Rosetta  2019.47
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Functions | Variables
rnp_ddg.cc File Reference
#include <core/pose/Pose.hh>
#include <core/import_pose/pose_stream/PoseInputStream.hh>
#include <core/import_pose/pose_stream/PoseInputStream.fwd.hh>
#include <core/import_pose/pose_stream/PDBPoseInputStream.hh>
#include <core/import_pose/pose_stream/SilentFilePoseInputStream.hh>
#include <core/pose/util.hh>
#include <core/pose/rna/util.hh>
#include <core/import_pose/import_pose.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/dssp/Dssp.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/pack_rotamers.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <core/io/silent/BinarySilentStruct.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/pose/full_model_info/FullModelInfo.hh>
#include <core/chemical/ChemicalManager.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <utility/pointer/owning_ptr.hh>
#include <basic/Tracer.hh>
#include <numeric/random/random.hh>
#include <iostream>
#include <fstream>
#include <devel/init.hh>
#include <protocols/moves/MonteCarlo.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <protocols/rigid/RigidBodyMover.hh>
#include <core/scoring/constraints/ConstraintIO.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <basic/options/keys/constraints.OptionKeys.gen.hh>
#include <basic/options/option_macros.hh>

Functions

std::pair< utility::vector1
< utility::vector1< std::pair
< core::Size, char >
> >, utility::vector1
< std::string > > 
get_mutations_from_file (std::string mut_file, core::pose::Pose const &pose)
 
utility::vector1< core::Size > find_residues_around_mutation (core::pose::Pose const &pose, utility::vector1< core::Size > mutant_residues)
 
utility::vector1< core::Size > find_residues_around_mutation (core::pose::Pose const &pose, utility::vector1< std::pair< core::Size, char > > const mutations)
 
core::scoring::ScoreFunctionOP setup_score_function ()
 
void simple_minimization (core::pose::Pose &pose, core::scoring::ScoreFunctionOP sfxn, utility::vector1< core::Size > const neighbor_residues, bool exclude_separation_jump=false)
 
void simple_minimization (core::pose::Pose &pose, core::scoring::ScoreFunctionOP sfxn, bool exclude_separation_jump=false)
 
void unbound_protein_minimization (core::pose::Pose &pose, core::scoring::ScoreFunctionOP sfxn)
 
void simple_packing (core::pose::Pose &pose, core::scoring::ScoreFunctionOP sfxn, utility::vector1< core::Size > const neighbor_residues)
 
void simple_packing (core::pose::Pose &pose, core::scoring::ScoreFunctionOP sfxn)
 
void make_mutations (core::pose::Pose &pose_to_mutate, core::scoring::ScoreFunctionOP sfxn, utility::vector1< std::pair< core::Size, char > > const mutations, utility::vector1< core::Size > const neighbor_residues, bool override_did_mutate_and_pack)
 
core::kinematics::FoldTree get_simple_RNA_protein_fold_tree (core::pose::Pose const &pose)
 
void delete_protein_from_pose (core::pose::Pose &pose)
 
void delete_RNA_from_pose (core::pose::Pose &pose)
 
std::string make_mutation_tag (utility::vector1< std::pair< core::Size, char > > mutations)
 
core::Real calculate_binding_energy (core::scoring::ScoreFunctionOP &sfxn, core::pose::Pose &pose, utility::vector1< std::pair< core::Size, char > > mutations)
 
core::Real get_complex_score (core::scoring::ScoreFunctionOP &sfxn, core::pose::Pose &pose)
 
core::Real calculate_binding_energy (core::scoring::ScoreFunctionOP &sfxn, core::pose::Pose &pose)
 
core::Real get_unbound_protein_score (core::scoring::ScoreFunctionOP &sfxn, core::pose::Pose const &pose)
 
void mutate_and_score_RNP ()
 
int main (int argc, char **argv)
 

Variables

static basic::Tracer TR ("apps.public.rnp_ddg.rnp_ddg")
 

Function Documentation

core::Real calculate_binding_energy ( core::scoring::ScoreFunctionOP &  sfxn,
core::pose::Pose pose,
utility::vector1< std::pair< core::Size, char > >  mutations 
)
core::Real calculate_binding_energy ( core::scoring::ScoreFunctionOP &  sfxn,
core::pose::Pose pose 
)
void delete_protein_from_pose ( core::pose::Pose pose)
void delete_RNA_from_pose ( core::pose::Pose pose)
utility::vector1< core::Size > find_residues_around_mutation ( core::pose::Pose const &  pose,
utility::vector1< core::Size >  mutant_residues 
)
utility::vector1< core::Size > find_residues_around_mutation ( core::pose::Pose const &  pose,
utility::vector1< std::pair< core::Size, char > > const  mutations 
)
core::Real get_complex_score ( core::scoring::ScoreFunctionOP &  sfxn,
core::pose::Pose pose 
)
std::pair< utility::vector1< utility::vector1< std::pair< core::Size, char > > >, utility::vector1< std::string > > get_mutations_from_file ( std::string  mut_file,
core::pose::Pose const &  pose 
)
core::kinematics::FoldTree get_simple_RNA_protein_fold_tree ( core::pose::Pose const &  pose)
core::Real get_unbound_protein_score ( core::scoring::ScoreFunctionOP &  sfxn,
core::pose::Pose const &  pose 
)
int main ( int  argc,
char **  argv 
)
std::string make_mutation_tag ( utility::vector1< std::pair< core::Size, char > >  mutations)
void make_mutations ( core::pose::Pose pose_to_mutate,
core::scoring::ScoreFunctionOP  sfxn,
utility::vector1< std::pair< core::Size, char > > const  mutations,
utility::vector1< core::Size > const  neighbor_residues,
bool  override_did_mutate_and_pack 
)
void mutate_and_score_RNP ( )
core::scoring::ScoreFunctionOP setup_score_function ( )
void simple_minimization ( core::pose::Pose pose,
core::scoring::ScoreFunctionOP  sfxn,
utility::vector1< core::Size > const  neighbor_residues,
bool  exclude_separation_jump = false 
)
void simple_minimization ( core::pose::Pose pose,
core::scoring::ScoreFunctionOP  sfxn,
bool  exclude_separation_jump = false 
)

References simple_minimization().

void simple_packing ( core::pose::Pose pose,
core::scoring::ScoreFunctionOP  sfxn,
utility::vector1< core::Size > const  neighbor_residues 
)
void simple_packing ( core::pose::Pose pose,
core::scoring::ScoreFunctionOP  sfxn 
)

References simple_packing().

void unbound_protein_minimization ( core::pose::Pose pose,
core::scoring::ScoreFunctionOP  sfxn 
)

Variable Documentation

basic::Tracer TR("apps.public.rnp_ddg.rnp_ddg")
static