#include <mpi.h>
#include <basic/options/option.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/option_macros.hh>
#include <basic/Tracer.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/Conformation.hh>
#include <devel/init.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/import_pose/import_pose.hh>
#include <core/conformation/util.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <numeric/xyz.functions.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <core/scoring/dssp/Dssp.hh>
#include <sstream>
#include <stdio.h>
#include <fstream>
#include <iostream>
#include <stdlib.h>
#include <math.h>
#include <string.h>
#include <protocols/simple_moves/MutateResidue.hh>
#include <protocols/relax/FastRelax.hh>
#include <core/kinematics/MoveMap.hh>
#include <numeric/random/random.hh>
#include <core/sequence/util.hh>
#include <core/sequence/Sequence.hh>
#include <numeric/xyzVector.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <core/optimization/CartesianMinimizer.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/scoring/func/CircularHarmonicFunc.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/constraints/AngleConstraint.hh>
#include <core/scoring/constraints/DihedralConstraint.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/chemical/AA.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/id/NamedAtomID.hh>
#include <protocols/constraint_movers/ConstraintSetMover.hh>
#include <core/import_pose/pose_stream/PoseInputStream.hh>
#include <core/import_pose/pose_stream/MetaPoseInputStream.hh>
#include <core/import_pose/pose_stream/PDBPoseInputStream.hh>
#include <core/import_pose/pose_stream/PDBPoseInputStream.fwd.hh>
#include <core/import_pose/pose_stream/SilentFilePoseInputStream.hh>
#include <core/import_pose/pose_stream/util.hh>
#include <core/io/silent/SilentStructFactory.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/io/silent/SilentStruct.hh>

Macros
#define	PI 3.1415926535897932384626433832795

#define	CNCa_ANGLE 121.7

#define	CNH_ANGLE 119.15

#define	CaCN_ANGLE 116.2

#define	OCN_ANGLE 123.01

Functions
	OPT_KEY (Integer, v_trialcount) OPT_KEY(Integer

v_relaxrounds	OPT_KEY (Real, v_MCtemperature) OPT_KEY(Real

v_relaxrounds v_kbt	OPT_KEY (Real, v_kbt_minimize) OPT_KEY(Integer

v_relaxrounds v_kbt v_MCminimize_replicates	OPT_KEY (Integer, v_MCminimize_steps) OPT_KEY(Real

v_relaxrounds v_kbt v_MCminimize_replicates v_bb_perturbation	OPT_KEY (Real, v_bb_perturbation_rand_fraction) OPT_KEY(Boolean

v_relaxrounds v_kbt v_MCminimize_replicates v_bb_perturbation v_rmspenalty	OPT_KEY (Real, v_rmspenalty_n) OPT_KEY(Boolean

v_relaxrounds v_kbt v_MCminimize_replicates v_bb_perturbation v_rmspenalty v_randseq	OPT_KEY (IntegerVector, v_ignoreresidue) OPT_KEY(IntegerVector

v_relaxrounds v_kbt v_MCminimize_replicates v_bb_perturbation v_rmspenalty v_randseq v_ignoreresidue_in_rms	OPT_KEY (Boolean, v_CB_in_rms) OPT_KEY(Boolean

v_relaxrounds v_kbt v_MCminimize_replicates v_bb_perturbation v_rmspenalty v_randseq v_ignoreresidue_in_rms v_removelowrms	OPT_KEY (Real, v_removelowrms_threshold) OPT_KEY(Real

v_relaxrounds v_kbt v_MCminimize_replicates v_bb_perturbation v_rmspenalty v_randseq v_ignoreresidue_in_rms v_removelowrms v_lambda	OPT_KEY (Boolean, v_use_cartesian_min) OPT_KEY(Boolean

v_relaxrounds v_kbt v_MCminimize_replicates v_bb_perturbation v_rmspenalty v_randseq v_ignoreresidue_in_rms v_removelowrms v_lambda v_cyclic	OPT_KEY (Boolean, v_use_cyclic_permutations) OPT_KEY(Integer

v_relaxrounds v_kbt v_MCminimize_replicates v_bb_perturbation v_rmspenalty v_randseq v_ignoreresidue_in_rms v_removelowrms v_lambda v_cyclic v_cyclic_permutation_offset	OPT_KEY (Boolean, v_strip_terminal_gly) OPT_KEY(FileVector

v_relaxrounds v_kbt v_MCminimize_replicates v_bb_perturbation v_rmspenalty v_randseq v_ignoreresidue_in_rms v_removelowrms v_lambda v_cyclic v_cyclic_permutation_offset v_PCAfiles	OPT_KEY (File, v_PCAfiles_list) OPT_KEY(File

v_relaxrounds v_kbt v_MCminimize_replicates v_bb_perturbation v_rmspenalty v_randseq v_ignoreresidue_in_rms v_removelowrms v_lambda v_cyclic v_cyclic_permutation_offset v_PCAfiles v_PCAfile_native	OPT_KEY (Boolean, v_allow_gly_mutation) OPT_KEY(Boolean

v_relaxrounds v_kbt v_MCminimize_replicates v_bb_perturbation v_rmspenalty v_randseq v_ignoreresidue_in_rms v_removelowrms v_lambda v_cyclic v_cyclic_permutation_offset v_PCAfiles v_PCAfile_native v_preserve_chirality	OPT_KEY (Boolean, v_split_replicates_over_processes) OPT_KEY(Boolean

v_relaxrounds v_kbt v_MCminimize_replicates v_bb_perturbation v_rmspenalty v_randseq v_ignoreresidue_in_rms v_removelowrms v_lambda v_cyclic v_cyclic_permutation_offset v_PCAfiles v_PCAfile_native v_preserve_chirality v_savememory	OPT_KEY (Boolean, v_scoreonly) OPT_KEY(IntegerVector

v_relaxrounds v_kbt v_MCminimize_replicates v_bb_perturbation v_rmspenalty v_randseq v_ignoreresidue_in_rms v_removelowrms v_lambda v_cyclic v_cyclic_permutation_offset v_PCAfiles v_PCAfile_native v_preserve_chirality v_savememory v_disulfide_positions	OPT_KEY (String, v_allowed_aminoacids) OPT_KEY(String

v_relaxrounds v_kbt v_MCminimize_replicates v_bb_perturbation v_rmspenalty v_randseq v_ignoreresidue_in_rms v_removelowrms v_lambda v_cyclic v_cyclic_permutation_offset v_PCAfiles v_PCAfile_native v_preserve_chirality v_savememory v_disulfide_positions v_allowed_betas	OPT_KEY (Integer, v_PCAlimit) OPT_KEY(File

v_relaxrounds v_kbt v_MCminimize_replicates v_bb_perturbation v_rmspenalty v_randseq v_ignoreresidue_in_rms v_removelowrms v_lambda v_cyclic v_cyclic_permutation_offset v_PCAfiles v_PCAfile_native v_preserve_chirality v_savememory v_disulfide_positions v_allowed_betas v_equivalent_positions	OPT_KEY (File, v_covalent_connections) OPT_KEY(File

v_relaxrounds v_kbt v_MCminimize_replicates v_bb_perturbation v_rmspenalty v_randseq v_ignoreresidue_in_rms v_removelowrms v_lambda v_cyclic v_cyclic_permutation_offset v_PCAfiles v_PCAfile_native v_preserve_chirality v_savememory v_disulfide_positions v_allowed_betas v_equivalent_positions v_cst_file	OPT_KEY (String, v_native_tag) OPT_KEY(StringVector

v_relaxrounds v_kbt v_MCminimize_replicates v_bb_perturbation v_rmspenalty v_randseq v_ignoreresidue_in_rms v_removelowrms v_lambda v_cyclic v_cyclic_permutation_offset v_PCAfiles v_PCAfile_native v_preserve_chirality v_savememory v_disulfide_positions v_allowed_betas v_equivalent_positions v_cst_file v_extra_rms_atoms	OPT_KEY (IntegerVector, v_norepack_positions) OPT_KEY(Boolean

v_relaxrounds v_kbt v_MCminimize_replicates v_bb_perturbation v_rmspenalty v_randseq v_ignoreresidue_in_rms v_removelowrms v_lambda v_cyclic v_cyclic_permutation_offset v_PCAfiles v_PCAfile_native v_preserve_chirality v_savememory v_disulfide_positions v_allowed_betas v_equivalent_positions v_cst_file v_extra_rms_atoms v_consider_all_replicates void	register_options ()

void	betapeptide_setphi (core::pose::Pose &pose, core::Size resnumber, core::Real angle)

void	betapeptide_settheta (core::pose::Pose &pose, core::Size resnumber, core::Real angle)

void	betapeptide_setpsi (core::pose::Pose &pose, core::Size resnumber, core::Real angle)

void	betapeptide_setomega (core::pose::Pose &pose, core::Size resnumber, core::Real angle)

void	get_beta_name (const char onelettercode, std::string &threelettercode)

bool	is_in_list (const core::Size val, const utility::vector1< core::Size > &vect)

core::Size	is_in_list_of_lists (const core::Size val, const utility::vector1< utility::vector1< core::Size > > &vect)

void	get_D_name (const char onelettercode, std::string &threelettercode)

void	parse_extra_atom_list (utility::vector1< core::id::NamedAtomID > &extra_atom_list)

bool	use_in_rmsd (core::pose::Pose const &pose1, core::pose::Pose const &pose2, core::Size resno, core::Size atomno, utility::vector1< core::id::NamedAtomID > const &extra_atom_list)

core::Real	get_distance_measure (const core::pose::Pose &pose1, const core::pose::Pose &pose2, utility::vector1< core::id::NamedAtomID > const &extra_rms_atoms)

core::Real	calc_sequence_score (utility::vector1< core::Real > &energies, utility::vector1< core::Real > &rmsvalues)

void	set_up_termini (core::pose::Pose &pose)

void	add_user_constraints (core::pose::Pose &mypose)

void	addcyclicconstraints (core::pose::Pose &mypose)

void	perturb_bb_and_relax (const core::Size replicates, const core::Size MCsteps, core::pose::Pose &pose, utility::vector1< std::pair< core::Size, core::Size > > &disulf_positions, numeric::random::RandomGenerator &RandGen, const core::Real bb_perturbation, protocols::relax::FastRelax &frlx, core::scoring::ScoreFunctionOP const &sfxn, const core::Real MCkbt, const utility::vector1< core::Real > &PCAvariances, const utility::vector1< utility::vector1< core::Real > > &PCAvectors)

void	vMPI_transmitpose (core::pose::Pose &pose, int thisproc, int sendingproc, int receivingproc)

void	vMPI_Bcastpose (core::pose::Pose &pose, int rootproc, int thisproc)

void	store_backbone (const core::pose::Pose &mypose, utility::vector1< core::Real > &outvect)

bool	strip_terminal_glycines (core::pose::Pose &mypose)

void	set_to_state (core::pose::Pose &mypose, const utility::vector1< core::Real > &bb_list)

void	mutate_to_sequence (const std::string &sequence, core::pose::Pose &mypose, const utility::vector1< bool > &dpositions, const utility::vector1< bool > &betapositions, bool const force_mutation)

void	transmit_additional_info (const int fromproc, const int toproc, const int thisproc, const int numelements, utility::vector1< core::Real > &datavector)

void	receive_silent_struct (core::pose::Pose &pose, const int fromproc, const int toproc, const int thisproc, bool const broadcast)

void	transmit_silent_struct (const int fromproc, const int toproc, const int thisproc, core::io::silent::SilentStructOP &silentstruct, bool const broadcast)

void	transmit_silent_struct (const int fromproc, const int toproc, const int thisproc, std::string const &tag, core::pose::Pose const &pose, bool const broadcast)

void	scoreall (const int procnum, const int proccount, const core::Size totalstatecount, const core::Size PCAvectorcomponentcount, std::string &sequence, utility::vector1< bool > &dpositions, utility::vector1< bool > &betapositions, utility::vector1< core::io::silent::SilentStructOP > &allstates_master, utility::vector1< std::pair< core::Size, core::Size > > &disulf_positions, utility::vector1< core::Real > &energyvals_current, utility::vector1< core::Real > &rmsvals_current, const core::pose::Pose &positive_master, core::pose::Pose &positive_current, numeric::random::RandomGenerator &RG, protocols::relax::FastRelax &frlx, core::scoring::ScoreFunctionOP const &sfxn, utility::vector1< utility::vector1< core::Real > > &PCAvariances, utility::vector1< utility::vector1< utility::vector1< core::Real > > > &PCAmatrices, utility::vector1< core::id::NamedAtomID > const &extra_rms_atoms)

void	set_up_covalent_connections (core::pose::Pose &pose, utility::vector1< std::pair< core::id::NamedAtomID, core::id::NamedAtomID > > const &conlist)

void	read_covalent_connections_file (utility::vector1< std::pair< core::id::NamedAtomID, core::id::NamedAtomID > > &conlist, core::Size const procnum)

void	read_equivalent_position_file (const char *filename, utility::vector1< utility::vector1< core::Size > > &equivalent_positions)

core::Size	read_PCAfile (const char *filename, utility::vector1< core::Real > &variances, utility::vector1< utility::vector1< core::Real > > &PCA_vectors, bool normalize_variances)

void	parsefilelist (const std::string &listfile, utility::vector1< std::string > &filevector)

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

Macro Definition Documentation

◆ CaCN_ANGLE

#define CaCN_ANGLE 116.2

◆ CNCa_ANGLE

#define CNCa_ANGLE 121.7

◆ CNH_ANGLE

#define CNH_ANGLE 119.15

◆ OCN_ANGLE

#define OCN_ANGLE 123.01

◆ PI

#define PI 3.1415926535897932384626433832795

Function Documentation

◆ add_user_constraints()

void add_user_constraints ( core::pose::Pose & mypose )

References basic::options::OptionKeys::enzdes::cstfile, basic::options::option, and basic::options::OptionKeys::inout::dbms::user.

Referenced by receive_silent_struct().

◆ addcyclicconstraints()

void addcyclicconstraints ( core::pose::Pose & mypose )

References betapeptide_setomega(), CaCN_ANGLE, CNCa_ANGLE, CNH_ANGLE, basic::options::OptionKeys::constraints::constraints, numeric::dihedral_degrees(), func, OCN_ANGLE, PI, beta_nonlocal::pose, residue_types_from_sequence(), and superimpose_pose().

Referenced by mutate_to_sequence(), and perturb_bb_and_relax().

◆ betapeptide_setomega()

void betapeptide_setomega	(	core::pose::Pose &	pose,
		core::Size	resnumber,
		core::Real	angle
	)

References basic::options::OptionKeys::hotspot::angle, and beta_nonlocal::pose.

Referenced by addcyclicconstraints(), perturb_bb_and_relax(), and set_to_state().

◆ betapeptide_setphi()

void betapeptide_setphi	(	core::pose::Pose &	pose,
		core::Size	resnumber,
		core::Real	angle
	)

References basic::options::OptionKeys::hotspot::angle, and beta_nonlocal::pose.

Referenced by perturb_bb_and_relax(), and set_to_state().

◆ betapeptide_setpsi()

void betapeptide_setpsi	(	core::pose::Pose &	pose,
		core::Size	resnumber,
		core::Real	angle
	)

References basic::options::OptionKeys::hotspot::angle, and beta_nonlocal::pose.

Referenced by perturb_bb_and_relax(), and set_to_state().

◆ betapeptide_settheta()

void betapeptide_settheta	(	core::pose::Pose &	pose,
		core::Size	resnumber,
		core::Real	angle
	)

References basic::options::OptionKeys::hotspot::angle, and beta_nonlocal::pose.

Referenced by perturb_bb_and_relax(), and set_to_state().

◆ calc_sequence_score()

core::Real calc_sequence_score	(	utility::vector1< core::Real > &	energies,
		utility::vector1< core::Real > &	rmsvalues
	)

References create_a3b_hbs::i, numeric::log(), basic::options::option, and ObjexxFCL::pow().

Referenced by main().

◆ get_beta_name()

void get_beta_name	(	const char	onelettercode,
		std::string &	threelettercode
	)

Referenced by mutate_to_sequence().

◆ get_D_name()

void get_D_name	(	const char	onelettercode,
		std::string &	threelettercode
	)

References enumerate_junctions::default.

Referenced by mutate_to_sequence().

◆ get_distance_measure()

core::Real get_distance_measure	(	const core::pose::Pose &	pose1,
		const core::pose::Pose &	pose2,
		utility::vector1< core::id::NamedAtomID > const &	extra_rms_atoms
	)

References basic::options::OptionKeys::cluster::energy_based_clustering::extra_rms_atoms, enumerate_junctions::int, test.T008_Serialization::pose1, test.T008_Serialization::pose2, and use_in_rmsd().

Referenced by main(), and scoreall().

◆ is_in_list()

bool is_in_list	(	const core::Size	val,
		const utility::vector1< core::Size > &	vect
	)

References create_a3b_hbs::i.

Referenced by is_in_list_of_lists().

◆ is_in_list_of_lists()

core::Size is_in_list_of_lists	(	const core::Size	val,
		const utility::vector1< utility::vector1< core::Size > > &	vect
	)

References create_a3b_hbs::i, and is_in_list().

Referenced by main().

◆ main()

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

References basic::options::OptionKeys::ralford::dump_rotamers::all_positions, argv, val2thr::atom, test.T005_Bindings::base, calc_sequence_score(), utility::options::OptionKeys::options::exit, basic::options::OptionKeys::cluster::energy_based_clustering::extra_rms_atoms, in::file::fasta(), clean_pdb_keep_ligand::fastaseq, utility::file_basename(), ObjexxFCL::get(), get_distance_measure(), create_a3b_hbs::i, create_a3b_hbs::ii, basic::init(), enumerate_junctions::int, is_in_list_of_lists(), create_a3b_hbs::j, create_a3b_hbs::k, in::file::l(), oop_conformations::length, mutate_to_sequence(), in::file::native(), create_a3b_hbs::nres, out::file::o(), basic::options::option, lactamize::outfile, parse_extra_atom_list(), parsefilelist(), beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, printf(), spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::prob, numeric::random::RandomGenerator::random_range(), read_covalent_connections_file(), read_equivalent_position_file(), read_PCAfile(), receive_silent_struct(), register_options(), numeric::random::rg(), runtime_assert_string_msg, in::file::s(), scoreall(), basic::options::OptionKeys::frags::scoring::scoring, set_up_covalent_connections(), set_up_termini(), test.T120_core::sfxn, in::file::silent(), subloop_histogram::size, build::stdout, strip_terminal_glycines(), basic::options::OptionKeys::motifs::target_aa, vancomycin::task, transmit_silent_struct(), numeric::random::uniform(), and basic::options::OptionKeys::inout::dbms::user.

◆ mutate_to_sequence()

void mutate_to_sequence	(	const std::string &	sequence,
		core::pose::Pose &	mypose,
		const utility::vector1< bool > &	dpositions,
		const utility::vector1< bool > &	betapositions,
		bool const	force_mutation
	)

References addcyclicconstraints(), utility::options::OptionKeys::options::exit, get_beta_name(), get_D_name(), create_a3b_hbs::i, basic::options::option, printf(), basic::options::OptionKeys::relax::sequence, subloop_histogram::size, and build::stdout.

Referenced by main(), and scoreall().

◆ OPT_KEY() [1/21]

v_relaxrounds v_kbt v_MCminimize_replicates v_bb_perturbation v_rmspenalty v_randseq v_ignoreresidue_in_rms v_removelowrms v_lambda v_cyclic v_cyclic_permutation_offset v_PCAfiles v_PCAfile_native OPT_KEY	(	Boolean	,
		v_allow_gly_mutation
	)

◆ OPT_KEY() [2/21]

v_relaxrounds v_kbt v_MCminimize_replicates v_bb_perturbation v_rmspenalty v_randseq v_ignoreresidue_in_rms OPT_KEY	(	Boolean	,
		v_CB_in_rms
	)

◆ OPT_KEY() [3/21]

v_relaxrounds v_kbt v_MCminimize_replicates v_bb_perturbation v_rmspenalty v_randseq v_ignoreresidue_in_rms v_removelowrms v_lambda v_cyclic v_cyclic_permutation_offset v_PCAfiles v_PCAfile_native v_preserve_chirality v_savememory OPT_KEY	(	Boolean	,
		v_scoreonly
	)

◆ OPT_KEY() [4/21]

v_relaxrounds v_kbt v_MCminimize_replicates v_bb_perturbation v_rmspenalty v_randseq v_ignoreresidue_in_rms v_removelowrms v_lambda v_cyclic v_cyclic_permutation_offset v_PCAfiles v_PCAfile_native v_preserve_chirality OPT_KEY	(	Boolean	,
		v_split_replicates_over_processes
	)

◆ OPT_KEY() [5/21]

v_relaxrounds v_kbt v_MCminimize_replicates v_bb_perturbation v_rmspenalty v_randseq v_ignoreresidue_in_rms v_removelowrms v_lambda v_cyclic v_cyclic_permutation_offset OPT_KEY	(	Boolean	,
		v_strip_terminal_gly
	)

◆ OPT_KEY() [6/21]

v_relaxrounds v_kbt v_MCminimize_replicates v_bb_perturbation v_rmspenalty v_randseq v_ignoreresidue_in_rms v_removelowrms v_lambda OPT_KEY	(	Boolean	,
		v_use_cartesian_min
	)

◆ OPT_KEY() [7/21]

v_relaxrounds v_kbt v_MCminimize_replicates v_bb_perturbation v_rmspenalty v_randseq v_ignoreresidue_in_rms v_removelowrms v_lambda v_cyclic OPT_KEY	(	Boolean	,
		v_use_cyclic_permutations
	)

◆ OPT_KEY() [8/21]

v_relaxrounds v_kbt v_MCminimize_replicates v_bb_perturbation v_rmspenalty v_randseq v_ignoreresidue_in_rms v_removelowrms v_lambda v_cyclic v_cyclic_permutation_offset v_PCAfiles v_PCAfile_native v_preserve_chirality v_savememory v_disulfide_positions v_allowed_betas v_equivalent_positions OPT_KEY	(	File	,
		v_covalent_connections
	)

◆ OPT_KEY() [9/21]

v_relaxrounds v_kbt v_MCminimize_replicates v_bb_perturbation v_rmspenalty v_randseq v_ignoreresidue_in_rms v_removelowrms v_lambda v_cyclic v_cyclic_permutation_offset v_PCAfiles OPT_KEY	(	File	,
		v_PCAfiles_list
	)

◆ OPT_KEY() [10/21]

v_relaxrounds v_kbt v_MCminimize_replicates OPT_KEY	(	Integer	,
		v_MCminimize_steps
	)

◆ OPT_KEY() [11/21]

v_relaxrounds v_kbt v_MCminimize_replicates v_bb_perturbation v_rmspenalty v_randseq v_ignoreresidue_in_rms v_removelowrms v_lambda v_cyclic v_cyclic_permutation_offset v_PCAfiles v_PCAfile_native v_preserve_chirality v_savememory v_disulfide_positions v_allowed_betas OPT_KEY	(	Integer	,
		v_PCAlimit
	)

◆ OPT_KEY() [12/21]

OPT_KEY	(	Integer	,
		v_trialcount
	)

◆ OPT_KEY() [13/21]

v_relaxrounds v_kbt v_MCminimize_replicates v_bb_perturbation v_rmspenalty v_randseq OPT_KEY	(	IntegerVector	,
		v_ignoreresidue
	)

◆ OPT_KEY() [14/21]

v_relaxrounds v_kbt v_MCminimize_replicates v_bb_perturbation v_rmspenalty v_randseq v_ignoreresidue_in_rms v_removelowrms v_lambda v_cyclic v_cyclic_permutation_offset v_PCAfiles v_PCAfile_native v_preserve_chirality v_savememory v_disulfide_positions v_allowed_betas v_equivalent_positions v_cst_file v_extra_rms_atoms OPT_KEY	(	IntegerVector	,
		v_norepack_positions
	)

◆ OPT_KEY() [15/21]

v_relaxrounds v_kbt v_MCminimize_replicates v_bb_perturbation OPT_KEY	(	Real	,
		v_bb_perturbation_rand_fraction
	)

◆ OPT_KEY() [16/21]

v_relaxrounds v_kbt OPT_KEY	(	Real	,
		v_kbt_minimize
	)

◆ OPT_KEY() [17/21]

v_relaxrounds OPT_KEY	(	Real	,
		v_MCtemperature
	)

◆ OPT_KEY() [18/21]

v_relaxrounds v_kbt v_MCminimize_replicates v_bb_perturbation v_rmspenalty v_randseq v_ignoreresidue_in_rms v_removelowrms OPT_KEY	(	Real	,
		v_removelowrms_threshold
	)

◆ OPT_KEY() [19/21]

v_relaxrounds v_kbt v_MCminimize_replicates v_bb_perturbation v_rmspenalty OPT_KEY	(	Real	,
		v_rmspenalty_n
	)

◆ OPT_KEY() [20/21]

v_relaxrounds v_kbt v_MCminimize_replicates v_bb_perturbation v_rmspenalty v_randseq v_ignoreresidue_in_rms v_removelowrms v_lambda v_cyclic v_cyclic_permutation_offset v_PCAfiles v_PCAfile_native v_preserve_chirality v_savememory v_disulfide_positions OPT_KEY	(	String	,
		v_allowed_aminoacids
	)

◆ OPT_KEY() [21/21]

v_relaxrounds v_kbt v_MCminimize_replicates v_bb_perturbation v_rmspenalty v_randseq v_ignoreresidue_in_rms v_removelowrms v_lambda v_cyclic v_cyclic_permutation_offset v_PCAfiles v_PCAfile_native v_preserve_chirality v_savememory v_disulfide_positions v_allowed_betas v_equivalent_positions v_cst_file OPT_KEY	(	String	,
		v_native_tag
	)

◆ parse_extra_atom_list()

void parse_extra_atom_list ( utility::vector1< core::id::NamedAtomID > & extra_atom_list )

References create_a3b_hbs::i, basic::options::option, res, extract_by_sidechain_sasa_score::tags, and basic::options::OptionKeys::inout::dbms::user.

Referenced by main().

◆ parsefilelist()

void parsefilelist	(	const std::string &	listfile,
		utility::vector1< std::string > &	filevector
	)

References getline(), basic::options::OptionKeys::in::in, and line.

Referenced by main().

◆ perturb_bb_and_relax()

void perturb_bb_and_relax	(	const core::Size	replicates,
		const core::Size	MCsteps,
		core::pose::Pose &	pose,
		utility::vector1< std::pair< core::Size, core::Size > > &	disulf_positions,
		numeric::random::RandomGenerator &	RandGen,
		const core::Real	bb_perturbation,
		protocols::relax::FastRelax &	frlx,
		core::scoring::ScoreFunctionOP const &	sfxn,
		const core::Real	MCkbt,
		const utility::vector1< core::Real > &	PCAvariances,
		const utility::vector1< utility::vector1< core::Real > > &	PCAvectors
	)

◆ read_covalent_connections_file()

void read_covalent_connections_file	(	utility::vector1< std::pair< core::id::NamedAtomID, core::id::NamedAtomID > > &	conlist,
		core::Size const	procnum
	)

References create_a3b_hbs::first, getline(), create_a3b_hbs::i, basic::options::OptionKeys::in::in, line, basic::options::option, printf(), erraser_analysis::res1, erraser_analysis::res2, and build::stdout.

Referenced by main().

◆ read_equivalent_position_file()

void read_equivalent_position_file	(	const char *	filename,
		utility::vector1< utility::vector1< core::Size > > &	equivalent_positions
	)

References lactamize::filename, getline(), basic::options::OptionKeys::in::in, and line.

Referenced by main().

◆ read_PCAfile()

core::Size read_PCAfile	(	const char *	filename,
		utility::vector1< core::Real > &	variances,
		utility::vector1< utility::vector1< core::Real > > &	PCA_vectors,
		bool	normalize_variances
	)

References fclose(), PREcst::FILE, lactamize::filename, create_a3b_hbs::i, create_a3b_hbs::j, basic::options::option, runtime_assert_string_msg, and basic::options::OptionKeys::inout::dbms::user.

Referenced by main().

◆ receive_silent_struct()

void receive_silent_struct	(	core::pose::Pose &	pose,
		const int	fromproc,
		const int	toproc,
		const int	thisproc,
		bool const	broadcast
	)

References add_user_constraints(), and beta_nonlocal::pose.

Referenced by main(), and scoreall().

◆ register_options()

v_relaxrounds v_kbt v_MCminimize_replicates v_bb_perturbation v_rmspenalty v_randseq v_ignoreresidue_in_rms v_removelowrms v_lambda v_cyclic v_cyclic_permutation_offset v_PCAfiles v_PCAfile_native v_preserve_chirality v_savememory v_disulfide_positions v_allowed_betas v_equivalent_positions v_cst_file v_extra_rms_atoms v_consider_all_replicates void register_options ( )

References NEW_OPT.

Referenced by main().

◆ scoreall()

void scoreall	(	const int	procnum,
		const int	proccount,
		const core::Size	totalstatecount,
		const core::Size	PCAvectorcomponentcount,
		std::string &	sequence,
		utility::vector1< bool > &	dpositions,
		utility::vector1< bool > &	betapositions,
		utility::vector1< core::io::silent::SilentStructOP > &	allstates_master,
		utility::vector1< std::pair< core::Size, core::Size > > &	disulf_positions,
		utility::vector1< core::Real > &	energyvals_current,
		utility::vector1< core::Real > &	rmsvals_current,
		const core::pose::Pose &	positive_master,
		core::pose::Pose &	positive_current,
		numeric::random::RandomGenerator &	RG,
		protocols::relax::FastRelax &	frlx,
		core::scoring::ScoreFunctionOP const &	sfxn,
		utility::vector1< utility::vector1< core::Real > > &	PCAvariances,
		utility::vector1< utility::vector1< utility::vector1< core::Real > > > &	PCAmatrices,
		utility::vector1< core::id::NamedAtomID > const &	extra_rms_atoms
	)

References basic::options::OptionKeys::cluster::energy_based_clustering::extra_rms_atoms, get_distance_measure(), create_a3b_hbs::ii, enumerate_junctions::int, mutate_to_sequence(), basic::options::option, perturb_bb_and_relax(), printf(), receive_silent_struct(), basic::RG, basic::options::OptionKeys::relax::sequence, test.T120_core::sfxn, build::stdout, transmit_additional_info(), transmit_silent_struct(), and basic::options::OptionKeys::inout::dbms::user.

Referenced by main().

◆ set_to_state()

void set_to_state	(	core::pose::Pose &	mypose,
		const utility::vector1< core::Real > &	bb_list
	)

References basic::options::OptionKeys::mean_field::bb_list, betapeptide_setomega(), betapeptide_setphi(), betapeptide_setpsi(), betapeptide_settheta(), create_a3b_hbs::nres, basic::options::option, and PI.

◆ set_up_covalent_connections()

void set_up_covalent_connections	(	core::pose::Pose &	pose,
		utility::vector1< std::pair< core::id::NamedAtomID, core::id::NamedAtomID > > const &	conlist
	)

References create_a3b_hbs::first, create_a3b_hbs::i, beta_nonlocal::pose, and runtime_assert_string_msg.

Referenced by main().

◆ set_up_termini()

void set_up_termini ( core::pose::Pose & pose )

References beta_nonlocal::pose.

Referenced by main().

◆ store_backbone()

void store_backbone	(	const core::pose::Pose &	mypose,
		utility::vector1< core::Real > &	outvect
	)

References numeric::dihedral_degrees(), create_a3b_hbs::nres, and basic::options::option.

◆ strip_terminal_glycines()

bool strip_terminal_glycines ( core::pose::Pose & mypose )

Referenced by main().

◆ transmit_additional_info()

void transmit_additional_info	(	const int	fromproc,
		const int	toproc,
		const int	thisproc,
		const int	numelements,
		utility::vector1< core::Real > &	datavector
	)

References create_a3b_hbs::i.

Referenced by scoreall().

◆ transmit_silent_struct() [1/2]

void transmit_silent_struct	(	const int	fromproc,
		const int	toproc,
		const int	thisproc,
		core::io::silent::SilentStructOP &	silentstruct,
		bool const	broadcast
	)

References header().

Referenced by main(), scoreall(), and transmit_silent_struct().

◆ transmit_silent_struct() [2/2]

void transmit_silent_struct	(	const int	fromproc,
		const int	toproc,
		const int	thisproc,
		std::string const &	tag,
		core::pose::Pose const &	pose,
		bool const	broadcast
	)

References beta_nonlocal::pose, tag, and transmit_silent_struct().

◆ use_in_rmsd()

bool use_in_rmsd	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		core::Size	resno,
		core::Size	atomno,
		utility::vector1< core::id::NamedAtomID > const &	extra_atom_list
	)

References val2thr::atom, create_a3b_hbs::i, basic::options::option, test.T008_Serialization::pose1, test.T008_Serialization::pose2, and subloop_histogram::size.

Referenced by get_distance_measure().

◆ vMPI_Bcastpose()

void vMPI_Bcastpose	(	core::pose::Pose &	pose,
		int	rootproc,
		int	thisproc
	)

References natoms(), and beta_nonlocal::pose.

◆ vMPI_transmitpose()

void vMPI_transmitpose	(	core::pose::Pose &	pose,
		int	thisproc,
		int	sendingproc,
		int	receivingproc
	)

References natoms(), and beta_nonlocal::pose.

Macros

Functions

Macro Definition Documentation

◆ CaCN_ANGLE

◆ CNCa_ANGLE

◆ CNH_ANGLE

◆ OCN_ANGLE

◆ PI

Function Documentation

◆ add_user_constraints()

◆ addcyclicconstraints()

◆ betapeptide_setomega()

◆ betapeptide_setphi()

◆ betapeptide_setpsi()

◆ betapeptide_settheta()

◆ calc_sequence_score()

◆ get_beta_name()

◆ get_D_name()

◆ get_distance_measure()

◆ is_in_list()

◆ is_in_list_of_lists()

◆ main()

◆ mutate_to_sequence()

◆ OPT_KEY() [1/21]

◆ OPT_KEY() [2/21]

◆ OPT_KEY() [3/21]

◆ OPT_KEY() [4/21]

◆ OPT_KEY() [5/21]

◆ OPT_KEY() [6/21]

◆ OPT_KEY() [7/21]

◆ OPT_KEY() [8/21]

◆ OPT_KEY() [9/21]

◆ OPT_KEY() [10/21]

◆ OPT_KEY() [11/21]

◆ OPT_KEY() [12/21]

◆ OPT_KEY() [13/21]

◆ OPT_KEY() [14/21]

◆ OPT_KEY() [15/21]

◆ OPT_KEY() [16/21]

◆ OPT_KEY() [17/21]

◆ OPT_KEY() [18/21]

◆ OPT_KEY() [19/21]

◆ OPT_KEY() [20/21]

◆ OPT_KEY() [21/21]

◆ parse_extra_atom_list()

◆ parsefilelist()

◆ perturb_bb_and_relax()

◆ read_covalent_connections_file()

◆ read_equivalent_position_file()

◆ read_PCAfile()

◆ receive_silent_struct()

◆ register_options()

◆ scoreall()

◆ set_to_state()

◆ set_up_covalent_connections()

◆ set_up_termini()

◆ store_backbone()

◆ strip_terminal_glycines()

◆ transmit_additional_info()

◆ transmit_silent_struct() [1/2]

◆ transmit_silent_struct() [2/2]

◆ use_in_rmsd()

◆ vMPI_Bcastpose()

◆ vMPI_transmitpose()