#include <MatcherTask.hh>

Inheritance diagram for protocols::match::MatcherTask:

Collaboration diagram for protocols::match::MatcherTask:

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...

	MatcherTask (MatcherTask const &other)

MatcherTask const &	operator= (MatcherTask const &rhs)

virtual	~MatcherTask ()

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< 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 (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 (Size geom_cst_id, utility::vector1< 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 (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	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 (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	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< Size > const &	upstream_pose_build_resids_for_geometric_constraint (Size cst_id) const

std::map< core::Size, core::Size > const &	upstream_only_geom_cst () const

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

Size	n_to_output_per_group () const

std::list< std::string > const &	filter_names () const

std::string const &	upstream_pose_name () const

std::string const &	cstfile_name () const

std::string const &	grouper_name () const

std::string const &	evaluator_name () const

std::string const &	output_writer_name () const

std::string const &	output_file_name () const

Real	grouper_ds_rmsd () const

bool	output_matchres_only () const

utility::vector1< core::Size > const &	geom_csts_downstream_output () const

toolbox::match_enzdes_util::EnzConstraintIOCOP	enz_input_data () const

bool	filter_upstream_residue_collisions () const

bool	filter_upstream_collisions_by_score () const

Real	upstream_residue_collision_tolerance () const

Real	upstream_residue_collision_score_cutoff () const

Real	upstream_residue_collision_Wfa_atr () const

Real	upstream_residue_collision_Wfa_rep () const

Real	upstream_residue_collision_Wfa_sol () const

bool	filter_upstream_downstream_collisions () const

bool	filter_upstream_downstream_collisions_by_score () const

Real	upstream_downstream_atom_collision_tolerance () const

Real	upstream_downstream_residue_collision_score_cutoff () const

Real	upstream_downstream_residue_collision_Wfa_atr () const

Real	upstream_downstream_residue_collision_Wfa_rep () const

Real	upstream_downstream_residue_collision_Wfa_sol () const

bool	define_match_by_single_downstream_positioning () const

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	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< Size >	generic_pose_build_resids_

utility::vector1 < utility::vector1< Size > >	per_cst_pose_build_resids_

std::map< core::Size, core::Size >	upstream_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< Size, Real > >	upstream_resids_and_radii_defining_active_site_

std::list< core::id::AtomID >	downstream_atoms_required_inside_active_site_

utility::vector1< Size >	downstream_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_

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_

bool	output_matchres_only_

utility::vector1< core::Size >	geom_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_

Member Typedef Documentation

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

typedef core::Real protocols::match::MatcherTask::Real

typedef core::Size protocols::match::MatcherTask::Size

typedef core::Vector protocols::match::MatcherTask::Vector

Constructor & Destructor Documentation

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

Construction and Destruction.

protocols::match::MatcherTask::MatcherTask ( MatcherTask const & other)

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

virtual

Member Function Documentation

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

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

References filter_names_.

void protocols::match::MatcherTask::append_downstream_atom_to_active_site_required_list ( core::id::AtomID atid)

References downstream_atoms_required_inside_active_site_.

void protocols::match::MatcherTask::append_upstream_resiue_as_defining_active_site	(	Size	resid,
		Real	radius
	)

References gridlig_active_site_definition_, protocols::match::TR(), and upstream_resids_and_radii_defining_active_site_.

void protocols::match::MatcherTask::clear_downstream_orientation_atoms ( )

References 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)

References gridlig_active_site_definition_, gridlig_fname_, protocols::match::TR(), and upstream_resids_and_radii_defining_active_site_.

void protocols::match::MatcherTask::define_active_site_from_residue_radii_list ( )

References gridlig_active_site_definition_.

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().

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

References define_match_by_single_downstream_positioning_.

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 enz_input_data_, relevant_downstream_atoms_, and upstream_only_geom_cst_.

Referenced by initialize_enzdes_input_data_from_command_line(), and set_enz_input_data().

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().

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().

core::pose::PoseCOP protocols::match::MatcherTask::downstream_pose ( ) const

References downstream_pose_.

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

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

References dynamic_grid_refinement_.

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

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

References enumerate_ligand_rotamers_.

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

toolbox::match_enzdes_util::EnzConstraintIOCOP protocols::match::MatcherTask::enz_input_data ( ) const

References enz_input_data_.

Referenced by initialize_enzdes_input_data_from_command_line(), and protocols::match::Matcher::initialize_from_task().

MatcherTask::Vector protocols::match::MatcherTask::euclidean_bin_widths ( ) const

References euclidean_bin_widths_.

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

MatcherTask::Vector protocols::match::MatcherTask::euler_bin_widths ( ) const

References euler_bin_widths_.

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

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)

References filter_upstream_collisions_by_score_, and filter_upstream_residue_collisions_.

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

References filter_upstream_collisions_by_score_.

void protocols::match::MatcherTask::filter_upstream_downstream_collisions ( bool setting)

References filter_upstream_and_downstream_residue_collisions_.

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

References filter_upstream_and_downstream_residue_collisions_.

void protocols::match::MatcherTask::filter_upstream_downstream_collisions_by_score ( bool setting)

References filter_upstream_and_downstream_collisions_by_score_.

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

References filter_upstream_and_downstream_collisions_by_score_.

void protocols::match::MatcherTask::filter_upstream_residue_collisions ( bool setting)

References filter_upstream_residue_collisions_.

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

References filter_upstream_residue_collisions_.

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().

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.

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().

void protocols::match::MatcherTask::initialize_enzdes_input_data_from_command_line ( )

private

References cstfile_name_, determine_all_match_relevant_downstream_atoms(), enz_input_data(), enz_input_data_, core::chemical::FA_STANDARD, and core::chemical::ChemicalManager::get_instance().

Referenced by initialize_from_command_line().

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

Initialize many parameters from the command line options.

References 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_.

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_, core::io::serialization::size(), protocols::match::TR(), and upstream_pose_.

Referenced by initialize_from_command_line().

void protocols::match::MatcherTask::initialize_orientation_atoms_from_command_line ( )

private

References downstream_orientation_atoms_, and downstream_pose_.

Referenced by initialize_from_command_line().

void protocols::match::MatcherTask::initialize_output_options_from_command_line ( )

private

References define_match_by_single_downstream_positioning_, enz_input_data_, geom_csts_downstream_output_, grouper_ds_rmsd_, grouper_name_, output_matchres_only_, output_writer_name_, and protocols::match::TR().

Referenced by initialize_from_command_line().

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(), per_cst_pose_build_resids_, share_build_points_for_geomcsts_, and upstream_pose_.

Referenced by initialize_from_command_line().

void protocols::match::MatcherTask::initialize_upstream_downstream_collision_filter_data_from_command_line ( )

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().

void protocols::match::MatcherTask::initialize_upstream_residue_collision_filter_data_from_command_line ( )

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().

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_, per_cst_pose_build_resids_, share_build_points_for_geomcsts_, core::io::pdb::split(), protocols::match::TR(), and upstream_pose_.

Referenced by initialize_from_command_line().

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

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

References n_to_output_per_group_.

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

References n_to_output_per_group_.

MatcherTask::BoundingBox const & protocols::match::MatcherTask::occ_space_bounding_box ( ) const

References occ_space_bounding_box_.

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

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().

MatcherTask const & protocols::match::MatcherTask::operator= ( MatcherTask const & rhs)

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_.

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

References permitted_overlap_.

Referenced by protocols::match::Matcher::initialize_from_task(), and set_permitted_overlap().

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().

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::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().

void protocols::match::MatcherTask::set_downstream_orientation_atoms ( utility::vector1< core::id::AtomID > const & orientation_atoms)

References downstream_orientation_atoms_, downstream_pose_, and validate_downstream_orientation_atoms().

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

References downstream_orientation_atoms_, downstream_pose_, and validate_downstream_orientation_atoms().

void protocols::match::MatcherTask::set_downstream_pose	(	core::pose::Pose const &	pose,
		utility::vector1< core::id::AtomID > const &	orientation_atoms
	)

References downstream_orientation_atoms_, downstream_pose_, and validate_downstream_orientation_atoms().

void protocols::match::MatcherTask::set_enumerate_ligand_rotamers ( bool setting)

References enumerate_ligand_rotamers_.

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)

References ignore_cmdline_for_build_points_.

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)

References only_enumerate_non_match_redundant_ligand_rotamers_.

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

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

References generic_pose_build_resids_, per_cst_pose_build_resids_, and share_build_points_for_geomcsts_.

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

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

References per_cst_pose_build_resids_, and share_build_points_for_geomcsts_.

Referenced by set_active_site_residue_list_to_preexisting_partial_match().

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)

Setup.

References core::pose::Pose::pdb_info(), upstream_pose_, and upstream_pose_name_.

void protocols::match::MatcherTask::upstream_downstream_atom_collision_tolerance ( Real setting)

References upstream_downstream_atom_collision_tolerance_.

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

References upstream_downstream_atom_collision_tolerance_.

void protocols::match::MatcherTask::upstream_downstream_residue_collision_score_cutoff ( Real setting)

References upstream_downstream_residue_collision_score_cutoff_.

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

References upstream_downstream_residue_collision_score_cutoff_.

void protocols::match::MatcherTask::upstream_downstream_residue_collision_Wfa_atr ( Real setting)

References upstream_downstream_residue_collision_Wfa_atr_.

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

References upstream_downstream_residue_collision_Wfa_atr_.

void protocols::match::MatcherTask::upstream_downstream_residue_collision_Wfa_rep ( Real setting)

References upstream_downstream_residue_collision_Wfa_rep_.

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

References upstream_downstream_residue_collision_Wfa_rep_.

void protocols::match::MatcherTask::upstream_downstream_residue_collision_Wfa_sol ( Real setting)

References upstream_downstream_residue_collision_Wfa_sol_.

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

References upstream_downstream_residue_collision_Wfa_sol_.

std::map< core::Size, core::Size > const & protocols::match::MatcherTask::upstream_only_geom_cst ( ) const

References upstream_only_geom_cst_.

core::pose::PoseCOP protocols::match::MatcherTask::upstream_pose ( ) const

References upstream_pose_.

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

utility::vector1< core::Size > const & protocols::match::MatcherTask::upstream_pose_build_resids_for_geometric_constraint ( 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().

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)

References upstream_residue_collision_score_cutoff_.

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

References upstream_residue_collision_score_cutoff_.

void protocols::match::MatcherTask::upstream_residue_collision_tolerance ( Real setting)

References upstream_residue_collision_tolerance_.

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

References upstream_residue_collision_tolerance_.

void protocols::match::MatcherTask::upstream_residue_collision_Wfa_atr ( Real setting)

References upstream_residue_collision_Wfa_atr_.

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

References upstream_residue_collision_Wfa_atr_.

void protocols::match::MatcherTask::upstream_residue_collision_Wfa_rep ( Real setting)

References upstream_residue_collision_Wfa_rep_.

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

References upstream_residue_collision_Wfa_rep_.

void protocols::match::MatcherTask::upstream_residue_collision_Wfa_sol ( Real setting)

References upstream_residue_collision_Wfa_sol_.

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

References upstream_residue_collision_Wfa_sol_.

void protocols::match::MatcherTask::use_different_build_points_for_each_geometric_constraint ( Size n_geometric_constraints)

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

References per_cst_pose_build_resids_, and share_build_points_for_geomcsts_.

Referenced by set_active_site_residue_list_to_preexisting_partial_match().

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

References use_input_sc_.

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

void protocols::match::MatcherTask::validate_downstream_orientation_atoms ( ) const

private

Referenced by set_downstream_orientation_atoms(), and set_downstream_pose().