Rosetta  2021.16
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Types | Public Member Functions | Static Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::abinitio::Templates Class Reference

#include <Templates.hh>

Inheritance diagram for protocols::abinitio::Templates:
Inheritance graph
[legend]

Public Types

typedef std::map< std::string,
TemplateOP
TemplateMap
 
typedef TemplateMap::const_iterator const_iterator
 
typedef utility::vector1
< TemplateCOP
TemplateList
 

Public Member Functions

 Templates (std::string const &config_file, core::pose::PoseCOP native=nullptr)
 
 ~Templates () override
 
core::fragment::FragSetOP pick_frags (core::fragment::FragSetOP, core::fragment::FragDataCOP frag_type, core::Size min_nr_frags, core::Size ncopies=1) const
 
core::Size pick_frags (core::fragment::FragSet &, core::fragment::FragDataCOP frag_type, core::Size ncopies=1) const
 
void read_pairings (std::string const &filename, core::scoring::dssp::PairingsList &) const
 
TemplateJumpSetupOP create_jump_def (core::fragment::SecondaryStructureCOP=nullptr) const
 
bool has_pairings () const
 
core::scoring::dssp::PairingsList
const & 
pairings () const
 
std::string const & target_sequence () const
 
std::string & target_sequence ()
 
core::Size target_total_residue () const
 
const_iterator begin () const
 
const_iterator end () const
 
TemplateList const & helixjump_picks () const
 
void add_target_constraints (core::scoring::constraints::ConstraintSetOP, core::pose::Pose const &) const
 
bool has_template (std::string const &ModelID) const
 
Template const & get_template (std::string const &ModelID) const
 
bool is_good () const
 
core::Size pick_large_frags (core::fragment::FragSet &frag_set, core::fragment::SingleResidueFragDataOP frag_type, core::Size ncopies=1) const
 
void set_native (core::pose::PoseCOP native)
 
PairingStatistics const & strand_pairing_stats ()
 
TemplatesCOP get_self_ptr () const
 
TemplatesOP get_self_ptr ()
 
TemplatesCAP get_self_weak_ptr () const
 
TemplatesAP get_self_weak_ptr ()
 

Static Public Member Functions

static void register_options ()
 

Private Member Functions

void get_cst_list (TemplateList &cst_list, TemplateList &cull_list) const
 
void scored_fragpick_list (TemplateList &frag_pick_list) const
 
void _get_scored_list (TemplateList &cst_list, core::Size topN, core::Real wTopol, core::Real wExtern) const
 

Private Attributes

bool good_
 
TemplateMap templates_
 
core::scoring::dssp::PairingsList pairings_
 
std::string target_sequence_
 
PairingStatisticsCOP strand_stats_
 
core::pose::PoseCOP native_
 
TemplateList cull_list_
 
TemplateList fragpick_list_
 
TemplateList helixjump_pick_list_
 

Member Typedef Documentation

typedef TemplateMap::const_iterator protocols::abinitio::Templates::const_iterator
typedef std::map< std::string, TemplateOP > protocols::abinitio::Templates::TemplateMap

Constructor & Destructor Documentation

protocols::abinitio::Templates::Templates ( std::string const &  config_file,
core::pose::PoseCOP  native = nullptr 
)
protocols::abinitio::Templates::~Templates ( )
overridedefault

Member Function Documentation

void protocols::abinitio::Templates::_get_scored_list ( TemplateList cst_list,
core::Size  topN,
core::Real  wTopol,
core::Real  wExtern 
) const
private
void protocols::abinitio::Templates::add_target_constraints ( core::scoring::constraints::ConstraintSetOP  cstset,
core::pose::Pose const &  pose 
) const
const_iterator protocols::abinitio::Templates::begin ( ) const
inline

References templates_.

TemplateJumpSetupOP protocols::abinitio::Templates::create_jump_def ( core::fragment::SecondaryStructureCOP  ss_def = nullptr) const
const_iterator protocols::abinitio::Templates::end ( ) const
inline

References templates_.

Referenced by _get_scored_list().

void protocols::abinitio::Templates::get_cst_list ( TemplateList cst_list,
TemplateList cull_list 
) const
private

References _get_scored_list(), and templates_.

Referenced by add_target_constraints().

TemplatesCOP protocols::abinitio::Templates::get_self_ptr ( ) const
inline

Referenced by create_jump_def().

TemplatesOP protocols::abinitio::Templates::get_self_ptr ( )
inline
TemplatesCAP protocols::abinitio::Templates::get_self_weak_ptr ( ) const
inline
TemplatesAP protocols::abinitio::Templates::get_self_weak_ptr ( )
inline
Template const& protocols::abinitio::Templates::get_template ( std::string const &  ModelID) const
inline

References templates_.

bool protocols::abinitio::Templates::has_pairings ( ) const
inline

References pairings_.

bool protocols::abinitio::Templates::has_template ( std::string const &  ModelID) const
inline

References templates_.

TemplateList const& protocols::abinitio::Templates::helixjump_picks ( ) const
inline

References helixjump_pick_list_.

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

References good_.

core::scoring::dssp::PairingsList const& protocols::abinitio::Templates::pairings ( ) const
inline

References pairings_.

core::fragment::FragSetOP protocols::abinitio::Templates::pick_frags ( core::fragment::FragSetOP  ,
core::fragment::FragDataCOP  frag_type,
core::Size  min_nr_frags,
core::Size  ncopies = 1 
) const

Referenced by create_jump_def().

core::Size protocols::abinitio::Templates::pick_frags ( core::fragment::FragSet ,
core::fragment::FragDataCOP  frag_type,
core::Size  ncopies = 1 
) const
Size protocols::abinitio::Templates::pick_large_frags ( core::fragment::FragSet frag_set,
core::fragment::SingleResidueFragDataOP  frag_type,
core::Size  ncopies = 1 
) const

References protocols::analysis::total, and tr().

void protocols::abinitio::Templates::read_pairings ( std::string const &  filename,
core::scoring::dssp::PairingsList pairings 
) const
void protocols::abinitio::Templates::register_options ( )
static
void protocols::abinitio::Templates::scored_fragpick_list ( TemplateList frag_pick_list) const
private

References _get_scored_list(), and templates_.

Referenced by Templates().

void protocols::abinitio::Templates::set_native ( core::pose::PoseCOP  native)

References native_.

PairingStatistics const& protocols::abinitio::Templates::strand_pairing_stats ( )
inline

References strand_stats_.

std::string const& protocols::abinitio::Templates::target_sequence ( ) const
inline

References target_sequence_.

Referenced by target_total_residue().

std::string& protocols::abinitio::Templates::target_sequence ( )
inline

References target_sequence_.

core::Size protocols::abinitio::Templates::target_total_residue ( ) const
inline

References target_sequence().

Referenced by create_jump_def().

Member Data Documentation

TemplateList protocols::abinitio::Templates::cull_list_
private
TemplateList protocols::abinitio::Templates::fragpick_list_
private

Referenced by Templates().

bool protocols::abinitio::Templates::good_
private

Referenced by is_good(), and Templates().

TemplateList protocols::abinitio::Templates::helixjump_pick_list_
private

Referenced by helixjump_picks(), and Templates().

core::pose::PoseCOP protocols::abinitio::Templates::native_
private

Referenced by set_native(), and Templates().

core::scoring::dssp::PairingsList protocols::abinitio::Templates::pairings_
private
PairingStatisticsCOP protocols::abinitio::Templates::strand_stats_
private
std::string protocols::abinitio::Templates::target_sequence_
private

Referenced by target_sequence(), and Templates().

TemplateMap protocols::abinitio::Templates::templates_
private

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