#include <MatcherTask.hh>
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 () |
Member Typedef Documentation
◆ BoundingBox
| typedef numeric::geometry::BoundingBox< Vector > protocols::match::MatcherTask::BoundingBox |
◆ Real
◆ Size
◆ Vector
Constructor & Destructor Documentation
◆ MatcherTask()
| protocols::match::MatcherTask::MatcherTask | ( | ) |
Construction and Destruction.
Member Function Documentation
◆ add_filter()
| 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_.
◆ append_downstream_atom_to_active_site_required_list()
| void protocols::match::MatcherTask::append_downstream_atom_to_active_site_required_list | ( | core::id::AtomID | atid | ) |
References downstream_atoms_required_inside_active_site_.
◆ append_upstream_resiue_as_defining_active_site()
| void protocols::match::MatcherTask::append_upstream_resiue_as_defining_active_site | ( | core::Size | resid, |
| Real | radius | ||
| ) |
◆ build_round1_hits_twice()
| bool protocols::match::MatcherTask::build_round1_hits_twice | ( | ) | const |
References build_round1_hits_twice_.
Referenced by protocols::match::Matcher::initialize_from_file(), and protocols::match::Matcher::initialize_from_task().
◆ clear_downstream_orientation_atoms()
| void protocols::match::MatcherTask::clear_downstream_orientation_atoms | ( | ) |
References downstream_orientation_atoms_.
◆ consolidate_matches() [1/2]
| bool protocols::match::MatcherTask::consolidate_matches | ( | ) | const |
References consolidate_matches_.
◆ consolidate_matches() [2/2]
| 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().
◆ cstfile_name()
| std::string const & protocols::match::MatcherTask::cstfile_name | ( | ) | const |
References cstfile_name_.
◆ define_active_site_from_gridlig_file()
| void protocols::match::MatcherTask::define_active_site_from_gridlig_file | ( | std::string const & | file_name | ) |
◆ define_active_site_from_residue_radii_list()
| void protocols::match::MatcherTask::define_active_site_from_residue_radii_list | ( | ) |
References gridlig_active_site_definition_.
◆ define_match_by_single_downstream_positioning() [1/2]
| bool protocols::match::MatcherTask::define_match_by_single_downstream_positioning | ( | ) | const |
References define_match_by_single_downstream_positioning_.
◆ define_match_by_single_downstream_positioning() [2/2]
| void protocols::match::MatcherTask::define_match_by_single_downstream_positioning | ( | bool | setting | ) |
References define_match_by_single_downstream_positioning_.
Referenced by protocols::match::Matcher::initialize_from_task().
◆ 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().
◆ downstream_atoms_required_inside_active_site()
| std::list< core::id::AtomID > const & protocols::match::MatcherTask::downstream_atoms_required_inside_active_site | ( | ) | const |
References downstream_atoms_required_inside_active_site_.
Referenced by protocols::match::Matcher::initialize_from_task().
◆ downstream_orientation_atoms()
| utility::vector1< core::id::AtomID > const & protocols::match::MatcherTask::downstream_orientation_atoms | ( | ) | const |
References downstream_orientation_atoms_.
Referenced by protocols::match::Matcher::initialize_from_task().
◆ downstream_pose()
| core::pose::PoseCOP protocols::match::MatcherTask::downstream_pose | ( | ) | const |
References downstream_pose_.
Referenced by protocols::match::Matcher::initialize_from_task().
◆ dynamic_grid_refinement()
| bool protocols::match::MatcherTask::dynamic_grid_refinement | ( | ) | const |
References dynamic_grid_refinement_.
Referenced by protocols::match::Matcher::initialize_from_task().
◆ enumerate_ligand_rotamers()
| bool protocols::match::MatcherTask::enumerate_ligand_rotamers | ( | ) | const |
References enumerate_ligand_rotamers_.
Referenced by protocols::match::Matcher::initialize_from_file().
◆ enz_input_data()
| toolbox::match_enzdes_util::EnzConstraintIOCOP protocols::match::MatcherTask::enz_input_data | ( | ) | const |
◆ euclidean_bin_widths()
| MatcherTask::Vector protocols::match::MatcherTask::euclidean_bin_widths | ( | ) | const |
References euclidean_bin_widths_.
Referenced by protocols::match::Matcher::initialize_from_task().
◆ euler_bin_widths()
| MatcherTask::Vector protocols::match::MatcherTask::euler_bin_widths | ( | ) | const |
References euler_bin_widths_.
Referenced by protocols::match::Matcher::initialize_from_task().
◆ evaluator_name() [1/2]
| std::string const & protocols::match::MatcherTask::evaluator_name | ( | ) | const |
References evaluator_name_.
◆ evaluator_name() [2/2]
| 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_.
◆ filter_names()
| std::list< std::string > const & protocols::match::MatcherTask::filter_names | ( | ) | const |
References filter_names_.
◆ filter_upstream_collisions_by_score() [1/2]
| bool protocols::match::MatcherTask::filter_upstream_collisions_by_score | ( | ) | const |
References filter_upstream_collisions_by_score_.
◆ filter_upstream_collisions_by_score() [2/2]
| void protocols::match::MatcherTask::filter_upstream_collisions_by_score | ( | bool | setting | ) |
References filter_upstream_collisions_by_score_, and filter_upstream_residue_collisions_.
◆ filter_upstream_downstream_collisions() [1/2]
| bool protocols::match::MatcherTask::filter_upstream_downstream_collisions | ( | ) | const |
◆ filter_upstream_downstream_collisions() [2/2]
| void protocols::match::MatcherTask::filter_upstream_downstream_collisions | ( | bool | setting | ) |
◆ filter_upstream_downstream_collisions_by_score() [1/2]
| bool protocols::match::MatcherTask::filter_upstream_downstream_collisions_by_score | ( | ) | const |
◆ filter_upstream_downstream_collisions_by_score() [2/2]
| void protocols::match::MatcherTask::filter_upstream_downstream_collisions_by_score | ( | bool | setting | ) |
◆ filter_upstream_residue_collisions() [1/2]
| bool protocols::match::MatcherTask::filter_upstream_residue_collisions | ( | ) | const |
References filter_upstream_residue_collisions_.
◆ filter_upstream_residue_collisions() [2/2]
| void protocols::match::MatcherTask::filter_upstream_residue_collisions | ( | bool | setting | ) |
References filter_upstream_residue_collisions_.
◆ geom_csts_downstream_output()
| utility::vector1< core::Size > const & protocols::match::MatcherTask::geom_csts_downstream_output | ( | ) | const |
References geom_csts_downstream_output_.
Referenced by protocols::match::Matcher::initialize_from_task().
◆ get_self_ptr() [1/2]
|
inline |
◆ get_self_ptr() [2/2]
|
inline |
self pointers
Referenced by modify_pose_build_resids_from_endes_input().
◆ gridlig_active_site_definition()
| 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().
◆ gridlig_file_name()
| 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().
◆ grouper_ds_rmsd()
| MatcherTask::Real protocols::match::MatcherTask::grouper_ds_rmsd | ( | ) | const |
References grouper_ds_rmsd_.
◆ grouper_name() [1/2]
| std::string const & protocols::match::MatcherTask::grouper_name | ( | ) | const |
References grouper_name_.
◆ grouper_name() [2/2]
| 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_.
◆ 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.
- 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).
- 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.
- 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:
- 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>
- 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>
- 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().
◆ initialize_enzdes_input_data_from_command_line()
|
private |
References cstfile_name_, determine_all_match_relevant_downstream_atoms(), enz_input_data(), enz_input_data_, and core::chemical::FA_STANDARD.
Referenced by initialize_from_command_line().
◆ initialize_enzdes_input_data_with_mcfi_list()
|
private |
References determine_all_match_relevant_downstream_atoms(), enz_input_data(), enz_input_data_, and core::chemical::FA_STANDARD.
Referenced by initialize_with_mcfi_list().
◆ initialize_from_command_line()
| void protocols::match::MatcherTask::initialize_from_command_line | ( | ) |
Initialize many parameters from the command line options.
References build_round1_hits_twice_, consolidate_matches_, dynamic_grid_refinement_, enumerate_ligand_rotamers_, euclidean_bin_widths_, euler_bin_widths_, ignore_cmdline_for_build_points_, initialize_active_site_definition_from_command_line(), initialize_enzdes_input_data_from_command_line(), initialize_occupied_space_bounding_box_from_command_line(), initialize_orientation_atoms_from_command_line(), initialize_output_options_from_command_line(), initialize_scaffold_active_site_residue_list_from_command_line(), initialize_upstream_downstream_collision_filter_data_from_command_line(), initialize_upstream_residue_collision_filter_data_from_command_line(), modify_pose_build_resids_from_endes_input(), n_to_output_per_group_, only_enumerate_non_match_redundant_ligand_rotamers_, permitted_overlap_, set_active_site_residue_list_to_preexisting_partial_match(), and use_input_sc_.
◆ 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 core::chemical::ResidueType::all_bb_atoms(), protocols::abinitio::filename(), core::conformation::Residue::is_protein(), occ_space_bounding_box_, protocols::match::TR(), core::conformation::Residue::type(), upstream_pose_, and core::conformation::Residue::xyz().
Referenced by initialize_from_command_line(), and initialize_with_mcfi_list().
◆ initialize_orientation_atoms_from_command_line()
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private |
References downstream_orientation_atoms_, and downstream_pose_.
Referenced by initialize_from_command_line(), and initialize_with_mcfi_list().
◆ initialize_output_options_from_command_line()
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private |
References define_match_by_single_downstream_positioning_, enz_input_data_, geom_csts_downstream_output_, grouper_ds_rmsd_, grouper_name_, output_matchres_only_, output_scores_, output_writer_name_, score_output_file_name(), and protocols::match::TR().
Referenced by initialize_from_command_line(), and initialize_with_mcfi_list().
◆ initialize_scaffold_active_site_residue_list_from_command_line()
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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::toolbox::match_enzdes_util::AllowedSeqposForGeomCst::num_seqpos_lists(), per_cst_pose_build_resids_, protocols::toolbox::match_enzdes_util::AllowedSeqposForGeomCst::seqpos_for_geomcst(), share_build_points_for_geomcsts_, core::id::to_string(), and upstream_pose_.
Referenced by initialize_from_command_line(), and initialize_with_mcfi_list().
◆ initialize_upstream_downstream_collision_filter_data_from_command_line()
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private |
References filter_upstream_and_downstream_collisions_by_score_, filter_upstream_and_downstream_residue_collisions_, upstream_downstream_atom_collision_tolerance_, upstream_downstream_residue_collision_score_cutoff_, upstream_downstream_residue_collision_Wfa_atr_, upstream_downstream_residue_collision_Wfa_rep_, and upstream_downstream_residue_collision_Wfa_sol_.
Referenced by initialize_from_command_line(), and initialize_with_mcfi_list().
◆ initialize_upstream_residue_collision_filter_data_from_command_line()
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private |
References filter_upstream_collisions_by_score_, filter_upstream_residue_collisions_, upstream_residue_collision_score_cutoff_, upstream_residue_collision_tolerance_, upstream_residue_collision_Wfa_atr_, upstream_residue_collision_Wfa_rep_, and upstream_residue_collision_Wfa_sol_.
Referenced by initialize_from_command_line(), and initialize_with_mcfi_list().
◆ initialize_with_mcfi_list()
| void protocols::match::MatcherTask::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.
References build_round1_hits_twice_, consolidate_matches_, dynamic_grid_refinement_, enumerate_ligand_rotamers_, euclidean_bin_widths_, euler_bin_widths_, ignore_cmdline_for_build_points_, initialize_active_site_definition_from_command_line(), initialize_enzdes_input_data_with_mcfi_list(), initialize_occupied_space_bounding_box_from_command_line(), initialize_orientation_atoms_from_command_line(), initialize_output_options_from_command_line(), initialize_scaffold_active_site_residue_list_from_command_line(), initialize_upstream_downstream_collision_filter_data_from_command_line(), initialize_upstream_residue_collision_filter_data_from_command_line(), modify_pose_build_resids_from_endes_input(), n_to_output_per_group_, only_enumerate_non_match_redundant_ligand_rotamers_, permitted_overlap_, set_active_site_residue_list_to_preexisting_partial_match(), and use_input_sc_.
◆ modify_pose_build_resids_from_endes_input()
| 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(), enz_input_data_, generic_pose_build_resids_, get_self_ptr(), per_cst_pose_build_resids_, share_build_points_for_geomcsts_, protocols::sparta::split(), protocols::match::TR(), and upstream_pose_.
Referenced by initialize_from_command_line(), and initialize_with_mcfi_list().
◆ n_to_output_per_group() [1/2]
| MatcherTask::Size protocols::match::MatcherTask::n_to_output_per_group | ( | ) | const |
References n_to_output_per_group_.
◆ n_to_output_per_group() [2/2]
| 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_.
◆ occ_space_bounding_box()
| MatcherTask::BoundingBox const & protocols::match::MatcherTask::occ_space_bounding_box | ( | ) | const |
References occ_space_bounding_box_.
Referenced by protocols::match::Matcher::initialize_from_task().
◆ only_enumerate_non_match_redundant_ligand_rotamers()
| bool protocols::match::MatcherTask::only_enumerate_non_match_redundant_ligand_rotamers | ( | ) | const |
References only_enumerate_non_match_redundant_ligand_rotamers_.
Referenced by protocols::match::Matcher::initialize_from_task().
◆ output_file_name() [1/2]
| std::string const & protocols::match::MatcherTask::output_file_name | ( | ) | const |
References output_file_name_.
◆ output_file_name() [2/2]
| 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_.
◆ output_matchres_only()
| bool protocols::match::MatcherTask::output_matchres_only | ( | ) | const |
References output_matchres_only_.
◆ output_scores()
| bool protocols::match::MatcherTask::output_scores | ( | ) | const |
References output_scores_.
◆ output_writer_name() [1/2]
| std::string const & protocols::match::MatcherTask::output_writer_name | ( | ) | const |
References output_writer_name_.
◆ output_writer_name() [2/2]
| 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_.
◆ permitted_overlap()
| MatcherTask::Real protocols::match::MatcherTask::permitted_overlap | ( | ) | const |
References permitted_overlap_.
Referenced by protocols::match::Matcher::initialize_from_task(), and set_permitted_overlap().
◆ relevant_downstream_atoms()
| utility::vector1< core::id::AtomID > const & protocols::match::MatcherTask::relevant_downstream_atoms | ( | ) | const |
References relevant_downstream_atoms_.
Referenced by protocols::match::Matcher::initialize_from_task().
◆ remove_downstream_object_from_upstream_pose()
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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().
◆ score_output_file_name() [1/2]
| std::string const & protocols::match::MatcherTask::score_output_file_name | ( | ) | const |
References score_output_file_name_.
Referenced by initialize_output_options_from_command_line().
◆ score_output_file_name() [2/2]
| 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_.
◆ set_active_site_residue_list_to_preexisting_partial_match()
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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().
◆ set_downstream_orientation_atoms()
| void protocols::match::MatcherTask::set_downstream_orientation_atoms | ( | utility::vector1< core::id::AtomID > const & | orientation_atoms | ) |
◆ set_downstream_pose() [1/2]
| void protocols::match::MatcherTask::set_downstream_pose | ( | core::pose::Pose const & | input_pose | ) |
◆ set_downstream_pose() [2/2]
| void protocols::match::MatcherTask::set_downstream_pose | ( | core::pose::Pose const & | pose, |
| utility::vector1< core::id::AtomID > const & | orientation_atoms | ||
| ) |
◆ set_enumerate_ligand_rotamers()
| void protocols::match::MatcherTask::set_enumerate_ligand_rotamers | ( | bool | setting | ) |
References enumerate_ligand_rotamers_.
◆ set_enz_input_data()
| 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_.
◆ set_hash_euclidean_bin_width()
| 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_.
◆ set_hash_euler_bin_width()
| 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_.
◆ set_ignore_cmdline_for_build_points()
| void protocols::match::MatcherTask::set_ignore_cmdline_for_build_points | ( | bool | setting | ) |
References ignore_cmdline_for_build_points_.
Referenced by protocols::match::MatcherMover::setup_seqpos_from_selectors().
◆ set_occupied_space_bounding_box()
| 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_.
◆ set_only_enumerate_non_match_redundant_ligand_rotamers()
| void protocols::match::MatcherTask::set_only_enumerate_non_match_redundant_ligand_rotamers | ( | bool | setting | ) |
◆ set_original_scaffold_build_points()
| 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_.
◆ set_original_scaffold_build_points_for_geometric_constraint()
| void protocols::match::MatcherTask::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.
References per_cst_pose_build_resids_, core::select::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().
◆ set_permitted_overlap()
| 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_.
◆ set_upstream_pose()
| void protocols::match::MatcherTask::set_upstream_pose | ( | core::pose::Pose const & | pose | ) |
Setup.
References protocols::hybridization::path, core::pose::Pose::pdb_info(), upstream_pose_, and upstream_pose_name_.
◆ upstream_downstream_atom_collision_tolerance() [1/2]
| MatcherTask::Real protocols::match::MatcherTask::upstream_downstream_atom_collision_tolerance | ( | ) | const |
References upstream_downstream_atom_collision_tolerance_.
◆ upstream_downstream_atom_collision_tolerance() [2/2]
| void protocols::match::MatcherTask::upstream_downstream_atom_collision_tolerance | ( | Real | setting | ) |
References upstream_downstream_atom_collision_tolerance_.
◆ upstream_downstream_residue_collision_score_cutoff() [1/2]
| MatcherTask::Real protocols::match::MatcherTask::upstream_downstream_residue_collision_score_cutoff | ( | ) | const |
◆ upstream_downstream_residue_collision_score_cutoff() [2/2]
| void protocols::match::MatcherTask::upstream_downstream_residue_collision_score_cutoff | ( | Real | setting | ) |
◆ upstream_downstream_residue_collision_Wfa_atr() [1/2]
| MatcherTask::Real protocols::match::MatcherTask::upstream_downstream_residue_collision_Wfa_atr | ( | ) | const |
References upstream_downstream_residue_collision_Wfa_atr_.
◆ upstream_downstream_residue_collision_Wfa_atr() [2/2]
| void protocols::match::MatcherTask::upstream_downstream_residue_collision_Wfa_atr | ( | Real | setting | ) |
References upstream_downstream_residue_collision_Wfa_atr_.
◆ upstream_downstream_residue_collision_Wfa_rep() [1/2]
| MatcherTask::Real protocols::match::MatcherTask::upstream_downstream_residue_collision_Wfa_rep | ( | ) | const |
References upstream_downstream_residue_collision_Wfa_rep_.
◆ upstream_downstream_residue_collision_Wfa_rep() [2/2]
| void protocols::match::MatcherTask::upstream_downstream_residue_collision_Wfa_rep | ( | Real | setting | ) |
References upstream_downstream_residue_collision_Wfa_rep_.
◆ upstream_downstream_residue_collision_Wfa_sol() [1/2]
| MatcherTask::Real protocols::match::MatcherTask::upstream_downstream_residue_collision_Wfa_sol | ( | ) | const |
References upstream_downstream_residue_collision_Wfa_sol_.
◆ upstream_downstream_residue_collision_Wfa_sol() [2/2]
| void protocols::match::MatcherTask::upstream_downstream_residue_collision_Wfa_sol | ( | Real | setting | ) |
References upstream_downstream_residue_collision_Wfa_sol_.
◆ upstream_only_geom_cst()
| std::map< core::Size, core::Size > const & protocols::match::MatcherTask::upstream_only_geom_cst | ( | ) | const |
References upstream_only_geom_cst_.
◆ upstream_pose()
| core::pose::PoseCOP protocols::match::MatcherTask::upstream_pose | ( | ) | const |
References upstream_pose_.
Referenced by protocols::match::Matcher::initialize_from_task().
◆ upstream_pose_build_resids_for_geometric_constraint()
| utility::vector1< core::Size > const & protocols::match::MatcherTask::upstream_pose_build_resids_for_geometric_constraint | ( | core::Size | cst_id | ) | const |
References generic_pose_build_resids_, per_cst_pose_build_resids_, and share_build_points_for_geomcsts_.
Referenced by protocols::match::Matcher::initialize_from_task().
◆ upstream_pose_name()
| std::string const & protocols::match::MatcherTask::upstream_pose_name | ( | ) | const |
References upstream_pose_name_.
◆ upstream_resids_and_radii_defining_active_site()
| 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().
◆ upstream_residue_collision_score_cutoff() [1/2]
| MatcherTask::Real protocols::match::MatcherTask::upstream_residue_collision_score_cutoff | ( | ) | const |
References upstream_residue_collision_score_cutoff_.
◆ upstream_residue_collision_score_cutoff() [2/2]
| void protocols::match::MatcherTask::upstream_residue_collision_score_cutoff | ( | Real | setting | ) |
References upstream_residue_collision_score_cutoff_.
◆ upstream_residue_collision_tolerance() [1/2]
| MatcherTask::Real protocols::match::MatcherTask::upstream_residue_collision_tolerance | ( | ) | const |
References upstream_residue_collision_tolerance_.
◆ upstream_residue_collision_tolerance() [2/2]
| void protocols::match::MatcherTask::upstream_residue_collision_tolerance | ( | Real | setting | ) |
References upstream_residue_collision_tolerance_.
◆ upstream_residue_collision_Wfa_atr() [1/2]
| MatcherTask::Real protocols::match::MatcherTask::upstream_residue_collision_Wfa_atr | ( | ) | const |
References upstream_residue_collision_Wfa_atr_.
◆ upstream_residue_collision_Wfa_atr() [2/2]
| void protocols::match::MatcherTask::upstream_residue_collision_Wfa_atr | ( | Real | setting | ) |
References upstream_residue_collision_Wfa_atr_.
◆ upstream_residue_collision_Wfa_rep() [1/2]
| MatcherTask::Real protocols::match::MatcherTask::upstream_residue_collision_Wfa_rep | ( | ) | const |
References upstream_residue_collision_Wfa_rep_.
◆ upstream_residue_collision_Wfa_rep() [2/2]
| void protocols::match::MatcherTask::upstream_residue_collision_Wfa_rep | ( | Real | setting | ) |
References upstream_residue_collision_Wfa_rep_.
◆ upstream_residue_collision_Wfa_sol() [1/2]
| MatcherTask::Real protocols::match::MatcherTask::upstream_residue_collision_Wfa_sol | ( | ) | const |
References upstream_residue_collision_Wfa_sol_.
◆ upstream_residue_collision_Wfa_sol() [2/2]
| void protocols::match::MatcherTask::upstream_residue_collision_Wfa_sol | ( | Real | setting | ) |
References upstream_residue_collision_Wfa_sol_.
◆ use_different_build_points_for_each_geometric_constraint()
| 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().
◆ use_input_sc()
| bool protocols::match::MatcherTask::use_input_sc | ( | ) | const |
References use_input_sc_.
Referenced by protocols::match::Matcher::initialize_from_task().
◆ validate_downstream_orientation_atoms()
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private |
Referenced by set_downstream_orientation_atoms(), and set_downstream_pose().
Member Data Documentation
◆ build_round1_hits_twice_
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private |
Referenced by build_round1_hits_twice(), initialize_from_command_line(), and initialize_with_mcfi_list().
◆ consolidate_matches_
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private |
Referenced by consolidate_matches(), initialize_from_command_line(), and initialize_with_mcfi_list().
◆ cstfile_name_
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private |
Referenced by cstfile_name(), and initialize_enzdes_input_data_from_command_line().
◆ define_match_by_single_downstream_positioning_
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private |
◆ downstream_atom_inds_used_in_matching_
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private |
◆ downstream_atoms_required_inside_active_site_
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private |
◆ downstream_orientation_atoms_
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private |
◆ downstream_pose_
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private |
◆ dynamic_grid_refinement_
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private |
Referenced by dynamic_grid_refinement(), initialize_from_command_line(), and initialize_with_mcfi_list().
◆ enumerate_ligand_rotamers_
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private |
◆ enz_input_data_
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private |
Referenced by determine_all_match_relevant_downstream_atoms(), enz_input_data(), initialize_enzdes_input_data_from_command_line(), initialize_enzdes_input_data_with_mcfi_list(), initialize_output_options_from_command_line(), initialize_scaffold_active_site_residue_list_from_command_line(), modify_pose_build_resids_from_endes_input(), set_active_site_residue_list_to_preexisting_partial_match(), and set_enz_input_data().
◆ euclidean_bin_widths_
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private |
◆ euler_bin_widths_
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private |
◆ evaluator_name_
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private |
Referenced by evaluator_name().
◆ filter_names_
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private |
Referenced by add_filter(), and filter_names().
◆ filter_upstream_and_downstream_collisions_by_score_
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private |
◆ filter_upstream_and_downstream_residue_collisions_
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private |
◆ filter_upstream_collisions_by_score_
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private |
◆ filter_upstream_residue_collisions_
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private |
◆ generic_pose_build_resids_
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private |
◆ geom_csts_downstream_output_
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private |
Referenced by geom_csts_downstream_output(), and initialize_output_options_from_command_line().
◆ gridlig_active_site_definition_
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private |
Referenced by append_upstream_resiue_as_defining_active_site(), define_active_site_from_gridlig_file(), define_active_site_from_residue_radii_list(), gridlig_active_site_definition(), gridlig_file_name(), initialize_active_site_definition_from_command_line(), and upstream_resids_and_radii_defining_active_site().
◆ gridlig_fname_
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private |
◆ grouper_ds_rmsd_
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private |
Referenced by grouper_ds_rmsd(), and initialize_output_options_from_command_line().
◆ grouper_name_
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private |
Referenced by grouper_name(), and initialize_output_options_from_command_line().
◆ ignore_cmdline_for_build_points_
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private |
◆ n_to_output_per_group_
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private |
MatchConsolidator vs MatchOutputter.
Referenced by initialize_from_command_line(), initialize_with_mcfi_list(), and n_to_output_per_group().
◆ occ_space_bounding_box_
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private |
◆ only_enumerate_non_match_redundant_ligand_rotamers_
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private |
◆ output_file_name_
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private |
Referenced by output_file_name().
◆ output_matchres_only_
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private |
Referenced by initialize_output_options_from_command_line(), and output_matchres_only().
◆ output_scores_
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private |
Referenced by initialize_output_options_from_command_line(), output_scores(), and score_output_file_name().
◆ output_writer_name_
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private |
Referenced by initialize_output_options_from_command_line(), and output_writer_name().
◆ per_cst_pose_build_resids_
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private |
Referenced by initialize_scaffold_active_site_residue_list_from_command_line(), modify_pose_build_resids_from_endes_input(), set_original_scaffold_build_points(), set_original_scaffold_build_points_for_geometric_constraint(), upstream_pose_build_resids_for_geometric_constraint(), and use_different_build_points_for_each_geometric_constraint().
◆ permitted_overlap_
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private |
Referenced by initialize_from_command_line(), initialize_with_mcfi_list(), permitted_overlap(), and set_permitted_overlap().
◆ relevant_downstream_atoms_
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private |
Referenced by determine_all_match_relevant_downstream_atoms(), and relevant_downstream_atoms().
◆ score_output_file_name_
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Referenced by score_output_file_name().
◆ share_build_points_for_geomcsts_
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Referenced by initialize_scaffold_active_site_residue_list_from_command_line(), modify_pose_build_resids_from_endes_input(), set_active_site_residue_list_to_preexisting_partial_match(), set_original_scaffold_build_points(), set_original_scaffold_build_points_for_geometric_constraint(), upstream_pose_build_resids_for_geometric_constraint(), and use_different_build_points_for_each_geometric_constraint().
◆ upstream_downstream_atom_collision_tolerance_
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◆ upstream_downstream_residue_collision_score_cutoff_
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◆ upstream_downstream_residue_collision_Wfa_atr_
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◆ upstream_downstream_residue_collision_Wfa_rep_
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◆ upstream_downstream_residue_collision_Wfa_sol_
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◆ upstream_only_geom_cst_
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Referenced by determine_all_match_relevant_downstream_atoms(), and upstream_only_geom_cst().
◆ upstream_pose_
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Referenced by initialize_active_site_definition_from_command_line(), initialize_occupied_space_bounding_box_from_command_line(), initialize_scaffold_active_site_residue_list_from_command_line(), modify_pose_build_resids_from_endes_input(), remove_downstream_object_from_upstream_pose(), set_active_site_residue_list_to_preexisting_partial_match(), set_upstream_pose(), and upstream_pose().
◆ upstream_pose_name_
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Referenced by set_upstream_pose(), and upstream_pose_name().
◆ upstream_resids_and_radii_defining_active_site_
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◆ upstream_residue_collision_score_cutoff_
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◆ upstream_residue_collision_tolerance_
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◆ upstream_residue_collision_Wfa_atr_
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◆ upstream_residue_collision_Wfa_rep_
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◆ upstream_residue_collision_Wfa_sol_
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◆ use_input_sc_
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Referenced by initialize_from_command_line(), initialize_with_mcfi_list(), and use_input_sc().
The documentation for this class was generated from the following files:
- src/protocols/match/MatcherTask.hh
- src/protocols/match/MatcherTask.cc
