#include <LigandConformerBuilder.hh>

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

Public Types
typedef DownstreamBuilder	parent

Public Types inherited from protocols::match::downstream::DownstreamBuilder
typedef utility::VirtualBase	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 &)

	~LigandConformerBuilder () override

DownstreamBuilderOP	clone () const override

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

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...

core::Size	assign_conformer_group_to_residue (core::conformation::Residue const &residue, utility::vector1< core::Size > const &relevant_atom_indices) const

void	set_bb_grid (BumpGridCOP bbgrid) override

bool	hits_potentially_incompatible () const override
	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...

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

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

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

ProbeRadius	atom1_radius () const override

ProbeRadius	atom2_radius () const override

ProbeRadius	atom3_radius () const override

bool	atom1_belongs_in_active_site () const override

bool	atom2_belongs_in_active_site () const override

bool	atom3_belongs_in_active_site () const override

Real	atom1_atom2_distance () const override

Real	atom2_atom3_distance () const override

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

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

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

core::Size	n_possible_hits_per_at3frame () const override

void	initialize_from_residue (core::Size atom1, core::Size atom2, core::Size atom3, core::Size orientation_atom1, core::Size orientation_atom2, core::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=nullptr)

void	ignore_h_collisions (bool setting)

void	set_idealize_conformers (bool setting)

void	set_rmsd_unique_cutoff (core::Real setting)

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

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

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

	DownstreamBuilder (DownstreamBuilder const &)

	~DownstreamBuilder () override

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 (core::Size const confgrp_id, HTReal const &atom3_frame, core::Size const scaffold_build_point_id, core::Size const upstream_conf_id, core::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< core::Size, 3 >	orientation_atoms_

utility::fixedsizearray1< core::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< core::Size >	non_collision_detection_atoms_reqd_in_active_site_

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

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

utility::vector1< core::Size >	conformer_group_for_conformer_

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

utility::vector1< utility::vector1< std::pair< core::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

Member Typedef Documentation

◆ parent

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

Constructor & Destructor Documentation

◆ LigandConformerBuilder() [1/2]

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

◆ LigandConformerBuilder() [2/2]

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

References lig_conformers_.

◆ ~LigandConformerBuilder()

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

overridedefault

Member Function Documentation

◆ assign_conformer_group_to_residue()

core::Size protocols::match::downstream::LigandConformerBuilder::assign_conformer_group_to_residue	(	core::conformation::Residue const &	residue,
		utility::vector1< core::Size > const &	relevant_atom_indices
	)		const

For results to make sense, the relevant atom indices being passed in should be identical to the ones that the conformer groups were determined with in the above function, although this isn't being enforced

References core::conformation::Residue::atom(), conformer_group_indices_, lig_conformers_, and core::conformation::Atom::xyz().

◆ atom1_atom2_atom3_angle()

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

overridevirtual

Returns an angle in degrees between the three downstream atoms.

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

References downstream_restype_, and lig_conformers_.

Referenced by initialize_conformers().

◆ atom1_atom2_distance()

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

overridevirtual

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

References downstream_restype_, and lig_conformers_.

Referenced by initialize_conformers().

◆ atom1_belongs_in_active_site()

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

overridevirtual

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

References ats123_reqd_in_active_site_.

◆ atom1_radius()

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

overridevirtual

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

References downstream_restype_, and radii_123_.

◆ atom2_atom3_distance()

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

overridevirtual

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

References downstream_restype_, and lig_conformers_.

Referenced by initialize_conformers().

◆ atom2_belongs_in_active_site()

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

overridevirtual

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

References ats123_reqd_in_active_site_.

◆ atom2_radius()

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

overridevirtual

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

References downstream_restype_, and radii_123_.

◆ atom3_belongs_in_active_site()

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

overridevirtual

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

References ats123_reqd_in_active_site_.

◆ atom3_radius()

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

overridevirtual

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

References downstream_restype_, and radii_123_.

◆ build()

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

overridevirtual

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

References build_conformer_group(), and conformer_group_indices_.

◆ build_conformer_group()

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

private

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(), conformer_group_indices_, 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.

Referenced by build().

◆ clone()

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

overridevirtual

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

◆ compatible() [1/2]

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

overridevirtual

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

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

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

◆ compatible() [2/2]

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

overridevirtual

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

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

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

◆ coordinates_from_hit()

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

overridevirtual

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

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

◆ determine_redundant_conformer_groups()

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

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

◆ downstream_pose_from_hit()

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

overridevirtual

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

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().

◆ get_lig_conformers()

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

overridevirtual

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

References lig_conformers_.

◆ get_upstream_restype()

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

overridevirtual

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

References upstream_restype_.

◆ hits_potentially_incompatible()

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

overridevirtual

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.

References conformer_group_indices_.

◆ ignore_h_collisions()

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

References downstream_restype_, and ignore_h_collisions_.

◆ initialize_conformers()

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

private

◆ initialize_from_residue()

void protocols::match::downstream::LigandConformerBuilder::initialize_from_residue	(	core::Size	atom1,
		core::Size	atom2,
		core::Size	atom3,
		core::Size	orientation_atom1,
		core::Size	orientation_atom2,
		core::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.

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_ptr(), and protocols::match::ZERO.

◆ initialize_upstream_nonbonded_min_separation_d2()

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

private

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().

◆ initialize_upstream_residue()

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

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.

◆ n_possible_hits_per_at3frame()

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

overridevirtual

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

References lig_conformers_.

◆ require_atom_to_reside_in_active_site()

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

overridevirtual

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

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_.

◆ set_bb_grid()

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

overridevirtual

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

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

◆ set_idealize_conformers()

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

References idealize_conformers_.

◆ set_rmsd_unique_cutoff()

void protocols::match::downstream::LigandConformerBuilder::set_rmsd_unique_cutoff ( core::Real setting )

References rmsd_unique_cutoff_.

Member Data Documentation

◆ atom_radii_

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

private

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

◆ atom_required_in_active_site_

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

private

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

◆ atoms_123_

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

private

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

◆ ats123_reqd_in_active_site_

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

private

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().

◆ conformer_group_for_conformer_

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

private

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

◆ conformer_group_indices_

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

private

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

◆ downstream_restype_

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

private

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().

◆ idealize_conformers_

bool protocols::match::downstream::LigandConformerBuilder::idealize_conformers_

private

Referenced by initialize_conformers(), and set_idealize_conformers().

◆ ignore_h_collisions_

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

private

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

◆ lig_conformers_

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

private

Referenced by assign_conformer_group_to_residue(), 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().

◆ min_sep_d2_from_upstream_atoms_

utility::vector1< utility::vector1< std::pair< core::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

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

◆ non_collision_detection_atoms_reqd_in_active_site_

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

private

Referenced by build_conformer_group(), and require_atom_to_reside_in_active_site().

◆ orientation_atoms_

utility::fixedsizearray1< core::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.

Referenced by initialize_conformers(), and initialize_from_residue().

◆ radii_123_

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

private

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

◆ rmsd_unique_cutoff_

Real protocols::match::downstream::LigandConformerBuilder::rmsd_unique_cutoff_

private

Grouped into sets compatible ligand conformers.

Referenced by determine_redundant_conformer_groups(), and set_rmsd_unique_cutoff().

◆ upstream_restype_

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

private

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

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

src/protocols/match/downstream/LigandConformerBuilder.hh
src/protocols/match/downstream/LigandConformerBuilder.cc

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

◆ parent

Constructor & Destructor Documentation

◆ LigandConformerBuilder() [1/2]

◆ LigandConformerBuilder() [2/2]

◆ ~LigandConformerBuilder()

Member Function Documentation

◆ assign_conformer_group_to_residue()

◆ atom1_atom2_atom3_angle()

◆ atom1_atom2_distance()

◆ atom1_belongs_in_active_site()

◆ atom1_radius()

◆ atom2_atom3_distance()

◆ atom2_belongs_in_active_site()

◆ atom2_radius()

◆ atom3_belongs_in_active_site()

◆ atom3_radius()

◆ build()

◆ build_conformer_group()

◆ clone()

◆ compatible() [1/2]

◆ compatible() [2/2]

◆ coordinates_from_hit()

◆ determine_redundant_conformer_groups()

◆ downstream_pose_from_hit()

◆ get_lig_conformers()

◆ get_upstream_restype()

◆ hits_potentially_incompatible()

◆ ignore_h_collisions()

◆ initialize_conformers()

◆ initialize_from_residue()

◆ initialize_upstream_nonbonded_min_separation_d2()

◆ initialize_upstream_residue()

◆ n_possible_hits_per_at3frame()

◆ require_atom_to_reside_in_active_site()

◆ set_bb_grid()

◆ set_idealize_conformers()

◆ set_rmsd_unique_cutoff()

Member Data Documentation

◆ atom_radii_

◆ atom_required_in_active_site_

◆ atoms_123_

◆ ats123_reqd_in_active_site_

◆ conformer_group_for_conformer_

◆ conformer_group_indices_

◆ downstream_restype_

◆ idealize_conformers_

◆ ignore_h_collisions_

◆ lig_conformers_

◆ min_sep_d2_from_upstream_atoms_

◆ non_collision_detection_atoms_reqd_in_active_site_

◆ orientation_atoms_

◆ radii_123_

◆ rmsd_unique_cutoff_

◆ upstream_restype_