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protocols::match::MatcherTask Class Reference

#include <MatcherTask.hh>

Inheritance diagram for protocols::match::MatcherTask:
Inheritance graph
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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. More...
 
MatcherTaskCOP get_self_ptr () const
 self pointers More...
 
MatcherTaskOP get_self_ptr ()
 
void set_upstream_pose (core::pose::Pose const &pose)
 Setup. More...
 
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_ignore_cmdline_for_build_points (bool setting)
 
void set_original_scaffold_build_points (utility::vector1< core::Size > const &resids)
 Uniformly consider the same set of build points for each of the geometric constrains. More...
 
void modify_pose_build_resids_from_endes_input ()
 modify the match positions according to what is specified in the cstfile More...
 
void use_different_build_points_for_each_geometric_constraint (core::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. More...
 
void set_original_scaffold_build_points_for_geometric_constraint (core::Size geom_cst_id, utility::vector1< core::Size > const &resids)
 Set the build point id's for a particular geometric constraint. More...
 
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 (core::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. More...
 
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. More...
 
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. More...
 
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. More...
 
void initialize_from_command_line ()
 Initialize many parameters from the command line options. More...
 
void initialize_with_mcfi_list (utility::vector1< toolbox::match_enzdes_util::MatchConstraintFileInfoListOP > mcfi_list_vec)
 Initialize all parameters except for the MatchConstraints from the command line. More...
 
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. More...
 
void n_to_output_per_group (core::Size setting)
 For use with the match consolidator; specify the number of output matches that the consolidator should select for each group. More...
 
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. More...
 
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. More...
 
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. More...
 
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. More...
 
void output_file_name (std::string const &setting)
 Indicate the name of the single output file to which the matches will be written. More...
 
void score_output_file_name (std::string const &setting)
 Set the name of the single output file to which the scores of matches will be written. More...
 
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. More...
 
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< core::Size >
const & 
upstream_pose_build_resids_for_geometric_constraint (core::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)? More...
 
std::string const & gridlig_file_name () const
 Accessor for the file name containing the active-site definition in gridlig format. More...
 
std::list< std::pair
< core::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. More...
 
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
 
core::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
 
std::string const & score_output_file_name () const
 
bool output_scores () 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
 
bool build_round1_hits_twice () const
 

Private Member Functions

void validate_downstream_orientation_atoms () const
 
void initialize_occupied_space_bounding_box_from_command_line ()
 Read the file describing the occupied space grid euclidean dimensions. The "details" tag for this function describes the file format used. More...
 
void initialize_scaffold_active_site_residue_list_from_command_line ()
 Read one of two files given on the command line that defines the set of residues on the scaffold to consider as potential launch points for the scaffold's active site. File formats are described in the "details" tag. More...
 
void set_active_site_residue_list_to_preexisting_partial_match ()
 in cases where the upstream pose to be matched already contains some of the desired interactions (as specified in the REMARK header, the match position list for every geomcst will be set to these positions More...
 
void remove_downstream_object_from_upstream_pose ()
 in case the upstream pose containts a copy of the downstream object (i.e. if a previously matched partial match is being read in again ) More...
 
void initialize_enzdes_input_data_from_command_line ()
 
void initialize_enzdes_input_data_with_mcfi_list (utility::vector1< toolbox::match_enzdes_util::MatchConstraintFileInfoListOP > mcfi_list_vec)
 
void determine_all_match_relevant_downstream_atoms ()
 queries the enzdes input for which atoms are relevant to the matcher, i.e. which atoms in the downstream object interact with any of the match residues More...
 
void initialize_orientation_atoms_from_command_line ()
 
void initialize_active_site_definition_from_command_line ()
 Read the command line arguments specifying the subset of downstream partner atoms that are required to be in the active site, as well as a definition of the region called the active site. The "details" tag for this function describes three file formats used in this function. More...
 
void initialize_upstream_residue_collision_filter_data_from_command_line ()
 
void initialize_upstream_downstream_collision_filter_data_from_command_line ()
 
void initialize_output_options_from_command_line ()
 

Private Attributes

core::pose::PoseCOP upstream_pose_
 
core::pose::PoseCOP downstream_pose_
 
utility::vector1
< core::id::AtomID
downstream_orientation_atoms_
 
utility::vector1
< core::id::AtomID
relevant_downstream_atoms_
 
bool enumerate_ligand_rotamers_
 
bool only_enumerate_non_match_redundant_ligand_rotamers_
 
bool ignore_cmdline_for_build_points_
 
bool share_build_points_for_geomcsts_
 
utility::vector1< core::Sizegeneric_pose_build_resids_
 
utility::vector1
< utility::vector1< core::Size > > 
per_cst_pose_build_resids_
 
std::map< core::Size, core::Sizeupstream_only_geom_cst_
 
bool gridlig_active_site_definition_
 
std::string gridlig_fname_
 
std::string upstream_pose_name_
 
std::string cstfile_name_
 
std::list< std::pair
< core::Size, Real > > 
upstream_resids_and_radii_defining_active_site_
 
std::list< core::id::AtomIDdownstream_atoms_required_inside_active_site_
 
utility::vector1< core::Sizedownstream_atom_inds_used_in_matching_
 
BoundingBox occ_space_bounding_box_
 
Vector euclidean_bin_widths_
 
Vector euler_bin_widths_
 
Real permitted_overlap_
 
bool use_input_sc_
 
bool dynamic_grid_refinement_
 
bool consolidate_matches_
 
core::Size n_to_output_per_group_
 MatchConsolidator vs MatchOutputter. More...
 
std::list< std::string > filter_names_
 
std::string grouper_name_
 
std::string evaluator_name_
 
std::string output_writer_name_
 
std::string output_file_name_
 
Real grouper_ds_rmsd_
 
std::string score_output_file_name_
 
bool output_scores_
 
bool output_matchres_only_
 
utility::vector1< core::Sizegeom_csts_downstream_output_
 
toolbox::match_enzdes_util::EnzConstraintIOCOP enz_input_data_
 
bool filter_upstream_residue_collisions_
 
bool filter_upstream_collisions_by_score_
 
Real upstream_residue_collision_tolerance_
 
Real upstream_residue_collision_score_cutoff_
 
Real upstream_residue_collision_Wfa_atr_
 
Real upstream_residue_collision_Wfa_rep_
 
Real upstream_residue_collision_Wfa_sol_
 
bool filter_upstream_and_downstream_residue_collisions_
 
bool filter_upstream_and_downstream_collisions_by_score_
 
Real upstream_downstream_atom_collision_tolerance_
 
Real upstream_downstream_residue_collision_score_cutoff_
 
Real upstream_downstream_residue_collision_Wfa_atr_
 
Real upstream_downstream_residue_collision_Wfa_rep_
 
Real upstream_downstream_residue_collision_Wfa_sol_
 
bool define_match_by_single_downstream_positioning_
 
bool build_round1_hits_twice_
 

Member Typedef Documentation

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

Constructor & Destructor Documentation

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

Construction and Destruction.

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.

References filter_names_.

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 ( core::Size  resid,
Real  radius 
)
bool protocols::match::MatcherTask::build_round1_hits_twice ( ) const
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.

References consolidate_matches_.

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

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

References consolidate_matches_.

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

References cstfile_name_.

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
void protocols::match::MatcherTask::determine_all_match_relevant_downstream_atoms ( )
private

queries the enzdes input for which atoms are relevant to the matcher, i.e. which atoms in the downstream object interact with any of the match residues

note: for the time being, this function sets all the residue numbers of the AtomIDs in relevant_downstream_atoms_ to 1, i.e. it will only function properly for cases where the downstream pose consists of one residue only (i.e. ligands )

References downstream_orientation_atoms_, enz_input_data_, relevant_downstream_atoms_, core::id::to_string(), and upstream_only_geom_cst_.

Referenced by initialize_enzdes_input_data_from_command_line(), initialize_enzdes_input_data_with_mcfi_list(), and set_enz_input_data().

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
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.

References evaluator_name_.

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

References evaluator_name_.

std::list< std::string > const & protocols::match::MatcherTask::filter_names ( ) const

References filter_names_.

void protocols::match::MatcherTask::filter_upstream_collisions_by_score ( bool  setting)
bool protocols::match::MatcherTask::filter_upstream_collisions_by_score ( ) const
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
void protocols::match::MatcherTask::filter_upstream_residue_collisions ( bool  setting)
bool protocols::match::MatcherTask::filter_upstream_residue_collisions ( ) const
utility::vector1< core::Size > const & protocols::match::MatcherTask::geom_csts_downstream_output ( ) const
MatcherTaskCOP protocols::match::MatcherTask::get_self_ptr ( ) const
inline

self pointers

Referenced by modify_pose_build_resids_from_endes_input().

MatcherTaskOP protocols::match::MatcherTask::get_self_ptr ( )
inline
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)?

References gridlig_active_site_definition_.

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.

References gridlig_active_site_definition_, and gridlig_fname_.

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

MatcherTask::Real protocols::match::MatcherTask::grouper_ds_rmsd ( ) const

References grouper_ds_rmsd_.

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.

References grouper_name_.

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

References grouper_name_.

void protocols::match::MatcherTask::initialize_active_site_definition_from_command_line ( )
private

Read the command line arguments specifying the subset of downstream partner atoms that are required to be in the active site, as well as a definition of the region called the active site. The "details" tag for this function describes three file formats used in this function.

This function reads three types of files relating to the active site. The file formats are described below.

  1. A file listing the atom names of those atoms in the downstream partner which are required to be in the active site – conformations of the downstream partner in which any of these atoms lie outside of the active site are excluded. This file format is only valid if the downstream partner is a single residue (e.g. a ligand).
  2. A file defining the active site geometry by listing residue indices of the scaffold and, for each residue i, a reach, r_i (a radius). A point in space is within the active site it is within r_i of any atom of residue i.
  3. A "gridlig" file from rosetta++ where a box in space whose voxels are labeled with 0's and 1's; voxels with 1's are part of the active site, those with 0's are not.

File formats:

  1. Active site atoms. The file lists on one or more lines the atom names for all atoms that are required to be present in the active site. The file format does not support comments. Example: <begin file>=""> C7 O2 O3 C22 C23 N5 <end file>="">
  2. Residue/reach pairs. Each line of the file should list a residue index (where residue numbering starts from 1) for a residue on the scaffold and a reach (a radius). Example. <begin file>=""> 10 5.5 12 7.2 13 7.0 23 10.0 25 7.0 58 5.5 60 7.0 <end file>="">
  3. Gridlig format The gridlig format specifies a discretization of euclidean space, and then gives the 0 and 1 values for each voxel. The first line in the liggrid file is "NAME: gridlig" The second line describes the coordinate of the lower corner: "BASE: <xcoord> <ycoord> <zcoord> The third line describes the number of voxels in each dimension: "SIZE: <xcount> <ycount> <zcount> The fourth line describes the length of each dimension describing a voxel: "LENGTH: <xlength> <ylength> <zlength> The subsequent lines are arranged in blocks sweeping through the grid in "row-major" order. Each line has zcount space-separated 0's and 1's. Lines are grouped into ycount blocks; a single empty line separates blocks. Example: <begin file>=""> NAME: gridlig BASE: 27.712 15.827 39.155 SIZE: 39 39 34 LENGTH: 0.500 0.500 0.500 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 1 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 <the file contains 1563 lines total>

References downstream_atoms_required_inside_active_site_, downstream_pose_, protocols::abinitio::filename(), gridlig_active_site_definition_, gridlig_fname_, protocols::match::TR(), upstream_pose_, and upstream_resids_and_radii_defining_active_site_.

Referenced by initialize_from_command_line(), and initialize_with_mcfi_list().

void protocols::match::MatcherTask::initialize_enzdes_input_data_from_command_line ( )
private
void protocols::match::MatcherTask::initialize_enzdes_input_data_with_mcfi_list ( utility::vector1< toolbox::match_enzdes_util::MatchConstraintFileInfoListOP mcfi_list_vec)
private
void protocols::match::MatcherTask::initialize_from_command_line ( )
void protocols::match::MatcherTask::initialize_occupied_space_bounding_box_from_command_line ( )
private

Read the file describing the occupied space grid euclidean dimensions. The "details" tag for this function describes the file format used.

This function reads a file specified on the command line through the -match::grid_boundary <filename> flag. The "grid boundary" specifies a bounding box inside which the third orientation atom of the downstream partner must lie for a downstream conformation to become a match. The orientation atoms are described in the match::orientation_atoms flag description. The format for the file describing this bounding box is the first four lines of the gridlig file format from rosetta++. The same file may be listed as both the grid_boundary file and the active_site_definition_by_gridlig file. Though the active_site_definition_by_gridlig flag is not required for the matcher to work, the grid_boundary flag is necessary.

Format: The gridlig format has been coopted. This file specifies voxels for a region of 3D. Though the occupied space bounding box does not require a discritization for its description, this gridlig file format does.

Gridlig format The gridlig format specifies a discretization of euclidean space, and then gives the 0 and 1 values for each voxel. The first line in the liggrid file is "NAME: gridlig" The second line describes the coordinate of the lower corner: "BASE: <xcoord> <ycoord> <zcoord> The third line describes the number of voxels in each dimension: "SIZE: <xcount> <ycount> <zcount> The fourth line describes the length of each dimension describing a voxel: "LENGTH: <xlength> <ylength> <zlength> Only the first four lines of the gridlig file are read. Additional lines are ignored. Example: <begin file>=""> NAME: gridlig BASE: 27.712 15.827 39.155 SIZE: 39 39 34 LENGTH: 0.500 0.500 0.500 <end file>="">

NOTE: The discritization of the occupied space bounding box has no impact on the hash size when detecting that two hits match. The -match::euclid_bin_size <Real> flag alone controls that behavior.

References protocols::abinitio::filename(), occ_space_bounding_box_, protocols::match::TR(), and upstream_pose_.

Referenced by initialize_from_command_line(), and initialize_with_mcfi_list().

void protocols::match::MatcherTask::initialize_orientation_atoms_from_command_line ( )
private
void protocols::match::MatcherTask::initialize_output_options_from_command_line ( )
private
void protocols::match::MatcherTask::initialize_scaffold_active_site_residue_list_from_command_line ( )
private

Read one of two files given on the command line that defines the set of residues on the scaffold to consider as potential launch points for the scaffold's active site. File formats are described in the "details" tag.

flo may '12, bulk of this function has been moved to AllowedSeqposForGeomCst file

References enz_input_data_, generic_pose_build_resids_, protocols::toolbox::match_enzdes_util::AllowedSeqposForGeomCst::initialize_from_command_line(), protocols::stepwise::modeler::is_protein(), per_cst_pose_build_resids_, share_build_points_for_geomcsts_, core::id::to_string(), and upstream_pose_.

Referenced by initialize_from_command_line(), and initialize_with_mcfi_list().

void protocols::match::MatcherTask::initialize_upstream_downstream_collision_filter_data_from_command_line ( )
private
void protocols::match::MatcherTask::initialize_upstream_residue_collision_filter_data_from_command_line ( )
private
void protocols::match::MatcherTask::initialize_with_mcfi_list ( utility::vector1< toolbox::match_enzdes_util::MatchConstraintFileInfoListOP mcfi_list_vec)
void protocols::match::MatcherTask::modify_pose_build_resids_from_endes_input ( )
void protocols::match::MatcherTask::n_to_output_per_group ( core::Size  setting)

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

References n_to_output_per_group_.

MatcherTask::Size protocols::match::MatcherTask::n_to_output_per_group ( ) const
MatcherTask::BoundingBox const & protocols::match::MatcherTask::occ_space_bounding_box ( ) const
bool protocols::match::MatcherTask::only_enumerate_non_match_redundant_ligand_rotamers ( ) 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.

References output_file_name_.

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

References output_file_name_.

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

References output_matchres_only_.

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

References output_scores_.

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.

References output_writer_name_.

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

References output_writer_name_.

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::remove_downstream_object_from_upstream_pose ( )
private

in case the upstream pose containts a copy of the downstream object (i.e. if a previously matched partial match is being read in again )

References downstream_pose_, protocols::match::TR(), and upstream_pose_.

Referenced by set_active_site_residue_list_to_preexisting_partial_match().

void protocols::match::MatcherTask::score_output_file_name ( std::string const &  setting)

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

Sets the output score filename and turns on score output boolean

References output_scores_, and score_output_file_name_.

std::string const & protocols::match::MatcherTask::score_output_file_name ( ) const
void protocols::match::MatcherTask::set_active_site_residue_list_to_preexisting_partial_match ( )
private

in cases where the upstream pose to be matched already contains some of the desired interactions (as specified in the REMARK header, the match position list for every geomcst will be set to these positions

go through all of the remarks in the pose and see if any of them specify already existing catalytic interactions

References enz_input_data_, generic_pose_build_resids_, remove_downstream_object_from_upstream_pose(), set_original_scaffold_build_points_for_geometric_constraint(), share_build_points_for_geomcsts_, protocols::toolbox::match_enzdes_util::split_up_remark_line(), protocols::match::TR(), upstream_pose_, and use_different_build_points_for_each_geometric_constraint().

Referenced by initialize_from_command_line(), and initialize_with_mcfi_list().

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 &  input_pose)
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_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.

References determine_all_match_relevant_downstream_atoms(), and enz_input_data_.

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.

References euclidean_bin_widths_.

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.

References euler_bin_widths_.

void protocols::match::MatcherTask::set_ignore_cmdline_for_build_points ( bool  setting)
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.

References occ_space_bounding_box_.

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< core::Size > const &  resids)

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

References generic_pose_build_resids_, per_cst_pose_build_resids_, core::select::resids(), and share_build_points_for_geomcsts_.

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

void protocols::match::MatcherTask::set_upstream_pose ( core::pose::Pose const &  pose)
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
void protocols::match::MatcherTask::upstream_downstream_residue_collision_Wfa_rep ( Real  setting)
MatcherTask::Real protocols::match::MatcherTask::upstream_downstream_residue_collision_Wfa_rep ( ) const
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 ( core::Size  cst_id) const
std::string const & protocols::match::MatcherTask::upstream_pose_name ( ) const

References upstream_pose_name_.

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.

References gridlig_active_site_definition_, and upstream_resids_and_radii_defining_active_site_.

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 ( core::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.

References per_cst_pose_build_resids_, and share_build_points_for_geomcsts_.

Referenced by set_active_site_residue_list_to_preexisting_partial_match(), and protocols::match::MatcherMover::setup_seqpos_from_selectors().

bool protocols::match::MatcherTask::use_input_sc ( ) const
void protocols::match::MatcherTask::validate_downstream_orientation_atoms ( ) const
private

Member Data Documentation

bool protocols::match::MatcherTask::build_round1_hits_twice_
private
bool protocols::match::MatcherTask::consolidate_matches_
private
std::string protocols::match::MatcherTask::cstfile_name_
private
bool protocols::match::MatcherTask::define_match_by_single_downstream_positioning_
private
utility::vector1< core::Size > protocols::match::MatcherTask::downstream_atom_inds_used_in_matching_
private
std::list< core::id::AtomID > protocols::match::MatcherTask::downstream_atoms_required_inside_active_site_
private
utility::vector1< core::id::AtomID > protocols::match::MatcherTask::downstream_orientation_atoms_
private
core::pose::PoseCOP protocols::match::MatcherTask::downstream_pose_
private
bool protocols::match::MatcherTask::dynamic_grid_refinement_
private
bool protocols::match::MatcherTask::enumerate_ligand_rotamers_
private
toolbox::match_enzdes_util::EnzConstraintIOCOP protocols::match::MatcherTask::enz_input_data_
private
Vector protocols::match::MatcherTask::euclidean_bin_widths_
private
Vector protocols::match::MatcherTask::euler_bin_widths_
private
std::string protocols::match::MatcherTask::evaluator_name_
private

Referenced by evaluator_name().

std::list< std::string > protocols::match::MatcherTask::filter_names_
private

Referenced by add_filter(), and filter_names().

bool protocols::match::MatcherTask::filter_upstream_and_downstream_collisions_by_score_
private
bool protocols::match::MatcherTask::filter_upstream_and_downstream_residue_collisions_
private
bool protocols::match::MatcherTask::filter_upstream_collisions_by_score_
private
bool protocols::match::MatcherTask::filter_upstream_residue_collisions_
private
utility::vector1< core::Size > protocols::match::MatcherTask::generic_pose_build_resids_
private
utility::vector1< core::Size > protocols::match::MatcherTask::geom_csts_downstream_output_
private
bool protocols::match::MatcherTask::gridlig_active_site_definition_
private
std::string protocols::match::MatcherTask::gridlig_fname_
private
Real protocols::match::MatcherTask::grouper_ds_rmsd_
private
std::string protocols::match::MatcherTask::grouper_name_
private
bool protocols::match::MatcherTask::ignore_cmdline_for_build_points_
private
core::Size protocols::match::MatcherTask::n_to_output_per_group_
private

MatchConsolidator vs MatchOutputter.

Referenced by initialize_from_command_line(), initialize_with_mcfi_list(), and n_to_output_per_group().

BoundingBox protocols::match::MatcherTask::occ_space_bounding_box_
private
bool protocols::match::MatcherTask::only_enumerate_non_match_redundant_ligand_rotamers_
private
std::string protocols::match::MatcherTask::output_file_name_
private

Referenced by output_file_name().

bool protocols::match::MatcherTask::output_matchres_only_
private
bool protocols::match::MatcherTask::output_scores_
private
std::string protocols::match::MatcherTask::output_writer_name_
private
utility::vector1< utility::vector1< core::Size > > protocols::match::MatcherTask::per_cst_pose_build_resids_
private
Real protocols::match::MatcherTask::permitted_overlap_
private
utility::vector1< core::id::AtomID > protocols::match::MatcherTask::relevant_downstream_atoms_
private
std::string protocols::match::MatcherTask::score_output_file_name_
private

Referenced by score_output_file_name().

bool protocols::match::MatcherTask::share_build_points_for_geomcsts_
private
Real protocols::match::MatcherTask::upstream_downstream_atom_collision_tolerance_
private
Real protocols::match::MatcherTask::upstream_downstream_residue_collision_score_cutoff_
private
Real protocols::match::MatcherTask::upstream_downstream_residue_collision_Wfa_atr_
private
Real protocols::match::MatcherTask::upstream_downstream_residue_collision_Wfa_rep_
private
Real protocols::match::MatcherTask::upstream_downstream_residue_collision_Wfa_sol_
private
std::map< core::Size, core::Size > protocols::match::MatcherTask::upstream_only_geom_cst_
private
core::pose::PoseCOP protocols::match::MatcherTask::upstream_pose_
private
std::string protocols::match::MatcherTask::upstream_pose_name_
private
std::list< std::pair< core::Size, Real > > protocols::match::MatcherTask::upstream_resids_and_radii_defining_active_site_
private
Real protocols::match::MatcherTask::upstream_residue_collision_score_cutoff_
private
Real protocols::match::MatcherTask::upstream_residue_collision_tolerance_
private
Real protocols::match::MatcherTask::upstream_residue_collision_Wfa_atr_
private
Real protocols::match::MatcherTask::upstream_residue_collision_Wfa_rep_
private
Real protocols::match::MatcherTask::upstream_residue_collision_Wfa_sol_
private
bool protocols::match::MatcherTask::use_input_sc_
private

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