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Namespaces | Functions
SheetDB.cc File Reference
#include <protocols/denovo_design/components/SheetDB.hh>
#include <protocols/denovo_design/util.hh>
#include <protocols/fldsgn/topology/Sheet.hh>
#include <protocols/fldsgn/topology/SS_Info2.hh>
#include <protocols/fldsgn/topology/util.hh>
#include <protocols/idealize/IdealizeMover.hh>
#include <protocols/moves/DsspMover.hh>
#include <protocols/toolbox/pose_manipulation/pose_manipulation.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <utility/graph/Graph.hh>
#include <utility/graph/graph_util.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/io/silent/SilentFileOptions.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/Pose.hh>
#include <core/pose/variant_util.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/util/SwitchResidueTypeSet.hh>
#include <basic/Tracer.hh>
#include <utility/io/izstream.hh>
#include <utility/VirtualBase.hh>
#include <boost/lexical_cast.hpp>
#include <map>
#include <stack>

Namespaces

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

Functions

static basic::Tracer TR ("protocols.denovo_design.components.SheetDB")
 
bool protocols::denovo_design::components::pose_matches_description (core::pose::Pose const &pose, std::string const &in_lengths_shifts)
 tells whether the given pose matches up with the given descriptor More...
 
std::string protocols::denovo_design::components::orientations_str (StrandOrientations const &orientations)
 
utility::graph::Graph protocols::denovo_design::components::graph_from_strandpairings (protocols::fldsgn::topology::StrandPairings const &spairs, std::map< core::Size, core::Size > &node_to_strand)
 
int protocols::denovo_design::components::add_to_pose (core::pose::PoseOP newpose, core::pose::Pose const &pose, core::Size s_start, core::Size s_stop)
 
utility::vector1
< core::pose::PoseOP
protocols::denovo_design::components::extract_sheets_from_strandlist (utility::vector1< core::pose::PoseOP > const &strands, core::Size const nstrands)
 
core::pose::PoseOP protocols::denovo_design::components::reorder_chains (core::pose::Pose &pose)
 
utility::vector1
< core::pose::PoseOP
protocols::denovo_design::components::extract_sheets_from_pose (core::pose::Pose const &pose, protocols::fldsgn::topology::StrandPairings const &spairs, protocols::fldsgn::topology::SS_Info2 const &ss_info, bool const idealize)
 
utility::vector1< boolprotocols::denovo_design::components::calc_paired_residues (core::pose::Pose &pose, protocols::fldsgn::topology::StrandPairingSet const &spairs)
 creates a list of whether a pose residue is beta-sheet-type paired to anything More...
 
std::string protocols::denovo_design::components::make_strand_info_str (architects::Lengths const &lengths, RegisterShifts const &shifts)
 creates a string key for lengths/shifts based on the given vectors for strand lengths and register shifts More...
 
std::string protocols::denovo_design::components::make_lengths_str (core::pose::Pose const &pose, utility::vector1< bool > const &paired, Lengths const &lengths, StrandOrientations const &orients, protocols::fldsgn::topology::StrandPairingSet const &spairs)
 
std::pair< std::string,
std::string > 
protocols::denovo_design::components::prune_unpaired_residues (core::pose::Pose &pose)
 using the pose secondary structure, remove residues that aren't paired. returns a list of paired strand lengths, which do not necessarily correspond to pose lengths due to beta-bulges and other weird things. More...
 
core::Size protocols::denovo_design::components::num_strands (core::pose::Pose const &pose)
 counts number of strands based on number of jumps. Pose must be a disconnected sheet More...
 
std::pair< std::string,
std::string > 
protocols::denovo_design::components::find_orientations_and_lengths (core::pose::Pose const &pose)
 gets a pair of strings, which refer to orientations, and lengths/shifts. Pose secstruct MUST be set More...
 
std::string protocols::denovo_design::components::reverse_orientations (std::string const &orient)
 
utility::vector1< boolprotocols::denovo_design::components::parse_orientations (std::string const &orientations)
 
std::pair< utility::vector1
< core::Size >
, utility::vector1< int > > 
protocols::denovo_design::components::parse_lengths (std::string const &lengths)
 
std::string protocols::denovo_design::components::reverse_lengths (std::string const &orientations, std::string const &lengths)
 
std::pair< std::string,
std::string > 
protocols::denovo_design::components::canonicalize (std::string const &orientations, std::string const &lengths)
 
std::string const & protocols::denovo_design::components::choose_canonical (std::string const &l1, std::string const &l2)
 
core::pose::PoseOP protocols::denovo_design::components::reverse_chains (core::pose::Pose const &pose)
 

Function Documentation

static basic::Tracer TR ( "protocols.denovo_design.components.SheetDB"  )
static