TorsionFragment.cc File Reference

#include <protocols/frags/TorsionFragment.hh>
#include <protocols/frags/VallData.hh>
#include <core/types.hh>
#include <core/pose/Pose.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/Conformation.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/id/types.hh>
#include <utility/io/izstream.hh>
#include <utility/vector1.functions.hh>
#include <numeric/random/random.hh>
#include <numeric/random/random_permutation.hh>
#include <numeric/conversions.hh>
#include <basic/Tracer.hh>
#include <ObjexxFCL/string.functions.hh>
#include <ObjexxFCL/format.hh>

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

Typedefs
using	protocols::frags::Sizes = utility::vector1< core::Size >

Functions
static basic::Tracer	protocols::frags::TR ("protocols.frags.TorsionFragment")
template<class T >
bool	protocols::frags::has_element (utility::vector1< T > const &v, T const &t)
	these will go into a helper file soon More...
template<class T >
bool	protocols::frags::has_element (T const &t, utility::vector1< T > const &v)
	never can remember the order... More...
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::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)
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)
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::get_min_and_max_contigs (Sizes const &seg_in, core::Size &min_seg, core::Size &max_seg)
void	protocols::frags::insert_random_fragments_in_flexible_protein_regions (Sizes const &flex_protein, FragLib const &frag_lib, pose::Pose &pose)

Variables
utility::vector1< core::Size > const	protocols::frags::empty_size_list