rnp_ddg.cc File Reference

#include <core/pose/Pose.hh>
#include <core/conformation/Residue.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/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/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 <utility/pointer/owning_ptr.hh>
#include <basic/Tracer.hh>
#include <fstream>
#include <devel/init.hh>
#include <protocols/rigid/RigidBodyMover.hh>
#include <core/scoring/constraints/ConstraintIO.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <basic/options/keys/constraints.OptionKeys.gen.hh>
#include <basic/options/option_macros.hh>
#include <core/pack/task/ResidueLevelTask.hh>
#include <utility/stream_util.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

calculate_binding_energy() [1/2]

core::Real calculate_binding_energy	(	core::scoring::ScoreFunctionOP &	sfxn,
		core::pose::Pose &	pose
	)

References calculate_binding_energy(), beta_nonlocal::pose, and test.T120_core::sfxn.

calculate_binding_energy() [2/2]

core::Real calculate_binding_energy	(	core::scoring::ScoreFunctionOP &	sfxn,
		core::pose::Pose &	pose,
		utility::vector1< std::pair< core::Size, char > >	mutations
	)

References delete_protein_from_pose(), find_residues_around_mutation(), get_simple_RNA_protein_fold_tree(), create_a3b_hbs::i, basic::options::OptionKeys::relax::range::kT, numeric::log(), make_mutation_tag(), make_mutations(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, basic::options::option, beta_nonlocal::pose, basic::options::OptionKeys::frags::scoring::scoring, test.T120_core::sfxn, simple_minimization(), simple_packing(), basic::options::TR, and basic::options::OptionKeys::inout::dbms::user.

Referenced by calculate_binding_energy(), and mutate_and_score_RNP().

delete_protein_from_pose()

void delete_protein_from_pose

(

core::pose::Pose &

pose

)

References end, create_a3b_hbs::first, create_a3b_hbs::i, offset, beta_nonlocal::pose, and basic::options::OptionKeys::cutoutdomain::start.

Referenced by calculate_binding_energy().

delete_RNA_from_pose()

void delete_RNA_from_pose

(

core::pose::Pose &

pose

)

References end, create_a3b_hbs::first, create_a3b_hbs::i, offset, beta_nonlocal::pose, and basic::options::OptionKeys::cutoutdomain::start.

Referenced by get_unbound_protein_score().

find_residues_around_mutation() [1/2]

utility::vector1< core::Size > find_residues_around_mutation	(	core::pose::Pose const &	pose,
		utility::vector1< core::Size >	mutant_residues
	)

References extract_by_sidechain_sasa_score::cutoff, build_jacobian::distance, utility::options::OptionKeys::options::exit, create_a3b_hbs::i, create_a3b_hbs::j, oop_conformations::length, basic::options::OptionKeys::frags::contacts::neighbors, basic::options::option, beta_nonlocal::pose, and basic::options::TR.

Referenced by calculate_binding_energy(), find_residues_around_mutation(), and mutate_and_score_RNP().

find_residues_around_mutation() [2/2]

utility::vector1< core::Size > find_residues_around_mutation	(	core::pose::Pose const &	pose,
		utility::vector1< std::pair< core::Size, char > > const	mutations
	)

References find_residues_around_mutation(), create_a3b_hbs::first, create_a3b_hbs::i, and beta_nonlocal::pose.

get_complex_score()

core::Real get_complex_score	(	core::scoring::ScoreFunctionOP &	sfxn,
		core::pose::Pose &	pose
	)

References beta_nonlocal::pose, basic::options::OptionKeys::frags::scoring::scoring, and test.T120_core::sfxn.

Referenced by mutate_and_score_RNP().

get_mutations_from_file()

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
	)

References build_restypes::elem, utility::options::OptionKeys::options::exit, create_a3b_hbs::i, basic::options::OptionKeys::ddg::mut_file, analyze_ddG_stability::mutation, basic::options::option, beta_nonlocal::pose, predPRE::resnum, runtime_assert, and basic::options::TR.

Referenced by mutate_and_score_RNP().

get_simple_RNA_protein_fold_tree()

core::kinematics::FoldTree get_simple_RNA_protein_fold_tree

(

core::pose::Pose const &

pose

)

References basic::Tracer::Debug, create_a3b_hbs::i, beta_nonlocal::pose, and basic::options::TR.

Referenced by calculate_binding_energy(), get_unbound_protein_score(), and mutate_and_score_RNP().

get_unbound_protein_score()

core::Real get_unbound_protein_score	(	core::scoring::ScoreFunctionOP &	sfxn,
		core::pose::Pose const &	pose
	)

References delete_RNA_from_pose(), get_simple_RNA_protein_fold_tree(), create_a3b_hbs::i, basic::options::option, beta_nonlocal::pose, basic::options::OptionKeys::frags::scoring::scoring, test.T120_core::sfxn, simple_packing(), basic::options::TR, and unbound_protein_minimization().

Referenced by mutate_and_score_RNP().

main()

int main	(	int	argc,
		char **	argv
	)

References argv, test.T009_Exceptions::e, basic::init(), mutate_and_score_RNP(), NEW_OPT, and basic::options::OptionKeys::recces::out_prefix.

make_mutation_tag()

std::string make_mutation_tag

(

utility::vector1< std::pair< core::Size, char > >

mutations

)

References utility::vectorL< L, T, A >::append(), create_a3b_hbs::i, basic::options::option, basic::options::OptionKeys::recces::out_prefix, and challenge::ss.

Referenced by calculate_binding_energy(), and mutate_and_score_RNP().

make_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
	)

References basic::Tracer::Debug, utility::options::OptionKeys::options::exit, detail::find(), create_a3b_hbs::first, create_a3b_hbs::i, basic::options::option, create_a3b_hbs::r, test.T120_core::sfxn, simple_minimization(), simple_packing(), and basic::options::TR.

Referenced by calculate_binding_energy(), and mutate_and_score_RNP().

mutate_and_score_RNP()

void mutate_and_score_RNP

(

)

References calculate_binding_energy(), basic::options::OptionKeys::constraints::cst_file, basic::Tracer::Debug, detail::find(), find_residues_around_mutation(), create_a3b_hbs::first, get_complex_score(), get_mutations_from_file(), get_simple_RNA_protein_fold_tree(), get_unbound_protein_score(), create_a3b_hbs::i, gaussian-sampling::input, make_mutation_tag(), make_mutations(), SmotifHasher::min_score, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, basic::options::option, closure_error::path, create_a3b_hbs::r, residue, execute::residues, basic::options::OptionKeys::frags::scoring::scoring, setup_score_function(), test.T120_core::sfxn, simple_minimization(), simple_packing(), subloop_histogram::size, basic::options::TR, and basic::options::OptionKeys::inout::dbms::user.

Referenced by main().

setup_score_function()

core::scoring::ScoreFunctionOP setup_score_function

(

)

References pyrosetta.io::create_score_function, pyrosetta.distributed.io::get_score_function(), basic::options::option, test.T120_core::sfxn, basic::options::OptionKeys::inout::dbms::user, and basic::options::OptionKeys::score::weights.

Referenced by mutate_and_score_RNP().

simple_minimization() [1/2]

void simple_minimization	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunctionOP	sfxn,
		bool	exclude_separation_jump = false
	)

References create_a3b_hbs::i, beta_nonlocal::pose, test.T120_core::sfxn, and simple_minimization().

simple_minimization() [2/2]

void simple_minimization	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunctionOP	sfxn,
		utility::vector1< core::Size > const	neighbor_residues,
		bool	exclude_separation_jump = false
	)

References create_a3b_hbs::i, beta_nonlocal::mm, basic::options::option, beta_nonlocal::pose, basic::options::OptionKeys::frags::scoring::scoring, test.T120_core::sfxn, and basic::options::TR.

Referenced by calculate_binding_energy(), make_mutations(), mutate_and_score_RNP(), and simple_minimization().

simple_packing() [1/2]

void simple_packing	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunctionOP	sfxn
	)

References create_a3b_hbs::i, beta_nonlocal::pose, test.T120_core::sfxn, and simple_packing().

simple_packing() [2/2]

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

References utility::vector1< T, A >::has_value(), create_a3b_hbs::i, beta_nonlocal::pose, basic::options::OptionKeys::frags::scoring::scoring, test.T120_core::sfxn, and basic::options::TR.

Referenced by calculate_binding_energy(), get_unbound_protein_score(), make_mutations(), mutate_and_score_RNP(), and simple_packing().

unbound_protein_minimization()

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

References create_a3b_hbs::i, beta_nonlocal::mm, basic::options::option, beta_nonlocal::pose, basic::options::OptionKeys::frags::scoring::scoring, test.T120_core::sfxn, and basic::options::TR.

Referenced by get_unbound_protein_score().

Variable Documentation

TR

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

static