Rosetta 3.4
Public Types | Public Member Functions
protocols::match::MatcherTask Class Reference

#include <MatcherTask.hh>

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List of all members.

Public Types

typedef core::Real Real
typedef core::Size Size
typedef core::Vector Vector
typedef
numeric::geometry::BoundingBox
< Vector
BoundingBox

Public Member Functions

 MatcherTask ()
 Construction and Destruction.
 MatcherTask (MatcherTask const &other)
MatcherTask const & operator= (MatcherTask const &rhs)
virtual ~MatcherTask ()
void set_upstream_pose (core::pose::Pose const &pose)
 Setup.
void set_downstream_pose (core::pose::Pose const &input_pose)
void set_downstream_pose (core::pose::Pose const &pose, utility::vector1< core::id::AtomID > const &orientation_atoms)
void set_downstream_orientation_atoms (utility::vector1< core::id::AtomID > const &orientation_atoms)
void set_enumerate_ligand_rotamers (bool setting)
void set_only_enumerate_non_match_redundant_ligand_rotamers (bool setting)
void clear_downstream_orientation_atoms ()
void set_original_scaffold_build_points (utility::vector1< Size > const &resids)
 Uniformly consider the same set of build points for each of the geometric constrains.
void modify_pose_build_resids_from_endes_input ()
 modify the match positions according to what is specified in the cstfile
void use_different_build_points_for_each_geometric_constraint (Size n_geometric_constraints)
 Set up the task so that it keeps different backbone build points for each geometric constraint -- the task then needs to know how many geometric constraints there are.
void set_original_scaffold_build_points_for_geometric_constraint (Size geom_cst_id, utility::vector1< Size > const &resids)
 Set the build point id's for a particular geometric constraint.
void define_active_site_from_gridlig_file (std::string const &file_name)
void define_active_site_from_residue_radii_list ()
void append_upstream_resiue_as_defining_active_site (Size resid, Real radius)
void append_downstream_atom_to_active_site_required_list (core::id::AtomID atid)
void set_occupied_space_bounding_box (BoundingBox const &bb)
 Set the bounding box for the region of space that the OccupiedSpaceHash should accept hits in side of. If the 3rd orientation atom of the downstream partner is outside of this bounding box, the hit will be rejected out of hand.
void set_hash_euclidean_bin_width (Real width)
 For the occupied space hash, set the euclidean-bin width to a uniform value for xy&z.
void set_hash_euler_bin_width (Real width)
 For the occupeid space hash, set the euler-bin width to a uniform value for phi,psi&theta.
void set_permitted_overlap (Real permitted_overlap)
 For collision detection, select the amount of collision that should be tolerated between heavy atoms. This should be a positive value in Angstroms.
void initialize_from_command_line ()
 Initialize many parameters from the command line options.
void consolidate_matches (bool setting)
 Matches may either be output as soon as they are generated, or they may be consolidated. When consolidating matches, the MatchProcessor (the MatchEvaluator) waits until all matches are seen before outputting any; it groups matches and selects the top N matches from each group to output. This can require a lot of memory if there are very many possible matches. MatchConsolidation is on by default.
void n_to_output_per_group (Size setting)
 For use with the match consolidator; specify the number of output matches that the consolidator should select for each group.
void add_filter (std::string const &filter_name)
 Add a filter by name to the set of filters being included. If that filter requires extra data (as, for example, the UpstreamCollisionFilter) then the task should be expanded to include all the data necessary to create and initialize that filter. No valid options currently.
void grouper_name (std::string const &setting)
 Specify the name of the match-consolidator related match-grouper class. This class will group matches together; the consolidator will then pick the top N from each group for output. Valid options include: SameChiBinComboGrouper, SameSequenceGrouper, and SameRotamerComboGrouper.
void evaluator_name (std::string const &setting)
 Specify the name of the match-consolidator related match-evaluator class. This class will rank each of the matches so that the consolidator may pick the top N. Valid options include: DownstreamRMSEvaluator. More evaluator options will be implemented shortly.
void output_writer_name (std::string const &setting)
 Specify the name of the class that will write the output. Valid options include: KinWriter. More output options will be implemented shortly.
void output_file_name (std::string const &setting)
 Indicate the name of the single output file to which the matches will be written.
void set_enz_input_data (toolbox::match_enzdes_util::EnzConstraintIOCOP data)
 Set the matcher-file input data. The Matcher will read this data when initializing itself.
void filter_upstream_residue_collisions (bool setting)
void filter_upstream_collisions_by_score (bool setting)
void upstream_residue_collision_tolerance (Real setting)
void upstream_residue_collision_score_cutoff (Real setting)
void upstream_residue_collision_Wfa_atr (Real setting)
void upstream_residue_collision_Wfa_rep (Real setting)
void upstream_residue_collision_Wfa_sol (Real setting)
void filter_upstream_downstream_collisions (bool setting)
void filter_upstream_downstream_collisions_by_score (bool setting)
void upstream_downstream_atom_collision_tolerance (Real setting)
void upstream_downstream_residue_collision_score_cutoff (Real setting)
void upstream_downstream_residue_collision_Wfa_atr (Real setting)
void upstream_downstream_residue_collision_Wfa_rep (Real setting)
void upstream_downstream_residue_collision_Wfa_sol (Real setting)
void define_match_by_single_downstream_positioning (bool setting)
core::pose::PoseCOP upstream_pose () const
core::pose::PoseCOP downstream_pose () const
utility::vector1
< core::id::AtomID > const & 
downstream_orientation_atoms () const
bool enumerate_ligand_rotamers () const
bool only_enumerate_non_match_redundant_ligand_rotamers () const
utility::vector1< Size > const & upstream_pose_build_resids_for_geometric_constraint (Size cst_id) const
std::map< core::Size,
core::Size > const & 
upstream_only_geom_cst () const
bool gridlig_active_site_definition () const
 Define the active site through a gridlig file (true), or by listing residue/radii paris (false)?
std::string const & gridlig_file_name () const
 Accessor for the file name containing the active-site definition in gridlig format.
std::list< std::pair< Size,
Real > > const & 
upstream_resids_and_radii_defining_active_site () const
 Accessor for the data defining the active site by-residue. This data is only active if gridlig_active_site_definition() returns false.
std::list< core::id::AtomID >
const & 
downstream_atoms_required_inside_active_site () const
utility::vector1
< core::id::AtomID > const & 
relevant_downstream_atoms () const
BoundingBox const & occ_space_bounding_box () const
Vector euclidean_bin_widths () const
Vector euler_bin_widths () const
Real permitted_overlap () const
bool use_input_sc () const
bool dynamic_grid_refinement () const
bool consolidate_matches () const
Size n_to_output_per_group () const
std::list< std::string > const & filter_names () const
std::string const & upstream_pose_name () const
std::string const & cstfile_name () const
std::string const & grouper_name () const
std::string const & evaluator_name () const
std::string const & output_writer_name () const
std::string const & output_file_name () const
Real grouper_ds_rmsd () const
bool output_matchres_only () const
utility::vector1< core::Size >
const & 
geom_csts_downstream_output () const
toolbox::match_enzdes_util::EnzConstraintIOCOP enz_input_data () const
bool filter_upstream_residue_collisions () const
bool filter_upstream_collisions_by_score () const
Real upstream_residue_collision_tolerance () const
Real upstream_residue_collision_score_cutoff () const
Real upstream_residue_collision_Wfa_atr () const
Real upstream_residue_collision_Wfa_rep () const
Real upstream_residue_collision_Wfa_sol () const
bool filter_upstream_downstream_collisions () const
bool filter_upstream_downstream_collisions_by_score () const
Real upstream_downstream_atom_collision_tolerance () const
Real upstream_downstream_residue_collision_score_cutoff () const
Real upstream_downstream_residue_collision_Wfa_atr () const
Real upstream_downstream_residue_collision_Wfa_rep () const
Real upstream_downstream_residue_collision_Wfa_sol () const
bool define_match_by_single_downstream_positioning () const

Member Typedef Documentation

typedef numeric::geometry::BoundingBox< Vector > protocols::match::MatcherTask::BoundingBox

Constructor & Destructor Documentation

protocols::match::MatcherTask::MatcherTask ( )

Construction and Destruction.

protocols::match::MatcherTask::MatcherTask ( MatcherTask const &  other)
protocols::match::MatcherTask::~MatcherTask ( ) [virtual]

Member Function Documentation

void protocols::match::MatcherTask::add_filter ( std::string const &  filter_name)

Add a filter by name to the set of filters being included. If that filter requires extra data (as, for example, the UpstreamCollisionFilter) then the task should be expanded to include all the data necessary to create and initialize that filter. No valid options currently.

void protocols::match::MatcherTask::append_downstream_atom_to_active_site_required_list ( core::id::AtomID  atid)
void protocols::match::MatcherTask::append_upstream_resiue_as_defining_active_site ( Size  resid,
Real  radius 
)
void protocols::match::MatcherTask::clear_downstream_orientation_atoms ( )
void protocols::match::MatcherTask::consolidate_matches ( bool  setting)

Matches may either be output as soon as they are generated, or they may be consolidated. When consolidating matches, the MatchProcessor (the MatchEvaluator) waits until all matches are seen before outputting any; it groups matches and selects the top N matches from each group to output. This can require a lot of memory if there are very many possible matches. MatchConsolidation is on by default.

Referenced by protocols::match::Matcher::initialize_from_task().

bool protocols::match::MatcherTask::consolidate_matches ( ) const
std::string const & protocols::match::MatcherTask::cstfile_name ( ) const
void protocols::match::MatcherTask::define_active_site_from_gridlig_file ( std::string const &  file_name)
void protocols::match::MatcherTask::define_active_site_from_residue_radii_list ( )
void protocols::match::MatcherTask::define_match_by_single_downstream_positioning ( bool  setting)
bool protocols::match::MatcherTask::define_match_by_single_downstream_positioning ( ) const
std::list< core::id::AtomID > const & protocols::match::MatcherTask::downstream_atoms_required_inside_active_site ( ) const
utility::vector1< core::id::AtomID > const & protocols::match::MatcherTask::downstream_orientation_atoms ( ) const
core::pose::PoseCOP protocols::match::MatcherTask::downstream_pose ( ) const
bool protocols::match::MatcherTask::dynamic_grid_refinement ( ) const
bool protocols::match::MatcherTask::enumerate_ligand_rotamers ( ) const
toolbox::match_enzdes_util::EnzConstraintIOCOP protocols::match::MatcherTask::enz_input_data ( ) const
MatcherTask::Vector protocols::match::MatcherTask::euclidean_bin_widths ( ) const
MatcherTask::Vector protocols::match::MatcherTask::euler_bin_widths ( ) const
std::string const & protocols::match::MatcherTask::evaluator_name ( ) const
void protocols::match::MatcherTask::evaluator_name ( std::string const &  setting)

Specify the name of the match-consolidator related match-evaluator class. This class will rank each of the matches so that the consolidator may pick the top N. Valid options include: DownstreamRMSEvaluator. More evaluator options will be implemented shortly.

std::list< std::string > const & protocols::match::MatcherTask::filter_names ( ) const
bool protocols::match::MatcherTask::filter_upstream_collisions_by_score ( ) const
void protocols::match::MatcherTask::filter_upstream_collisions_by_score ( bool  setting)
void protocols::match::MatcherTask::filter_upstream_downstream_collisions ( bool  setting)
bool protocols::match::MatcherTask::filter_upstream_downstream_collisions ( ) const
void protocols::match::MatcherTask::filter_upstream_downstream_collisions_by_score ( bool  setting)
bool protocols::match::MatcherTask::filter_upstream_downstream_collisions_by_score ( ) const
bool protocols::match::MatcherTask::filter_upstream_residue_collisions ( ) const
void protocols::match::MatcherTask::filter_upstream_residue_collisions ( bool  setting)
utility::vector1< core::Size > const & protocols::match::MatcherTask::geom_csts_downstream_output ( ) const
bool protocols::match::MatcherTask::gridlig_active_site_definition ( ) const

Define the active site through a gridlig file (true), or by listing residue/radii paris (false)?

Referenced by protocols::match::Matcher::initialize_from_task().

std::string const & protocols::match::MatcherTask::gridlig_file_name ( ) const

Accessor for the file name containing the active-site definition in gridlig format.

Referenced by protocols::match::Matcher::initialize_from_task().

MatcherTask::Real protocols::match::MatcherTask::grouper_ds_rmsd ( ) const
std::string const & protocols::match::MatcherTask::grouper_name ( ) const
void protocols::match::MatcherTask::grouper_name ( std::string const &  setting)

Specify the name of the match-consolidator related match-grouper class. This class will group matches together; the consolidator will then pick the top N from each group for output. Valid options include: SameChiBinComboGrouper, SameSequenceGrouper, and SameRotamerComboGrouper.

void protocols::match::MatcherTask::initialize_from_command_line ( )
void protocols::match::MatcherTask::modify_pose_build_resids_from_endes_input ( )

modify the match positions according to what is specified in the cstfile

References protocols::match::create_match_position_modifier(), core::io::pdb::split(), and protocols::match::TR().

Referenced by initialize_from_command_line().

MatcherTask::Size protocols::match::MatcherTask::n_to_output_per_group ( ) const
void protocols::match::MatcherTask::n_to_output_per_group ( Size  setting)

For use with the match consolidator; specify the number of output matches that the consolidator should select for each group.

MatcherTask::BoundingBox const & protocols::match::MatcherTask::occ_space_bounding_box ( ) const
bool protocols::match::MatcherTask::only_enumerate_non_match_redundant_ligand_rotamers ( ) const
MatcherTask const & protocols::match::MatcherTask::operator= ( MatcherTask const &  rhs)
std::string const & protocols::match::MatcherTask::output_file_name ( ) const
void protocols::match::MatcherTask::output_file_name ( std::string const &  setting)

Indicate the name of the single output file to which the matches will be written.

bool protocols::match::MatcherTask::output_matchres_only ( ) const
void protocols::match::MatcherTask::output_writer_name ( std::string const &  setting)

Specify the name of the class that will write the output. Valid options include: KinWriter. More output options will be implemented shortly.

std::string const & protocols::match::MatcherTask::output_writer_name ( ) const
MatcherTask::Real protocols::match::MatcherTask::permitted_overlap ( ) const
utility::vector1< core::id::AtomID > const & protocols::match::MatcherTask::relevant_downstream_atoms ( ) const
void protocols::match::MatcherTask::set_downstream_orientation_atoms ( utility::vector1< core::id::AtomID > const &  orientation_atoms)
void protocols::match::MatcherTask::set_downstream_pose ( core::pose::Pose const &  pose,
utility::vector1< core::id::AtomID > const &  orientation_atoms 
)
void protocols::match::MatcherTask::set_downstream_pose ( core::pose::Pose const &  input_pose)
void protocols::match::MatcherTask::set_enumerate_ligand_rotamers ( bool  setting)
void protocols::match::MatcherTask::set_enz_input_data ( toolbox::match_enzdes_util::EnzConstraintIOCOP  data)

Set the matcher-file input data. The Matcher will read this data when initializing itself.

void protocols::match::MatcherTask::set_hash_euclidean_bin_width ( Real  width)

For the occupied space hash, set the euclidean-bin width to a uniform value for xy&z.

void protocols::match::MatcherTask::set_hash_euler_bin_width ( Real  width)

For the occupeid space hash, set the euler-bin width to a uniform value for phi,psi&theta.

void protocols::match::MatcherTask::set_occupied_space_bounding_box ( BoundingBox const &  bb)

Set the bounding box for the region of space that the OccupiedSpaceHash should accept hits in side of. If the 3rd orientation atom of the downstream partner is outside of this bounding box, the hit will be rejected out of hand.

void protocols::match::MatcherTask::set_only_enumerate_non_match_redundant_ligand_rotamers ( bool  setting)
void protocols::match::MatcherTask::set_original_scaffold_build_points ( utility::vector1< Size > const &  resids)

Uniformly consider the same set of build points for each of the geometric constrains.

void protocols::match::MatcherTask::set_original_scaffold_build_points_for_geometric_constraint ( Size  geom_cst_id,
utility::vector1< Size > const &  resids 
)

Set the build point id's for a particular geometric constraint.

void protocols::match::MatcherTask::set_permitted_overlap ( Real  permitted_overlap)

For collision detection, select the amount of collision that should be tolerated between heavy atoms. This should be a positive value in Angstroms.

References permitted_overlap().

void protocols::match::MatcherTask::set_upstream_pose ( core::pose::Pose const &  pose)

Setup.

References core::pose::Pose::pdb_info().

void protocols::match::MatcherTask::upstream_downstream_atom_collision_tolerance ( Real  setting)
MatcherTask::Real protocols::match::MatcherTask::upstream_downstream_atom_collision_tolerance ( ) const
void protocols::match::MatcherTask::upstream_downstream_residue_collision_score_cutoff ( Real  setting)
MatcherTask::Real protocols::match::MatcherTask::upstream_downstream_residue_collision_score_cutoff ( ) const
void protocols::match::MatcherTask::upstream_downstream_residue_collision_Wfa_atr ( Real  setting)
MatcherTask::Real protocols::match::MatcherTask::upstream_downstream_residue_collision_Wfa_atr ( ) const
MatcherTask::Real protocols::match::MatcherTask::upstream_downstream_residue_collision_Wfa_rep ( ) const
void protocols::match::MatcherTask::upstream_downstream_residue_collision_Wfa_rep ( Real  setting)
void protocols::match::MatcherTask::upstream_downstream_residue_collision_Wfa_sol ( Real  setting)
MatcherTask::Real protocols::match::MatcherTask::upstream_downstream_residue_collision_Wfa_sol ( ) const
std::map< core::Size, core::Size > const & protocols::match::MatcherTask::upstream_only_geom_cst ( ) const
core::pose::PoseCOP protocols::match::MatcherTask::upstream_pose ( ) const
utility::vector1< core::Size > const & protocols::match::MatcherTask::upstream_pose_build_resids_for_geometric_constraint ( Size  cst_id) const
std::string const & protocols::match::MatcherTask::upstream_pose_name ( ) const
std::list< std::pair< MatcherTask::Size, MatcherTask::Real > > const & protocols::match::MatcherTask::upstream_resids_and_radii_defining_active_site ( ) const

Accessor for the data defining the active site by-residue. This data is only active if gridlig_active_site_definition() returns false.

Referenced by protocols::match::Matcher::initialize_from_task().

void protocols::match::MatcherTask::upstream_residue_collision_score_cutoff ( Real  setting)
MatcherTask::Real protocols::match::MatcherTask::upstream_residue_collision_score_cutoff ( ) const
void protocols::match::MatcherTask::upstream_residue_collision_tolerance ( Real  setting)
MatcherTask::Real protocols::match::MatcherTask::upstream_residue_collision_tolerance ( ) const
void protocols::match::MatcherTask::upstream_residue_collision_Wfa_atr ( Real  setting)
MatcherTask::Real protocols::match::MatcherTask::upstream_residue_collision_Wfa_atr ( ) const
void protocols::match::MatcherTask::upstream_residue_collision_Wfa_rep ( Real  setting)
MatcherTask::Real protocols::match::MatcherTask::upstream_residue_collision_Wfa_rep ( ) const
void protocols::match::MatcherTask::upstream_residue_collision_Wfa_sol ( Real  setting)
MatcherTask::Real protocols::match::MatcherTask::upstream_residue_collision_Wfa_sol ( ) const
void protocols::match::MatcherTask::use_different_build_points_for_each_geometric_constraint ( Size  n_geometric_constraints)

Set up the task so that it keeps different backbone build points for each geometric constraint -- the task then needs to know how many geometric constraints there are.

bool protocols::match::MatcherTask::use_input_sc ( ) const

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