#include <RigidLigandBuilder.hh>

Inheritance diagram for protocols::match::downstream::RigidLigandBuilder:

Collaboration diagram for protocols::match::downstream::RigidLigandBuilder:

Public Types
typedef DownstreamBuilder	parent

Public Types inherited from protocols::match::downstream::DownstreamBuilder
typedef utility::pointer::ReferenceCount	parent

typedef core::id::AtomID	AtomID

typedef core::Vector	Vector

typedef core::Real	Real

typedef numeric::HomogeneousTransform < Real >	HTReal

Public Member Functions
	RigidLigandBuilder ()

	RigidLigandBuilder (RigidLigandBuilder const &)

virtual	~RigidLigandBuilder ()

virtual DownstreamBuilderOP	clone () const

virtual std::list< Hit >	build (HTReal const &atom3_frame, Size const scaffold_build_point_id, Size const upstream_conf_id, Size const external_geometry_id, core::conformation::Residue const &upstream_residue) const

virtual void	set_bb_grid (BumpGridCOP bbgrid)

virtual bool	hits_potentially_incompatible () const
	In case downstream builders can return hits that are incompatible with each other (e.g. different ligand conformations ) the matcher needs to know about this to allow for speedy match enumeration. More...

virtual bool	compatible (Hit const &my_hit, DownstreamBuilder const &other, Hit const &other_hit, bool first_dispatch=true) const

virtual bool	compatible (Hit const &my_hit, RigidLigandBuilder const &other, Hit const &other_hit, bool first_dispatch=true) const

virtual void	require_atom_to_reside_in_active_site (core::id::AtomID const &id)

virtual ProbeRadius	atom1_radius () const

virtual ProbeRadius	atom2_radius () const

virtual ProbeRadius	atom3_radius () const

virtual bool	atom1_belongs_in_active_site () const

virtual bool	atom2_belongs_in_active_site () const

virtual bool	atom3_belongs_in_active_site () const

virtual Real	atom1_atom2_distance () const

virtual Real	atom2_atom3_distance () const

virtual Real	atom1_atom2_atom3_angle () const
	Returns an angle in degrees between the three downstream atoms. More...

virtual void	coordinates_from_hit (Hit const &hit, utility::vector1< AtomID > const &atom_indices, utility::vector1< Vector > &atom_coords) const

virtual core::pose::PoseCOP	downstream_pose_from_hit (Hit const &hit) const

virtual Size	n_possible_hits_per_at3frame () const

virtual toolbox::match_enzdes_util::LigandConformerOP	get_lig_conformers (core::Size conf_id) const

virtual core::chemical::ResidueTypeCOP	get_upstream_restype () const

void	initialize_from_residue (Size atom1, Size atom2, Size atom3, Size orientation_atom1, Size orientation_atom2, Size orientation_atom3, core::conformation::Residue const &residue)
	Specify the residue, with coordinates, that's being used as the downstream partner. This class is meant to be used in conjuction with the ClassicMatchAglrotihm, and therefore the initialization routines are specific for that algorithm. In this initialization function, one must list atoms "D1, D2 and D3" in the convention of describing the rigid-body orientation between three atoms of the upstream partner (atoms U3, U2 & U1) and three atoms of the downstream partner (atoms D1, D2 & D3) in terms of 2 angles, 1 distance, and 3 dihedrals. The user must also list the 3 atoms used to define the orientation frame of the downstream ligand. It is essential to the matching algorithm that the same three orientation atoms are used for all RigidLigandBuilders. More...

void	initialize_upstream_residue (core::chemical::ResidueTypeCOP upstream_res, core::scoring::etable::count_pair::CountPairFunctionCOP count_pair=0)

void	ignore_h_collisions (bool setting)

Public Member Functions inherited from protocols::match::downstream::DownstreamBuilder
	DownstreamBuilder ()

	DownstreamBuilder (DownstreamBuilder const &)

virtual	~DownstreamBuilder ()

void	set_occupied_space_hash (OccupiedSpaceHashCOP occ_space)

void	set_active_site_grid (ActiveSiteGridCOP active_site_grid)

virtual bool	compatible (Hit const &my_hit, LigandConformerBuilder const &other, Hit const &other_hit, bool first_dispatch=true) const

Private Member Functions
void	initialize_upstream_nonbonded_min_separation_d2 ()

Private Attributes
core::chemical::ResidueTypeCOP	downstream_restype_

core::chemical::ResidueTypeCOP	upstream_restype_

bool	ignore_h_collisions_

utility::fixedsizearray1< Size, 3 >	orientation_atoms_

utility::fixedsizearray1< Size, 3 >	atoms_123_

utility::fixedsizearray1 < ProbeRadius, 3 >	radii_123_

utility::fixedsizearray1< bool, 3 >	ats123_reqd_in_active_site_

utility::vector1< ProbeRadius >	atom_radii_

utility::vector1< bool >	atom_required_in_active_site_

utility::vector1< Size >	non_collision_detection_atoms_reqd_in_active_site_

utility::vector1 < toolbox::match_enzdes_util::LigandConformerOP >	lig_conformers_

utility::vector1 < utility::vector1< std::pair < Size, Real > > >	min_sep_d2_from_upstream_atoms_

Additional Inherited Members
Protected Member Functions inherited from protocols::match::downstream::DownstreamBuilder
bool	bbgrid_set () const

BumpGrid const &	bbgrid () const

bool	occ_space_set () const

OccupiedSpaceHash const &	occ_space () const

bool	active_site_grid_set () const

ActiveSiteGrid const &	active_site_grid () const

Detailed Description

Definition at line 55 of file RigidLigandBuilder.hh.

Member Typedef Documentation

typedef DownstreamBuilder protocols::match::downstream::RigidLigandBuilder::parent

Definition at line 57 of file RigidLigandBuilder.hh.

Constructor & Destructor Documentation

protocols::match::downstream::RigidLigandBuilder::RigidLigandBuilder ( )

Definition at line 51 of file RigidLigandBuilder.cc.

Referenced by clone().

protocols::match::downstream::RigidLigandBuilder::RigidLigandBuilder ( RigidLigandBuilder const & other)

Definition at line 58 of file RigidLigandBuilder.cc.

References lig_conformers_.

protocols::match::downstream::RigidLigandBuilder::~RigidLigandBuilder ( )

virtual

Definition at line 96 of file RigidLigandBuilder.cc.

Member Function Documentation

RigidLigandBuilder::Real protocols::match::downstream::RigidLigandBuilder::atom1_atom2_atom3_angle ( ) const

virtual

Returns an angle in degrees between the three downstream atoms.

Implements protocols::match::downstream::DownstreamBuilder.

Definition at line 309 of file RigidLigandBuilder.cc.

References downstream_restype_, and lig_conformers_.

RigidLigandBuilder::Real protocols::match::downstream::RigidLigandBuilder::atom1_atom2_distance ( ) const

virtual

Implements protocols::match::downstream::DownstreamBuilder.

Definition at line 292 of file RigidLigandBuilder.cc.

References downstream_restype_, and lig_conformers_.

bool protocols::match::downstream::RigidLigandBuilder::atom1_belongs_in_active_site ( ) const

virtual

Implements protocols::match::downstream::DownstreamBuilder.

Definition at line 274 of file RigidLigandBuilder.cc.

References ats123_reqd_in_active_site_.

ProbeRadius protocols::match::downstream::RigidLigandBuilder::atom1_radius ( ) const

virtual

Implements protocols::match::downstream::DownstreamBuilder.

Definition at line 249 of file RigidLigandBuilder.cc.

References downstream_restype_, and radii_123_.

RigidLigandBuilder::Real protocols::match::downstream::RigidLigandBuilder::atom2_atom3_distance ( ) const

virtual

Implements protocols::match::downstream::DownstreamBuilder.

Definition at line 300 of file RigidLigandBuilder.cc.

References downstream_restype_, and lig_conformers_.

bool protocols::match::downstream::RigidLigandBuilder::atom2_belongs_in_active_site ( ) const

virtual

Implements protocols::match::downstream::DownstreamBuilder.

Definition at line 280 of file RigidLigandBuilder.cc.

References ats123_reqd_in_active_site_.

ProbeRadius protocols::match::downstream::RigidLigandBuilder::atom2_radius ( ) const

virtual

Implements protocols::match::downstream::DownstreamBuilder.

Definition at line 258 of file RigidLigandBuilder.cc.

References downstream_restype_, and radii_123_.

bool protocols::match::downstream::RigidLigandBuilder::atom3_belongs_in_active_site ( ) const

virtual

Implements protocols::match::downstream::DownstreamBuilder.

Definition at line 286 of file RigidLigandBuilder.cc.

References ats123_reqd_in_active_site_.

ProbeRadius protocols::match::downstream::RigidLigandBuilder::atom3_radius ( ) const

virtual

Implements protocols::match::downstream::DownstreamBuilder.

Definition at line 266 of file RigidLigandBuilder.cc.

References downstream_restype_, and radii_123_.

std::list< Hit > protocols::match::downstream::RigidLigandBuilder::build	(	HTReal const &	atom3_frame,
		Size const	scaffold_build_point_id,
		Size const	upstream_conf_id,
		Size const	external_geometry_id,
		core::conformation::Residue const &	upstream_residue
	)		const

virtual

Implements protocols::match::downstream::DownstreamBuilder.

Definition at line 106 of file RigidLigandBuilder.cc.

References protocols::match::downstream::DownstreamBuilder::active_site_grid(), atom_radii_, atom_required_in_active_site_, protocols::match::downstream::DownstreamBuilder::bbgrid(), protocols::match::downstream::DownstreamBuilder::bbgrid_set(), downstream_restype_, protocols::match::Hit::first(), lig_conformers_, min_sep_d2_from_upstream_atoms_, non_collision_detection_atoms_reqd_in_active_site_, protocols::match::downstream::DownstreamBuilder::occ_space(), protocols::match::downstream::DownstreamBuilder::occ_space_set(), protocols::match::Hit::second(), core::conformation::Residue::type(), upstream_restype_, core::conformation::Residue::xyz(), and protocols::match::ZERO.

DownstreamBuilderOP protocols::match::downstream::RigidLigandBuilder::clone ( ) const

virtual

Implements protocols::match::downstream::DownstreamBuilder.

Definition at line 99 of file RigidLigandBuilder.cc.

References RigidLigandBuilder().

bool protocols::match::downstream::RigidLigandBuilder::compatible	(	Hit const &	my_hit,
		DownstreamBuilder const &	other,
		Hit const &	other_hit,
		bool	first_dispatch = `true`
	)		const

virtual

Reimplemented from protocols::match::downstream::DownstreamBuilder.

Definition at line 204 of file RigidLigandBuilder.cc.

References protocols::match::downstream::DownstreamBuilder::compatible().

Referenced by protocols::match::downstream::DownstreamBuilder::compatible().

bool protocols::match::downstream::RigidLigandBuilder::compatible	(	Hit const &	my_hit,
		RigidLigandBuilder const &	other,
		Hit const &	other_hit,
		bool	first_dispatch = `true`
	)		const

virtual

RigidLigandBuilder hits are always compatible, because there is only one ligand conformation.

Reimplemented from protocols::match::downstream::DownstreamBuilder.

Definition at line 217 of file RigidLigandBuilder.cc.

void protocols::match::downstream::RigidLigandBuilder::coordinates_from_hit	(	Hit const &	hit,
		utility::vector1< AtomID > const &	atom_indices,
		utility::vector1< Vector > &	atom_coords
	)		const

virtual

Implements protocols::match::downstream::DownstreamBuilder.

Definition at line 317 of file RigidLigandBuilder.cc.

References lig_conformers_, and protocols::match::Hit::second().

core::pose::PoseCOP protocols::match::downstream::RigidLigandBuilder::downstream_pose_from_hit ( Hit const & hit) const

virtual

Implements protocols::match::downstream::DownstreamBuilder.

Definition at line 334 of file RigidLigandBuilder.cc.

References downstream_restype_, lig_conformers_, core::conformation::Residue::natoms(), protocols::match::Hit::second(), and core::conformation::Residue::set_xyz().

toolbox::match_enzdes_util::LigandConformerOP protocols::match::downstream::RigidLigandBuilder::get_lig_conformers ( core::Size conf_id) const

virtual

Implements protocols::match::downstream::DownstreamBuilder.

Definition at line 612 of file RigidLigandBuilder.cc.

References lig_conformers_.

core::chemical::ResidueTypeCOP protocols::match::downstream::RigidLigandBuilder::get_upstream_restype ( ) const

virtual

Implements protocols::match::downstream::DownstreamBuilder.

Definition at line 624 of file RigidLigandBuilder.cc.

References upstream_restype_.

virtual bool protocols::match::downstream::RigidLigandBuilder::hits_potentially_incompatible ( ) const

inlinevirtual

In case downstream builders can return hits that are incompatible with each other (e.g. different ligand conformations ) the matcher needs to know about this to allow for speedy match enumeration.

Implements protocols::match::downstream::DownstreamBuilder.

Definition at line 90 of file RigidLigandBuilder.hh.

void protocols::match::downstream::RigidLigandBuilder::ignore_h_collisions ( bool setting)

Definition at line 582 of file RigidLigandBuilder.cc.

References downstream_restype_, and ignore_h_collisions_.

void protocols::match::downstream::RigidLigandBuilder::initialize_from_residue	(	Size	atom1,
		Size	atom2,
		Size	atom3,
		Size	orientation_atom1,
		Size	orientation_atom2,
		Size	orientation_atom3,
		core::conformation::Residue const &	residue
	)

Specify the residue, with coordinates, that's being used as the downstream partner. This class is meant to be used in conjuction with the ClassicMatchAglrotihm, and therefore the initialization routines are specific for that algorithm. In this initialization function, one must list atoms "D1, D2 and D3" in the convention of describing the rigid-body orientation between three atoms of the upstream partner (atoms U3, U2 & U1) and three atoms of the downstream partner (atoms D1, D2 & D3) in terms of 2 angles, 1 distance, and 3 dihedrals. The user must also list the 3 atoms used to define the orientation frame of the downstream ligand. It is essential to the matching algorithm that the same three orientation atoms are used for all RigidLigandBuilders.

Definition at line 367 of file RigidLigandBuilder.cc.

References core::conformation::Residue::atom(), atom_radii_, atom_required_in_active_site_, core::conformation::Residue::atom_type(), atoms_123_, downstream_restype_, core::chemical::AtomType::element(), ignore_h_collisions_, lig_conformers_, core::conformation::Residue::natoms(), orientation_atoms_, protocols::match::probe_radius_for_atom_type(), radii_123_, core::conformation::Atom::type(), core::conformation::Residue::type(), and protocols::match::ZERO.

void protocols::match::downstream::RigidLigandBuilder::initialize_upstream_nonbonded_min_separation_d2 ( )

private

Definition at line 593 of file RigidLigandBuilder.cc.

References atom_radii_, protocols::match::downstream::DownstreamBuilder::bbgrid(), protocols::match::downstream::DownstreamBuilder::bbgrid_set(), lig_conformers_, min_sep_d2_from_upstream_atoms_, protocols::match::probe_radius_for_atom_type(), protocols::match::BumpGrid::required_separation_distance(), and upstream_restype_.

Referenced by initialize_upstream_residue(), and set_bb_grid().

void protocols::match::downstream::RigidLigandBuilder::initialize_upstream_residue	(	core::chemical::ResidueTypeCOP	upstream_res,
		core::scoring::etable::count_pair::CountPairFunctionCOP	count_pair = `0`
	)

Definition at line 412 of file RigidLigandBuilder.cc.

References atom_radii_, atoms_123_, protocols::match::downstream::DownstreamBuilder::bbgrid_set(), downstream_restype_, initialize_upstream_nonbonded_min_separation_d2(), lig_conformers_, min_sep_d2_from_upstream_atoms_, radii_123_, upstream_restype_, and protocols::match::ZERO.

RigidLigandBuilder::Size protocols::match::downstream::RigidLigandBuilder::n_possible_hits_per_at3frame ( ) const

virtual

Implements protocols::match::downstream::DownstreamBuilder.

Definition at line 359 of file RigidLigandBuilder.cc.

void protocols::match::downstream::RigidLigandBuilder::require_atom_to_reside_in_active_site ( core::id::AtomID const & id)

virtual

Implements protocols::match::downstream::DownstreamBuilder.

Definition at line 229 of file RigidLigandBuilder.cc.

References atom_required_in_active_site_, atoms_123_, ats123_reqd_in_active_site_, downstream_restype_, lig_conformers_, and non_collision_detection_atoms_reqd_in_active_site_.

void protocols::match::downstream::RigidLigandBuilder::set_bb_grid ( BumpGridCOP bbgrid)

virtual

Reimplemented from protocols::match::downstream::DownstreamBuilder.

Definition at line 193 of file RigidLigandBuilder.cc.

References initialize_upstream_nonbonded_min_separation_d2(), protocols::match::downstream::DownstreamBuilder::set_bb_grid(), and upstream_restype_.

Member Data Documentation

utility::vector1< ProbeRadius > protocols::match::downstream::RigidLigandBuilder::atom_radii_

private

Definition at line 242 of file RigidLigandBuilder.hh.

Referenced by build(), initialize_from_residue(), initialize_upstream_nonbonded_min_separation_d2(), and initialize_upstream_residue().

utility::vector1< bool > protocols::match::downstream::RigidLigandBuilder::atom_required_in_active_site_

private

Definition at line 243 of file RigidLigandBuilder.hh.

Referenced by build(), initialize_from_residue(), and require_atom_to_reside_in_active_site().

utility::fixedsizearray1< Size, 3 > protocols::match::downstream::RigidLigandBuilder::atoms_123_

private

Definition at line 238 of file RigidLigandBuilder.hh.

Referenced by initialize_from_residue(), initialize_upstream_residue(), and require_atom_to_reside_in_active_site().

utility::fixedsizearray1< bool, 3 > protocols::match::downstream::RigidLigandBuilder::ats123_reqd_in_active_site_

private

Definition at line 240 of file RigidLigandBuilder.hh.

Referenced by atom1_belongs_in_active_site(), atom2_belongs_in_active_site(), atom3_belongs_in_active_site(), and require_atom_to_reside_in_active_site().

core::chemical::ResidueTypeCOP protocols::match::downstream::RigidLigandBuilder::downstream_restype_

private

Definition at line 229 of file RigidLigandBuilder.hh.

Referenced by atom1_atom2_atom3_angle(), atom1_atom2_distance(), atom1_radius(), atom2_atom3_distance(), atom2_radius(), atom3_radius(), build(), downstream_pose_from_hit(), ignore_h_collisions(), initialize_from_residue(), initialize_upstream_residue(), and require_atom_to_reside_in_active_site().

bool protocols::match::downstream::RigidLigandBuilder::ignore_h_collisions_

private

Definition at line 232 of file RigidLigandBuilder.hh.

Referenced by ignore_h_collisions(), and initialize_from_residue().

utility::vector1< toolbox::match_enzdes_util::LigandConformerOP > protocols::match::downstream::RigidLigandBuilder::lig_conformers_

private

Definition at line 248 of file RigidLigandBuilder.hh.

Referenced by atom1_atom2_atom3_angle(), atom1_atom2_distance(), atom2_atom3_distance(), build(), coordinates_from_hit(), downstream_pose_from_hit(), get_lig_conformers(), initialize_from_residue(), initialize_upstream_nonbonded_min_separation_d2(), initialize_upstream_residue(), require_atom_to_reside_in_active_site(), and RigidLigandBuilder().

utility::vector1< utility::vector1< std::pair< Size, Real > > > protocols::match::downstream::RigidLigandBuilder::min_sep_d2_from_upstream_atoms_

private

Detect collision between the upstream residue (sidechain?!) conformation and the atoms of the downstream residue

Definition at line 252 of file RigidLigandBuilder.hh.

Referenced by build(), initialize_upstream_nonbonded_min_separation_d2(), and initialize_upstream_residue().

utility::vector1< Size > protocols::match::downstream::RigidLigandBuilder::non_collision_detection_atoms_reqd_in_active_site_

private

Definition at line 245 of file RigidLigandBuilder.hh.

Referenced by build(), and require_atom_to_reside_in_active_site().

utility::fixedsizearray1< Size, 3 > protocols::match::downstream::RigidLigandBuilder::orientation_atoms_

private

The indices of the three atoms defining the orientation of the ligand in the global coordinate frame These indices are in the restype indexing of atoms.

Definition at line 237 of file RigidLigandBuilder.hh.

Referenced by initialize_from_residue().

utility::fixedsizearray1< ProbeRadius, 3 > protocols::match::downstream::RigidLigandBuilder::radii_123_

private

Definition at line 239 of file RigidLigandBuilder.hh.

Referenced by atom1_radius(), atom2_radius(), atom3_radius(), initialize_from_residue(), and initialize_upstream_residue().