Rosetta Protocols  2014.35
Public Types | Public Member Functions | Protected Member Functions | Private Attributes | List of all members
protocols::match::downstream::DownstreamBuilder Class Referenceabstract

#include <DownstreamBuilder.hh>

Public Types

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

 DownstreamBuilder ()
 
 DownstreamBuilder (DownstreamBuilder const &)
 
virtual ~DownstreamBuilder ()
 
virtual DownstreamBuilderOP clone () const =0
 
virtual std::list< Hit > build (HTReal const &atom6_frame, Size const scaffold_build_point_id, Size const upstream_conf_id, Size const external_geometry_id, core::conformation::Residue const &upstream_residue) const =0
 
virtual void set_bb_grid (BumpGridCOP bbgrid)
 
void set_occupied_space_hash (OccupiedSpaceHashCOP occ_space)
 
void set_active_site_grid (ActiveSiteGridCOP active_site_grid)
 
virtual bool hits_potentially_incompatible () const =0
 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 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)=0
 
virtual ProbeRadius atom1_radius () const =0
 
virtual ProbeRadius atom2_radius () const =0
 
virtual ProbeRadius atom3_radius () const =0
 
virtual bool atom1_belongs_in_active_site () const =0
 
virtual bool atom2_belongs_in_active_site () const =0
 
virtual bool atom3_belongs_in_active_site () const =0
 
virtual Real atom1_atom2_distance () const =0
 
virtual Real atom2_atom3_distance () const =0
 
virtual Real atom1_atom2_atom3_angle () const =0
 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 =0
 
virtual
toolbox::match_enzdes_util::LigandConformerOP 		get_lig_conformers (core::Size conf_id) const =0
 
virtual
core::chemical::ResidueTypeCOP 		get_upstream_restype () const =0
 
virtual core::pose::PoseCOP downstream_pose_from_hit (Hit const &hit) const =0
 
virtual Size n_possible_hits_per_at3frame () const =0
 

Protected Member Functions

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
 

Private Attributes

BumpGridCOP bb_grid_
 
OccupiedSpaceHashCOP space_
 
ActiveSiteGridCOP active_site_grid_
 

Member Typedef Documentation

typedef core::id::AtomID protocols::match::downstream::DownstreamBuilder::AtomID
typedef numeric::HomogeneousTransform< Real > protocols::match::downstream::DownstreamBuilder::HTReal
typedef utility::pointer::ReferenceCount protocols::match::downstream::DownstreamBuilder::parent
typedef core::Real protocols::match::downstream::DownstreamBuilder::Real
typedef core::Vector protocols::match::downstream::DownstreamBuilder::Vector

Constructor & Destructor Documentation

protocols::match::downstream::DownstreamBuilder::DownstreamBuilder ( )
protocols::match::downstream::DownstreamBuilder::DownstreamBuilder ( DownstreamBuilder const &  other)
protocols::match::downstream::DownstreamBuilder::~DownstreamBuilder ( )
virtual

Member Function Documentation

ActiveSiteGrid const& protocols::match::downstream::DownstreamBuilder::active_site_grid ( ) const
inlineprotected

References active_site_grid_.

Referenced by protocols::match::downstream::RigidLigandBuilder::build(), protocols::match::downstream::LigandConformerBuilder::build_conformer_group(), and set_active_site_grid().

bool protocols::match::downstream::DownstreamBuilder::active_site_grid_set ( ) const
inlineprotected

References active_site_grid_.

virtual Real protocols::match::downstream::DownstreamBuilder::atom1_atom2_atom3_angle ( ) const
pure virtual

Returns an angle in degrees between the three downstream atoms.

Implemented in protocols::match::downstream::LigandConformerBuilder, and protocols::match::downstream::RigidLigandBuilder.

virtual Real protocols::match::downstream::DownstreamBuilder::atom1_atom2_distance ( ) const
pure virtual

Implemented in protocols::match::downstream::LigandConformerBuilder, and protocols::match::downstream::RigidLigandBuilder.

virtual bool protocols::match::downstream::DownstreamBuilder::atom1_belongs_in_active_site ( ) const
pure virtual

Implemented in protocols::match::downstream::LigandConformerBuilder, and protocols::match::downstream::RigidLigandBuilder.

virtual ProbeRadius protocols::match::downstream::DownstreamBuilder::atom1_radius ( ) const
pure virtual

Implemented in protocols::match::downstream::LigandConformerBuilder, and protocols::match::downstream::RigidLigandBuilder.

virtual Real protocols::match::downstream::DownstreamBuilder::atom2_atom3_distance ( ) const
pure virtual

Implemented in protocols::match::downstream::LigandConformerBuilder, and protocols::match::downstream::RigidLigandBuilder.

virtual bool protocols::match::downstream::DownstreamBuilder::atom2_belongs_in_active_site ( ) const
pure virtual

Implemented in protocols::match::downstream::LigandConformerBuilder, and protocols::match::downstream::RigidLigandBuilder.

virtual ProbeRadius protocols::match::downstream::DownstreamBuilder::atom2_radius ( ) const
pure virtual

Implemented in protocols::match::downstream::LigandConformerBuilder, and protocols::match::downstream::RigidLigandBuilder.

virtual bool protocols::match::downstream::DownstreamBuilder::atom3_belongs_in_active_site ( ) const
pure virtual

Implemented in protocols::match::downstream::LigandConformerBuilder, and protocols::match::downstream::RigidLigandBuilder.

virtual ProbeRadius protocols::match::downstream::DownstreamBuilder::atom3_radius ( ) const
pure virtual

Implemented in protocols::match::downstream::LigandConformerBuilder, and protocols::match::downstream::RigidLigandBuilder.

BumpGrid const& protocols::match::downstream::DownstreamBuilder::bbgrid ( ) const
inlineprotected

References bb_grid_.

Referenced by protocols::match::downstream::RigidLigandBuilder::build(), protocols::match::downstream::LigandConformerBuilder::build_conformer_group(), protocols::match::downstream::RigidLigandBuilder::initialize_upstream_nonbonded_min_separation_d2(), protocols::match::downstream::LigandConformerBuilder::initialize_upstream_nonbonded_min_separation_d2(), and set_bb_grid().

bool protocols::match::downstream::DownstreamBuilder::bbgrid_set ( ) const
inlineprotected

References bb_grid_, and utility::pointer::owning_ptr< T >::get().

Referenced by protocols::match::downstream::RigidLigandBuilder::build(), protocols::match::downstream::LigandConformerBuilder::build_conformer_group(), protocols::match::downstream::RigidLigandBuilder::initialize_upstream_nonbonded_min_separation_d2(), protocols::match::downstream::LigandConformerBuilder::initialize_upstream_nonbonded_min_separation_d2(), protocols::match::downstream::RigidLigandBuilder::initialize_upstream_residue(), and protocols::match::downstream::LigandConformerBuilder::initialize_upstream_residue().

virtual std::list< Hit > protocols::match::downstream::DownstreamBuilder::build ( HTReal const &  atom6_frame,
Size const  scaffold_build_point_id,
Size const  upstream_conf_id,
Size const  external_geometry_id,
core::conformation::Residue const &  upstream_residue 
) const
pure virtual

Implemented in protocols::match::downstream::LigandConformerBuilder, and protocols::match::downstream::RigidLigandBuilder.

virtual DownstreamBuilderOP protocols::match::downstream::DownstreamBuilder::clone ( ) const
pure virtual

Implemented in protocols::match::downstream::LigandConformerBuilder, and protocols::match::downstream::RigidLigandBuilder.

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

Reimplemented in protocols::match::downstream::LigandConformerBuilder, and protocols::match::downstream::RigidLigandBuilder.

References compatible(), and utility_exit_with_message.

Referenced by protocols::match::downstream::RigidLigandBuilder::compatible(), compatible(), and protocols::match::downstream::LigandConformerBuilder::compatible().

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

Reimplemented in protocols::match::downstream::RigidLigandBuilder.

References protocols::match::downstream::RigidLigandBuilder::compatible(), and utility_exit_with_message.

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

Reimplemented in protocols::match::downstream::LigandConformerBuilder.

References protocols::match::downstream::LigandConformerBuilder::compatible(), and utility_exit_with_message.

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

Implemented in protocols::match::downstream::LigandConformerBuilder, and protocols::match::downstream::RigidLigandBuilder.

virtual core::pose::PoseCOP protocols::match::downstream::DownstreamBuilder::downstream_pose_from_hit ( Hit const &  hit) const
pure virtual

Implemented in protocols::match::downstream::LigandConformerBuilder, and protocols::match::downstream::RigidLigandBuilder.

virtual toolbox::match_enzdes_util::LigandConformerOP protocols::match::downstream::DownstreamBuilder::get_lig_conformers ( core::Size  conf_id) const
pure virtual

Implemented in protocols::match::downstream::LigandConformerBuilder, and protocols::match::downstream::RigidLigandBuilder.

virtual core::chemical::ResidueTypeCOP protocols::match::downstream::DownstreamBuilder::get_upstream_restype ( ) const
pure virtual

Implemented in protocols::match::downstream::LigandConformerBuilder, and protocols::match::downstream::RigidLigandBuilder.

virtual bool protocols::match::downstream::DownstreamBuilder::hits_potentially_incompatible ( ) const
pure 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.

Implemented in protocols::match::downstream::LigandConformerBuilder, and protocols::match::downstream::RigidLigandBuilder.

virtual Size protocols::match::downstream::DownstreamBuilder::n_possible_hits_per_at3frame ( ) const
pure virtual

Implemented in protocols::match::downstream::LigandConformerBuilder, and protocols::match::downstream::RigidLigandBuilder.

OccupiedSpaceHash const& protocols::match::downstream::DownstreamBuilder::occ_space ( ) const
inlineprotected

References space_.

Referenced by protocols::match::downstream::RigidLigandBuilder::build(), protocols::match::downstream::LigandConformerBuilder::build_conformer_group(), and set_occupied_space_hash().

bool protocols::match::downstream::DownstreamBuilder::occ_space_set ( ) const
inlineprotected

References space_.

Referenced by protocols::match::downstream::RigidLigandBuilder::build(), and protocols::match::downstream::LigandConformerBuilder::build_conformer_group().

virtual void protocols::match::downstream::DownstreamBuilder::require_atom_to_reside_in_active_site ( core::id::AtomID const &  id)
pure virtual

Implemented in protocols::match::downstream::LigandConformerBuilder, and protocols::match::downstream::RigidLigandBuilder.

void protocols::match::downstream::DownstreamBuilder::set_active_site_grid ( ActiveSiteGridCOP  active_site_grid)

References active_site_grid(), and active_site_grid_.

void protocols::match::downstream::DownstreamBuilder::set_bb_grid ( BumpGridCOP  bbgrid)
virtual

Reimplemented in protocols::match::downstream::LigandConformerBuilder, and protocols::match::downstream::RigidLigandBuilder.

References bb_grid_, and bbgrid().

Referenced by protocols::match::downstream::RigidLigandBuilder::set_bb_grid(), and protocols::match::downstream::LigandConformerBuilder::set_bb_grid().

void protocols::match::downstream::DownstreamBuilder::set_occupied_space_hash ( OccupiedSpaceHashCOP  occ_space)

References occ_space(), and space_.

Member Data Documentation

ActiveSiteGridCOP protocols::match::downstream::DownstreamBuilder::active_site_grid_
private

Referenced by active_site_grid(), active_site_grid_set(), and set_active_site_grid().

BumpGridCOP protocols::match::downstream::DownstreamBuilder::bb_grid_
private

Referenced by bbgrid(), bbgrid_set(), and set_bb_grid().

OccupiedSpaceHashCOP protocols::match::downstream::DownstreamBuilder::space_
private

Referenced by occ_space(), occ_space_set(), and set_occupied_space_hash().

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