util.cc File Reference

#include <protocols/nonlocal/util.hh>
#include <iostream>
#include <string>
#include <basic/Tracer.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/OptionKeys.hh>
#include <basic/options/keys/abinitio.OptionKeys.gen.hh>
#include <basic/options/keys/rigid.OptionKeys.gen.hh>
#include <numeric/random/random.hh>
#include <numeric/xyzVector.hh>
#include <utility/vector1.hh>
#include <core/types.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/id/NamedAtomID.hh>
#include <core/pose/Pose.hh>
#include <core/sequence/Sequence.hh>
#include <core/sequence/SequenceAlignment.hh>
#include <core/scoring/EnergyMap.hh>
#include <core/scoring/Energies.hh>
#include <protocols/comparative_modeling/util.hh>
#include <protocols/loops/Loop.hh>
#include <protocols/loops/Loops.hh>

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

Functions
static basic::Tracer	protocols::nonlocal::TR ("protocols.nonlocal.util")
void	protocols::nonlocal::chunks_by_CA_CA_distance (const core::pose::Pose &pose, protocols::loops::LoopsOP chunks)
	Computes the distance between consecutive CA atoms. If the distance exceeds a user-specified threshold, creates a new chunk and adds it to <chunks>. CA-CA distance threshold is retrieved from the option system (rigid::max_ca_ca_dist). More...
void	protocols::nonlocal::chunks_by_CA_CA_distance (const core::pose::Pose &pose, protocols::loops::LoopsOP chunks, core::Real threshold)
	Computes the distance between consecutive CA atoms. If the distance exceeds <threshold>, creates a new chunk and adds it to <chunks>. More...
protocols::loops::Loops	protocols::nonlocal::combine_and_trim (core::Size min_chunk_sz, core::Size num_residues, const protocols::loops::LoopsOP aligned_regions, const protocols::loops::LoopsOP unaligned_regions)
	Combine aligned and unaligned regions, limit size of final loop. More...
void	protocols::nonlocal::limit_chunk_size (core::Size min_chunk_sz, core::Size max_chunk_sz, protocols::loops::LoopsOP &regions)
	Best-effort attempt to limit the length of a chunk by recursively decomposing <regions> such that min_chunk_sz <= |chunk| <= max_chunk_sz. More...
void	protocols::nonlocal::decompose (core::Size min_chunk_sz, core::Size max_chunk_sz, const protocols::loops::Loop &loop, utility::vector1< protocols::loops::Loop > *pieces)
	Recursively decomposes <loop> into a series of <pieces>, each having length less than or equal to <max_length>. More...
void	protocols::nonlocal::find_regions_with_minimum_size (const core::sequence::SequenceAlignment &alignment, const core::Size unaligned_region_min_sz, protocols::loops::LoopsOP &aligned_regions, protocols::loops::LoopsOP &unaligned_regions)
void	protocols::nonlocal::emit_intermediate (const core::pose::Pose &pose, const std::string &file)
	If -abinitio:debug is enabled, writes <pose> to <file>. More...
core::Real	protocols::nonlocal::get_per_residue_score (core::Size rsd_idx, core::scoring::ScoreType scoretype, core::pose::Pose const &pose)
	Returns the unweighted score of the ScoreType for the given residue. Assumes that the Pose has recently been scored by ScoreFunction with non-zero weight for the ScoreType. More...

Detailed Description

Author

Christopher Miles (cmile.nosp@m.s@uw.nosp@m..edu)