctionOP const &  sfx)

set the full-atom level score function

References fullatom_sfx_.

RemodelMover::TaskFactoryOP protocols::forge::remodel::RemodelMover::generic_taskfactory ( )
private

return a TaskFactory useable as a starting point for either design or refinement

Returns a TaskFactory useable as a starting point for either design or refinement. Only adds the NoRepackDisulfides, IncludeCurrent, and Init from command line ops. ReadResfile is not included.

Referenced by confirm_sequence(), and design_refine().

std::string protocols::forge::remodel::RemodelMover::get_name ( ) const
overridevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

References mover_name().

static String protocols::forge::remodel::RemodelMover::loops_buns_polar_calc_name ( )
inlinestatic

the name for the loops' buried unsatisfied polars calculator

Referenced by apply().

void protocols::forge::remodel::RemodelMover::max_linear_chainbreak ( Real const  threshold)
inline

add instruction to the manager of this RemodelMover (no copy)

Parameters
[in]biBuildInstruction
[in]aa_during_design_refineThe allowed amino acid sequence during design. Only applicable to BuildInstructions like SegmentRebuild and SegmentInsert. Make sure the length of this string matches up properly, and remember to use any special characters, e.g. the insertion character for SegmentInsert the maximum allowed linear chainbreak

References max_linear_chainbreak_.

std::string protocols::forge::remodel::RemodelMover::mover_name ( )
static
static String protocols::forge::remodel::RemodelMover::neighborhood_buns_polar_calc_name ( )
inlinestatic

the name for the loops' neighborhood buried unsatisfied polars calculator

Referenced by apply().

static String protocols::forge::remodel::RemodelMover::neighborhood_calc_name ( )
inlinestatic

the name for the loops' neighborhood calculator

Referenced by apply(), confirm_sequence(), and design_refine().

RemodelMover& protocols::forge::remodel::RemodelMover::operator= ( RemodelMover const &  rval)
private

copy assignment

Remarks
Mover base class prevents this from working properly...
void protocols::forge::remodel::RemodelMover::parse_my_tag ( TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
void protocols::forge::remodel::RemodelMover::process_continuous_design_string ( Interval const &  original_interval,
String const &  design_str,
Original2Modified const &  original2modified_interval_endpoints,
TaskFactoryOP  design_tf 
)
private

process a continuous design string, adding appropriate operations to the TaskFactory

References core::chemical::aa_from_oneletter_code(), allowed_surface_aa(), and protocols::forge::build::Interval::left.

void protocols::forge::remodel::RemodelMover::process_insert_design_string ( Interval const &  original_interval,
String const &  design_str,
Original2Modified const &  original2modified_interval_endpoints,
TaskFactoryOP  design_tf 
)
private
void protocols::forge::remodel::RemodelMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::forge::remodel::RemodelMover::redesign_loop_neighborhood ( bool const  flag)
inline

redesign the neighborhood around the loop? if false, then just repacks during the design phase

References redesign_loop_neighborhood_.

void protocols::forge::remodel::RemodelMover::register_user_options ( )
private

Checks for presence of any score term weight override options and calls set_weight on the centroid scorefunction. Note: options only get applied to centroid scorefunction - fullatom scorefunction left as is.

References core::scoring::cbeta, core::scoring::cenpack, centroid_sfx_, core::scoring::hbond_lr_bb, core::scoring::hbond_sr_bb, core::scoring::rama, core::scoring::rg, core::scoring::rg_local, core::scoring::rsigma, core::scoring::ss_pair, protocols::forge::remodel::TR(), and core::scoring::vdw.

Referenced by RemodelMover().

bool protocols::forge::remodel::RemodelMover::SamePose ( Pose const &  pose1,
Pose const &  pose2 
)
private

Apply method for Mover. Checks the values of the following options -remodel::checkpoint -remodel::domainFusion::insert_segment_from_pdb -remodel::bypass_fragments, -remodel::num_trajectory, -remodel::repeat_structure -remodel::build_disulf -remodel::quick_and_dirty -remodel::use_pose_relax -remodel::run_confirmation -enzdes::cstfile -symmetry::symmetry_definition -run::show_simulation_in_pymol.

References core::pose::Pose::omega(), core::pose::Pose::phi(), core::pose::Pose::psi(), and core::pose::Pose::size().

Referenced by apply().

void protocols::forge::remodel::RemodelMover::set_param_from_options ( )
private
forge::remodel::RemodelData protocols::forge::remodel::RemodelMover::setup_remodel_data_for_loop_btw_parametric_components ( core::pose::Pose pose)
private

sets up remodel data for combining blueprint with parametric mode

References blueprint_, protocols::simple_filters::dssp(), core::scoring::dssp::Dssp::dssp_reduced(), core::pose::Pose::split_by_chain(), and protocols::forge::remodel::TR().

Referenced by apply().

Member Data Documentation

forge::remodel::RemodelAccumulator protocols::forge::remodel::RemodelMover::accumulator_
private

Referenced by apply().

String protocols::forge::remodel::RemodelMover::blueprint_
private
String protocols::forge::remodel::RemodelMover::centroid_loop_mover_str_
private

the loop mover string to use during centroid build (default "RemodelLoopMover")

Remarks
set to either a string the create_loop_mover() LoopMoverFactory recognizes or the "RemodelLoopMover"

Referenced by centroid_build(), centroid_loop_mover_str(), and RemodelMover().

ScoreFunctionOP protocols::forge::remodel::RemodelMover::centroid_sfx_
private

the centroid scorefunction to use, default "remodel_cen"

Referenced by apply(), centroid_build(), centroid_scorefunction(), register_user_options(), and RemodelMover().

DesignInfo protocols::forge::remodel::RemodelMover::design_info_
private

Stores instructions' original interval and a string denoting the sequence during design.

Remarks
This is only for instructions such as SegmentRebuild or SegmentInsert. Non-applicable instructions will not have any data stored here.
core::Real protocols::forge::remodel::RemodelMover::disulf_fa_max_
private

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

core::Size protocols::forge::remodel::RemodelMover::dr_cycles_
private

name of the resfile to use during design-refine; empty string implies no resfile String resfile_;

the number of design-refine cycles to perform, default 3

Referenced by design_refine(), design_refine_cart_relax(), design_refine_seq_relax(), dr_cycles(), and RemodelMover().

ScoreFunctionOP protocols::forge::remodel::RemodelMover::fullatom_sfx_
private

the full-atom scorefunction to use

Referenced by apply(), confirm_sequence(), fullatom_scorefunction(), and RemodelMover().

core::pose::PoseOP protocols::forge::remodel::RemodelMover::last_input_pose_
private

Referenced by apply(), and RemodelMover().

BuildManager protocols::forge::remodel::RemodelMover::manager_
private
Real protocols::forge::remodel::RemodelMover::max_linear_chainbreak_
private

use sequence biased fragments when building the loop? (default false) bool use_sequence_bias_;

the maximum allowed linear chainbreak (default 0.07)

Referenced by centroid_build(), design_refine(), max_linear_chainbreak(), and RemodelMover().

Pose protocols::forge::remodel::RemodelMover::native_pose_
private

Referenced by apply(), and confirm_sequence().

bool protocols::forge::remodel::RemodelMover::redesign_loop_neighborhood_
private

redesign the neighborhood around the loop? if false, then just repacks during the design phase (default true)

Referenced by redesign_loop_neighborhood(), and RemodelMover().

bool protocols::forge::remodel::RemodelMover::relax_bb_for_disulf_
private

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

RemodelData protocols::forge::remodel::RemodelMover::remodel_data_
private

holds all the blueprint info, contains build manager

Referenced by apply(), centroid_build(), confirm_sequence(), design_refine(), and design_refine_cart_relax().

bool protocols::forge::remodel::RemodelMover::rosetta_scripts_
private

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

bool protocols::forge::remodel::RemodelMover::rosetta_scripts_build_disulfide_
private

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

bool protocols::forge::remodel::RemodelMover::rosetta_scripts_bypass_fragments_
private
bool protocols::forge::remodel::RemodelMover::rosetta_scripts_fast_disulfide_
private
bool protocols::forge::remodel::RemodelMover::rosetta_scripts_include_current_ds_
private

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

bool protocols::forge::remodel::RemodelMover::rosetta_scripts_keep_current_ds_
private

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

core::Real protocols::forge::remodel::RemodelMover::rosetta_scripts_match_rt_limit_
private

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

core::Size protocols::forge::remodel::RemodelMover::rosetta_scripts_max_disulfides_
private

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

core::Size protocols::forge::remodel::RemodelMover::rosetta_scripts_min_disulfides_
private

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

core::Size protocols::forge::remodel::RemodelMover::rosetta_scripts_min_loop_
private

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

bool protocols::forge::remodel::RemodelMover::rosetta_scripts_quick_and_dirty_
private

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

bool protocols::forge::remodel::RemodelMover::use_disulf_fa_score_
private

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

bool protocols::forge::remodel::RemodelMover::use_match_rt_
private

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

VarLengthBuildOP protocols::forge::remodel::RemodelMover::vlb_
private

VLB for centroid_build.

Remarks
Store it here instead of re-instantiation each centroid_build() call so fragment caching works.
Warning
Remember to set this to null if the BuildManager changes.

Referenced by centroid_build(), and RemodelMover().

RemodelWorkingSet protocols::forge::remodel::RemodelMover::working_model_
private

working set holds all the modified index that is required for the remodeling task

Referenced by apply(), and centroid_build().


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