#include <LigandBindingResPlacer.hh>

Inheritance diagram for protocols::sewing::hashing::LigandBindingResPlacer:

Public Member Functions
	LigandBindingResPlacer ()
	Default constructor. More...

	LigandBindingResPlacer (utility::pointer::shared_ptr< std::map< char, LigandHashMap > > coords, data_storage::LigandResidueOP ligand_residue)
	Constructor with arguments. More...

std::map< std::pair < core::Size, core::Size > , std::set< LigandCoordInfo > >	identify_possible_binders (data_storage::SmartAssemblyCOP assembly)
	Checks all residue stubs in assembly vs metal coordinates to determine which residues are potentially metal-coordinating. Return a set of SmartSewingResidueOP. More...

core::conformation::ResidueOP	make_aligned_residue (data_storage::SmartSewingResidueOP, std::string)

std::pair < data_storage::SmartSegmentOP, bool >	choose_best_metal_coordinator (data_storage::SmartAssemblyOP assembly)
	Finds the best residue/rotamer to coordinate metal (Main function for class) More...

std::pair< LigandCoordInfo, core::Real >	best_rotamer_for_residue (std::pair< core::Size, core::Size > res, std::set< LigandCoordInfo > res_coord, data_storage::SmartAssemblyOP assembly)
	Finds the best residue/rotamer to coordinate metal for a given residue and returns for each residue type a pair of (LigandCoordInfo, distance) where distance is the distance of the metal from its ideal position. More...

void	replace_chimaera_ligand_parent (data_storage::SmartAssemblyOP assembly, data_storage::SmartSegmentOP chimaeric_segment, data_storage::LigandSegmentOP replacement_ligseg, bool change_n_terminal_parent, bool first_basis_is_n_terminal, core::Size chimaeric_contact_resnum, utility::vector1< std::pair< std::pair< core::Size, core::Size >, std::pair< LigandCoordInfo, core::Real > > > res_scores)

void	revert_last_added_contact (data_storage::SmartAssemblyOP assembly)

data_storage::LigandResidueOP	get_ligand () const

std::map< std::pair < core::Size, core::Size > , std::set< LigandCoordInfo > > const &	get_possible_coordinations () const

utility::pointer::shared_ptr < std::map< char, LigandHashMap > const >	get_ligand_local_coords () const

core::Size	contacts_remaining () const

core::Real	get_geometry_score_weight () const

core::Real	get_best_geometry_score () const

void	set_ligand (data_storage::LigandResidueOP lig)

void	set_geometry_score_weight (core::Real)

void	set_best_geometry_score (core::Real)

void	set_ligand_local_coords (utility::pointer::shared_ptr< std::map< char, LigandHashMap > > ligand_local_coords)

Static Public Member Functions
static void	parse_ligand_files (utility::vector1< data_storage::LigandDescription > &ligands)
	Parses the ligand file format. More...

static HashKey	generate_ligand_key (numeric::xyzVector< core::Real >)
	Generates a HashKey from an xyzVector of core::Real. More...

static void	parse_ideal_contacts (utility::tag::TagCOP tag, utility::vector1< data_storage::LigandDescription > &ligands)

static void	define_ideal_contacts_subelement (utility::tag::XMLSchemaSimpleSubelementList &subs, utility::tag::XMLSchemaDefinition &xsd)

static std::string	ligand_subtag_ct_namer (std::string tag)

Private Attributes
data_storage::LigandResidueOP	ligand_

utility::pointer::shared_ptr < std::map< char, LigandHashMap > >	ligand_local_coords_

std::map< std::pair < core::Size, core::Size > , std::set< LigandCoordInfo > >	possible_coordinations_

core::Size	contacts_to_make_

data_storage::LigandContactOP	last_contact_added_

core::Real	geometry_score_weight_

core::Real	best_geometry_score_ = 0

core::chemical::AtomTypeSetCAP	atom_types_

Detailed Description

Given a ligand and an assembly, this class identifies the potential best mutations (with chi angles) to make to add a coordinating residue to the ligand. Another class will test the geometries and make the mutations.

Constructor & Destructor Documentation

protocols::sewing::hashing::LigandBindingResPlacer::LigandBindingResPlacer ( )

Default constructor.

References atom_types_.

protocols::sewing::hashing::LigandBindingResPlacer::LigandBindingResPlacer	(	utility::pointer::shared_ptr< std::map< char, LigandHashMap > >	coords,
		data_storage::LigandResidueOP	ligand_residue
	)

Constructor with arguments.

References atom_types_, contacts_to_make_, protocols::simple_filters::coords(), ligand_, and ligand_local_coords_.

Member Function Documentation

std::pair< LigandCoordInfo, core::Real > protocols::sewing::hashing::LigandBindingResPlacer::best_rotamer_for_residue	(	std::pair< core::Size, core::Size >	res,
		std::set< LigandCoordInfo >	res_coord,
		data_storage::SmartAssemblyOP	assembly
	)

Finds the best residue/rotamer to coordinate metal for a given residue and returns for each residue type a pair of (LigandCoordInfo, distance) where distance is the distance of the metal from its ideal position.

References core::conformation::Residue::atom(), core::chemical::ResidueType::atom_base(), core::chemical::ResidueType::atom_name(), atom_types_, core::kinematics::distance(), ligand_, make_aligned_residue(), protocols::sewing::hashing::IdealContact::max_contacts, protocols::mean_field::min(), core::conformation::Residue::natoms(), protocols::sewing::hashing::IdealContact::preferred_contact_angle, protocols::sewing::hashing::IdealContact::preferred_dihedral_1, protocols::sewing::hashing::IdealContact::preferred_dihedral_2, protocols::sewing::hashing::IdealContact::preferred_distance, protocols::hybridization::score, protocols::TR(), core::conformation::Atom::type(), core::conformation::Residue::type(), and core::conformation::Atom::xyz().

Referenced by choose_best_metal_coordinator().

std::pair< data_storage::SmartSegmentOP, bool > protocols::sewing::hashing::LigandBindingResPlacer::choose_best_metal_coordinator ( data_storage::SmartAssemblyOP assembly )

Finds the best residue/rotamer to coordinate metal (Main function for class)

References best_geometry_score_, best_rotamer_for_residue(), contacts_to_make_, geometry_score_weight_, core::pose::full_model_info::get_residue(), identify_possible_binders(), last_contact_added_, core::sequence::left, ligand_, protocols::sewing::data_storage::SmartSegment::link_to(), make_aligned_residue(), core::scoring::pair, possible_coordinations_, replace_chimaera_ligand_parent(), protocols::sewing::data_storage::SmartSegment::set_is_vital(), and protocols::TR().

core::Size protocols::sewing::hashing::LigandBindingResPlacer::contacts_remaining ( ) const

References contacts_to_make_.

void protocols::sewing::hashing::LigandBindingResPlacer::define_ideal_contacts_subelement	(	utility::tag::XMLSchemaSimpleSubelementList &	subs,
		utility::tag::XMLSchemaDefinition &	xsd
	)

static

References ligand_subtag_ct_namer().

Referenced by protocols::sewing::hashing::AlignmentFileGeneratorMover::append_ligands_subelement().

HashKey protocols::sewing::hashing::LigandBindingResPlacer::generate_ligand_key ( numeric::xyzVector< core::Real > coords )

static

Generates a HashKey from an xyzVector of core::Real.

First identify possible metal binding residues Iterate over all residues in the set Find best coordinating rotamer for each residue per restype

References protocols::noesy_assign::round().

Referenced by identify_possible_binders(), and parse_ligand_files().

core::Real protocols::sewing::hashing::LigandBindingResPlacer::get_best_geometry_score ( ) const

References best_geometry_score_.

core::Real protocols::sewing::hashing::LigandBindingResPlacer::get_geometry_score_weight ( ) const

References geometry_score_weight_.

data_storage::LigandResidueOP protocols::sewing::hashing::LigandBindingResPlacer::get_ligand ( ) const

References ligand_.

utility::pointer::shared_ptr< std::map< char, LigandHashMap > const > protocols::sewing::hashing::LigandBindingResPlacer::get_ligand_local_coords ( ) const

References ligand_local_coords_.

std::map< std::pair< core::Size, core::Size >, std::set< LigandCoordInfo > > const & protocols::sewing::hashing::LigandBindingResPlacer::get_possible_coordinations ( ) const

References possible_coordinations_.

std::map< std::pair< core::Size, core::Size >, std::set< LigandCoordInfo > > protocols::sewing::hashing::LigandBindingResPlacer::identify_possible_binders ( data_storage::SmartAssemblyCOP assembly )

Checks all residue stubs in assembly vs metal coordinates to determine which residues are potentially metal-coordinating. Return a set of SmartSewingResidueOP.

First format: Map of (secstruct, map( restype, vector< LigandCoordInfo> ) ) Second format: Map of secstruct to a std::set of zinc HashKeys (generated the same basic way we do in Hasher)

References atom_types_, core::kinematics::distance(), core::sequence::end, generate_ligand_key(), core::kinematics::Stub::global2local(), ligand_, ligand_local_coords_, and protocols::TR().

Referenced by choose_best_metal_coordinator().

std::string protocols::sewing::hashing::LigandBindingResPlacer::ligand_subtag_ct_namer ( std::string tag )

static

Referenced by define_ideal_contacts_subelement().

core::conformation::ResidueOP protocols::sewing::hashing::LigandBindingResPlacer::make_aligned_residue	(	data_storage::SmartSewingResidueOP	base_res,
		std::string	type
	)

Iterate over all segments Iterate over all residues in the segment If it's a required residue, skip it Otherwise, convert it to a stub Transform the ligand's coordinates into the stub's local coordinates Convert the ligand atoms' coordinates into HashKeys Look for the HashKeys in the appropriate HashMap for this DSSP, and compare the atom name to see if it's a real match If it's there, add this residue to the map with the corresponding entries from LigandCoordInfo

References protocols::TR(), and protocols::kinmatch::xyz().

Referenced by best_rotamer_for_residue(), choose_best_metal_coordinator(), and replace_chimaera_ligand_parent().

void protocols::sewing::hashing::LigandBindingResPlacer::parse_ideal_contacts	(	utility::tag::TagCOP	tag,
		utility::vector1< data_storage::LigandDescription > &	ligands
	)

static

Referenced by protocols::sewing::movers::LigandBindingAssemblyMover::parse_my_tag().

void protocols::sewing::hashing::LigandBindingResPlacer::parse_ligand_files ( utility::vector1< data_storage::LigandDescription > & ligands )

static

Parses the ligand file format.

References protocols::simple_filters::dssp(), generate_ligand_key(), core::conformation::membrane::in, protocols::sewing::data_storage::ligand, protocols::sewing::hashing::LigandCoordInfo::local_coords, and protocols::TR().

Referenced by protocols::sewing::movers::LigandBindingAssemblyMover::parse_my_tag().

void protocols::sewing::hashing::LigandBindingResPlacer::replace_chimaera_ligand_parent	(	data_storage::SmartAssemblyOP	assembly,
		data_storage::SmartSegmentOP	chimaeric_segment,
		data_storage::LigandSegmentOP	replacement_ligseg,
		bool	change_n_terminal_parent,
		bool	first_basis_is_n_terminal,
		core::Size	chimaeric_contact_resnum,
		utility::vector1< std::pair< std::pair< core::Size, core::Size >, std::pair< LigandCoordInfo, core::Real > > >	res_scores
	)

For the given residue, does the following: 1) Looks the residue up in possible_coordinations_ Make a residue of the appropriate type and transform it onto res Iterate over LigandCoorInfo and for each one set the chi angles

References ligand_, and make_aligned_residue().

Referenced by choose_best_metal_coordinator().

void protocols::sewing::hashing::LigandBindingResPlacer::revert_last_added_contact ( data_storage::SmartAssemblyOP assembly )

References contacts_to_make_, protocols::sewing::data_storage::LigandSegment::get_nonconst_ligand_contact_indices(), last_contact_added_, and ligand_.

void protocols::sewing::hashing::LigandBindingResPlacer::set_best_geometry_score ( core::Real best )

References best_geometry_score_.

void protocols::sewing::hashing::LigandBindingResPlacer::set_geometry_score_weight ( core::Real gsw )

References geometry_score_weight_.

void protocols::sewing::hashing::LigandBindingResPlacer::set_ligand ( data_storage::LigandResidueOP lig )

References contacts_to_make_, and ligand_.

void protocols::sewing::hashing::LigandBindingResPlacer::set_ligand_local_coords ( utility::pointer::shared_ptr< std::map< char, LigandHashMap > > ligand_local_coords )

References ligand_local_coords_.

Member Data Documentation

core::chemical::AtomTypeSetCAP protocols::sewing::hashing::LigandBindingResPlacer::atom_types_

private

Referenced by best_rotamer_for_residue(), identify_possible_binders(), and LigandBindingResPlacer().

core::Real protocols::sewing::hashing::LigandBindingResPlacer::best_geometry_score_ = 0

private

Referenced by choose_best_metal_coordinator(), get_best_geometry_score(), and set_best_geometry_score().

core::Size protocols::sewing::hashing::LigandBindingResPlacer::contacts_to_make_

private

Referenced by choose_best_metal_coordinator(), contacts_remaining(), LigandBindingResPlacer(), revert_last_added_contact(), and set_ligand().

core::Real protocols::sewing::hashing::LigandBindingResPlacer::geometry_score_weight_

private

Referenced by choose_best_metal_coordinator(), get_geometry_score_weight(), and set_geometry_score_weight().

data_storage::LigandContactOP protocols::sewing::hashing::LigandBindingResPlacer::last_contact_added_

private

Referenced by choose_best_metal_coordinator(), and revert_last_added_contact().

data_storage::LigandResidueOP protocols::sewing::hashing::LigandBindingResPlacer::ligand_

private

Referenced by best_rotamer_for_residue(), choose_best_metal_coordinator(), get_ligand(), identify_possible_binders(), LigandBindingResPlacer(), replace_chimaera_ligand_parent(), revert_last_added_contact(), and set_ligand().

utility::pointer::shared_ptr< std::map< char, LigandHashMap > > protocols::sewing::hashing::LigandBindingResPlacer::ligand_local_coords_

private

Referenced by get_ligand_local_coords(), identify_possible_binders(), LigandBindingResPlacer(), and set_ligand_local_coords().

std::map< std::pair< core::Size, core::Size >, std::set< LigandCoordInfo> > protocols::sewing::hashing::LigandBindingResPlacer::possible_coordinations_

private

Referenced by choose_best_metal_coordinator(), and get_possible_coordinations().

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

src/protocols/sewing/hashing/LigandBindingResPlacer.hh
src/protocols/sewing/hashing/LigandBindingResPlacer.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation