Rosetta  2021.07
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Public Types | Public Member Functions | Static Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::abinitio::Template Class Reference

#include <Template.hh>

Inheritance diagram for protocols::abinitio::Template:
Inheritance graph
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Public Types

typedef utility::vector1
< core::scoring::constraints::AtomPairConstraintOP
AtomPairConstraintList
 
typedef utility::vector1
< core::scoring::constraints::Obsolet_NamedAtomPairConstraintOP
NamedAtomPairConstraintList
 

Public Member Functions

 ~Template () override
 Automatically generated virtual destructor for class deriving directly from VirtualBase. More...
 
 Template (std::string const &name, core::pose::PoseCOP, core::sequence::DerivedSequenceMapping const &mapping)
 
 Template (std::string const &name, core::pose::PoseCOP, std::string const &map_file, int offset, core::Real score)
 
core::Size steal_frags (core::fragment::FrameList const &target_frames, core::fragment::FragSet &accumulator, core::Size ncopies=1) const
 good for continuous fragments: no torsions from insertions are mapped More...
 
void map_pairings2template (core::scoring::dssp::PairingList const &in, core::scoring::dssp::PairingList &out) const
 
void map_pairings2target (core::scoring::dssp::PairingList const &in, core::scoring::dssp::PairingList &out) const
 
void map2target (core::fragment::FrameList const &template_frames, core::fragment::FrameList &target_frames) const
 
void map2target (core::fragment::FrameList &) const
 
void map2template (core::fragment::FrameList const &target_frames, core::fragment::FrameList &template_frames) const
 
void map2template (core::fragment::FrameList &) const
 
core::Size pick_large_frags (core::fragment::FragSet &frag_set, core::fragment::SingleResidueFragDataOP frag_type, core::Size ncopies=1) const
 
void map2target (NamedAtomPairConstraintList const &, NamedAtomPairConstraintList &) const
 
void map2template (NamedAtomPairConstraintList const &, NamedAtomPairConstraintList &) const
 
void cull_violators (NamedAtomPairConstraintList const &target_list, NamedAtomPairConstraintList &culled_list) const
 
void read_constraints (std::string const &cst_file)
 
bool has_constraints () const
 
core::scoring::dssp::StrandPairingSet
const & 
strand_pairings () const
 
NamedAtomPairConstraintList const & constraints () const
 
std::string const & name () const
 
core::Real external_score () const
 
std::string query_sequence () const
 
core::Real topology_score () const
 
void topology_score (core::Real setting)
 
bool is_good () const
 

Static Public Member Functions

static void register_options ()
 

Private Member Functions

bool map_pairing (core::scoring::dssp::Pairing const &, core::scoring::dssp::Pairing &, core::sequence::DerivedSequenceMapping const &map) const
 
void _read_constraints (std::string const &cst_file) const
 

Private Attributes

core::sequence::DerivedSequenceMapping mapping_
 
core::sequence::DerivedSequenceMapping reverse_mapping_
 
core::pose::PoseCOP pose_
 
std::string name_
 
core::Real score_
 
core::Real topol_score_
 
NamedAtomPairConstraintList cstset_
 
core::scoring::dssp::StrandPairingSetOP strand_pairings_
 
std::string cstfile_
 
bool good_
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::abinitio::Template::~Template ( )
overridedefault

Automatically generated virtual destructor for class deriving directly from VirtualBase.

Auto-generated virtual destructor

protocols::abinitio::Template::Template ( std::string const &  name,
core::pose::PoseCOP  pose,
core::sequence::DerivedSequenceMapping const &  mapping 
)
protocols::abinitio::Template::Template ( std::string const &  name,
core::pose::PoseCOP  pose,
std::string const &  map_file,
int  offset,
core::Real  score 
)

Member Function Documentation

void protocols::abinitio::Template::_read_constraints ( std::string const &  cst_file) const
private

References cstset_, pose_, and tr().

Referenced by constraints().

NamedAtomPairConstraintList const& protocols::abinitio::Template::constraints ( ) const
inline
void protocols::abinitio::Template::cull_violators ( NamedAtomPairConstraintList const &  target_list,
NamedAtomPairConstraintList culled_list 
) const

References mapping_, pose_, and tr().

core::Real protocols::abinitio::Template::external_score ( ) const
inline

References score_.

bool protocols::abinitio::Template::has_constraints ( ) const
inline

References cstfile_.

bool protocols::abinitio::Template::is_good ( ) const
inline

References good_.

void protocols::abinitio::Template::map2target ( core::fragment::FrameList const &  template_frames,
core::fragment::FrameList target_frames 
) const
void protocols::abinitio::Template::map2target ( core::fragment::FrameList ) const
void protocols::abinitio::Template::map2target ( NamedAtomPairConstraintList const &  template_list,
NamedAtomPairConstraintList target_list 
) const

References reverse_mapping_, and tr().

void protocols::abinitio::Template::map2template ( core::fragment::FrameList const &  target_frames,
core::fragment::FrameList template_frames 
) const

Referenced by steal_frags().

void protocols::abinitio::Template::map2template ( core::fragment::FrameList ) const
void protocols::abinitio::Template::map2template ( NamedAtomPairConstraintList const &  target_list,
NamedAtomPairConstraintList template_list 
) const

References mapping_, and tr().

bool protocols::abinitio::Template::map_pairing ( core::scoring::dssp::Pairing const &  in,
core::scoring::dssp::Pairing out,
core::sequence::DerivedSequenceMapping const &  map 
) const
private
void protocols::abinitio::Template::map_pairings2target ( core::scoring::dssp::PairingList const &  in,
core::scoring::dssp::PairingList out 
) const
void protocols::abinitio::Template::map_pairings2template ( core::scoring::dssp::PairingList const &  in,
core::scoring::dssp::PairingList out 
) const

References map_pairing(), and mapping_.

std::string const& protocols::abinitio::Template::name ( ) const
inline
Size protocols::abinitio::Template::pick_large_frags ( core::fragment::FragSet frag_set,
core::fragment::SingleResidueFragDataOP  frag_type,
core::Size  ncopies = 1 
) const
std::string protocols::abinitio::Template::query_sequence ( ) const
inline
void protocols::abinitio::Template::read_constraints ( std::string const &  cst_file)

References cstfile_.

void protocols::abinitio::Template::register_options ( )
static
Size protocols::abinitio::Template::steal_frags ( core::fragment::FrameList const &  target_frames,
core::fragment::FragSet accumulator,
core::Size  ncopies = 1 
) const

good for continuous fragments: no torsions from insertions are mapped

References map2target(), map2template(), name(), pose_, protocols::analysis::total, and tr().

core::scoring::dssp::StrandPairingSet const& protocols::abinitio::Template::strand_pairings ( ) const
inline
core::Real protocols::abinitio::Template::topology_score ( ) const
inline

References topol_score_.

void protocols::abinitio::Template::topology_score ( core::Real  setting)
inline

References topol_score_.

Member Data Documentation

std::string protocols::abinitio::Template::cstfile_
private
NamedAtomPairConstraintList protocols::abinitio::Template::cstset_
mutableprivate

Referenced by _read_constraints(), and constraints().

bool protocols::abinitio::Template::good_
private

Referenced by is_good(), and Template().

core::sequence::DerivedSequenceMapping protocols::abinitio::Template::mapping_
private
std::string protocols::abinitio::Template::name_
private

Referenced by name().

core::pose::PoseCOP protocols::abinitio::Template::pose_
private
core::sequence::DerivedSequenceMapping protocols::abinitio::Template::reverse_mapping_
private
core::Real protocols::abinitio::Template::score_
private

Referenced by external_score().

core::scoring::dssp::StrandPairingSetOP protocols::abinitio::Template::strand_pairings_
private

Referenced by strand_pairings(), and Template().

core::Real protocols::abinitio::Template::topol_score_
private

Referenced by topology_score().


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