#include <protocols/frags/VallData.hh>
#include <protocols/frags/TorsionFragment.hh>
#include <numeric/random/random_permutation.hh>
#include <core/scoring/dna/setup.hh>
#include <core/scoring/dna/base_geometry.hh>
#include <core/scoring/dna/BasePartner.hh>
#include <core/scoring/GenBornPotential.hh>
#include <core/scoring/LREnergyContainer.hh>
#include <core/scoring/methods/Methods.hh>
#include <protocols/simple_moves/BackboneMover.hh>
#include <protocols/minimization_packing/MinMover.hh>
#include <protocols/moves/MonteCarlo.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/moves/MoverContainer.hh>
#include <protocols/moves/OutputMovers.hh>
#include <protocols/rigid/RigidBodyMover.hh>
#include <protocols/moves/TrialMover.hh>
#include <protocols/minimization_packing/PackRotamersMover.hh>
#include <protocols/minimization_packing/RotamerTrialsMover.hh>
#include <protocols/moves/RepeatMover.hh>
#include <protocols/loops/ccd_closure.hh>
#include <protocols/loops/loops_main.hh>
#include <protocols/viewer/viewers.hh>
#include <core/types.hh>
#include <core/scoring/sasa.hh>
#include <core/id/SequenceMapping.hh>
#include <core/chemical/AtomTypeSet.hh>
#include <core/chemical/MMAtomTypeSet.hh>
#include <core/chemical/AA.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueMatcher.hh>
#include <core/pack/rotamer_set/RotamerCouplings.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/ResidueTypeSelector.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/chemical/VariantType.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/scoring/etable/Etable.hh>
#include <core/scoring/ScoringManager.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/Ramachandran.hh>
#include <core/pack/dunbrack/RotamerLibrary.hh>
#include <core/pack/dunbrack/RotamerLibraryScratchSpace.hh>
#include <core/scoring/hbonds/HBondSet.hh>
#include <core/scoring/hbonds/hbonds.hh>
#include <core/scoring/etable/count_pair/CountPairFunction.hh>
#include <core/pack/rotamer_trials.hh>
#include <core/pack/pack_rotamers.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/TaskOperation.hh>
#include <core/kinematics/FoldTree.hh>
#include <protocols/viewer/visualize.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/kinematics/util.hh>
#include <core/id/AtomID_Map.hh>
#include <core/mm/MMTorsionLibrary.hh>
#include <core/mm/MMTorsionLibrary.fwd.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/pose/PDBPoseMap.hh>
#include <core/pose/PDBInfo.hh>
#include <basic/options/util.hh>
#include <basic/basic.hh>
#include <basic/database/open.hh>
#include <devel/init.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <utility/vector1.hh>
#include <numeric/xyzVector.hh>
#include <numeric/random/random.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.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/fragment/picking/FragmentLibraryManager.hh>
#include <core/fragment/picking/vall/VallLibrarian.hh>
#include <core/fragment/picking/vall/gen/LengthGen.hh>
#include <core/fragment/picking/vall/scores/VallFragmentScore.hh>
#include <cstdlib>
#include <fstream>
#include <iostream>
#include <string>
#include <basic/Tracer.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/pep_spec.OptionKeys.gen.hh>
#include <basic/options/keys/constraints.OptionKeys.gen.hh>
#include <mpi.h>
#include <core/import_pose/import_pose.hh>

Functions
Size	get_n_pep_nbrs (pose::Pose const &pose, vector1< bool > const is_pep, Real const cutoff_cg)

void	dump_efactor_pdb (pose::Pose &pose, core::scoring::ScoreFunctionOP const scorefxn, std::string const &tag)

bool	has_clash (pose::Pose &pose, vector1< bool > is_checked, scoring::ScoreFunctionOP const &scorefxn, Real const clash_threshold)

void	normalize_res_freqs (vector1< Real > &res_freqs, Size n)

void	minimize_ref_weights (vector1< Real > &ref_weights, vector1< Real > res_freqs, vector1< Real > ideal_res_freqs, Real stepsize)

void	print_res_freqs (vector1< Real > res_freqs, vector1< Real > ideal_res_freqs, std::string res_freqs_file_name_str)

vector1< Real >	operator+ (vector1< Real > v1, vector1< Real > v2)

void	print_scorefxn (ScoreFunctionOP scorefxn, vector1< Real > ref_weights, std::string wts_file_name_str)

Size	aa2index (chemical::AA aa)

void	send_string_to_node (int destination, std::string const &string_to_send)

std::string	receive_string_from_node (int source)

void	RunPepSpec ()

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

Function Documentation

◆ aa2index()

Size aa2index ( chemical::AA aa )

References aa, enumerate_junctions::default, and ObjexxFCL::index().

Referenced by RunPepSpec().

◆ dump_efactor_pdb()

void dump_efactor_pdb	(	pose::Pose &	pose,
		core::scoring::ScoreFunctionOP const	scorefxn,
		std::string const &	tag
	)

References val2thr::atom, predPRE::chain, chains, ObjexxFCL::format::F(), lactamize::filename, create_a3b_hbs::i, test.T110_numeric::I, create_a3b_hbs::j, create_a3b_hbs::nres, basic::options::option, erraser_single_res_analysis::out, basic::options::OptionKeys::out::file::output_virtual, beta_nonlocal::pose, oop_conformations::scorefxn, and tag.

◆ get_n_pep_nbrs()

Size get_n_pep_nbrs	(	pose::Pose const &	pose,
		vector1< bool > const	is_pep,
		Real const	cutoff_cg
	)

References create_a3b_hbs::i, create_a3b_hbs::ii, create_a3b_hbs::j, beta_nonlocal::jj, beta_nonlocal::pose, test.T200_Scoring::rsd1, and test.T200_Scoring::rsd2.

◆ has_clash()

bool has_clash	(	pose::Pose &	pose,
		vector1< bool >	is_checked,
		scoring::ScoreFunctionOP const &	scorefxn,
		Real const	clash_threshold
	)

References clash(), test.T200_Scoring::emap, utility::graph::Edge::get_node(), is_clash(), utility::graph::Node::lower_edge_list_end(), beta_nonlocal::pose, basic::options::OptionKeys::frags::scoring::scoring, and utility::graph::Node::upper_edge_list_end().

◆ main()

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

References argv, test.T009_Exceptions::e, basic::init(), and RunPepSpec().

◆ minimize_ref_weights()

void minimize_ref_weights	(	vector1< Real > &	ref_weights,
		vector1< Real >	res_freqs,
		vector1< Real >	ideal_res_freqs,
		Real	stepsize
	)

References ObjexxFCL::abs(), create_a3b_hbs::i, and loops_kic::tol.

Referenced by RunPepSpec().

◆ normalize_res_freqs()

void normalize_res_freqs	(	vector1< Real > &	res_freqs,
		Size	n
	)

References create_a3b_hbs::i, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::n.

Referenced by RunPepSpec().

◆ operator+()

vector1< Real > operator+	(	vector1< Real >	v1,
		vector1< Real >	v2
	)

References create_a3b_hbs::i, oop_scan::v1, and oop_scan::v2.

◆ print_res_freqs()

void print_res_freqs	(	vector1< Real >	res_freqs,
		vector1< Real >	ideal_res_freqs,
		std::string	res_freqs_file_name_str
	)

References create_a3b_hbs::i, erraser_single_res_analysis::out, ObjexxFCL::pow(), average_rmsds::rmsd, and ObjexxFCL::string_of().

Referenced by RunPepSpec().

◆ print_scorefxn()

void print_scorefxn	(	ScoreFunctionOP	scorefxn,
		vector1< Real >	ref_weights,
		std::string	wts_file_name_str
	)

References create_a3b_hbs::ii, erraser_single_res_analysis::out, and oop_conformations::scorefxn.

Referenced by RunPepSpec().

◆ receive_string_from_node()

std::string receive_string_from_node ( int source )

References ObjexxFCL::len(), str(), and tag.

Referenced by RunPepSpec().

◆ RunPepSpec()

void RunPepSpec ( )

References aa2index(), utility::io::oc::cout, pyrosetta::create_score_function, create_a3b_hbs::f, getline(), create_a3b_hbs::i, create_a3b_hbs::ii, beta_nonlocal::jj, make_sequence_change(), minimize_ref_weights(), normalize_res_freqs(), out::file::o(), option, demo.D010_Pose_structure::pdb_filename, bur_nodon_tyr::pdb_list, basic::options::OptionKeys::pepspec::pep_anchor, pep_begin(), basic::options::OptionKeys::pepspec::pep_chain, pep_end(), beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, print_res_freqs(), print_scorefxn(), numeric::random::random_permutation(), receive_string_from_node(), numeric::random::rg(), oop_conformations::scorefxn, send_string_to_node(), ObjexxFCL::string_of(), numeric::random::RandomGenerator::uniform(), basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

Referenced by main().

◆ send_string_to_node()

void send_string_to_node	(	int	destination,
		std::string const &	string_to_send
	)

References ObjexxFCL::len(), and tag.

Referenced by RunPepSpec().

Functions

Function Documentation

◆ aa2index()

◆ dump_efactor_pdb()

◆ get_n_pep_nbrs()

◆ has_clash()

◆ main()

◆ minimize_ref_weights()

◆ normalize_res_freqs()

◆ operator+()

◆ print_res_freqs()

◆ print_scorefxn()

◆ receive_string_from_node()

◆ RunPepSpec()

◆ send_string_to_node()