myspace Namespace Reference

Classes
struct	DataStruct
class	Evaluator
class	Scheduler
struct	DatumStruct
class	DataClass
struct	InputData
class	GraftTester

Typedefs
typedef std::map< std::string, utility::vector1< DatumStruct > >	DatastoreType

Functions
Real	periodic (Real ang)
Real	nonperiodic (Real ang)
bool	is_contacting (conformation::Residue const &rsd1, conformation::Residue const &rsd2)
Size	find_nearest_rot (utility::vector1< Real > chi, utility::vector1< pack::dunbrack::Real4 > rotchis)
Size	aa_to_id (std::string const &aa)
std::string	id_to_aa (Size const &id)
void	get_data_index (pose::Pose const &pose, Size const ires, utility::vector1< DataStruct > const &data, Size &data_index, Size &rot_index)
void	scan_contact (pose::Pose const &pose, Size const &winsize, utility::vector1< DataStruct > &data)
void	collect_silent (pose::Pose &pose, Size const &winsize, utility::vector1< DataStruct > &data)
utility::vector1< DataStruct >	initialize_data ()
void	write_silent (utility::vector1< DataStruct > &data, std::string const prefix)
void	read_contact (std::string const infile, utility::vector1< DataStruct > &data)
void	CArmsd_and_superimpose_pose (pose::Pose &pose, pose::Pose &ref_pose, std::map< Size, Size > const resmap, Real &gdtmm, Real &rmsd)
void	get_resmap (pose::Pose const &pose, pose::Pose const &ref_pose, std::map< Size, Size > &resmap, std::map< Size, Size > &pose_resmap)
void	find_best_projection (pose::Pose const &pose, pose::Pose const &pose_ref, std::map< Size, Size > const resmap, std::map< Size, Size > const pose_resmap, utility::vector1< utility::vector1< Vector > > const vecs, utility::vector1< Real > const importance, utility::vector1< Real > &proj_scale, utility::vector1< Vector > &proj_vec)
utility::vector1< Vector >	project (Real const scale, utility::vector1< Real > const proj_scale, utility::vector1< utility::vector1< Vector > > const vecs)
pose::Pose	generate_proj_pose (pose::Pose const &pose_init, utility::vector1< Vector > proj_vec)
Real	stdev (utility::vector1< Real > const &vals, Real const &mean)
void	report_data (utility::vector1< DataStruct > const &data, bool report_verb)
void	scan_Evalue (pose::Pose &pose, scoring::ScoreFunctionOP sfxn, utility::vector1< DataStruct > &data, bool const rotscan)
utility::vector1< InputData >	read_input (std::string const filename)
pose::Pose	pose_from_scratch (InputData input)
Size	get_clash_type (pose::Pose const &pose,)
void	check_clash (pose::Pose &pose, chemical::ResidueTypeSetCAP rsd_set, pack::dunbrack::RotamerLibrary const &rotlib, InputData input)
void	scan_Evalue (pose::Pose &pose, scoring::ScoreFunctionOP sfxn, chemical::ResidueTypeSetCAP rsd_set, pack::dunbrack::RotamerLibrary const &rotlib, InputData input)
utility::vector1< pose::Pose >	test_NMrelaxer (pose::Pose const pose, scoring::ScoreFunctionCOP sfxn, optimization::MinimizerOptionsCOP minoptions, Size const nstruct, bool const cartesian, bool const repack)
utility::vector1< pose::Pose >	test_MD (pose::Pose const pose, scoring::ScoreFunctionCOP sfxn, scoring::ScoreFunctionCOP sfxn_obj, optimization::MinimizerOptionsCOP minoptions, Size const nstruct, Size const nper_trj)
utility::vector1< pose::Pose >	test_relax (pose::Pose const pose, scoring::ScoreFunctionCOP sfxn, Size const nstruct)
utility::vector1< pose::Pose >	test_recombine (pose::Pose const pose, pose::Pose const pose2, scoring::ScoreFunctionCOP sfxn, optimization::MinimizerOptionsCOP minoptions, Size const nstruct, bool const repack)
utility::vector1< pose::Pose >	test_bbgauss (pose::Pose const pose, scoring::ScoreFunctionCOP sfxn, optimization::MinimizerOptionsCOP minoptions, Size const nstruct)
utility::vector1< pose::Pose >	test_loophash (pose::Pose const pose, scoring::ScoreFunctionCOP sfxn, optimization::MinimizerOptionsCOP minoptions, Size const nstruct, bool const local)
utility::vector1< pose::Pose >	test_relax (pose::Pose const pose, scoring::ScoreFunctionCOP sfxn, Size const nstruct, bool const cartesian)
utility::vector1< Size >	get_touched_res (pose::Pose const pose, utility::vector1< Size > const loopres)
kinematics::MoveMapOP	get_movemap (pose::Pose const pose, utility::vector1< Size > loopres, bool const nonideal)
kinematics::MoveMapOP	get_movemap (bool const nonideal)
protocols::minimization_packing::PackRotamersMoverOP	setup_packer (pose::Pose const &pose, kinematics::MoveMap const mm, scoring::ScoreFunctionCOP sfxn)
void	ramp_repack_min (pose::Pose &pose, kinematics::MoveMap const mm, scoring::ScoreFunctionCOP sfxn, optimization::MinimizerOptionsCOP minoptions, bool const cartesian)
std::map< Size, Size >	get_resmap (pose::Pose const &pose, pose::Pose const &ref_pose)
void	evaluate_and_write (scoring::ScoreFunctionCOP sfxn, pose::Pose const &native_pose, pose::Pose const &pose0, utility::vector1< pose::Pose > const &poses)
utility::vector1< pose::Pose >	test_bbgauss (pose::Pose const pose, scoring::ScoreFunctionCOP sfxn, optimization::MinimizerOptionsCOP minoptions, Size const nstruct, Size const report_step)

Typedef Documentation

DatastoreType

typedef std::map< std::string, utility::vector1< DatumStruct > > myspace::DatastoreType

Function Documentation

aa_to_id()

Size myspace::aa_to_id

(

std::string const &

aa

)

References aa.

Referenced by get_data_index(), read_contact(), and scan_Evalue().

CArmsd_and_superimpose_pose()

void myspace::CArmsd_and_superimpose_pose	(	pose::Pose &	pose,
		pose::Pose &	ref_pose,
		std::map< Size, Size > const	resmap,
		Real &	gdtmm,
		Real &	rmsd
	)

References basic::options::OptionKeys::cluster::gdtmm, beta_nonlocal::pose, and average_rmsds::rmsd.

Referenced by main().

check_clash()

void myspace::check_clash	(	pose::Pose &	pose,
		chemical::ResidueTypeSetCAP	rsd_set,
		pack::dunbrack::RotamerLibrary const &	rotlib,
		InputData	input
	)

References utility::io::oc::cout, create_a3b_hbs::i, gaussian-sampling::input, create_a3b_hbs::j, create_a3b_hbs::k, predPRE::pdbname, beta_nonlocal::pose, printf(), legacy_score_vs_rmsd::scores, test.T120_core::sfxn, and subloop_histogram::size.

Referenced by main().

collect_silent()

void myspace::collect_silent	(	pose::Pose &	pose,
		Size const &	winsize,
		utility::vector1< DataStruct > &	data
	)

References utility::io::oc::cerr, myspace::DataStruct::contact_exist, data, get_data_index(), make_symmdef_file_denovo::pos, beta_nonlocal::pose, basic::options::OptionKeys::in::file::residue_type_set, basic::options::OptionKeys::relax::sequence, myspace::DataStruct::silents, challenge::ss, and tag.

Referenced by main().

evaluate_and_write()

void myspace::evaluate_and_write	(	scoring::ScoreFunctionCOP	sfxn,
		pose::Pose const &	native_pose,
		pose::Pose const &	pose0,
		utility::vector1< pose::Pose > const &	poses
	)

References utility::io::oc::cout, basic::options::OptionKeys::cluster::gdtmm, get_resmap(), create_a3b_hbs::i, docking::native_pose, option, predPRE::pdbname, beta_nonlocal::pose, basic::options::OptionKeys::mp::assembly::poses, out::prefix(), printf(), and average_rmsds::rmsd.

Referenced by main().

find_best_projection()

void myspace::find_best_projection	(	pose::Pose const &	pose,
		pose::Pose const &	pose_ref,
		std::map< Size, Size > const	resmap,
		std::map< Size, Size > const	pose_resmap,
		utility::vector1< utility::vector1< Vector > > const	vecs,
		utility::vector1< Real > const	importance,
		utility::vector1< Real > &	proj_scale,
		utility::vector1< Vector > &	proj_vec
	)

References basic::options::OptionKeys::msd::corr, utility::io::oc::cout, numeric::xyzVector< T >::dot_product(), subloop_histogram::iterator, beta_nonlocal::pose, and vec().

Referenced by main().

find_nearest_rot()

Size myspace::find_nearest_rot	(	utility::vector1< Real >	chi,
		utility::vector1< pack::dunbrack::Real4 >	rotchis
	)

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

Referenced by get_data_index(), and scan_Evalue().

generate_proj_pose()

pose::Pose myspace::generate_proj_pose	(	pose::Pose const &	pose_init,
		utility::vector1< Vector >	proj_vec
	)

get_clash_type()

Size myspace::get_clash_type

(

pose::Pose const &

pose

)

get_data_index()

void myspace::get_data_index	(	pose::Pose const &	pose,
		Size const	ires,
		utility::vector1< DataStruct > const &	data,
		Size &	data_index,
		Size &	rot_index
	)

References aa_to_id(), utility::io::oc::cerr, data, find_nearest_rot(), nonperiodic(), and beta_nonlocal::pose.

Referenced by collect_silent(), and scan_contact().

get_movemap() [1/2]

kinematics::MoveMapOP myspace::get_movemap ( bool const  nonideal )

inline

References spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::D, beta_nonlocal::mm, basic::options::OptionKeys::optimization::nonideal, and THETA.

get_movemap() [2/2]

kinematics::MoveMapOP myspace::get_movemap	(	pose::Pose const	pose,
		utility::vector1< Size >	loopres,
		bool const	nonideal
	)

References spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::D, get_touched_res(), beta_nonlocal::mm, basic::options::OptionKeys::optimization::nonideal, beta_nonlocal::pose, and THETA.

Referenced by UniformPerturber::perturb_chain(), test_bbgauss(), test_loophash(), test_MD(), test_NMrelaxer(), and test_recombine().

get_resmap() [1/2]

std::map< Size, Size> myspace::get_resmap	(	pose::Pose const &	pose,
		pose::Pose const &	ref_pose
	)

References create_a3b_hbs::ii, beta_nonlocal::jj, and beta_nonlocal::pose.

get_resmap() [2/2]

void myspace::get_resmap	(	pose::Pose const &	pose,
		pose::Pose const &	ref_pose,
		std::map< Size, Size > &	resmap,
		std::map< Size, Size > &	pose_resmap
	)

References utility::io::oc::cout, create_a3b_hbs::ii, beta_nonlocal::jj, and beta_nonlocal::pose.

Referenced by evaluate_and_write(), and main().

get_touched_res()

utility::vector1< Size > myspace::get_touched_res	(	pose::Pose const	pose,
		utility::vector1< Size > const	loopres
	)

References utility::vectorL< L, T, A >::contains(), numeric::xyzVector< T >::distance(), create_a3b_hbs::i, and beta_nonlocal::pose.

Referenced by get_movemap().

id_to_aa()

std::string myspace::id_to_aa

(

Size const &

id

)

Referenced by initialize_data().

initialize_data()

utility::vector1< DataStruct > myspace::initialize_data

(

)

References myspace::DataStruct::aa, myspace::DataStruct::chis, myspace::DataStruct::contact_exist, data, id_to_aa(), create_a3b_hbs::j, create_a3b_hbs::k, periodic(), oop_conformations::phi, myspace::DataStruct::phi, myspace::DataStruct::prob, oop_conformations::psi, myspace::DataStruct::psi, and myspace::DataStruct::silents.

Referenced by main().

is_contacting()

bool myspace::is_contacting	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2
	)

References numeric::xyzVector< T >::dot_product(), test.T200_Scoring::rsd1, and test.T200_Scoring::rsd2.

Referenced by scan_contact().

nonperiodic()

Real myspace::nonperiodic

(

Real

ang

)

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::ang.

Referenced by get_data_index(), scan_Evalue(), and write_silent().

periodic()

Real myspace::periodic

(

Real

ang

)

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::ang.

Referenced by initialize_data(), and numeric::interpolation::InterpolatedPotential< N >::set_periodic().

pose_from_scratch()

pose::Pose myspace::pose_from_scratch

(

InputData

input

)

References create_a3b_hbs::i, gaussian-sampling::input, make_symmdef_file_denovo::pos, beta_nonlocal::pose, basic::options::OptionKeys::in::file::residue_type_set, and basic::options::OptionKeys::relax::sequence.

Referenced by main().

project()

utility::vector1< Vector > myspace::project	(	Real const	scale,
		utility::vector1< Real > const	proj_scale,
		utility::vector1< utility::vector1< Vector > > const	vecs
	)

References spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::scale, subloop_histogram::size, and vec().

ramp_repack_min()

void myspace::ramp_repack_min	(	pose::Pose &	pose,
		kinematics::MoveMap const	mm,
		scoring::ScoreFunctionCOP	sfxn,
		optimization::MinimizerOptionsCOP	minoptions,
		bool const	cartesian
	)

References basic::options::OptionKeys::ddg::cartesian, create_a3b_hbs::i, beta_nonlocal::mm, beta_nonlocal::pose, setup_packer(), and test.T120_core::sfxn.

Referenced by test_recombine().

read_contact()

void myspace::read_contact	(	std::string const	infile,
		utility::vector1< DataStruct > &	data
	)

References aa_to_id(), utility::io::oc::cerr, and data.

Referenced by main().

read_input()

utility::vector1< InputData > myspace::read_input

(

std::string const

filename

)

References lactamize::filename, getline(), gaussian-sampling::input, line, and utility::io::izstream::open().

Referenced by main().

report_data()

void myspace::report_data	(	utility::vector1< DataStruct > const &	data,
		bool	report_verb
	)

References utility::io::oc::cout, data, create_a3b_hbs::i, create_a3b_hbs::j, create_a3b_hbs::k, min(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::ndata, kmeans_bb_dependent_rotlib::nrot, and stdev().

Referenced by GlycanClashCheckMover::apply(), and main().

scan_contact()

void myspace::scan_contact	(	pose::Pose const &	pose,
		Size const &	winsize,
		utility::vector1< DataStruct > &	data
	)

References myspace::DataStruct::contact_exist, utility::io::oc::cout, data, get_data_index(), is_contacting(), create_a3b_hbs::k, myspace::DataStruct::phi, beta_nonlocal::pose, and myspace::DataStruct::psi.

Referenced by main().

scan_Evalue() [1/2]

void myspace::scan_Evalue	(	pose::Pose &	pose,
		scoring::ScoreFunctionOP	sfxn,
		chemical::ResidueTypeSetCAP	rsd_set,
		pack::dunbrack::RotamerLibrary const &	rotlib,
		InputData	input
	)

References utility::io::oc::cout, test.T200_Scoring::emap, create_a3b_hbs::i, gaussian-sampling::input, create_a3b_hbs::j, create_a3b_hbs::k, predPRE::pdbname, beta_nonlocal::pose, printf(), legacy_score_vs_rmsd::scores, test.T120_core::sfxn, and subloop_histogram::size.

scan_Evalue() [2/2]

void myspace::scan_Evalue	(	pose::Pose &	pose,
		scoring::ScoreFunctionOP	sfxn,
		utility::vector1< DataStruct > &	data,
		bool const	rotscan
	)

References aa_to_id(), data, find_nearest_rot(), create_a3b_hbs::j, create_a3b_hbs::k, nonperiodic(), beta_nonlocal::pose, and test.T120_core::sfxn.

Referenced by main().

setup_packer()

protocols::minimization_packing::PackRotamersMoverOP myspace::setup_packer	(	pose::Pose const &	pose,
		kinematics::MoveMap const	mm,
		scoring::ScoreFunctionCOP	sfxn
	)

References beta_nonlocal::mm, vancomycin::pack, beta_nonlocal::pose, test.T120_core::sfxn, and vancomycin::task.

Referenced by ramp_repack_min(), and test_loophash().

stdev()

Real myspace::stdev	(	utility::vector1< Real > const &	vals,
		Real const &	mean
	)

References create_a3b_hbs::i, and basic::options::OptionKeys::ddg::mean.

Referenced by apps::pilot::SampleSecondaryStructureAlignmentMover::add_gap_constraints_to_pose(), HotspotPlacementMover::apply(), numeric::calc_zscore(), ClosabilityScore::gap_bound_cst_score(), gaussian_angle_move(), lariat_modeling(), main(), report_data(), and update_torsion_set().

test_bbgauss() [1/2]

utility::vector1< pose::Pose > myspace::test_bbgauss	(	pose::Pose const	pose,
		scoring::ScoreFunctionCOP	sfxn,
		optimization::MinimizerOptionsCOP	minoptions,
		Size const	nstruct
	)

References local::nstruct, and basic::options::OptionKeys::mp::assembly::poses.

Referenced by main().

test_bbgauss() [2/2]

utility::vector1< pose::Pose > myspace::test_bbgauss	(	pose::Pose const	pose,
		scoring::ScoreFunctionCOP	sfxn,
		optimization::MinimizerOptionsCOP	minoptions,
		Size const	nstruct,
		Size const	report_step
	)

References utility::io::oc::cout, get_movemap(), basic::options::OptionKeys::relax::range::kT, beta_nonlocal::mm, basic::options::OptionKeys::MonteCarlo::MonteCarlo, local::nstruct, beta_nonlocal::pose, basic::options::OptionKeys::mp::assembly::poses, spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::prob, numeric::random::rg(), test.T120_core::sfxn, and numeric::random::RandomGenerator::uniform().

test_loophash()

utility::vector1< pose::Pose > myspace::test_loophash	(	pose::Pose const	pose,
		scoring::ScoreFunctionCOP	sfxn,
		optimization::MinimizerOptionsCOP	minoptions,
		Size const	nstruct,
		bool const	local
	)

References get_movemap(), create_a3b_hbs::i, loop_hash_library, beta_nonlocal::mm, create_a3b_hbs::nres, local::nstruct, beta_nonlocal::pose, basic::options::OptionKeys::mp::assembly::poses, RG, setup_packer(), test.T120_core::sfxn, and numeric::random::RandomGenerator::uniform().

Referenced by main().

test_MD()

utility::vector1< pose::Pose > myspace::test_MD	(	pose::Pose const	pose,
		scoring::ScoreFunctionCOP	sfxn,
		scoring::ScoreFunctionCOP	sfxn_obj,
		optimization::MinimizerOptionsCOP	minoptions,
		Size const	nstruct,
		Size const	nper_trj
	)

References get_movemap(), create_a3b_hbs::i, beta_nonlocal::mm, local::nstruct, beta_nonlocal::pose, basic::options::OptionKeys::mp::assembly::poses, and test.T120_core::sfxn.

Referenced by main().

test_NMrelaxer()

utility::vector1< pose::Pose > myspace::test_NMrelaxer	(	pose::Pose const	pose,
		scoring::ScoreFunctionCOP	sfxn,
		optimization::MinimizerOptionsCOP	minoptions,
		Size const	nstruct,
		bool const	cartesian,
		bool const	repack
	)

References basic::options::OptionKeys::ddg::cartesian, get_movemap(), create_a3b_hbs::i, beta_nonlocal::mm, beta_nonlocal::pose, basic::options::OptionKeys::mp::assembly::poses, spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::scale, and test.T120_core::sfxn.

Referenced by main().

test_recombine()

utility::vector1< pose::Pose > myspace::test_recombine	(	pose::Pose const	pose,
		pose::Pose const	pose2,
		scoring::ScoreFunctionCOP	sfxn,
		optimization::MinimizerOptionsCOP	minoptions,
		Size const	nstruct,
		bool const	repack
	)

References get_movemap(), beta_nonlocal::mm, local::nstruct, beta_nonlocal::pose, test.T008_Serialization::pose2, basic::options::OptionKeys::mp::assembly::poses, ramp_repack_min(), and test.T120_core::sfxn.

Referenced by main().

test_relax() [1/2]

utility::vector1< pose::Pose > myspace::test_relax	(	pose::Pose const	pose,
		scoring::ScoreFunctionCOP	sfxn,
		Size const	nstruct
	)

References local::nstruct, basic::options::option, beta_nonlocal::pose, basic::options::OptionKeys::mp::assembly::poses, basic::options::OptionKeys::abinitio::relax, basic::options::OptionKeys::relax::script, and test.T120_core::sfxn.

Referenced by main().

test_relax() [2/2]

utility::vector1< pose::Pose > myspace::test_relax	(	pose::Pose const	pose,
		scoring::ScoreFunctionCOP	sfxn,
		Size const	nstruct,
		bool const	cartesian
	)

write_silent()

void myspace::write_silent	(	utility::vector1< DataStruct > &	data,
		std::string const	prefix
	)

References myspace::DataStruct::aa, myspace::DataStruct::contact_exist, data, nonperiodic(), myspace::DataStruct::phi, create_a3b_hbs::prefix, myspace::DataStruct::psi, sfd, myspace::DataStruct::silents, and challenge::ss.

Referenced by main().