easy_target_test.cc File Reference

#include <core/scoring/rms_util.hh>
#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueMatcher.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/ResidueTypeSelector.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/chemical/VariantType.hh>
#include <core/chemical/util.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/sequence/util.hh>
#include <core/scoring/constraints/DihedralConstraint.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/scoring/func/PeriodicFunc.hh>
#include <core/scoring/constraints/DOF_Constraint.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/constraints/ConstraintIO.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/tree/Atom.hh>
#include <core/id/AtomID_Map.hh>
#include <core/id/AtomID_Map.Pose.hh>
#include <core/id/AtomID.hh>
#include <core/id/DOF_ID.hh>
#include <core/kinematics/AtomTree.hh>
#include <core/kinematics/Jump.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/io/silent/ProteinSilentStruct.hh>
#include <core/io/silent/NonIdealProteinSilentStruct.hh>
#include <core/io/silent/BinarySilentStruct.hh>
#include <core/io/silent/SilentFileData.hh>
#include <protocols/evaluation/RmsdEvaluator.hh>
#include <core/pack/pack_rotamers.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <core/options/option.hh>
#include <core/options/after_opts.hh>
#include <core/options/util.hh>
#include <core/options/option_macros.hh>
#include <protocols/idealize.hh>
#include <protocols/relax_protocols.hh>
#include <protocols/viewer/viewers.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/util/basic.hh>
#include <core/io/database/open.hh>
#include <devel/init.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <utility/vector1.hh>
#include <utility/io/ozstream.hh>
#include <utility/io/izstream.hh>
#include <numeric/xyzVector.hh>
#include <numeric/conversions.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <core/scoring/TenANeighborGraph.hh>
#include <protocols/branch_angle/BranchAngleOptimizer.hh>
#include <protocols/backrub/BackrubMover.hh>
#include <protocols/moves/MonteCarlo.hh>
#include <protocols/simple_moves/sidechain_moves/SidechainMover.hh>
#include <core/scoring/dssp/Dssp.hh>
#include <fstream>
#include <iostream>
#include <string>
#include <core/util/Tracer.hh>
#include <core/options/keys/out.OptionKeys.gen.hh>
#include <core/options/keys/score.OptionKeys.gen.hh>
#include <core/options/keys/OptionKeys.OptionKeys.gen.hh>
#include <core/options/keys/run.OptionKeys.gen.hh>
#include <core/options/keys/in.OptionKeys.gen.hh>
#include <core/options/keys/backrub.OptionKeys.gen.hh>

Typedefs
typedef numeric::xyzMatrix< Real >	Matrix

Functions
Size	read_alignment_fasta_file (utility::vector1< std::string > &sequences, utility::vector1< std::string > &pdb_names, std::string const &fasta_file)
void	setup_mask (FArray1D_bool &sequence_mask, utility::vector1< std::string > const &sequences)
void	setup_alignment_map (utility::vector1< std::map< Size, Size > > &alignment2sequence, utility::vector1< std::string > const &sequences)
std::string	apply_mask (FArray1D_bool &sequence_mask, utility::vector1< std::map< Size, Size > > &alignment2sequence, utility::vector1< std::string > const &pdb_names, std::string const &which_file, pose::Pose &pose)
void	setup_t469_zn_tether (pose::Pose &pose)
void	prepare_start_model (pose::Pose const &template_pose, pose::Pose const &pose_with_desired_sequence, scoring::ScoreFunction &scorefxn_input, pose::Pose &pose, FArray1D_bool &conserved)
void	prepare_start_model (pose::Pose const &template_pose, std::string desired_sequence, scoring::ScoreFunction &scorefxn_input, pose::Pose &pose, FArray1D_bool &conserved)
void	repack (pose::Pose &pose, scoring::ScoreFunction const &scorefxn)
void	check_chi_correct (pose::Pose const &native_pose, pose::Pose const &pose, Size const &i, bool &chi1_exists, bool &chi2_exists, bool &chi1_correct, bool &chi1_chi2_correct)
void	output_backbone_stats (pose::Pose &native_pose, pose::Pose &pose)
void	output_chi_stats (pose::Pose &native_pose, pose::Pose &pose, FArray1D_bool sequence_mask, utility::io::ozstream &out, std::string const &pdb_file, Size const n)
void	setup_secstruct (pose::Pose &template_pose, std::string const &template_secstruct_file)
void	setup_secstruct_dssp (pose::Pose &pose)
Size	find_middle_of_vector (utility::vector1< Size > v)
void	setup_rhiju_fold_tree (pose::Pose &pose)
void	read_soft_segment_file (FArray1D_bool &in_soft_segment)
void	setup_CA_constraints (pose::Pose &pose, pose::Pose const &src_pose)
void	vary_geometry_sidechains (pose::Pose &pose, kinematics::MoveMap &mm)
void	mask_out_loop (pose::Pose const &pose, utility::vector1< std::map< Size, Size > > &alignment2sequence, FArray1D_bool &sequence_mask)
void	vary_geometry_backbone (pose::Pose &pose, kinematics::MoveMap &mm)
void	setup_constraints (std::string const cst_file_name, pose::Pose &pose)
void	output_constraints (pose::Pose const &pose, std::string const &filename, std::map< Size, Size > &alignment2full)
void	output_constraints (pose::Pose const &pose, std::string const &filename)
void	backrub_protocol (pose::Pose const &native_pose, pose::PoseOP &pose, scoring::ScoreFunctionOP &score_fxn)
void	minimize_protocol (pose::Pose const &native_pose, pose::Pose &pose, scoring::ScoreFunctionOP &scorefxn)
void	output_constraints_for_full_length (pose::Pose const &pose, std::map< Size, Size > &alignment2sequence_target, FArray1D_bool const &sequence_mask, std::string const &filename)
void	easy_target_test ()
void	prepare_full_length_start_model (pose::Pose &template_pose, pose::Pose &pose, utility::vector1< std::string > const &sequences, FArray1D_bool const &sequence_mask, utility::vector1< std::map< Size, Size > > &alignment2sequence, utility::vector1< std::string > const &pdb_names, std::string const &which_file)
void	easy_loop_model_test ()
void	initialize_sequence_mask (pose::Pose &pose, FArray1D_bool &sequence_mask)
void	chi_stats_test ()
void	cst_relax_test ()
void *	my_main (void *)
int	main (int argc, char *argv[])

Typedef Documentation

Matrix

typedef numeric::xyzMatrix< Real > Matrix

Function Documentation

apply_mask()

std::string apply_mask	(	FArray1D_bool &	sequence_mask,
		utility::vector1< std::map< Size, Size > > &	alignment2sequence,
		utility::vector1< std::string > const &	pdb_names,
		std::string const &	which_file,
		pose::Pose &	pose
	)

References count, utility::io::oc::cout, create_a3b_hbs::i, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, beta_nonlocal::pose, subloop_histogram::size, and utility_exit_with_message.

Referenced by easy_target_test().

backrub_protocol()

void backrub_protocol	(	pose::Pose const &	native_pose,
		pose::PoseOP &	pose,
		scoring::ScoreFunctionOP &	score_fxn
	)

References basic::options::OptionKeys::constraints::constraints, utility::io::oc::cout, create_a3b_hbs::i, test.T110_numeric::I, backrub::max_atoms(), mc, backrub::mc_kt(), backrub::min_atoms(), beta_nonlocal::mm, backrub::mm_bend_weight(), basic::options::OptionKeys::MonteCarlo::MonteCarlo, docking::native_pose, backrub::ntrials(), basic::options::OptionKeys::optimization::optimization, option, options, backrub::pivot_atoms(), backrub::pivot_residues(), beta_nonlocal::pose, create_a3b_hbs::r, numeric::random::rg(), average_rmsds::rmsd, backrub::sc_prob(), backrub::sc_prob_uniform(), beta_nonlocal::score_fxn, basic::options::OptionKeys::frags::scoring::scoring, vancomycin::task, numeric::random::uniform(), and basic::options::OptionKeys::inout::dbms::user.

Referenced by easy_target_test(), and my_main().

check_chi_correct()

void check_chi_correct	(	pose::Pose const &	native_pose,
		pose::Pose const &	pose,
		Size const &	i,
		bool &	chi1_exists,
		bool &	chi2_exists,
		bool &	chi1_correct,
		bool &	chi1_chi2_correct
	)

References ObjexxFCL::abs(), create_a3b_hbs::i, docking::native_pose, and beta_nonlocal::pose.

Referenced by output_chi_stats().

chi_stats_test()

void chi_stats_test

(

)

References utility::io::oc::cout, initialize_sequence_mask(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, in::file::native(), docking::native_pose, out::file::o(), option, erraser_single_res_analysis::out, lactamize::outfile, output_chi_stats(), beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, in::file::s(), oop_conformations::scorefxn, and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by my_main().

cst_relax_test()

void cst_relax_test

(

)

References utility::io::oc::cout, basic::options::OptionKeys::cluster::energy_based_clustering::cst_file, create_a3b_hbs::j, ObjexxFCL::lead_zero_string_of(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, in::file::native(), local::nstruct, out::nstruct(), option, basic::options::OptionKeys::lh::fragpdb::out_path, out::path::path(), beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, docking::s, in::file::s(), basic::options::OptionKeys::carbohydrates::glycopeptide_docking::score_only, run::score_only(), oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, setup_constraints(), basic::options::OptionKeys::in::file::silent, out::file::silent(), basic::options::start_files(), and basic::options::OptionKeys::inout::dbms::user.

Referenced by my_main().

easy_loop_model_test()

void easy_loop_model_test

(

)

References in::file::fasta(), in::file::native(), docking::native_pose, option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, prepare_full_length_start_model(), read_alignment_fasta_file(), in::file::s(), basic::options::OptionKeys::frags::scoring::scoring, setup_alignment_map(), and setup_mask().

Referenced by my_main().

easy_target_test()

void easy_target_test

(

)

References apply_mask(), backrub_protocol(), utility::io::oc::cout, basic::options::OptionKeys::cluster::energy_based_clustering::cst_file, in::file::fasta(), mask_out_loop(), minimize_protocol(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, in::file::native(), docking::native_pose, option, erraser_single_res_analysis::out, output_backbone_stats(), output_chi_stats(), output_constraints(), output_constraints_for_full_length(), beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, prepare_start_model(), read_alignment_fasta_file(), in::file::s(), oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, setup_alignment_map(), setup_CA_constraints(), setup_constraints(), setup_mask(), setup_rhiju_fold_tree(), setup_secstruct_dssp(), and basic::options::OptionKeys::inout::dbms::user.

Referenced by my_main().

find_middle_of_vector()

Size find_middle_of_vector

(

utility::vector1< Size >

v

)

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::v, and value.

Referenced by setup_rhiju_fold_tree().

initialize_sequence_mask()

void initialize_sequence_mask	(	pose::Pose &	pose,
		FArray1D_bool &	sequence_mask
	)

References getline(), line, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, option, beta_nonlocal::pose, and basic::options::OptionKeys::inout::dbms::user.

Referenced by chi_stats_test().

main()

int main	(	int	argc,
		char *	argv[]
	)

References argv, basic::options::OptionKeys::cluster::energy_based_clustering::cst_file, test.T009_Exceptions::e, basic::init(), backrub::max_atoms(), backrub::mc_kt(), backrub::min_atoms(), backrub::mm_bend_weight(), my_main(), NEW_OPT, backrub::ntrials(), backrub::pivot_atoms(), backrub::pivot_residues(), basic::options::OptionKeys::lh::rounds, backrub::sc_prob(), backrub::sc_prob_uniform(), basic::options::OptionKeys::rna::denovo::secstruct_file, basic::options::OptionKeys::rna::vary_geometry, and viewer_main().

mask_out_loop()

void mask_out_loop	(	pose::Pose const &	pose,
		utility::vector1< std::map< Size, Size > > &	alignment2sequence,
		FArray1D_bool &	sequence_mask
	)

References create_a3b_hbs::i, beta_nonlocal::pose, and subloop_histogram::size.

Referenced by easy_target_test().

minimize_protocol()

void minimize_protocol	(	pose::Pose const &	native_pose,
		pose::Pose &	pose,
		scoring::ScoreFunctionOP &	scorefxn
	)

References basic::options::OptionKeys::constraints::constraints, utility::io::oc::cout, beta_nonlocal::mm, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, docking::native_pose, basic::options::OptionKeys::optimization::optimization, option, options, beta_nonlocal::pose, repack(), average_rmsds::rmsd, basic::options::OptionKeys::lh::rounds, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::rna::vary_geometry, vary_geometry_backbone(), and vary_geometry_sidechains().

Referenced by easy_target_test().

my_main()

void* my_main

(

void *

)

References chi_stats_test(), cst_relax_test(), easy_loop_model_test(), easy_target_test(), utility::options::OptionKeys::options::exit, and option.

Referenced by main().

output_backbone_stats()

void output_backbone_stats	(	pose::Pose &	native_pose,
		pose::Pose &	pose
	)

References create_a3b_hbs::i, docking::native_pose, create_a3b_hbs::nres, erraser_single_res_analysis::out, and beta_nonlocal::pose.

Referenced by easy_target_test().

output_chi_stats()

void output_chi_stats	(	pose::Pose &	native_pose,
		pose::Pose &	pose,
		FArray1D_bool	sequence_mask,
		utility::io::ozstream &	out,
		std::string const &	pdb_file,
		Size const	n
	)

References spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::A, check_chi_correct(), utility::io::oc::cout, ObjexxFCL::format::F(), create_a3b_hbs::i, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, docking::native_pose, create_a3b_hbs::nres, and beta_nonlocal::pose.

Referenced by chi_stats_test(), and easy_target_test().

output_constraints() [1/2]

void output_constraints	(	pose::Pose const &	pose,
		std::string const &	filename
	)

References lactamize::filename, create_a3b_hbs::i, output_constraints(), and beta_nonlocal::pose.

output_constraints() [2/2]

void output_constraints	(	pose::Pose const &	pose,
		std::string const &	filename,
		std::map< Size, Size > &	alignment2full
	)

References spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::A, basic::options::OptionKeys::constraints::constraints, basic::options::OptionKeys::templates::cst::cst, lactamize::filename, create_a3b_hbs::i, test.T110_numeric::I, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, erraser_single_res_analysis::out, and beta_nonlocal::pose.

Referenced by easy_target_test(), output_constraints(), and output_constraints_for_full_length().

output_constraints_for_full_length()

void output_constraints_for_full_length	(	pose::Pose const &	pose,
		std::map< Size, Size > &	alignment2sequence_target,
		FArray1D_bool const &	sequence_mask,
		std::string const &	filename
	)

References count, lactamize::filename, create_a3b_hbs::i, output_constraints(), and beta_nonlocal::pose.

Referenced by easy_target_test().

prepare_full_length_start_model()

void prepare_full_length_start_model	(	pose::Pose &	template_pose,
		pose::Pose &	pose,
		utility::vector1< std::string > const &	sequences,
		FArray1D_bool const &	sequence_mask,
		utility::vector1< std::map< Size, Size > > &	alignment2sequence,
		utility::vector1< std::string > const &	pdb_names,
		std::string const &	which_file
	)

References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, end, create_a3b_hbs::first, create_a3b_hbs::i, basic::options::OptionKeys::cluster::loops, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, beta_nonlocal::pose, subloop_histogram::size, and basic::options::OptionKeys::cutoutdomain::start.

Referenced by easy_loop_model_test().

prepare_start_model() [1/2]

void prepare_start_model	(	pose::Pose const &	template_pose,
		pose::Pose const &	pose_with_desired_sequence,
		scoring::ScoreFunction &	scorefxn_input,
		pose::Pose &	pose,
		FArray1D_bool &	conserved
	)

References basic::options::OptionKeys::constraints::constraints, create_a3b_hbs::i, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, option, beta_nonlocal::pose, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, setup_t469_zn_tether(), and vancomycin::task.

Referenced by easy_target_test().

prepare_start_model() [2/2]

void prepare_start_model	(	pose::Pose const &	template_pose,
		std::string	desired_sequence,
		scoring::ScoreFunction &	scorefxn_input,
		pose::Pose &	pose,
		FArray1D_bool &	conserved
	)

References basic::options::OptionKeys::constraints::constraints, utility::io::oc::cout, create_a3b_hbs::i, beta_nonlocal::pose, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, and vancomycin::task.

read_alignment_fasta_file()

Size read_alignment_fasta_file	(	utility::vector1< std::string > &	sequences,
		utility::vector1< std::string > &	pdb_names,
		std::string const &	fasta_file
	)

References utility::io::oc::cout, utility::io::izstream::fail(), getline(), line, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, basic::options::OptionKeys::relax::sequence, subloop_histogram::size, and utility_exit_with_message.

Referenced by easy_loop_model_test(), and easy_target_test().

read_soft_segment_file()

void read_soft_segment_file

(

FArray1D_bool &

in_soft_segment

)

References getline(), create_a3b_hbs::i, line, option, and basic::options::OptionKeys::inout::dbms::user.

Referenced by setup_CA_constraints().

repack()

void repack	(	pose::Pose &	pose,
		scoring::ScoreFunction const &	scorefxn
	)

References basic::options::OptionKeys::constraints::constraints, create_a3b_hbs::i, beta_nonlocal::pose, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, and vancomycin::task.

Referenced by minimize_protocol().

setup_alignment_map()

void setup_alignment_map	(	utility::vector1< std::map< Size, Size > > &	alignment2sequence,
		utility::vector1< std::string > const &	sequences
	)

References count, create_a3b_hbs::i, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, and subloop_histogram::size.

Referenced by easy_loop_model_test(), and easy_target_test().

setup_CA_constraints()

void setup_CA_constraints	(	pose::Pose &	pose,
		pose::Pose const &	src_pose
	)

References basic::options::OptionKeys::constraints::constraints, utility::io::oc::cout, create_a3b_hbs::i, enumerate_junctions::int, create_a3b_hbs::j, oop_conformations::length, create_a3b_hbs::nres, offset, option, beta_nonlocal::pose, and read_soft_segment_file().

Referenced by easy_target_test().

setup_constraints()

void setup_constraints	(	std::string const	cst_file_name,
		pose::Pose &	pose
	)

References basic::options::OptionKeys::constraints::constraints, and beta_nonlocal::pose.

Referenced by cst_relax_test(), and easy_target_test().

setup_mask()

void setup_mask	(	FArray1D_bool &	sequence_mask,
		utility::vector1< std::string > const &	sequences
	)

References count, utility::io::oc::cout, create_a3b_hbs::i, enumerate_junctions::int, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, offset, option, and erraser_single_res_analysis::out.

Referenced by easy_loop_model_test(), and easy_target_test().

setup_rhiju_fold_tree()

void setup_rhiju_fold_tree

(

pose::Pose &

pose

)

References count, utility::io::oc::cout, ObjexxFCL::FArray2D< T >::dimension(), ObjexxFCL::FArray1D< T >::dimension(), end, create_a3b_hbs::f, find_middle_of_vector(), create_a3b_hbs::first, create_a3b_hbs::i, create_a3b_hbs::j, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, create_a3b_hbs::nres, beta_nonlocal::pose, basic::options::OptionKeys::cutoutdomain::start, and basic::options::OptionKeys::sc::verbose.

Referenced by easy_target_test().

setup_secstruct()

void setup_secstruct	(	pose::Pose &	template_pose,
		std::string const &	template_secstruct_file
	)

References getline(), create_a3b_hbs::i, and line.

setup_secstruct_dssp()

void setup_secstruct_dssp

(

pose::Pose &

pose

)

References basic::options::OptionKeys::in::file::dssp, create_a3b_hbs::i, and beta_nonlocal::pose.

Referenced by easy_target_test().

setup_t469_zn_tether()

void setup_t469_zn_tether

(

pose::Pose &

pose

)

References basic::options::OptionKeys::constraints::constraints, and beta_nonlocal::pose.

Referenced by prepare_start_model().

vary_geometry_backbone()

void vary_geometry_backbone	(	pose::Pose &	pose,
		kinematics::MoveMap &	mm
	)

References basic::options::OptionKeys::constraints::constraints, utility::io::oc::cout, spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::D, create_a3b_hbs::i, test.T110_numeric::I, beta_nonlocal::mm, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, beta_nonlocal::pose, basic::options::OptionKeys::frags::scoring::scoring, and utility_exit_with_message.

Referenced by minimize_protocol().

vary_geometry_sidechains()

void vary_geometry_sidechains	(	pose::Pose &	pose,
		kinematics::MoveMap &	mm
	)

References basic::options::OptionKeys::constraints::constraints, utility::io::oc::cout, spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::D, create_a3b_hbs::i, test.T110_numeric::I, beta_nonlocal::mm, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, beta_nonlocal::pose, basic::options::OptionKeys::frags::scoring::scoring, and utility_exit_with_message.

Referenced by minimize_protocol().