#include <protocols/simple_moves/ScoreMover.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/pose/util.hh>
#include <core/scoring/symmetry/SymmetricScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/import_pose/import_pose.hh>
#include <core/id/TorsionID.hh>
#include <protocols/cluster/cluster.hh>
#include <protocols/loops/Loops.hh>
#include <core/import_pose/pose_stream/MetaPoseInputStream.hh>
#include <core/import_pose/pose_stream/util.hh>
#include <basic/options/option.hh>
#include <basic/options/option_macros.hh>
#include <devel/init.hh>
#include <iostream>
#include <string>
#include <deque>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/cluster.OptionKeys.gen.hh>
#include <basic/options/keys/symmetry.OptionKeys.gen.hh>
#include <utility/vector1.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/rms_util.tmpl.hh>
#include <core/scoring/Energies.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <protocols/minimization_packing/RepackSidechainsMover.hh>
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <protocols/simple_moves/MutateResidue.hh>
#include <protocols/relax/FastRelax.hh>
#include <numeric/model_quality/rms.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 <numeric/EulerAngles.hh>
#include <numeric/PCA.hh>
#include <core/io/silent/SilentStructFactory.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/io/silent/SilentFileOptions.hh>
#include <core/io/silent/SilentStruct.hh>
#include <protocols/constraint_movers/ConstraintSetMover.hh>
#include <protocols/cyclic_peptide/CycpepSymmetryFilter.hh>
#include <protocols/cyclic_peptide/DeclareBond.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 (Boolean, v_prerelax) OPT_KEY(Integer

v_relaxrounds	OPT_KEY (String, v_clusterby) OPT_KEY(Real

v_relaxrounds v_clusterradius	OPT_KEY (Boolean, v_weightbyenergy) OPT_KEY(Real

v_relaxrounds v_clusterradius v_kbt	OPT_KEY (Boolean, v_CB) OPT_KEY(IntegerVector

v_relaxrounds v_clusterradius v_kbt v_ignoreresidue	OPT_KEY (IntegerVector, v_ignorechain) OPT_KEY(Integer

v_relaxrounds v_clusterradius v_kbt v_ignoreresidue v_limit_structures_per_cluster	OPT_KEY (Integer, v_limit_clusters) OPT_KEY(Boolean

v_relaxrounds v_clusterradius v_kbt v_ignoreresidue v_limit_structures_per_cluster v_cyclic	OPT_KEY (Integer, v_cyclic_symmetry) OPT_KEY(Boolean

v_relaxrounds v_clusterradius v_kbt v_ignoreresidue v_limit_structures_per_cluster v_cyclic v_cyclic_symmetry_mirroring	OPT_KEY (Real, v_cyclic_symmetry_threshold) OPT_KEY(Boolean

v_relaxrounds v_clusterradius v_kbt v_ignoreresidue v_limit_structures_per_cluster v_cyclic v_cyclic_symmetry_mirroring v_cluster_cyclic_permutations	OPT_KEY (Integer, v_cyclic_permutation_offset) OPT_KEY(Boolean

v_relaxrounds v_clusterradius v_kbt v_ignoreresidue v_limit_structures_per_cluster v_cyclic v_cyclic_symmetry_mirroring v_cluster_cyclic_permutations v_mutate_to_ala	OPT_KEY (IntegerVector, v_disulfide_positions) OPT_KEY(Boolean

v_relaxrounds v_clusterradius v_kbt v_ignoreresidue v_limit_structures_per_cluster v_cyclic v_cyclic_symmetry_mirroring v_cluster_cyclic_permutations v_mutate_to_ala v_homooligomer_swap	OPT_KEY (Boolean, v_silentoutput) OPT_KEY(File

v_relaxrounds v_clusterradius v_kbt v_ignoreresidue v_limit_structures_per_cluster v_cyclic v_cyclic_symmetry_mirroring v_cluster_cyclic_permutations v_mutate_to_ala v_homooligomer_swap v_cst_file	OPT_KEY (StringVector, v_extra_rms_atoms) OPT_KEY(Boolean

v_relaxrounds v_clusterradius v_kbt v_ignoreresidue v_limit_structures_per_cluster v_cyclic v_cyclic_symmetry_mirroring v_cluster_cyclic_permutations v_mutate_to_ala v_homooligomer_swap v_cst_file v_skip_PCA void	register_options ()

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

bool	use_in_rmsd_offset (core::pose::Pose const &pose1, core::pose::Pose const &pose2, core::Size resno2, core::Size atomno, const core::Size pose1_offset, utility::vector1< core::id::NamedAtomID > const &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)

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)

bool	is_beta_aminoacid (const core::conformation::Residue &rsd)
	Function to determine whether an amino acid is a beta amino acid. Added 23 August 2013 by Vikram K. Mulligan. More...

bool	is_beta_aminoacid (const core::pose::Pose &mypose, const core::Size position)

core::Size	count_bb_dihedrals (const core::pose::Pose &mypose)

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

void	check_angle_bounds (utility::vector1< core::Real > anglevector, utility::vector1< core::Size > skiplist)

void	check_angle_bounds (utility::vector1< core::Real > anglevector)

void	make_disulfides (core::pose::Pose outputpose)

void	storeposedata (const core::pose::Pose &pose, utility::vector1< core::Real > &posedata, FArray2D< core::Real > &alignmentdata, const core::Size clustermode, utility::vector1< core::id::NamedAtomID > const &extra_atom_list)

void	storeposedata (const core::pose::Pose &pose, utility::vector1< utility::vector1< core::Real > > &posedata, utility::vector1< FArray2D< core::Real > > &alignmentdata, const core::Size clustermode, utility::vector1< core::id::NamedAtomID > const &extra_atom_list)

core::Real	elementdiff (const core::Real &n1, const core::Real &n2, const core::Size &clustmode)

void	pose_from_posedata (const core::pose::Pose &inputpose, core::pose::Pose &outputpose, const core::Size clustermode, const utility::vector1< core::Real > &posedata, const bool set_chi=true)

core::Size	alignment_atoms_in_res (const core::pose::Pose &pose, const core::Size position)

core::Size	alignment_torsions_in_res (const core::pose::Pose &pose, const core::Size position)

core::Size	factorial (core::Size val)

core::Size	get_start_index (const core::Size aa_number, const core::pose::Pose &refpose)

core::Size	get_start_aa (const core::Size chainnumber, const core::pose::Pose &refpose)

void	swapchains (core::pose::Pose &currentpose, const core::Size permutation_number)

void	swapalignmentvector (const FArray2D< core::Real > &parentvect, FArray2D< core::Real > &swappedvect, const core::pose::Pose &refpose, core::Size permutation_number)

void	swapvector (const utility::vector1< core::Real > &parentvect, utility::vector1< core::Real > &swappedvect, const core::pose::Pose &, core::Size)

core::Real	calc_dist (const utility::vector1< core::Real > &vect1, const utility::vector1< core::Real > &vect2, const core::Size clustmode, const FArray2D< core::Real > &alignmentvect1, const FArray2D< core::Real > &alignmentvect2, const core::Size nresidues, const core::pose::Pose &firstpose)

core::Real	calc_dist (const utility::vector1< core::Real > &vect1, const utility::vector1< core::Real > &vect2, const core::Size clustmode, const FArray2D< core::Real > &alignmentvect1, const FArray2D< core::Real > &alignmentvect2, const core::Size nresidues, const core::pose::Pose &firstpose, core::Size &offset, core::Size &permutation)

void	slidearound (utility::vector1< core::Real > &dihedrals, const core::Size offset, const core::Size rescount, const core::pose::Pose &pose)

void	trim_and_add_jump_data (utility::vector1< core::Real > &myvect, const core::Size numdihedrals, const core::pose::Pose &mypose)

void	shift_center_and_PCA (utility::vector1< core::Real > &clustcenter, utility::vector1< utility::vector1< core::Real > > &pca_vector_list, utility::vector1< core::Real > &coeff_list, const core::Size clustcenterindex, const utility::vector1< utility::vector1< core::Real > > &posedata, const utility::vector1< core::Real > &poseenergies, const utility::vector1< core::Size > &statesincluster, const core::Size currentclusterindex, const core::Size clustmode, const core::pose::Pose &firstpose, const utility::vector1< core::Size > &cluster_offsets, const utility::vector1< core::Size > &cluster_oligomer_permutations, utility::vector1< core::id::NamedAtomID > const &extra_atom_list)

void	output_PCA (const utility::vector1< utility::vector1< core::Real > > &pca_vector_list, const utility::vector1< core::Real > &coeff_list, const core::Size &clustnumber)

void	sortclusterlist (utility::vector1< core::Size > &statelist, utility::vector1< core::Real > &poseenergies)

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

void	align_with_offset (core::pose::Pose &pose1, const core::pose::Pose &pose2, const core::Size offset, utility::vector1< core::id::NamedAtomID > const &extra_atom_list)

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

bool	contains_beta (const core::pose::Pose &mypose)

bool	betas_match (const core::pose::Pose &pose1, const core::pose::Pose &pose2)

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

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, option, and basic::options::OptionKeys::inout::dbms::user.

Referenced by main().

◆ addcyclicconstraints()

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

References CaCN_ANGLE, CNCa_ANGLE, CNH_ANGLE, basic::options::OptionKeys::constraints::constraints, numeric::dihedral_degrees(), func, OCN_ANGLE, PI, basic::options::OptionKeys::in::file::residue_type_set, and superimpose_pose().

Referenced by main().

◆ align_with_offset()

void align_with_offset	(	core::pose::Pose &	pose1,
		const core::pose::Pose &	pose2,
		const core::Size	offset,
		utility::vector1< core::id::NamedAtomID > const &	extra_atom_list
	)

References offset, test.T008_Serialization::pose1, test.T008_Serialization::pose2, superimpose_pose(), and use_in_rmsd_offset().

Referenced by main().

◆ alignment_atoms_in_res()

core::Size alignment_atoms_in_res	(	const core::pose::Pose &	pose,
		const core::Size	position
	)

References is_beta_aminoacid(), option, and beta_nonlocal::pose.

Referenced by calc_dist(), get_start_index(), and swapalignmentvector().

◆ alignment_torsions_in_res()

core::Size alignment_torsions_in_res	(	const core::pose::Pose &	pose,
		const core::Size	position
	)

References is_beta_aminoacid(), and beta_nonlocal::pose.

Referenced by calc_dist(), and slidearound().

◆ 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 pose_from_posedata().

◆ 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 pose_from_posedata().

◆ 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 pose_from_posedata().

◆ 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 pose_from_posedata().

◆ betas_match()

bool betas_match	(	const core::pose::Pose &	pose1,
		const core::pose::Pose &	pose2
	)

References is_beta_aminoacid(), create_a3b_hbs::nres, test.T008_Serialization::pose1, and test.T008_Serialization::pose2.

Referenced by main().

◆ calc_dist() [1/2]

core::Real calc_dist	(	const utility::vector1< core::Real > &	vect1,
		const utility::vector1< core::Real > &	vect2,
		const core::Size	clustmode,
		const FArray2D< core::Real > &	alignmentvect1,
		const FArray2D< core::Real > &	alignmentvect2,
		const core::Size	nresidues,
		const core::pose::Pose &	firstpose
	)

References elementdiff(), utility::options::OptionKeys::options::exit, create_a3b_hbs::i, ObjexxFCL::index(), is_beta_aminoacid(), create_a3b_hbs::j, option, ObjexxFCL::pow(), printf(), numeric::model_quality::rms_wrapper(), subloop_histogram::size, ObjexxFCL::FArray2D< T >::size2(), and build::stdout.

Referenced by calc_dist(), and main().

◆ calc_dist() [2/2]

core::Real calc_dist	(	const utility::vector1< core::Real > &	vect1,
		const utility::vector1< core::Real > &	vect2,
		const core::Size	clustmode,
		const FArray2D< core::Real > &	alignmentvect1,
		const FArray2D< core::Real > &	alignmentvect2,
		const core::Size	nresidues,
		const core::pose::Pose &	firstpose,
		core::Size &	offset,
		core::Size &	permutation
	)

References alignment_atoms_in_res(), alignment_torsions_in_res(), calc_dist(), dist(), factorial(), create_a3b_hbs::i, ObjexxFCL::index(), offset, option, ObjexxFCL::FArray2D< T >::size2(), swapalignmentvector(), swapvector(), and oop_scan::v2.

◆ check_angle_bounds() [1/2]

void check_angle_bounds ( utility::vector1< core::Real > anglevector )

References check_angle_bounds().

◆ check_angle_bounds() [2/2]

void check_angle_bounds	(	utility::vector1< core::Real >	anglevector,
		utility::vector1< core::Size >	skiplist
	)

References create_a3b_hbs::i, and is_in_list().

Referenced by check_angle_bounds(), shift_center_and_PCA(), and storeposedata().

◆ contains_beta()

bool contains_beta ( const core::pose::Pose & mypose )

References is_beta_aminoacid(), and create_a3b_hbs::nres.

Referenced by main().

◆ count_bb_dihedrals()

core::Size count_bb_dihedrals ( const core::pose::Pose & mypose )

References is_beta_aminoacid(), create_a3b_hbs::nres, and option.

Referenced by shift_center_and_PCA().

◆ elementdiff()

core::Real elementdiff	(	const core::Real &	n1,
		const core::Real &	n2,
		const core::Size &	clustmode
	)

References erraser_analysis::diff.

Referenced by calc_dist(), and shift_center_and_PCA().

◆ factorial()

core::Size factorial ( core::Size val )

Referenced by calc_dist().

◆ get_start_aa()

core::Size get_start_aa	(	const core::Size	chainnumber,
		const core::pose::Pose &	refpose
	)

References create_a3b_hbs::nres.

Referenced by swapalignmentvector(), and swapchains().

◆ get_start_index()

core::Size get_start_index	(	const core::Size	aa_number,
		const core::pose::Pose &	refpose
	)

References alignment_atoms_in_res(), demo.D060_Folding::counter, and create_a3b_hbs::nres.

Referenced by swapalignmentvector().

◆ is_beta_aminoacid() [1/2]

bool KinematicMover::is_beta_aminoacid ( const core::conformation::Residue & rsd )

Function to determine whether an amino acid is a beta amino acid. Added 23 August 2013 by Vikram K. Mulligan.

Referenced by alignment_atoms_in_res(), alignment_torsions_in_res(), betas_match(), calc_dist(), contains_beta(), count_bb_dihedrals(), is_beta_aminoacid(), mutate_to_ala(), pose_from_posedata(), and storeposedata().

◆ is_beta_aminoacid() [2/2]

bool is_beta_aminoacid	(	const core::pose::Pose &	mypose,
		const core::Size	position
	)

References is_beta_aminoacid().

◆ is_in_list()

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

References create_a3b_hbs::i.

Referenced by check_angle_bounds(), shift_center_and_PCA(), and storeposedata().

◆ main()

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

◆ make_disulfides()

void make_disulfides ( core::pose::Pose outputpose )

References create_a3b_hbs::i, option, subloop_histogram::size, and basic::options::OptionKeys::inout::dbms::user.

Referenced by main(), and pose_from_posedata().

◆ mutate_to_ala()

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

References is_beta_aminoacid().

Referenced by main().

◆ OPT_KEY() [1/12]

v_relaxrounds v_clusterradius v_kbt OPT_KEY	(	Boolean	,
		v_CB
	)

◆ OPT_KEY() [2/12]

OPT_KEY	(	Boolean	,
		v_prerelax
	)

◆ OPT_KEY() [3/12]

v_relaxrounds v_clusterradius v_kbt v_ignoreresidue v_limit_structures_per_cluster v_cyclic v_cyclic_symmetry_mirroring v_cluster_cyclic_permutations v_mutate_to_ala v_homooligomer_swap OPT_KEY	(	Boolean	,
		v_silentoutput
	)

◆ OPT_KEY() [4/12]

v_relaxrounds v_clusterradius OPT_KEY	(	Boolean	,
		v_weightbyenergy
	)

◆ OPT_KEY() [5/12]

v_relaxrounds v_clusterradius v_kbt v_ignoreresidue v_limit_structures_per_cluster v_cyclic v_cyclic_symmetry_mirroring v_cluster_cyclic_permutations OPT_KEY	(	Integer	,
		v_cyclic_permutation_offset
	)

◆ OPT_KEY() [6/12]

v_relaxrounds v_clusterradius v_kbt v_ignoreresidue v_limit_structures_per_cluster v_cyclic OPT_KEY	(	Integer	,
		v_cyclic_symmetry
	)

◆ OPT_KEY() [7/12]

v_relaxrounds v_clusterradius v_kbt v_ignoreresidue v_limit_structures_per_cluster OPT_KEY	(	Integer	,
		v_limit_clusters
	)

◆ OPT_KEY() [8/12]

v_relaxrounds v_clusterradius v_kbt v_ignoreresidue v_limit_structures_per_cluster v_cyclic v_cyclic_symmetry_mirroring v_cluster_cyclic_permutations v_mutate_to_ala OPT_KEY	(	IntegerVector	,
		v_disulfide_positions
	)

◆ OPT_KEY() [9/12]

v_relaxrounds v_clusterradius v_kbt v_ignoreresidue OPT_KEY	(	IntegerVector	,
		v_ignorechain
	)

◆ OPT_KEY() [10/12]

v_relaxrounds v_clusterradius v_kbt v_ignoreresidue v_limit_structures_per_cluster v_cyclic v_cyclic_symmetry_mirroring OPT_KEY	(	Real	,
		v_cyclic_symmetry_threshold
	)

◆ OPT_KEY() [11/12]

v_relaxrounds OPT_KEY	(	String	,
		v_clusterby
	)

◆ OPT_KEY() [12/12]

v_relaxrounds v_clusterradius v_kbt v_ignoreresidue v_limit_structures_per_cluster v_cyclic v_cyclic_symmetry_mirroring v_cluster_cyclic_permutations v_mutate_to_ala v_homooligomer_swap v_cst_file OPT_KEY	(	StringVector	,
		v_extra_rms_atoms
	)

◆ output_PCA()

void output_PCA	(	const utility::vector1< utility::vector1< core::Real > > &	pca_vector_list,
		const utility::vector1< core::Real > &	coeff_list,
		const core::Size &	clustnumber
	)

References fclose(), PREcst::FILE, lactamize::filename, fprintf(), create_a3b_hbs::i, create_a3b_hbs::j, printf(), subloop_histogram::size, and build::stdout.

Referenced by main().

◆ parse_extra_atom_list()

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

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

Referenced by main().

◆ pose_from_posedata()

void pose_from_posedata	(	const core::pose::Pose &	inputpose,
		core::pose::Pose &	outputpose,
		const core::Size	clustermode,
		const utility::vector1< core::Real > &	posedata,
		const bool	set_chi = `true`
	)

◆ register_options()

v_relaxrounds v_clusterradius v_kbt v_ignoreresidue v_limit_structures_per_cluster v_cyclic v_cyclic_symmetry_mirroring v_cluster_cyclic_permutations v_mutate_to_ala v_homooligomer_swap v_cst_file v_skip_PCA void register_options ( )

References NEW_OPT.

Referenced by main().

◆ shift_center_and_PCA()

void shift_center_and_PCA	(	utility::vector1< core::Real > &	clustcenter,
		utility::vector1< utility::vector1< core::Real > > &	pca_vector_list,
		utility::vector1< core::Real > &	coeff_list,
		const core::Size	clustcenterindex,
		const utility::vector1< utility::vector1< core::Real > > &	posedata,
		const utility::vector1< core::Real > &	poseenergies,
		const utility::vector1< core::Size > &	statesincluster,
		const core::Size	currentclusterindex,
		const core::Size	clustmode,
		const core::pose::Pose &	firstpose,
		const utility::vector1< core::Size > &	cluster_offsets,
		const utility::vector1< core::Size > &	cluster_oligomer_permutations,
		utility::vector1< core::id::NamedAtomID > const &	extra_atom_list
	)

References check_angle_bounds(), count_bb_dihedrals(), demo.D060_Folding::counter, elementdiff(), create_a3b_hbs::i, is_in_list(), create_a3b_hbs::j, min(), option, pose_from_posedata(), numeric::principal_components_and_eigenvalues_ndimensions(), printf(), slidearound(), build::stdout, storeposedata(), swapchains(), and trim_and_add_jump_data().

Referenced by main().

◆ slidearound()

void slidearound	(	utility::vector1< core::Real > &	dihedrals,
		const core::Size	offset,
		const core::Size	rescount,
		const core::pose::Pose &	pose
	)

References alignment_torsions_in_res(), ObjexxFCL::index(), offset, and beta_nonlocal::pose.

Referenced by shift_center_and_PCA().

◆ sortclusterlist()

void sortclusterlist	(	utility::vector1< core::Size > &	statelist,
		utility::vector1< core::Real > &	poseenergies
	)

References create_a3b_hbs::i, and create_a3b_hbs::j.

Referenced by main().

◆ storeposedata() [1/2]

void storeposedata	(	const core::pose::Pose &	pose,
		utility::vector1< core::Real > &	posedata,
		FArray2D< core::Real > &	alignmentdata,
		const core::Size	clustermode,
		utility::vector1< core::id::NamedAtomID > const &	extra_atom_list
	)

References check_angle_bounds(), enumerate_junctions::default, numeric::dihedral_degrees(), create_a3b_hbs::i, is_beta_aminoacid(), is_in_list(), create_a3b_hbs::nres, option, beta_nonlocal::pose, ObjexxFCL::FArray2D< T >::redimension(), subloop_histogram::size, and use_in_rmsd().

Referenced by main(), shift_center_and_PCA(), and storeposedata().

◆ storeposedata() [2/2]

void storeposedata	(	const core::pose::Pose &	pose,
		utility::vector1< utility::vector1< core::Real > > &	posedata,
		utility::vector1< FArray2D< core::Real > > &	alignmentdata,
		const core::Size	clustermode,
		utility::vector1< core::id::NamedAtomID > const &	extra_atom_list
	)

References beta_nonlocal::pose, and storeposedata().

◆ swapalignmentvector()

void swapalignmentvector	(	const FArray2D< core::Real > &	parentvect,
		FArray2D< core::Real > &	swappedvect,
		const core::pose::Pose &	refpose,
		core::Size	permutation_number
	)

References alignment_atoms_in_res(), demo.D060_Folding::counter, get_start_aa(), get_start_index(), create_a3b_hbs::i, and create_a3b_hbs::nres.

Referenced by calc_dist().

◆ swapchains()

void swapchains	(	core::pose::Pose &	currentpose,
		const core::Size	permutation_number
	)

References get_start_aa(), create_a3b_hbs::i, and create_a3b_hbs::nres.

Referenced by main(), and shift_center_and_PCA().

◆ swapvector()

void swapvector	(	const utility::vector1< core::Real > &	parentvect,
		utility::vector1< core::Real > &	swappedvect,
		const core::pose::Pose &	,
		core::Size
	)

Referenced by calc_dist().

◆ trim_and_add_jump_data()

void trim_and_add_jump_data	(	utility::vector1< core::Real > &	myvect,
		const core::Size	numdihedrals,
		const core::pose::Pose &	mypose
	)

References demo.D060_Folding::counter, create_a3b_hbs::i, create_a3b_hbs::j, numeric::EulerAngles< T >::phi_degrees(), numeric::EulerAngles< T >::psi_degrees(), and numeric::EulerAngles< T >::theta_degrees().

Referenced by shift_center_and_PCA().

◆ 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, option, test.T008_Serialization::pose1, test.T008_Serialization::pose2, and subloop_histogram::size.

Referenced by storeposedata().

◆ use_in_rmsd_offset()

bool use_in_rmsd_offset	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		core::Size	resno2,
		core::Size	atomno,
		const core::Size	pose1_offset,
		utility::vector1< core::id::NamedAtomID > const &	extra_atom_list
	)

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

Referenced by align_with_offset().

Macros

Functions

Macro Definition Documentation

◆ CaCN_ANGLE

◆ CNCa_ANGLE

◆ CNH_ANGLE

◆ OCN_ANGLE

◆ PI

Function Documentation

◆ add_user_constraints()

◆ addcyclicconstraints()

◆ align_with_offset()

◆ alignment_atoms_in_res()

◆ alignment_torsions_in_res()

◆ betapeptide_setomega()

◆ betapeptide_setphi()

◆ betapeptide_setpsi()

◆ betapeptide_settheta()

◆ betas_match()

◆ calc_dist() [1/2]

◆ calc_dist() [2/2]

◆ check_angle_bounds() [1/2]

◆ check_angle_bounds() [2/2]

◆ contains_beta()

◆ count_bb_dihedrals()

◆ elementdiff()

◆ factorial()

◆ get_start_aa()

◆ get_start_index()

◆ is_beta_aminoacid() [1/2]

◆ is_beta_aminoacid() [2/2]

◆ is_in_list()

◆ main()

◆ make_disulfides()

◆ mutate_to_ala()

◆ OPT_KEY() [1/12]

◆ OPT_KEY() [2/12]

◆ OPT_KEY() [3/12]

◆ OPT_KEY() [4/12]

◆ OPT_KEY() [5/12]

◆ OPT_KEY() [6/12]

◆ OPT_KEY() [7/12]

◆ OPT_KEY() [8/12]

◆ OPT_KEY() [9/12]

◆ OPT_KEY() [10/12]

◆ OPT_KEY() [11/12]

◆ OPT_KEY() [12/12]

◆ output_PCA()

◆ parse_extra_atom_list()

◆ pose_from_posedata()

◆ register_options()

◆ shift_center_and_PCA()

◆ slidearound()

◆ sortclusterlist()

◆ storeposedata() [1/2]

◆ storeposedata() [2/2]

◆ swapalignmentvector()

◆ swapchains()

◆ swapvector()

◆ trim_and_add_jump_data()

◆ use_in_rmsd()

◆ use_in_rmsd_offset()