coiled_coil.cc File Reference

#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/conformation/symmetry/SymmData.hh>
#include <core/pose/symmetry/util.hh>
#include <core/conformation/symmetry/util.hh>
#include <core/fragment/FragmentIO.hh>
#include <core/fragment/FragSet.hh>
#include <devel/init.hh>
#include <basic/database/open.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/kinematics/MoveMap.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/option.hh>
#include <basic/options/util.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pose/util.hh>
#include <core/scoring/constraints/AmbiguousConstraint.hh>
#include <core/scoring/constraints/AngleConstraint.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/constraints/CoordinateConstraint.hh>
#include <core/scoring/constraints/DihedralConstraint.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/scoring/constraints/util.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/symmetry/SymmetricScoreFunction.hh>
#include <basic/Tracer.hh>
#include <numeric/model_quality/rms.hh>
#include <numeric/random/random.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/xyz.io.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <protocols/abinitio/FragmentMover.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/minimization_packing/symmetry/SymMinMover.hh>
#include <protocols/minimization_packing/symmetry/SymPackRotamersMover.hh>
#include <protocols/symmetric_docking/SymDockingLowRes.hh>
#include <sstream>
#include <utility/io/izstream.hh>
#include <utility/io/ozstream.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/util/SwitchResidueTypeSet.hh>

Classes
struct	CCParam

Typedefs
typedef numeric::xyzVector< Real >	Vec
typedef utility::vector1< Vec >	Vecs
typedef numeric::xyzMatrix< Real >	Mat
typedef ScoreFunctionOP	SFOP

Functions
Vec	helix_axis (core::pose::Pose const &pose)
Vec	center_of_mass (core::pose::Pose const &pose, Size nres=0)
void	trans_pose (core::pose::Pose &pose, Vec const &trans)
void	rot_pose (core::pose::Pose &pose, Mat const &rot)
void	rot_pose (core::pose::Pose &pose, Mat const &rot, Vec const &cen)
void	rot_pose (core::pose::Pose &pose, Vec const &axis, Real const &ang)
void	rot_pose (core::pose::Pose &pose, Vec const &axis, Real const &ang, Vec const &cen)
core::pose::Pose	make_helix (std::string seq)
core::conformation::symmetry::SymmData	make_symm_data (core::pose::Pose const &pose, core::Real rot, core::Real trans, core::Size n)
core::pose::Pose	make_coiled_coil (CCParam &p)
core::kinematics::MoveMapOP	make_move_map (core::pose::Pose &pose)
Real	rg2d (core::pose::Pose &pose)
void	addcc (core::pose::Pose &pose, core::id::AtomID aid, core::id::AtomID anchor, core::Real mult=1.0)
void	add_apc (core::pose::Pose &pose, core::id::AtomID aid1, core::id::AtomID aid2, core::Real mean, core::Real sd)
void	add_agc (core::pose::Pose &pose, core::id::AtomID aid1, core::id::AtomID aid2, core::id::AtomID aid3, core::Real mean, core::Real sd)
void	add_dhc (core::pose::Pose &pose, core::id::AtomID aid1, core::id::AtomID aid2, core::id::AtomID aid3, core::id::AtomID aid4, core::Real mean, core::Real sd)
void	repack (core::pose::Pose &cc, ScoreFunctionOP sf)
void	design_target (core::pose::Pose &cc, ScoreFunctionOP sf)
void	design_all (core::pose::Pose &cc, ScoreFunctionOP sf)
void	design_FILV (core::pose::Pose &cc, ScoreFunctionOP sf)
void	design_AFILV (core::pose::Pose &cc, ScoreFunctionOP sf)
void	design_AL (core::pose::Pose &cc, ScoreFunctionOP sf)
void	design_FILVEK (core::pose::Pose &cc, ScoreFunctionOP sf)
void	design_AFILVEK (core::pose::Pose &cc, ScoreFunctionOP sf)
void	minimize (core::pose::Pose &cc, ScoreFunctionOP sf)
Size	natoms (core::pose::Pose &cc, Size nres)
Real	zcyl_score (core::pose::Pose &cc, Size nres, Real trans)
void	add_fa_cst (core::pose::Pose &cc, CCParam &p)
void	make_sf (SFOP &sfc, SFOP &sfd, SFOP &sf1, SFOP &sf2, SFOP &sf3, SFOP &sf4, SFOP &sf5)
Real	sq (Real x)
core::Real	align_sf4 (core::pose::Pose const &cc, CCParam &p, core::pose::Pose &tp, Size c1, Size c2, Size c3, Size c4, core::Real dissdv, core::Real angsdv)
utility::vector1< utility::vector1< Size > >	place_sf4 (core::pose::Pose &cc, CCParam &p, core::Real cstthresh, core::Real dissdv, core::Real angsdv)
bool	add_symm_sf4 (core::pose::Pose &cc, CCParam &p, SFOP sf, core::Real cstthresh, core::Real dissdv, core::Real angsdv)
void	do_centroid_stuff (core::pose::Pose &cenpose, ScoreFunctionOP sfc)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("coiled_coil")

Typedef Documentation

Mat

typedef numeric::xyzMatrix<Real> Mat

SFOP

typedef ScoreFunctionOP SFOP

Vec

typedef numeric::xyzVector<Real> Vec

Vecs

typedef utility::vector1<Vec> Vecs

Function Documentation

add_agc()

void add_agc	(	core::pose::Pose &	pose,
		core::id::AtomID	aid1,
		core::id::AtomID	aid2,
		core::id::AtomID	aid3,
		core::Real	mean,
		core::Real	sd
	)

References basic::options::OptionKeys::ddg::mean, beta_nonlocal::pose, and sd().

Referenced by add_fa_cst(), add_symm_sf4(), and align_sf4().

add_apc()

void add_apc	(	core::pose::Pose &	pose,
		core::id::AtomID	aid1,
		core::id::AtomID	aid2,
		core::Real	mean,
		core::Real	sd
	)

References basic::options::OptionKeys::ddg::mean, beta_nonlocal::pose, and sd().

Referenced by add_fa_cst(), add_symm_sf4(), and align_sf4().

add_dhc()

void add_dhc	(	core::pose::Pose &	pose,
		core::id::AtomID	aid1,
		core::id::AtomID	aid2,
		core::id::AtomID	aid3,
		core::id::AtomID	aid4,
		core::Real	mean,
		core::Real	sd
	)

References basic::options::OptionKeys::constraints::constraints, basic::options::OptionKeys::ddg::mean, beta_nonlocal::pose, and sd().

Referenced by add_fa_cst(), add_symm_sf4(), and align_sf4().

add_fa_cst()

void add_fa_cst	(	core::pose::Pose &	cc,
		CCParam &	p
	)

References add_agc(), add_apc(), add_dhc(), addcc(), create_a3b_hbs::j, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, and numeric::conversions::radians().

Referenced by main().

add_symm_sf4()

bool add_symm_sf4	(	core::pose::Pose &	cc,
		CCParam &	p,
		SFOP	sf,
		core::Real	cstthresh,
		core::Real	dissdv,
		core::Real	angsdv
	)

References add_agc(), add_apc(), add_dhc(), align_sf4(), basic::options::OptionKeys::chemical::chemical, create_a3b_hbs::i, create_a3b_hbs::ii, make_symm_data(), sign::minus, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, place_sf4(), beta_nonlocal::pose, numeric::conversions::radians(), erraser_analysis::res1, erraser_analysis::res2, basic::options::OptionKeys::in::file::residue_type_set, create_a3b_hbs::score, sd(), beta_sc_scan::seq, basic::options::OptionKeys::symmetry::symmetry, predPRE::t, and TR.

Referenced by main().

addcc()

void addcc	(	core::pose::Pose &	pose,
		core::id::AtomID	aid,
		core::id::AtomID	anchor,
		core::Real	mult = 1.0
	)

References basic::options::OptionKeys::AnchoredDesign::anchor, and beta_nonlocal::pose.

Referenced by add_fa_cst().

align_sf4()

core::Real align_sf4	(	core::pose::Pose const &	cc,
		CCParam &	p,
		core::pose::Pose &	tp,
		Size	c1,
		Size	c2,
		Size	c3,
		Size	c4,
		core::Real	dissdv,
		core::Real	angsdv
	)

References add_agc(), add_apc(), add_dhc(), basic::options::OptionKeys::chemical::chemical, test.T009_Exceptions::e, create_a3b_hbs::i, numeric::xyzVector< T >::length(), numeric::max(), max(), numeric::min(), min(), sign::minus, beta_nonlocal::mm, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, numeric::conversions::radians(), basic::options::OptionKeys::in::file::residue_type_set, basic::options::OptionKeys::out::sf, sq(), and numeric::xyzVector< T >::z().

Referenced by add_symm_sf4(), and place_sf4().

center_of_mass()

Vec center_of_mass ( core::pose::Pose const &  pose, Size  nres = 0  )

inline

References count, natoms(), create_a3b_hbs::nres, and beta_nonlocal::pose.

Referenced by DetectSymmetry::apply(), SwapElementsMover1::apply(), SwapElementsMover2::apply(), get_change_in_distance(), get_moment_of_inertia(), make_helix(), spinner_test(), and apps::pilot::SampleSecondaryStructureAlignmentMover::translate_virt_to_CoM().

design_AFILV()

void design_AFILV	(	core::pose::Pose &	cc,
		ScoreFunctionOP	sf
	)

References create_a3b_hbs::i, repack(), basic::options::OptionKeys::out::sf, and vancomycin::task.

Referenced by main().

design_AFILVEK()

void design_AFILVEK	(	core::pose::Pose &	cc,
		ScoreFunctionOP	sf
	)

References create_a3b_hbs::i, repack(), basic::options::OptionKeys::out::sf, and vancomycin::task.

Referenced by main().

design_AL()

void design_AL	(	core::pose::Pose &	cc,
		ScoreFunctionOP	sf
	)

References create_a3b_hbs::i, repack(), basic::options::OptionKeys::out::sf, and vancomycin::task.

Referenced by main().

design_all()

void design_all	(	core::pose::Pose &	cc,
		ScoreFunctionOP	sf
	)

References create_a3b_hbs::i, repack(), basic::options::OptionKeys::out::sf, and vancomycin::task.

design_FILV()

void design_FILV	(	core::pose::Pose &	cc,
		ScoreFunctionOP	sf
	)

References create_a3b_hbs::i, repack(), basic::options::OptionKeys::out::sf, and vancomycin::task.

Referenced by main().

design_FILVEK()

void design_FILVEK	(	core::pose::Pose &	cc,
		ScoreFunctionOP	sf
	)

References create_a3b_hbs::i, repack(), basic::options::OptionKeys::out::sf, and vancomycin::task.

design_target()

void design_target	(	core::pose::Pose &	cc,
		ScoreFunctionOP	sf
	)

References create_a3b_hbs::i, basic::options::option, repack(), basic::options::OptionKeys::out::sf, basic::options::OptionKeys::in::target_residues, and vancomycin::task.

do_centroid_stuff()

void do_centroid_stuff	(	core::pose::Pose &	cenpose,
		ScoreFunctionOP	sfc
	)

References make_move_map(), and basic::options::OptionKeys::in::file::movemap.

Referenced by main().

helix_axis()

Vec helix_axis

(

core::pose::Pose const &

pose

)

References create_a3b_hbs::i, numeric::xyzVector< T >::normalize(), and beta_nonlocal::pose.

Referenced by SampleTiltProtocol::apply(), and make_helix().

main()

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

References add_fa_cst(), add_symm_sf4(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::ang, argv, utility::io::ocstream::clear(), utility::io::oc::cout, design_AFILV(), design_AFILVEK(), design_AL(), design_FILV(), do_centroid_stuff(), test.T009_Exceptions::e, ObjexxFCL::format::F(), utility::io::ocstream::flush(), test.T110_numeric::I, if(), basic::init(), create_a3b_hbs::k, ObjexxFCL::format::LJ(), make_coiled_coil(), make_sf(), minimize(), natoms(), basic::options::OptionKeys::out::file::o, basic::options::option, option, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, repack(), basic::options::OptionKeys::frags::scoring::scoring, sfd, in::file::silent_energy_cut(), ObjexxFCL::string_of(), tag, vancomycin::task, TR, numeric::random::uniform(), and zcyl_score().

make_coiled_coil()

core::pose::Pose make_coiled_coil

(

CCParam &

p

)

References create_a3b_hbs::i, make_helix(), make_symm_data(), natoms(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, beta_nonlocal::pose, rot_pose(), beta_sc_scan::seq, basic::options::OptionKeys::symmetry::symmetry, trans_pose(), and predPRE::z.

Referenced by main().

make_helix()

core::pose::Pose make_helix

(

std::string

seq

)

References center_of_mass(), helix_axis(), create_a3b_hbs::i, make_symmdef_file_denovo::pos, beta_nonlocal::pose, rot, rot_pose(), numeric::rotation_matrix_radians(), beta_sc_scan::seq, trans_pose(), numeric::random::uniform(), and predPRE::z.

Referenced by main(), and make_coiled_coil().

make_move_map()

core::kinematics::MoveMapOP make_move_map

(

core::pose::Pose &

pose

)

References create_a3b_hbs::i, subloop_histogram::iterator, basic::options::OptionKeys::in::file::movemap, beta_nonlocal::pose, erraser_analysis::res1, erraser_analysis::res2, and basic::options::OptionKeys::symmetry::symmetry.

Referenced by do_centroid_stuff(), and minimize().

make_sf()

void make_sf	(	SFOP &	sfc,
		SFOP &	sfd,
		SFOP &	sf1,
		SFOP &	sf2,
		SFOP &	sf3,
		SFOP &	sf4,
		SFOP &	sf5
	)

References pyrosetta::create_score_function, basic::options::OptionKeys::frags::scoring::scoring, and sfd.

Referenced by main().

make_symm_data()

core::conformation::symmetry::SymmData make_symm_data	(	core::pose::Pose const &	pose,
		core::Real	rot,
		core::Real	trans,
		core::Size	n
	)

References basic::options::OptionKeys::AnchoredDesign::anchor, create_a3b_hbs::i, test.T008_Serialization::iss, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, beta_nonlocal::pose, rot, docking::s, ObjexxFCL::string_of(), and trans.

Referenced by add_symm_sf4(), and make_coiled_coil().

minimize()

void minimize	(	core::pose::Pose &	cc,
		ScoreFunctionOP	sf
	)

References test.T009_Exceptions::e, kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, make_move_map(), basic::options::OptionKeys::in::file::movemap, and basic::options::OptionKeys::out::sf.

Referenced by main().

natoms()

Size natoms	(	core::pose::Pose &	cc,
		Size	nres
	)

References count, and CCParam::nres.

Referenced by alignhelix(), analyze_poses_for_convergence(), MinTestMover::apply(), SuperDeviationMover::apply(), SpartaSuperDeviationMover::apply(), RDF_Mover::apply(), MyScoreMover::apply(), SetupMover::apply(), ColorByLipidType::apply(), Hit::apply(), apps::pilot::AlignChunkMover::apply_transform(), apply_transform(), atoms_have_bond_to_bonded_atoms(), atoms_have_mutual_bond_to_atom(), back_in_time_1d(), HBondReporter::bfactor(), best_beta_backbones::bump_check(), bump_check(), demo.D090_Ala_scan::calc_binding_energy(), numeric::model_quality::calc_rms(), calc_rmsf_and_avrg(), GlycanClashCheckMover::calculate_atom_clashes(), calculate_moments(), center_of_mass(), change_floating_sc_geometry(), check_filter_rmsd(), check_rmsd(), coarse_frag_test(), coarse_to_full_test(), concave_shell(), cone_FA_nc_anyatom_calculator(), copy_xyz_by_chunk(), DockFragmentsMover::cut_from_map(), cyclic_perm(), ddg(), detect_neighbors(), doit_refine(), PoseWrap::dump_pdb(), fast_clash_check(), files_for_openMM_test(), find_centerest_residue(), forward_in_time(), get_contacts(), get_distances(), get_lig_rmsd(), get_moment_of_inertia(), get_RNA_binding_residues(), apps::pilot::AlignChunkMover::get_superposition_transformation(), get_superposition_transformation(), GetRmsd(), ik_arg_asp_frnt(), ik_arg_asp_side(), ik_arg_glu_frnt(), ik_arg_glu_side(), ik_lys_ctp_asp(), ik_lys_ctp_glu(), interface_rmsd(), is_atom_clash(), GlycanClashCheckMover::is_clashing(), local_rms(), local_rms_window(), main(), make_coiled_coil(), move_it(), nosuper_CA_rmsd(), optimal_rotation(), output_local_minima(), output_minipose_coords_test(), output_single_motif(), passes_quality_check(), pep_rmsd_analysis(), pose_from_posedata(), SuperDeviationMover::print_stats(), SpartaSuperDeviationMover::print_stats(), read_input_weights(), reorient_to_base_pair_coordinate_system(), numeric::model_quality::rms_wrapper(), numeric::model_quality::rms_wrapper_slow_and_correct(), abbinding::rmsd_frmk_chothia_num_ab(), rmsd_over_base(), rna_fullatom_multiscore_test(), rot_pose(), run(), run_3bpy(), beta_sc_scan::set_up_movemap(), sicdock_thread_num(), slice_ellipsoid_envelope(), apps::pilot::HelixMover::slide_non_ideal_helix(), slow_clash(), slow_nbcount(), sphere_FA_nc_anyatom_calculator(), superimpose_pose(), PoseWrap::switch_to_cen(), switch_to_cen(), PoseWrap::switch_to_fa(), switch_to_fa(), test_actcoord(), trans_pose(), HBondedPairIterator::update_hb(), vMPI_Bcastpose(), vMPI_transmitpose(), PBPotentialMover::write_APBS_config(), xform_pose(), and xform_pose_rev().

place_sf4()

utility::vector1< utility::vector1<Size> > place_sf4	(	core::pose::Pose &	cc,
		CCParam &	p,
		core::Real	cstthresh,
		core::Real	dissdv,
		core::Real	angsdv
	)

References a, aa, align_sf4(), compute_difference::b, kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, numeric::distance_squared(), numeric::xyzVector< T >::distance_squared(), create_a3b_hbs::i, kmeans_adaptive_kernel_density_bb_dependent_rotlib::idx, create_a3b_hbs::j, create_a3b_hbs::k, extract_by_sidechain_sasa_score::l, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, and TR.

Referenced by add_symm_sf4().

repack()

void repack	(	core::pose::Pose &	cc,
		ScoreFunctionOP	sf
	)

References basic::options::OptionKeys::out::sf, and vancomycin::task.

Referenced by design_AFILV(), design_AFILVEK(), design_AL(), design_all(), design_FILV(), design_FILVEK(), design_target(), and main().

rg2d()

Real rg2d

(

core::pose::Pose &

pose

)

References count, numeric::min(), beta_nonlocal::pose, basic::options::OptionKeys::remodel::rg, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

rot_pose() [1/4]

void rot_pose ( core::pose::Pose &  pose, Mat const &  rot  )

inline

References natoms(), beta_nonlocal::pose, and rot.

Referenced by make_coiled_coil(), make_helix(), and rot_pose().

rot_pose() [2/4]

void rot_pose ( core::pose::Pose &  pose, Mat const &  rot, Vec const &  cen  )

inline

References beta_nonlocal::pose, rot, rot_pose(), and trans_pose().

rot_pose() [3/4]

void rot_pose ( core::pose::Pose &  pose, Vec const &  axis, Real const &  ang  )

inline

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::ang, beta_nonlocal::pose, rot_pose(), and numeric::rotation_matrix_degrees().

rot_pose() [4/4]

void rot_pose ( core::pose::Pose &  pose, Vec const &  axis, Real const &  ang, Vec const &  cen  )

inline

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::ang, beta_nonlocal::pose, rot_pose(), and numeric::rotation_matrix_degrees().

sq()

Real sq ( Real  x )

inline

References CCParam::x.

Referenced by align_sf4(), utility::CSI_Sequence::CSI_Sequence(), and utility::CSI::operator<<().

trans_pose()

void trans_pose ( core::pose::Pose &  pose, Vec const &  trans  )

inline

References natoms(), beta_nonlocal::pose, and trans.

Referenced by make_coiled_coil(), make_helix(), and rot_pose().

zcyl_score()

Real zcyl_score	(	core::pose::Pose &	cc,
		Size	nres,
		Real	trans
	)

References CCParam::nres, CCParam::trans, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

Referenced by main().

Variable Documentation

TR

basic::Tracer TR("coiled_coil") ( "coiled_coil"  )

static

Referenced by add_symm_sf4(), main(), place_sf4(), and CCParam::show().