ConstraintConfig Struct Reference

Public Member Functions
virtual	~ConstraintConfig ()
	ConstraintConfig ()
	ConstraintConfig (string cfgfile)
void	init ()
std::string	ssstr () const
void	parse_config_file (string infname)
Strings	residue_names_from_sequence (string s) const
void	show_sequence (std::ostream &out=TR) const
void	show_cst_grids (std::ostream &out=TR) const
Sizes	parse_residues (string s, bool aliases=true) const
Sizes	parse_residues (Strings s, bool aliases=true) const
Size	resi_to_primary (Size resi) const
vector1< Strings >	parse_sequence (string s) const
void	add_sym_cst (Pose &p, AtomID id1, AtomID id2, Real d, Real sd) const
int	hub_seq_sep (int r1, int r2) const
void	parse_config_file (std::istream &in)
void	apply_bb_csts (Pose &p, Size ssep=0, bool earlycst=false)
void	apply_dcsts (Pose &p, Size ssep=0)
void	apply_cen_csts (Pose &p, Size ssep=0, bool earlycst=false)
void	apply_fa_csts (Pose &p, Size ssep=0)
void	apply_csts (Pose &p, Size ssep=0, bool earlycst=false)
void	reset_csts ()
std::string	pick_sequence () const
int	get_highest_intrahub_seqsep ()

Public Attributes
Size	nres
Size	nsub
Size	nhub
Size	hubpos
Real	CSTSDMULT
string	fname
string	template_seq_sc
string	template_seq_bb
vector1< char >	ss
std::map< string, Sizes >	ssmap
std::map< Size, Strings >	seq
Strings	templates_fname
vector1< PoseOP >	templates_fa
vector1< PoseOP >	templates_cen
vector1< std::map< Size, Size > >	template_map
vector1< Size >	template_sc
vector1< Size >	template_sc_resi
vector1< CST >	cst_sc
vector1< CST >	cst_bb
vector1< DCST >	dcst
Size	ncst
Size	nintracst
Size	nintercst
core::chemical::ResidueTypeSetCOP	crs
core::chemical::ResidueTypeSetCOP	frs

Constructor & Destructor Documentation

~ConstraintConfig()

virtual ConstraintConfig::~ConstraintConfig ( )

inlinevirtual

ConstraintConfig() [1/2]

ConstraintConfig::ConstraintConfig ( )

inline

References basic::init().

ConstraintConfig() [2/2]

ConstraintConfig::ConstraintConfig ( string  cfgfile )

inline

References PREcst::fname, basic::init(), basic::options::option, basic::options::TR, and utility_exit_with_message.

Member Function Documentation

add_sym_cst()

void ConstraintConfig::add_sym_cst ( Pose &  p, AtomID  id1, AtomID  id2, Real  d, Real  sd  ) const

inline

References basic::options::OptionKeys::constraints::constraints, create_a3b_hbs::nres, make_symmdef_file_denovo::nsub, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, sd(), str(), and utility_exit_with_message.

apply_bb_csts()

void ConstraintConfig::apply_bb_csts ( Pose &  p, Size  ssep = 0, bool  earlycst = false  )

inline

References basic::options::OptionKeys::constraints::constraints, create_a3b_hbs::i, create_a3b_hbs::nres, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, predPRE::t, and numeric::random::uniform().

apply_cen_csts()

void ConstraintConfig::apply_cen_csts ( Pose &  p, Size  ssep = 0, bool  earlycst = false  )

inline

References basic::options::OptionKeys::constraints::constraints, create_a3b_hbs::i, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, predPRE::t, and utility_exit_with_message.

apply_csts()

void ConstraintConfig::apply_csts ( Pose &  p, Size  ssep = 0, bool  earlycst = false  )

inline

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, and utility_exit_with_message.

Referenced by HubDenovo::cen_fold(), HubDenovo::min_as_poly_ala(), and HubDenovo::run().

apply_dcsts()

void ConstraintConfig::apply_dcsts ( Pose &  p, Size  ssep = 0  )

inline

References basic::options::OptionKeys::constraints::constraints, create_a3b_hbs::i, subloop_histogram::iterator, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, str(), basic::options::TR, and utility_exit_with_message.

apply_fa_csts()

void ConstraintConfig::apply_fa_csts ( Pose &  p, Size  ssep = 0  )

inline

References docking::a1, docking::a2, basic::options::OptionKeys::constraints::constraints, create_a3b_hbs::i, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, predPRE::t, basic::options::TR, utility_exit_with_message, and basic::Tracer::Warning.

get_highest_intrahub_seqsep()

int ConstraintConfig::get_highest_intrahub_seqsep ( )

inline

References create_a3b_hbs::i, and create_a3b_hbs::nres.

Referenced by HubDenovo::cen_fold().

hub_seq_sep()

int ConstraintConfig::hub_seq_sep ( int  r1, int  r2  ) const

inline

References enumerate_junctions::int, create_a3b_hbs::nres, make_symmdef_file_denovo::nsub, basic::options::OptionKeys::motifs::r1, basic::options::OptionKeys::motifs::r2, and utility_exit_with_message.

init()

void ConstraintConfig::init ( )

inline

parse_config_file() [1/2]

void ConstraintConfig::parse_config_file ( std::istream &  in )

inline

References cal_vdw_radius_pool::buf, ERROR_UINT, getline(), create_a3b_hbs::i, create_a3b_hbs::j, kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, create_a3b_hbs::nres, make_symmdef_file_denovo::nsub, basic::options::option, parse_sequence(), peek(), pyrosetta.distributed.io::pose_from_file, create_a3b_hbs::r, basic::options::OptionKeys::motifs::r1, basic::options::OptionKeys::motifs::r2, read_ignore_comments(), test.T200_Scoring::rsd1, test.T200_Scoring::rsd2, docking::s, sd(), beta_sc_scan::seq, subloop_histogram::size, challenge::ss, str(), basic::options::TR, utility_exit_with_message, kmeans_adaptive_kernel_density_bb_dependent_rotlib::v, and basic::Tracer::Warning.

parse_config_file() [2/2]

void ConstraintConfig::parse_config_file ( string  infname )

inline

References basic::options::OptionKeys::in::in, and utility_exit_with_message.

parse_residues() [1/2]

Sizes ConstraintConfig::parse_residues ( string  s, bool  aliases = true  ) const

inline

References create_a3b_hbs::i, create_a3b_hbs::r, docking::s, basic::options::OptionKeys::stepwise::s1, basic::options::OptionKeys::stepwise::s2, and utility_exit_with_message.

parse_residues() [2/2]

Sizes ConstraintConfig::parse_residues ( Strings  s, bool  aliases = true  ) const

inline

References create_a3b_hbs::i, create_a3b_hbs::r, res, and docking::s.

parse_sequence()

vector1<Strings > ConstraintConfig::parse_sequence ( string  s ) const

inline

References create_a3b_hbs::r, and docking::s.

pick_sequence()

std::string ConstraintConfig::pick_sequence ( ) const

inline

References utility::io::oc::cerr, run_backbone::choices, create_a3b_hbs::i, create_a3b_hbs::nres, basic::options::option, docking::s, beta_sc_scan::seq, challenge::ss, basic::options::TR, numeric::random::uniform(), and utility_exit_with_message.

Referenced by HubDenovo::make_start_pose().

reset_csts()

void ConstraintConfig::reset_csts ( )

inline

References create_a3b_hbs::i, and subloop_histogram::iterator.

Referenced by HubDenovo::run().

resi_to_primary()

Size ConstraintConfig::resi_to_primary ( Size  resi ) const

inline

References create_a3b_hbs::nres, make_symmdef_file_denovo::nsub, pna::resi, and utility_exit_with_message.

residue_names_from_sequence()

Strings ConstraintConfig::residue_names_from_sequence ( string  s ) const

inline

References create_a3b_hbs::i, create_a3b_hbs::r, residue_types_from_sequence(), docking::s, and str().

show_cst_grids()

void ConstraintConfig::show_cst_grids ( std::ostream &  out = TR ) const

inline

References compute_difference::alpha, numeric::crick_equations::ALPHA(), basic::options::OptionKeys::docking::ligand::grid::grid, create_a3b_hbs::i, max(), min(), create_a3b_hbs::nres, make_symmdef_file_denovo::nsub, residue, subloop_histogram::size, challenge::ss, and str().

show_sequence()

void ConstraintConfig::show_sequence ( std::ostream &  out = TR ) const

inline

References create_a3b_hbs::i, test.T110_numeric::I, create_a3b_hbs::j, create_a3b_hbs::nres, beta_sc_scan::seq, and challenge::ss.

ssstr()

std::string ConstraintConfig::ssstr ( ) const

inline

References create_a3b_hbs::i, create_a3b_hbs::nres, docking::s, and challenge::ss.

Referenced by HubDenovo::HubDenovo().

Member Data Documentation

crs

core::chemical::ResidueTypeSetCOP ConstraintConfig::crs

cst_bb

vector1<CST> ConstraintConfig::cst_bb

Referenced by HubDenovo::HubDenovo().

cst_sc

vector1<CST> ConstraintConfig::cst_sc

CSTSDMULT

Real ConstraintConfig::CSTSDMULT

dcst

vector1<DCST> ConstraintConfig::dcst

fname

string ConstraintConfig::fname

Referenced by options.KeepSameFile::close(), and HubDenovo::run().

frs

core::chemical::ResidueTypeSetCOP ConstraintConfig::frs

Referenced by HubDenovo::make_start_pose().

hubpos

Size ConstraintConfig::hubpos

ncst

Size ConstraintConfig::ncst

nhub

Size ConstraintConfig::nhub

Referenced by HubDenovo::make_start_pose(), and HubDenovo::stupid_ddg().

nintercst

Size ConstraintConfig::nintercst

nintracst

Size ConstraintConfig::nintracst

nres

Size ConstraintConfig::nres

Referenced by HubDenovo::cen_fold(), HubDenovo::design(), HubDenovo::HubDenovo(), HubDenovo::make_start_pose(), HubDenovo::min_as_poly_ala(), and HubDenovo::stupid_ddg().

nsub

Size ConstraintConfig::nsub

Referenced by HubDenovo::cen_fold(), and HubDenovo::stupid_ddg().

seq

std::map<Size,Strings> ConstraintConfig::seq

Referenced by HubDenovo::design().

ss

vector1<char> ConstraintConfig::ss

Referenced by HubDenovo::HubDenovo().

ssmap

std::map<string,Sizes> ConstraintConfig::ssmap

Referenced by HubDenovo::HubDenovo().

template_map

vector1<std::map<Size,Size> > ConstraintConfig::template_map

template_sc

vector1<Size> ConstraintConfig::template_sc

template_sc_resi

vector1<Size> ConstraintConfig::template_sc_resi

template_seq_bb

string ConstraintConfig::template_seq_bb

Referenced by HubDenovo::make_start_pose().

template_seq_sc

string ConstraintConfig::template_seq_sc

Referenced by HubDenovo::make_start_pose().

templates_cen

vector1<PoseOP> ConstraintConfig::templates_cen

templates_fa

vector1<PoseOP> ConstraintConfig::templates_fa

templates_fname

Strings ConstraintConfig::templates_fname

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The documentation for this struct was generated from the following file:

• src/apps/pilot/will/old/hubdenovo.cc