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Classes | Namespaces | Functions
TorsionFragment.hh File Reference
#include <protocols/frags/TorsionFragment.fwd.hh>
#include <core/types.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/kinematics/MoveMap.hh>
#include <protocols/moves/Mover.hh>
#include <utility>
#include <utility/vector1.hh>
#include <utility/VirtualBase.hh>
#include <map>

Classes

class  protocols::frags::TorsionFragment
 a class for single piece of torsion fragment More...
 
class  protocols::frags::SingleResidueTorsionFragmentLibrary
 a class for collection of fragments for a single residue position More...
 
class  protocols::frags::TorsionFragmentLibrary
 a class for classic Rosetta fragment library More...
 
class  protocols::frags::FragLib
 
class  protocols::frags::TorsionFragmentMover
 

Namespaces

 protocols
 The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
 
 protocols::frags
 

Functions

std::ostream & protocols::frags::operator<< (std::ostream &out, TorsionFragment const &f)
 
std::istream & protocols::frags::operator>> (std::istream &data, TorsionFragment &f)
 
std::ostream & protocols::frags::operator<< (std::ostream &out, SingleResidueTorsionFragmentLibrary const &lib)
 
std::istream & protocols::frags::operator>> (std::istream &data, SingleResidueTorsionFragmentLibrary &lib)
 
std::ostream & protocols::frags::operator<< (std::ostream &out, TorsionFragmentLibrary const &lib)
 
std::istream & protocols::frags::operator>> (std::istream &data, TorsionFragmentLibrary &lib)
 
std::ostream & protocols::frags::operator<< (std::ostream &out, FragLib const &lib)
 
std::istream & protocols::frags::operator>> (std::istream &data, FragLib &lib)
 
void protocols::frags::add_vall_fragments (utility::vector1< core::Size > const &frag_sizes, core::Size const nfrags, pose::Pose const &pose, core::kinematics::MoveMap const &mm, std::string const &secstruct, Real const seq_weight, Real const ss_weight, FragLib &frag_lib, utility::vector1< core::Size > const &homs_to_exclude, Real const bb_weight, std::string const &bigbins, std::string const &inputseq)
 
void protocols::frags::add_vall_fragments (utility::vector1< core::Size > const &frag_sizes, core::Size const nfrags, pose::Pose const &pose, core::kinematics::MoveMap const &mm, utility::vector1< std::map< char, core::Real > > const &target_ss, Real const seq_weight, Real const ss_weight, FragLib &frag_lib, utility::vector1< core::Size > const &homs_to_exclude, Real const bb_weight, std::string const &bigbins, std::string const &inputseq)
 
FragLibOP protocols::frags::setup_vall_fragments (utility::vector1< core::Size > const &frag_sizes, core::Size const nfrags, pose::Pose const &pose, core::kinematics::MoveMap const &mm, std::string const &secstruct, Real const seq_weight, Real const ss_weight, utility::vector1< core::Size > const &homs_to_exclude)
 
void protocols::frags::add_vall_cheating_fragments (utility::vector1< core::Size > const &frag_sizes, core::Size const nfrags, pose::Pose const &pose, core::kinematics::MoveMap const &mm, std::string const &secstruct, Real const seq_weight, Real const ss_weight, Real const torsion_weight, Real const min_torsion_dev, Real const max_torsion_dev, FragLib &frag_lib, utility::vector1< core::Size > const &homs_to_exclude)
 
FragLibOP protocols::frags::setup_vall_cheating_fragments (utility::vector1< core::Size > const &frag_sizes, core::Size const nfrags, pose::Pose const &pose, core::kinematics::MoveMap const &mm, std::string const &secstruct, Real const seq_weight, Real const ss_weight, Real const torsion_weight, Real const min_torsion_dev, Real const max_torsion_dev, utility::vector1< core::Size > const &homs_to_exclude)
 
void protocols::frags::fill_in_gaps (core::Size const nfrags, pose::Pose const &pose, std::string const &secstruct, Real const seq_weight, Real const ss_weight, FragLib &frag_lib, utility::vector1< core::Size > const &homs_to_exclude, bool const allow_uninitialized_secstruct)
 
bool protocols::frags::ss_length_check (core::Size const min_len_helix, core::Size const min_len_strand, core::pose::Pose const &pose)
 
void protocols::frags::insert_fragment (core::Size const begin, core::Size const end, pose::Pose &pose, TorsionFragmentLibrary const &lib, core::Size const desired_insert_pos)
 
void protocols::frags::insert_random_fragments_in_flexible_protein_regions (utility::vector1< core::Size > const &flex_protein, FragLib const &frag_lib, core::pose::Pose &pose)