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
	)

References delete_protein_from_pose(), find_residues_around_mutation(), get_simple_RNA_protein_fold_tree(), basic::options::OptionKeys::relax::range::kT, numeric::log(), make_mutation_tag(), make_mutations(), basic::options::option, options, demo.D010_Pose_structure::pose, basic::options::OptionKeys::frags::scoring::scoring, simple_minimization(), simple_packing(), basic::options::TR, and basic::options::OptionKeys::inout::dbms::user.

Referenced by calculate_binding_energy(), and mutate_and_score_RNP().

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

References calculate_binding_energy().

void delete_protein_from_pose

(

core::pose::Pose &

pose

)

References basic::options::OptionKeys::cutoutdomain::end, assign_charges::first, basic::options::OptionKeys::rna::denovo::offset, and basic::options::OptionKeys::cutoutdomain::start.

Referenced by calculate_binding_energy().

void delete_RNA_from_pose

(

core::pose::Pose &

pose

)

References basic::options::OptionKeys::cutoutdomain::end, assign_charges::first, basic::options::OptionKeys::rna::denovo::offset, and basic::options::OptionKeys::cutoutdomain::start.

Referenced by get_unbound_protein_score().

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

References basic::options::OptionKeys::cp::cutoff, distance(), utility::options::OptionKeys::options::exit, basic::options::OptionKeys::frags::j, make_symmdef_file_denovo::length, basic::options::OptionKeys::frags::contacts::neighbors, basic::options::option, options, and basic::options::TR.

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

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(), and assign_charges::first.

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

References options, demo.D010_Pose_structure::pose, and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by mutate_and_score_RNP().

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 utility::options::OptionKeys::options::exit, basic::options::OptionKeys::mp::mutate_relax::mutation, basic::options::option, clean_pdb_keep_ligand::resnum, runtime_assert, and basic::options::TR.

Referenced by mutate_and_score_RNP().

core::kinematics::FoldTree get_simple_RNA_protein_fold_tree

(

core::pose::Pose const &

pose

)

References basic::Tracer::Debug, and basic::options::TR.

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

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(), basic::options::option, options, demo.D010_Pose_structure::pose, basic::options::OptionKeys::frags::scoring::scoring, simple_packing(), basic::options::TR, and unbound_protein_minimization().

Referenced by mutate_and_score_RNP().

int main	(	int	argc,
		char **	argv
	)

References test.T009_Exceptions::e, devel::init(), utility::excn::Exception::msg(), mutate_and_score_RNP(), NEW_OPT, options, basic::options::OptionKeys::recces::out_prefix, and basic::options::TR.

std::string make_mutation_tag

(

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

mutations

)

References utility::vectorL< SSize, T, A >::append(), basic::options::option, basic::options::OptionKeys::recces::out_prefix, and basic::options::OptionKeys::mh::match::ss.

Referenced by calculate_binding_energy(), and mutate_and_score_RNP().

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, assign_charges::first, ObjexxFCL::index(), basic::options::option, simple_minimization(), simple_packing(), and basic::options::TR.

Referenced by calculate_binding_energy(), and mutate_and_score_RNP().

void mutate_and_score_RNP

(

)

References calculate_binding_energy(), basic::options::OptionKeys::constraints::cst_file, basic::Tracer::Debug, find_residues_around_mutation(), assign_charges::first, get_complex_score(), get_mutations_from_file(), get_simple_RNA_protein_fold_tree(), get_unbound_protein_score(), make_mutation_tag(), make_mutations(), basic::options::OptionKeys::score::saxs::min_score, basic::options::option, options, basic::options::OptionKeys::in::path::path, basic::options::OptionKeys::hotspot::residue, basic::options::OptionKeys::willmatch::residues, basic::options::OptionKeys::frags::scoring::scoring, setup_score_function(), test.T220_AtomAtomPairEnergies::sfxn, simple_minimization(), simple_packing(), amino_acids::size, basic::options::TR, and basic::options::OptionKeys::inout::dbms::user.

Referenced by main().

core::scoring::ScoreFunctionOP setup_score_function

(

)

References pyrosetta::create_score_function, basic::options::option, test.T220_AtomAtomPairEnergies::sfxn, basic::options::OptionKeys::inout::dbms::user, and basic::options::OptionKeys::score::weights.

Referenced by mutate_and_score_RNP().

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

References loops_kic::mm, basic::options::option, basic::options::OptionKeys::frags::scoring::scoring, and basic::options::TR.

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

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
	)

References utility::vector1< T, A >::has_value(), basic::options::OptionKeys::frags::scoring::scoring, and basic::options::TR.

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

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
	)

References loops_kic::mm, basic::options::option, basic::options::OptionKeys::frags::scoring::scoring, and basic::options::TR.

Referenced by get_unbound_protein_score().

Variable Documentation

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

static