motif_utils.cc File Reference

Motif helper/conversion/io functions. More...

#include <protocols/motifs/motif_utils.hh>
#include <protocols/motifs/BuildPosition.hh>
#include <protocols/motifs/Motif.hh>
#include <protocols/motifs/MotifLibrary.hh>
#include <protocols/motifs/SingleMotif.hh>
#include <protocols/dna/DnaDesignDef.hh>
#include <protocols/dna/util.hh>
#include <protocols/loops/Loops.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/Residue.functions.hh>
#include <core/conformation/ResidueFactory.hh>
#include <utility/graph/Graph.hh>
#include <core/id/AtomID.hh>
#include <core/kinematics/Jump.hh>
#include <core/kinematics/RT.hh>
#include <core/pack/pack_rotamers.hh>
#include <core/pack/packer_neighbors.hh>
#include <core/pack/rotamer_set/RotamerSet.hh>
#include <core/pack/rotamer_set/RotamerSetFactory.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/PDBPoseMap.hh>
#include <core/pose/util.hh>
#include <core/scoring/constraints/CoordinateConstraint.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/scoring/dna/base_geometry.hh>
#include <core/scoring/dna/BasePartner.hh>
#include <core/scoring/dna/setup.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/types.hh>
#include <basic/Tracer.hh>
#include <utility/exit.hh>
#include <utility/file/file_sys_util.hh>
#include <utility/file/FileName.hh>
#include <utility/io/izstream.hh>
#include <utility/tools/make_map.hh>
#include <utility/tools/make_vector1.hh>
#include <utility/string_util.hh>
#include <utility/vector1.hh>
#include <utility/vector0.hh>
#include <numeric/xyzVector.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/dna.OptionKeys.gen.hh>
#include <basic/options/keys/motifs.OptionKeys.gen.hh>
#include <core/import_pose/import_pose.hh>

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

Functions
static basic::Tracer	protocols::motifs::mu_tr ("protocols.motifs.motif_utils", basic::t_info)
SingleMotifOP	protocols::motifs::single_motif_from_filename (utility::file::FileName const &motif_filename)
SingleMotifOP	protocols::motifs::single_motif_from_stream (utility::io::izstream &motif_info)
SingleMotifOP	protocols::motifs::single_motif_from_stream (std::istream &motif_info)
SingleMotifOP	protocols::motifs::single_ligand_motif_from_stream (std::istream &motif_info)
core::Real	protocols::motifs::parallel_base_test (core::conformation::Residue const &pose_dna, core::conformation::Residue const &motif_dna)
core::Real	protocols::motifs::backbone_stub_match (core::conformation::Residue const &r1, core::conformation::Residue const &r2)
void	protocols::motifs::add_motif_bb_constraints (core::scoring::constraints::ConstraintSetOP cst_set, core::pose::Pose &pose, core::Size this_pos, core::conformation::Residue const &inv_rotamer)
void	protocols::motifs::add_motif_sc_constraints (core::scoring::constraints::ConstraintSetOP cst_set, core::pose::Pose &pose, core::Size this_pos, core::conformation::Residue const &inv_rotamer, MotifCOP this_motif, bool const is_it_forward)
void	protocols::motifs::mutate_position_vector_for_search (core::pose::Pose &pose, utility::vector1< core::Size > &trim_positions)
void	protocols::motifs::mutate_loops_for_search (core::pose::Pose &pose, protocols::loops::Loops &flex_regions)
MotifLibrary const	protocols::motifs::get_MotifLibrary_user ()
MotifLibrary const	protocols::motifs::get_LigandMotifLibrary_user ()
utility::vector1 < core::conformation::ResidueOP > const	protocols::motifs::get_targetconformers_user ()
std::map< std::string, utility::vector1 < core::conformation::ResidueOP > > const	protocols::motifs::setup_conformer_map (utility::vector1< core::conformation::ResidueOP > const &conformerOPs)
utility::vector1< core::Size >	protocols::motifs::get_target_positions_make_dna_mutations (core::pose::Pose &pose)
std::map< core::Size, std::set < std::string > >	protocols::motifs::get_target_position_map_make_dna_mutations (core::pose::Pose &pose)
void	protocols::motifs::make_dna_mutations (core::pose::Pose &pose)
void	protocols::motifs::make_dna_mutations (core::pose::Pose &pose, protocols::dna::DnaDesignDefOPs const &target)
utility::vector1< core::Size >	protocols::motifs::defs2vector (core::pose::Pose const &pose, protocols::dna::DnaDesignDefOPs const &targets)
utility::vector1< std::pair < core::Size, utility::vector1 < std::string > > >	protocols::motifs::defs2allowedtypes (core::pose::Pose const &pose, protocols::dna::DnaDesignDefOPs const &targets)
std::map< core::Size, std::set < std::string > >	protocols::motifs::defs2map (core::pose::Pose const &pose, protocols::dna::DnaDesignDefOPs const &targets)
std::map< core::Size, std::set < std::string > >	protocols::motifs::bpdefs2map (core::pose::Pose const &pose, protocols::dna::DnaDesignDefOPs const &targets)
std::string	protocols::motifs::name3_from_oneletter (std::string const &oneletter)
utility::vector1< core::Size >	protocols::motifs::get_motif_build_positions_user (core::pose::Pose const &pose)
utility::vector1 < protocols::dna::DnaDesignDefOP >	protocols::motifs::get_motif_build_position_defs_user ()
void	protocols::motifs::load_build_position_data (BuildPosition &bp, std::string const &filename, core::pose::Pose &pose, core::Size const ligand_marker)
utility::vector1 < utility::file::FileName >	protocols::motifs::get_filenames (utility::vector1< utility::file::FileName > const &listnames)
core::conformation::ResidueOP	protocols::motifs::single_residue_from_stream (utility::io::izstream &residue_info)
utility::vector1< bool >	protocols::motifs::bools_from_sizes (core::Size const nres, utility::vector1< core::Size > const &v)
void	protocols::motifs::make_base_pair_mutation (core::pose::Pose &pose, core::Size const seqpos, core::chemical::AA const &na)
core::Real	protocols::motifs::atom_specific_rms (core::conformation::Residue const &rsd1, core::conformation::Residue const &rsd2, utility::vector1< core::Size > const &atoms)
core::Real	protocols::motifs::atom_specific_rms (core::conformation::Residue const &rsd1, core::conformation::Residue const &rsd2, utility::vector1< std::string > const &atoms)
core::pack::rotamer_set::RotamerSetOP	protocols::motifs::build_rotamers_lite (core::pose::Pose &pose, core::Size const rotamer_build_position, utility::vector1< bool > aa_info, core::Size const ex_, bool bump_check)

Detailed Description

Motif helper/conversion/io functions.

Author

havranek, sthyme (sthym.nosp@m.e@gm.nosp@m.ail.c.nosp@m.om)