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util.cc File Reference

set of utilities used in comparative modeling of protein structures More...

#include <core/types.hh>
#include <basic/Tracer.hh>
#include <core/pose/util.hh>
#include <core/pose/Pose.hh>
#include <core/chemical/util.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/conformation/Residue.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreType.hh>
#include <core/pose/symmetry/util.hh>
#include <core/conformation/symmetry/SymmetricConformation.hh>
#include <core/conformation/symmetry/SymmetryInfo.hh>
#include <core/sequence/util.hh>
#include <core/sequence/Sequence.hh>
#include <core/sequence/Sequence.fwd.hh>
#include <core/sequence/AlignerFactory.hh>
#include <core/sequence/SequenceProfile.hh>
#include <core/id/SequenceMapping.hh>
#include <core/sequence/ScoringScheme.fwd.hh>
#include <core/sequence/ScoringSchemeFactory.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/cm.OptionKeys.gen.hh>
#include <protocols/comparative_modeling/util.hh>
#include <protocols/comparative_modeling/AlignmentSet.hh>
#include <protocols/loops/loops_main.hh>
#include <protocols/loops/Loop.hh>
#include <protocols/loops/Loops.hh>
#include <protocols/loops/loop_mover/LoopMover.hh>
#include <protocols/loops/LoopMoverFactory.hh>
#include <utility/vector1.hh>
#include <utility/string_util.hh>
#include <utility/file/FileName.hh>
#include <utility/file/file_sys_util.hh>
#include <core/chemical/ChemicalManager.fwd.hh>
#include <core/id/NamedAtomID.hh>
#include <core/sequence/Aligner.hh>
#include <core/sequence/ScoringScheme.hh>
#include <numeric/random/random.hh>
#include <core/import_pose/import_pose.hh>
#include <core/util/SwitchResidueTypeSet.hh>

Namespaces

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

Constant Groups

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

Macros

#define NO_LOOP_SIZE_CST   0
 

Functions

static
numeric::random::RandomGenerator 
protocols::comparative_modeling::RG (298211)
 
static basic::Tracer protocols::comparative_modeling::tr ("protocols.comparative_modeling.util")
 
core::sequence::SequenceAlignment protocols::comparative_modeling::alignment_from_cmd_line ()
 
void protocols::comparative_modeling::bounded_loops_from_alignment (const core::Size num_residues, const core::Size min_size, const core::sequence::SequenceAlignment &alignment, protocols::loops::LoopsOP &unaligned_regions)
 Identifies consecutive stretches of unaligned residues by scanning the alignment. Each unaligned region is guaranteed to have length at least <min_size>. Aligned regions share this property as well, and can be obtained by calling the invert() method on the output parameter <unaligned_regions>. More...
 
protocols::loops::LoopsOP protocols::comparative_modeling::loops_from_alignment (core::Size nres, core::sequence::SequenceAlignment const &aln, core::Size const min_loop_size)
 
protocols::loops::LoopsOP protocols::comparative_modeling::loops_from_transitive_alignments (core::Size nres1, core::sequence::SequenceAlignment const &aln1, core::Size nres2, core::sequence::SequenceAlignment const &aln2, core::Size const min_loop_size)
 
protocols::loops::LoopsOP protocols::comparative_modeling::pick_loops_unaligned (core::Size nres, utility::vector1< core::Size > const &unaligned_residues, core::Size min_loop_size)
 
protocols::loops::LoopsOP protocols::comparative_modeling::pick_loops_chainbreak (core::pose::Pose &query_pose, core::Size min_loop_size)
 
void protocols::comparative_modeling::rebuild_loops_until_closed (core::pose::Pose &query_pose, core::Size const min_loop_size, core::Size const max_rebuild, std::string const &loop_mover_name)
 
void protocols::comparative_modeling::steal_ligands (core::pose::Pose &dest_pose, core::pose::Pose const &source_pose_in, core::id::NamedAtomID const anchor_atom_dest, core::id::NamedAtomID const anchor_atom_source, utility::vector1< core::id::NamedAtomID > const ligand_indices)
 Function for stealing ligands from a given Pose and adding them to source_pose. More...
 
void protocols::comparative_modeling::initialize_ss (core::pose::Pose &pose)
 
utility::vector1
< core::pose::Pose
protocols::comparative_modeling::templates_from_cmd_line ()
 
bool protocols::comparative_modeling::loops_are_closed (core::pose::Pose &pose)
 
std::map< std::string,
core::pose::Pose
protocols::comparative_modeling::poses_from_cmd_line (utility::vector1< std::string > const &fn_list)
 
AlignmentSet protocols::comparative_modeling::alignments_from_cmd_line ()
 
void protocols::comparative_modeling::randomize_selected_atoms (core::pose::Pose &query_pose, core::id::AtomID_Mask const &selected)
 

Detailed Description

set of utilities used in comparative modeling of protein structures

Author
James Thompson

Macro Definition Documentation

#define NO_LOOP_SIZE_CST   0