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NucleotideMutation.cc File Reference

Substitutes amino acids in pose based on mutations in nucleotide space. More...

#include <protocols/evolution/NucleotideMutation.hh>
#include <protocols/evolution/NucleotideMutationCreator.hh>
#include <core/pose/symmetry/util.hh>
#include <protocols/minimization_packing/PackRotamersMover.hh>
#include <protocols/relax/FastRelax.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/pose/extra_pose_info_util.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <basic/Tracer.hh>
#include <core/scoring/ScoreFunction.hh>
#include <utility/tag/Tag.hh>
#include <numeric/random/random.hh>
#include <numeric/random/random_permutation.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/NucleotideTools.hh>
#include <utility/vector1.hh>
#include <basic/datacache/DataMap.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/rosetta_scripts/util.hh>
#include <sstream>
#include <core/chemical/AA.hh>
#include <core/import_pose/import_pose.hh>
#include <protocols/task_operations/ThreadSequenceOperation.hh>
#include <utility/vector0.hh>
#include <map>
#include <cmath>
#include <ctime>
#include <core/conformation/Residue.hh>
#include <core/kinematics/Jump.hh>
#include <utility/tag/XMLSchemaGeneration.hh>
#include <protocols/moves/mover_schemas.hh>

Namespaces

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

Functions

static basic::Tracer protocols::evolution::TR ("protocols.evolution.NucleotideMutation")
 

Detailed Description

Substitutes amino acids in pose based on mutations in nucleotide space.

Translate amino acid sequence to nucleotide sequence, introduce random mutation, and affectuates the amino acid substitution in pose. Stop codons are avoided and with default setting nucleotide mutations will continue untill a non-silent mutation occurs.

Author
Christoffer Norn (ch.no.nosp@m.rn@g.nosp@m.mail..nosp@m.com)