Rosetta 3.4
Public Types | Public Member Functions
protocols::match::upstream::ProteinUpstreamBuilder Class Reference

#include <ProteinUpstreamBuilder.hh>

Inheritance diagram for protocols::match::upstream::ProteinUpstreamBuilder:
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List of all members.

Public Types

typedef core::Vector Vector
typedef core::Real Real
typedef
numeric::HomogeneousTransform
< Real
HTReal
typedef
core::pack::dunbrack::DunbrackRotamerSampleData 
DunbrackRotamerSampleData
typedef utility::vector1
< DunbrackRotamerSampleData
DunbrackRotamerSampleDataVector

Public Member Functions

 ProteinUpstreamBuilder ()
virtual ~ProteinUpstreamBuilder ()
UpstreamBuilderOP clone () const
virtual std::list< Hitbuild (ScaffoldBuildPoint const &build_point) const
 Iterate across possible conformations for the upstream half of the hit, and for each (non-coliding) conformation, sample all external geometries specified by the external_sampler to construct the three coordinates of the downstream sampler. Return a list of hits.
virtual void recover_hit (Hit const &hit, ScaffoldBuildPoint const &build_point, UpstreamResidueProcessor &processor) const
 Regenerate the rotamer for a particular hit and give that rotamer to the UpstreamResidueProcessor.
virtual void recover_hits (std::list< Hit >::const_iterator hits_begin, std::list< Hit >::const_iterator hits_end, ScaffoldBuildPoint const &build_point, UpstreamResidueProcessor &processor) const
 Regenerate a set of rotamers for a subset of hits bound by the two input hit-list iterators.
virtual Size n_restypes_to_build () const
virtual
core::chemical::ResidueTypeCAP 
restype (Size which_restype) const
virtual bool compatible (Hit const &my_hit, ScaffoldBuildPoint const &build_point_mine, UpstreamBuilder const &other, Hit const &other_hit, ScaffoldBuildPoint const &build_point_other, bool first_dispatch=true) const
 The side chain for two.
virtual bool compatible (Hit const &my_hit, ScaffoldBuildPoint const &build_point_mine, ProteinUpstreamBuilder const &other, Hit const &other_hit, ScaffoldBuildPoint const &build_point_other, bool first_dispatch=true) const
void add_build_set (BuildSet const &build_set)
Size n_build_sets () const
BuildSet const & build_set (core::chemical::ResidueTypeCAP restype) const
BuildSetbuild_set (core::chemical::ResidueTypeCAP restype)
void set_sampler (ProteinSCSamplerCOP sampler)
void set_use_input_sidechain (bool setting)
void set_native_flag (bool native)

Member Typedef Documentation

typedef numeric::HomogeneousTransform< Real > protocols::match::upstream::ProteinUpstreamBuilder::HTReal

Constructor & Destructor Documentation

protocols::match::upstream::ProteinUpstreamBuilder::ProteinUpstreamBuilder ( )

Referenced by clone().

protocols::match::upstream::ProteinUpstreamBuilder::~ProteinUpstreamBuilder ( ) [virtual]

Member Function Documentation

void protocols::match::upstream::ProteinUpstreamBuilder::add_build_set ( BuildSet const &  build_set)
std::list< Hit > protocols::match::upstream::ProteinUpstreamBuilder::build ( ScaffoldBuildPoint const &  build_point) const [virtual]

Iterate across possible conformations for the upstream half of the hit, and for each (non-coliding) conformation, sample all external geometries specified by the external_sampler to construct the three coordinates of the downstream sampler. Return a list of hits.

This is the main workhorse function for the upstream builder. There are lots of ways to customize the way the loops in this function work, but custom code should be written in subroutines called by this function and should not change the function itself. It is crucial here that the rotamers are created in the same way they were counted in insert(). Make sure that if you change build()'s behavior, that insert()'s behavior changes, too!

DO NOT LET THIS FUNCTION EXCEED 150 LINES. CLEAR CODE IS SHORT.

Implements protocols::match::upstream::UpstreamBuilder.

References core::conformation::Residue::chi(), protocols::match::upstream::FullChiSampleSet::chi_sample(), protocols::match::upstream::UpstreamResTypeGeometry::chitip_atom(), protocols::match::upstream::FullChiSampleSet::frame(), core::pack::dunbrack::RotamerLibrary::get_instance(), protocols::match::upstream::UpstreamResTypeGeometry::ht_for_chitip_atom(), protocols::match::upstream::ScaffoldBuildPoint::index(), core::conformation::Residue::mainchain_torsions(), protocols::match::upstream::UpstreamResTypeGeometry::n_nonchitip_atoms_for_chi(), protocols::match::upstream::FullChiSampleSet::n_samples_per_chi(), protocols::match::upstream::UpstreamResTypeGeometry::nonchitip_atom(), protocols::match::upstream::FullChiSampleSet::num_chi_samples_total(), protocols::match::upstream::ScaffoldBuildPoint::original_insertion_point(), protocols::match::upstream::ProteinBackboneBuildPoint::phi(), protocols::match::upstream::UpstreamResTypeGeometry::points_for_nonchitip_atoms(), protocols::match::upstream::ProteinBackboneBuildPoint::psi(), restype(), core::conformation::Residue::set_xyz(), protocols::match::upstream::TR(), and core::conformation::Residue::type().

BuildSet const & protocols::match::upstream::ProteinUpstreamBuilder::build_set ( core::chemical::ResidueTypeCAP  restype) const

Referenced by add_build_set().

BuildSet & protocols::match::upstream::ProteinUpstreamBuilder::build_set ( core::chemical::ResidueTypeCAP  restype)
UpstreamBuilderOP protocols::match::upstream::ProteinUpstreamBuilder::clone ( ) const [virtual]
bool protocols::match::upstream::ProteinUpstreamBuilder::compatible ( Hit const &  my_hit,
ScaffoldBuildPoint const &  build_point_mine,
ProteinUpstreamBuilder const &  other,
Hit const &  other_hit,
ScaffoldBuildPoint const &  build_point_other,
bool  first_dispatch = true 
) const [virtual]
bool protocols::match::upstream::ProteinUpstreamBuilder::compatible ( Hit const &  my_hit,
ScaffoldBuildPoint const &  build_point_mine,
UpstreamBuilder const &  other,
Hit const &  other_hit,
ScaffoldBuildPoint const &  build_point_other,
bool  first_dispatch = true 
) const [virtual]
Size protocols::match::upstream::ProteinUpstreamBuilder::n_build_sets ( ) const [inline]
ProteinUpstreamBuilder::Size protocols::match::upstream::ProteinUpstreamBuilder::n_restypes_to_build ( ) const [virtual]
void protocols::match::upstream::ProteinUpstreamBuilder::recover_hit ( Hit const &  hit,
ScaffoldBuildPoint const &  build_point,
UpstreamResidueProcessor processor 
) const [virtual]

Regenerate the rotamer for a particular hit and give that rotamer to the UpstreamResidueProcessor.

Replace residue for the amino acid corresponding to the rotamer indicated in the hit at the Pose position seqpos_to_insert_at.

It is crucial here that the rotamers are counted in the same way they were iterated across in build. Make sure that if build() changes its behavior, that this function also changes its behavior!

Implements protocols::match::upstream::UpstreamBuilder.

References recover_hits().

void protocols::match::upstream::ProteinUpstreamBuilder::recover_hits ( std::list< Hit >::const_iterator  hits_begin,
std::list< Hit >::const_iterator  hits_end,
ScaffoldBuildPoint const &  build_point,
UpstreamResidueProcessor processor 
) const [virtual]
core::chemical::ResidueTypeCAP protocols::match::upstream::ProteinUpstreamBuilder::restype ( Size  which_restype) const [virtual]
void protocols::match::upstream::ProteinUpstreamBuilder::set_native_flag ( bool  native)
void protocols::match::upstream::ProteinUpstreamBuilder::set_sampler ( ProteinSCSamplerCOP  sampler)
void protocols::match::upstream::ProteinUpstreamBuilder::set_use_input_sidechain ( bool  setting)

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