#include <LigandConformer.hh>

Inheritance diagram for protocols::toolbox::match_enzdes_util::LigandConformer:

Collaboration diagram for protocols::toolbox::match_enzdes_util::LigandConformer:

Public Types
typedef utility::pointer::ReferenceCount	parent

typedef core::Size	Size

typedef core::Real	Real

typedef core::Vector	Vector

typedef numeric::geometry::hashing::Real6	Real6

typedef numeric::HomogeneousTransform < Real >	HTReal

Public Member Functions
	LigandConformer ()

	LigandConformer (LigandConformer const &)

virtual	~LigandConformer ()

Real	atom1_atom2_distance () const

Real	atom2_atom3_distance () const

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

Real	oatom1_oatom2_distance () const
	returns the distance between orientation atom 1 and orientation atom 2 More...

Real	oatom2_oatom3_distance () const
	returns the distance between orientation atom 2 and orientation atom 3 More...

Real	oatom1_oatom2_oatom3_angle () const
	Returns an angle in degrees between the three orientation atoms. More...

void	coordinates_from_orientation (Real6 const &orientation, utility::vector1< core::id::AtomID > const &atom_indices, utility::vector1< Vector > &atom_coords) const

void	initialize_from_residue (Size D1, Size D2, Size D3, 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 LigandConformers. More...

void	ignore_h_collisions (bool setting)

Real6	global_orientation_from_frame3 (HTReal const &frame3) const
	The orientaton frame at orientation atom 3 given the coordinate frame at D3 (this frame is called frame3) More...

HTReal	frame_from_global_orientation (Real6 orientation) const
	The orientation frame at orientation atom 3 given orientation atom 3's xyz coordinates and the euler angles describing the frame. More...

void	move_atoms_to_collcheck_begin (utility::vector1< Size > const &restype_atnos_to_move_early)

Size	n_collision_check_atoms () const

Size	restype_id_2_collision_check_id (Size restype_atomno) const

Size	collision_check_id_2_restype_id (Size coll_check_id) const

Vector	coordinate_in_D3_frame (Size restype_atomno, HTReal const &frame3) const

Vector	coordinate_in_global_frame (Size restype_atomno, HTReal const &orientation_frame) const

void	get_global_coords_as_FArray2D (ObjexxFCL::FArray2D< numeric::Real > &coords, HTReal const &orientation_frame, utility::vector1< core::Size > const &restype_atomnos) const
	@ brief helper function to get the coordinates in 2D FArray format More...

core::chemical::ResidueType	get_lig_restype () const

Private Member Functions
void	create_collcheck_ordering (utility::vector1< bool > selected, Size count_from)

Private Attributes
core::chemical::ResidueTypeCOP	ligand_restype_

utility::fixedsizearray1< Size, 3 >	orientation_atoms_

utility::fixedsizearray1 < Vector, 3 >	oats_in_D3_frame_

HTReal	oframe_in_D3frame_

utility::vector1< Vector >	points_in_global_orintation_frame_
	The coordinates of all the ligand atoms in the global orientation frame. More...

utility::fixedsizearray1< Size, 3 >	atoms_123_

Real	d12_

Real	d23_

Real	ang123_

utility::vector1< Vector >	points_in_D3_frame_
	angle between D1, D2 and D3 More...

bool	ignore_h_collisions_

utility::vector1< Size >	collision_check_id_2_restype_id_

utility::vector1< Size >	restype_id_2_collision_check_id_

Detailed Description

Definition at line 51 of file LigandConformer.hh.

Member Typedef Documentation

typedef numeric::HomogeneousTransform< Real > protocols::toolbox::match_enzdes_util::LigandConformer::HTReal

Definition at line 58 of file LigandConformer.hh.

typedef utility::pointer::ReferenceCount protocols::toolbox::match_enzdes_util::LigandConformer::parent

Definition at line 53 of file LigandConformer.hh.

typedef core::Real protocols::toolbox::match_enzdes_util::LigandConformer::Real

Definition at line 55 of file LigandConformer.hh.

typedef numeric::geometry::hashing::Real6 protocols::toolbox::match_enzdes_util::LigandConformer::Real6

Definition at line 57 of file LigandConformer.hh.

typedef core::Size protocols::toolbox::match_enzdes_util::LigandConformer::Size

Definition at line 54 of file LigandConformer.hh.

typedef core::Vector protocols::toolbox::match_enzdes_util::LigandConformer::Vector

Definition at line 56 of file LigandConformer.hh.

Constructor & Destructor Documentation

protocols::toolbox::match_enzdes_util::LigandConformer::LigandConformer ( )

Definition at line 39 of file LigandConformer.cc.

protocols::toolbox::match_enzdes_util::LigandConformer::LigandConformer ( LigandConformer const & other)

Definition at line 47 of file LigandConformer.cc.

protocols::toolbox::match_enzdes_util::LigandConformer::~LigandConformer ( )

virtual

Definition at line 63 of file LigandConformer.cc.

Member Function Documentation

LigandConformer::Real protocols::toolbox::match_enzdes_util::LigandConformer::atom1_atom2_atom3_angle ( ) const

Returns an angle in degrees between the three downstream atoms.

Definition at line 83 of file LigandConformer.cc.

References ang123_, and ligand_restype_.

LigandConformer::Real protocols::toolbox::match_enzdes_util::LigandConformer::atom1_atom2_distance ( ) const

Definition at line 66 of file LigandConformer.cc.

References d12_, and ligand_restype_.

LigandConformer::Real protocols::toolbox::match_enzdes_util::LigandConformer::atom2_atom3_distance ( ) const

Definition at line 74 of file LigandConformer.cc.

References d23_, and ligand_restype_.

Size protocols::toolbox::match_enzdes_util::LigandConformer::collision_check_id_2_restype_id ( Size coll_check_id) const

inline

Definition at line 151 of file LigandConformer.hh.

References collision_check_id_2_restype_id_.

Referenced by protocols::match::downstream::SecondaryMatcherToDownstreamResidue::prepare_for_hit_generation_for_geomcst().

Vector protocols::toolbox::match_enzdes_util::LigandConformer::coordinate_in_D3_frame	(	Size	restype_atomno,
		HTReal const &	frame3
	)		const

inline

Definition at line 157 of file LigandConformer.hh.

References points_in_D3_frame_.

Vector protocols::toolbox::match_enzdes_util::LigandConformer::coordinate_in_global_frame	(	Size	restype_atomno,
		HTReal const &	orientation_frame
	)		const

inline

Definition at line 163 of file LigandConformer.hh.

References points_in_global_orintation_frame_.

void protocols::toolbox::match_enzdes_util::LigandConformer::coordinates_from_orientation	(	Real6 const &	orientation,
		utility::vector1< core::id::AtomID > const &	atom_indices,
		utility::vector1< Vector > &	atom_coords
	)		const

Definition at line 119 of file LigandConformer.cc.

References frame_from_global_orientation(), and points_in_global_orintation_frame_.

void protocols::toolbox::match_enzdes_util::LigandConformer::create_collcheck_ordering	(	utility::vector1< bool >	selected,
		Size	count_from
	)

private

Definition at line 369 of file LigandConformer.cc.

References collision_check_id_2_restype_id_, ignore_h_collisions_, ligand_restype_, points_in_D3_frame_, and restype_id_2_collision_check_id_.

Referenced by initialize_from_residue(), and move_atoms_to_collcheck_begin().

LigandConformer::HTReal protocols::toolbox::match_enzdes_util::LigandConformer::frame_from_global_orientation ( Real6 orientation) const

The orientation frame at orientation atom 3 given orientation atom 3's xyz coordinates and the euler angles describing the frame.

Definition at line 286 of file LigandConformer.cc.

Referenced by coordinates_from_orientation().

void protocols::toolbox::match_enzdes_util::LigandConformer::get_global_coords_as_FArray2D	(	ObjexxFCL::FArray2D< numeric::Real > &	coords,
		HTReal const &	orientation_frame,
		utility::vector1< core::Size > const &	restype_atomnos
	)		const

@ brief helper function to get the coordinates in 2D FArray format

Definition at line 353 of file LigandConformer.cc.

References points_in_global_orintation_frame_.

core::chemical::ResidueType protocols::toolbox::match_enzdes_util::LigandConformer::get_lig_restype ( ) const

Definition at line 418 of file LigandConformer.cc.

References ligand_restype_.

LigandConformer::Real6 protocols::toolbox::match_enzdes_util::LigandConformer::global_orientation_from_frame3 ( HTReal const & frame3) const

The orientaton frame at orientation atom 3 given the coordinate frame at D3 (this frame is called frame3)

Definition at line 225 of file LigandConformer.cc.

References oframe_in_D3frame_.

void protocols::toolbox::match_enzdes_util::LigandConformer::ignore_h_collisions ( bool setting)

Definition at line 315 of file LigandConformer.cc.

References ignore_h_collisions_, and ligand_restype_.

void protocols::toolbox::match_enzdes_util::LigandConformer::initialize_from_residue	(	Size	D1,
		Size	D2,
		Size	D3,
		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 LigandConformers.

Definition at line 147 of file LigandConformer.cc.

References ang123_, core::conformation::Residue::atom_type(), atoms_123_, collision_check_id_2_restype_id_, create_collcheck_ordering(), d12_, d23_, core::chemical::AtomType::element(), ignore_h_collisions_, ligand_restype_, core::chemical::AtomType::name(), core::conformation::Residue::natoms(), core::conformation::Residue::nheavyatoms(), oats_in_D3_frame_, oframe_in_D3frame_, orientation_atoms_, points_in_D3_frame_, points_in_global_orintation_frame_, restype_id_2_collision_check_id_, core::conformation::Residue::type(), and core::conformation::Residue::xyz().

void protocols::toolbox::match_enzdes_util::LigandConformer::move_atoms_to_collcheck_begin ( utility::vector1< Size > const & restype_atnos_to_move_early)

Definition at line 325 of file LigandConformer.cc.

References atoms_123_, collision_check_id_2_restype_id_, create_collcheck_ordering(), points_in_D3_frame_, and restype_id_2_collision_check_id_.

Size protocols::toolbox::match_enzdes_util::LigandConformer::n_collision_check_atoms ( ) const

inline

Definition at line 139 of file LigandConformer.hh.

References collision_check_id_2_restype_id_.

Referenced by protocols::match::downstream::SecondaryMatcherToDownstreamResidue::prepare_for_hit_generation_for_geomcst().

LigandConformer::Real protocols::toolbox::match_enzdes_util::LigandConformer::oatom1_oatom2_distance ( ) const

returns the distance between orientation atom 1 and orientation atom 2

Definition at line 91 of file LigandConformer.cc.

References ligand_restype_, orientation_atoms_, and points_in_D3_frame_.

LigandConformer::Real protocols::toolbox::match_enzdes_util::LigandConformer::oatom1_oatom2_oatom3_angle ( ) const

Returns an angle in degrees between the three orientation atoms.

Definition at line 107 of file LigandConformer.cc.

References ligand_restype_, orientation_atoms_, and points_in_D3_frame_.

LigandConformer::Real protocols::toolbox::match_enzdes_util::LigandConformer::oatom2_oatom3_distance ( ) const

returns the distance between orientation atom 2 and orientation atom 3

Definition at line 99 of file LigandConformer.cc.

References ligand_restype_, orientation_atoms_, and points_in_D3_frame_.

Size protocols::toolbox::match_enzdes_util::LigandConformer::restype_id_2_collision_check_id ( Size restype_atomno) const

inline

Definition at line 145 of file LigandConformer.hh.

References restype_id_2_collision_check_id_.

Member Data Documentation

Real protocols::toolbox::match_enzdes_util::LigandConformer::ang123_

private

Definition at line 202 of file LigandConformer.hh.

Referenced by atom1_atom2_atom3_angle(), and initialize_from_residue().

utility::fixedsizearray1< Size, 3 > protocols::toolbox::match_enzdes_util::LigandConformer::atoms_123_

private

The indices for the three atoms defining the location of the downstream partner from the upstream partner. D1 D2 and D3. These indices are in the restype indexing of atoms.

Definition at line 199 of file LigandConformer.hh.

Referenced by initialize_from_residue(), and move_atoms_to_collcheck_begin().

utility::vector1< Size > protocols::toolbox::match_enzdes_util::LigandConformer::collision_check_id_2_restype_id_

private

Definition at line 207 of file LigandConformer.hh.

Referenced by collision_check_id_2_restype_id(), create_collcheck_ordering(), initialize_from_residue(), move_atoms_to_collcheck_begin(), and n_collision_check_atoms().

Real protocols::toolbox::match_enzdes_util::LigandConformer::d12_

private

Definition at line 200 of file LigandConformer.hh.

Referenced by atom1_atom2_distance(), and initialize_from_residue().

Real protocols::toolbox::match_enzdes_util::LigandConformer::d23_

private

Definition at line 201 of file LigandConformer.hh.

Referenced by atom2_atom3_distance(), and initialize_from_residue().

bool protocols::toolbox::match_enzdes_util::LigandConformer::ignore_h_collisions_

private

Definition at line 206 of file LigandConformer.hh.

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

core::chemical::ResidueTypeCOP protocols::toolbox::match_enzdes_util::LigandConformer::ligand_restype_

private

Definition at line 185 of file LigandConformer.hh.

Referenced by atom1_atom2_atom3_angle(), atom1_atom2_distance(), atom2_atom3_distance(), create_collcheck_ordering(), get_lig_restype(), ignore_h_collisions(), initialize_from_residue(), oatom1_oatom2_distance(), oatom1_oatom2_oatom3_angle(), and oatom2_oatom3_distance().

utility::fixedsizearray1< Vector, 3 > protocols::toolbox::match_enzdes_util::LigandConformer::oats_in_D3_frame_

private

Definition at line 191 of file LigandConformer.hh.

Referenced by initialize_from_residue().

HTReal protocols::toolbox::match_enzdes_util::LigandConformer::oframe_in_D3frame_

private

Definition at line 192 of file LigandConformer.hh.

Referenced by global_orientation_from_frame3(), and initialize_from_residue().

utility::fixedsizearray1< Size, 3 > protocols::toolbox::match_enzdes_util::LigandConformer::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 190 of file LigandConformer.hh.

Referenced by initialize_from_residue(), oatom1_oatom2_distance(), oatom1_oatom2_oatom3_angle(), and oatom2_oatom3_distance().