#include <LigandConformerBuilder.hh>

Inheritance diagram for protocols::match::downstream::LigandConformerBuilder:

Collaboration diagram for protocols::match::downstream::LigandConformerBuilder:

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
	LigandConformerBuilder ()

	LigandConformerBuilder (LigandConformerBuilder const &)

virtual	~LigandConformerBuilder ()

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

void	determine_redundant_conformer_groups (utility::vector1< core::Size > const &relevant_atom_indices)
	goes through the list of conformers and does rms calculations (overlaid on the relevant_atom_indices) between them. any conformers that have an rms < rmsd_unique_cutoff_ will be grouped together in a conformer_group More...

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, LigandConformerBuilder 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

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 LigandConformerBuilders. 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)

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

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

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, RigidLigandBuilder const &other, Hit const &other_hit, bool first_dispatch=true) const

Private Member Functions
std::list< Hit >	build_conformer_group (Size const confgrp_id, 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

void	initialize_upstream_nonbonded_min_separation_d2 ()

void	initialize_conformers (core::conformation::Residue const &residue)

Private Attributes
core::chemical::ResidueTypeCOP	downstream_restype_

core::chemical::ResidueTypeCOP	upstream_restype_

bool	ignore_h_collisions_

bool	idealize_conformers_

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_

Real	rmsd_unique_cutoff_
	Grouped into sets compatible ligand conformers. More...

utility::vector1 < utility::vector1< Size > >	conformer_group_indices_

utility::vector1< Size >	conformer_group_for_conformer_

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 57 of file LigandConformerBuilder.hh.

Member Typedef Documentation

typedef DownstreamBuilder protocols::match::downstream::LigandConformerBuilder::parent

Definition at line 59 of file LigandConformerBuilder.hh.

Constructor & Destructor Documentation

protocols::match::downstream::LigandConformerBuilder::LigandConformerBuilder ( )

Definition at line 64 of file LigandConformerBuilder.cc.

Referenced by clone().

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

Definition at line 73 of file LigandConformerBuilder.cc.

References lig_conformers_.

protocols::match::downstream::LigandConformerBuilder::~LigandConformerBuilder ( )

virtual

Definition at line 117 of file LigandConformerBuilder.cc.

Member Function Documentation

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

virtual

Returns an angle in degrees between the three downstream atoms.

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

Definition at line 313 of file LigandConformerBuilder.cc.

References downstream_restype_, and lig_conformers_.

Referenced by initialize_conformers().

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

virtual

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

Definition at line 296 of file LigandConformerBuilder.cc.

References downstream_restype_, and lig_conformers_.

Referenced by initialize_conformers().

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

virtual

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

Definition at line 278 of file LigandConformerBuilder.cc.

References ats123_reqd_in_active_site_.

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

virtual

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

Definition at line 253 of file LigandConformerBuilder.cc.

References downstream_restype_, and radii_123_.

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

virtual

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

Definition at line 304 of file LigandConformerBuilder.cc.

References downstream_restype_, and lig_conformers_.

Referenced by initialize_conformers().

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

virtual

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

Definition at line 284 of file LigandConformerBuilder.cc.

References ats123_reqd_in_active_site_.

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

virtual

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

Definition at line 262 of file LigandConformerBuilder.cc.

References downstream_restype_, and radii_123_.

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

virtual

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

Definition at line 290 of file LigandConformerBuilder.cc.

References ats123_reqd_in_active_site_.

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

virtual

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

Definition at line 270 of file LigandConformerBuilder.cc.

References downstream_restype_, and radii_123_.

std::list< Hit > protocols::match::downstream::LigandConformerBuilder::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 127 of file LigandConformerBuilder.cc.

References build_conformer_group(), and conformer_group_indices_.

std::list< Hit > protocols::match::downstream::LigandConformerBuilder::build_conformer_group	(	Size const	confgrp_id,
		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

private

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

virtual

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

Definition at line 120 of file LigandConformerBuilder.cc.

References LigandConformerBuilder().

bool protocols::match::downstream::LigandConformerBuilder::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 207 of file LigandConformerBuilder.cc.

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

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

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

virtual

LigandConformerBuilder checks whether the ligand conformers in both hits are in the same conformer group

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

Definition at line 220 of file LigandConformerBuilder.cc.

References conformer_group_for_conformer_, and protocols::match::Hit::downstream_conf_id().

void protocols::match::downstream::LigandConformerBuilder::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 321 of file LigandConformerBuilder.cc.

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

void protocols::match::downstream::LigandConformerBuilder::determine_redundant_conformer_groups ( utility::vector1< core::Size > const & relevant_atom_indices)

goes through the list of conformers and does rms calculations (overlaid on the relevant_atom_indices) between them. any conformers that have an rms < rmsd_unique_cutoff_ will be grouped together in a conformer_group

Definition at line 145 of file LigandConformerBuilder.cc.

References conformer_group_for_conformer_, conformer_group_indices_, lig_conformers_, rmsd_unique_cutoff_, and protocols::match::downstream::TR().

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

virtual

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

Definition at line 335 of file LigandConformerBuilder.cc.

References protocols::match::Hit::downstream_conf_id(), 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::LigandConformerBuilder::get_lig_conformers ( core::Size conf_id) const

virtual

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

Definition at line 806 of file LigandConformerBuilder.cc.

References lig_conformers_.

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

virtual

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

Definition at line 818 of file LigandConformerBuilder.cc.

References upstream_restype_.

bool protocols::match::downstream::LigandConformerBuilder::hits_potentially_incompatible ( ) const

virtual

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 200 of file LigandConformerBuilder.cc.

References conformer_group_indices_.

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

Definition at line 490 of file LigandConformerBuilder.cc.

References downstream_restype_, and ignore_h_collisions_.

void protocols::match::downstream::LigandConformerBuilder::initialize_conformers ( core::conformation::Residue const & residue)

private

Definition at line 624 of file LigandConformerBuilder.cc.

References core::pose::Pose::append_residue_by_jump(), protocols::idealize::IdealizeMover::apply(), atom1_atom2_atom3_angle(), atom1_atom2_distance(), atom2_atom3_distance(), core::conformation::Residue::atom_name(), atoms_123_, conformer_group_for_conformer_, conformer_group_indices_, core::pack::dunbrack::RotamerLibrary::get_instance(), core::pack::dunbrack::RotamerLibrary::get_rsd_library(), idealize_conformers_, ignore_h_collisions_, lig_conformers_, core::conformation::Residue::name(), core::conformation::Residue::nheavyatoms(), orientation_atoms_, core::pose::Pose::replace_residue(), protocols::idealize::IdealizeMover::report_CA_rmsd(), core::pose::Pose::residue(), core::scoring::rms, protocols::match::downstream::TR(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

Referenced by initialize_from_residue().

void protocols::match::downstream::LigandConformerBuilder::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 LigandConformerBuilders.

Definition at line 369 of file LigandConformerBuilder.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_, initialize_conformers(), core::conformation::Residue::name(), core::conformation::Residue::natoms(), orientation_atoms_, protocols::match::probe_radius_for_atom_type(), radii_123_, protocols::match::downstream::TR(), core::conformation::Atom::type(), core::conformation::Residue::type(), and protocols::match::ZERO.

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

private

Definition at line 603 of file LigandConformerBuilder.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::LigandConformerBuilder::initialize_upstream_residue	(	core::chemical::ResidueTypeCOP	upstream_res,
		core::scoring::etable::count_pair::CountPairFunctionCOP	count_pair = `0`
	)

Definition at line 414 of file LigandConformerBuilder.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.

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

virtual

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

Definition at line 361 of file LigandConformerBuilder.cc.

References lig_conformers_.

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

virtual

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

Definition at line 233 of file LigandConformerBuilder.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::LigandConformerBuilder::set_bb_grid ( BumpGridCOP bbgrid)

virtual

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

Definition at line 189 of file LigandConformerBuilder.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::LigandConformerBuilder::atom_radii_

private

Definition at line 267 of file LigandConformerBuilder.hh.

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

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

private

Definition at line 268 of file LigandConformerBuilder.hh.

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

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

private

Definition at line 263 of file LigandConformerBuilder.hh.

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

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

private

Definition at line 265 of file LigandConformerBuilder.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().

utility::vector1< Size > protocols::match::downstream::LigandConformerBuilder::conformer_group_for_conformer_

private

Definition at line 275 of file LigandConformerBuilder.hh.

Referenced by compatible(), determine_redundant_conformer_groups(), and initialize_conformers().

utility::vector1< utility::vector1< Size > > protocols::match::downstream::LigandConformerBuilder::conformer_group_indices_

private

Definition at line 274 of file LigandConformerBuilder.hh.

Referenced by build(), build_conformer_group(), determine_redundant_conformer_groups(), hits_potentially_incompatible(), and initialize_conformers().

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

private

Definition at line 253 of file LigandConformerBuilder.hh.

Referenced by atom1_atom2_atom3_angle(), atom1_atom2_distance(), atom1_radius(), atom2_atom3_distance(), atom2_radius(), atom3_radius(), build_conformer_group(), 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::LigandConformerBuilder::idealize_conformers_

private

Definition at line 257 of file LigandConformerBuilder.hh.

Referenced by initialize_conformers().

bool protocols::match::downstream::LigandConformerBuilder::ignore_h_collisions_

private

Definition at line 256 of file LigandConformerBuilder.hh.

Referenced by ignore_h_collisions(), initialize_conformers(), and initialize_from_residue().

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

private

Definition at line 276 of file LigandConformerBuilder.hh.

Referenced by atom1_atom2_atom3_angle(), atom1_atom2_distance(), atom2_atom3_distance(), build_conformer_group(), coordinates_from_hit(), determine_redundant_conformer_groups(), downstream_pose_from_hit(), get_lig_conformers(), initialize_conformers(), initialize_upstream_nonbonded_min_separation_d2(), initialize_upstream_residue(), LigandConformerBuilder(), n_possible_hits_per_at3frame(), and require_atom_to_reside_in_active_site().

utility::vector1< utility::vector1< std::pair< Size, Real > > > protocols::match::downstream::LigandConformerBuilder::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 280 of file LigandConformerBuilder.hh.

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

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

private

Definition at line 270 of file LigandConformerBuilder.hh.

Referenced by build_conformer_group(), and require_atom_to_reside_in_active_site().

utility::fixedsizearray1< Size, 3 > protocols::match::downstream::LigandConformerBuilder::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 262 of file LigandConformerBuilder.hh.

Referenced by initialize_conformers(), and initialize_from_residue().

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

private

Definition at line 264 of file LigandConformerBuilder.hh.

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