util.cc File Reference

#include <protocols/medal/util.hh>
#include <cmath>
#include <set>
#include <boost/unordered/unordered_set.hpp>
#include <numeric/prob_util.hh>
#include <utility/iter_util.hh>
#include <utility/vector1.hh>
#include <core/types.hh>
#include <core/chemical/ChemicalManager.fwd.hh>
#include <core/id/SequenceMapping.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/pose/Pose.hh>
#include <core/sequence/SequenceAlignment.hh>
#include <core/util/SwitchResidueTypeSet.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::medal

Typedefs
using	protocols::medal::Probabilities = utility::vector1< core::Real >

Functions
void	protocols::medal::end_bias_probabilities (const core::Size num_residues, Probabilities *p)
	Lower sampling probability near termini. More...
void	protocols::medal::alignment_probabilities (core::Size const num_residues, const core::sequence::SequenceAlignment &alignment, Probabilities *p)
	Computes per-residue alignment probabilities. To minimize assumptions about the fold tree, the number of residues in the pose is an explicit input. More...
void	protocols::medal::chunk_probabilities (const protocols::loops::Loops &chunks, Probabilities *p)
	Computes per-residue chunk probabilities. A linear voting scheme is used to bias sampling toward larger chunks. More...
void	protocols::medal::cutpoint_probabilities (core::Size const num_residues, const core::kinematics::FoldTree &tree, Probabilities *p)
	Computes per-residue cutpoint probabilities. Sampling is biased toward residues proximal to a cutpoint. More...
void	protocols::medal::invalidate_residues_spanning_cuts (const core::kinematics::FoldTree &tree, const core::Size fragment_len, Probabilities *probs)
	Zeroes out the probability of residues for which fragment insertion would cross cutpoint boundaries. More...
void	protocols::medal::as_set (protocols::loops::LoopsCOP loops, boost::unordered_set< core::Size > *s)
	Populates a hash table with the residues contained in loops. More...
void	protocols::medal::to_centroid (core::pose::Pose *pose)

Detailed Description

Author

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