detect_tight_clusters.cc File Reference

#include <devel/init.hh>
#include <core/import_pose/import_pose.hh>
#include <basic/options/option.hh>
#include <basic/Tracer.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/rms_util.tmpl.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/Energies.hh>
#include <protocols/minimization_packing/MinMover.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/conformation/Residue.hh>
#include <core/types.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/pack_rotamers.hh>
#include <protocols/relax/FastRelax.hh>
#include <core/pack/min_pack.hh>
#include <core/pack/rotamer_trials.hh>
#include <core/pack/rtmin.hh>
#include <protocols/rotamer_recovery/RRComparer.hh>
#include <protocols/backrub/BackrubMover.hh>
#include <protocols/simple_moves/sidechain_moves/SidechainMover.hh>
#include <protocols/moves/MonteCarlo.hh>
#include <utility/vector1.hh>
#include <utility/io/ozstream.hh>
#include <utility/excn/Exceptions.hh>
#include <numeric/xyzVector.hh>
#include <numeric/random/random.hh>
#include <core/pack/task/ResidueLevelTask.hh>
#include <basic/options/option_macros.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/packing.OptionKeys.gen.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <map>

Functions
	OPT_1GRP_KEY (Boolean, detect_tight_clusters, generate_output_structures) OPT_1GRP_KEY(Boolean
require_renumbered_structures	OPT_1GRP_KEY (Boolean, detect_tight_clusters, repack_8A_sphere) OPT_1GRP_KEY(IntegerVector
require_renumbered_structures chi_deviation_thresholds	OPT_1GRP_KEY (Real, detect_tight_clusters, backrub_sc_prob) OPT_1GRP_KEY(Boolean
require_renumbered_structures chi_deviation_thresholds detect_interchain_clusters	OPT_1GRP_KEY (Real, detect_tight_clusters, min_num_neighbors) OPT_1GRP_KEY(Real
require_renumbered_structures chi_deviation_thresholds detect_interchain_clusters heavy_atom_dist	OPT_1GRP_KEY (Real, detect_tight_clusters, b_factor_threshold) OPT_1GRP_KEY(StringVector
require_renumbered_structures chi_deviation_thresholds detect_interchain_clusters heavy_atom_dist external_cluster bool	sort_min (const std::pair< core::Size, core::Real > &left, const std::pair< core::Size, core::Real > &right)
void	detect_neighbors (const core::pose::Pose &p, const core::Size pos, const core::Real radius, std::map< core::Size, bool > &neighbor_map)
void	compare_chi1_2_angles (const core::pose::Pose &native_p, const core::pose::Pose &repacked_p, const std::set< core::Size > &cluster, utility::vector1< int > &chi_dev_lst, utility::vector1< std::string > &chi_dev_details)
core::kinematics::MoveMapOP	derive_MoveMap_from_cluster_lst (core::pose::Pose const &pose, utility::vector1< bool > const &is_flexible, bool allow_bb_move=false)
void	sidechain_fastrelax (core::scoring::ScoreFunctionOP scorefxn, utility::vector1< bool > const &is_flexible, bool const cartesian_min, core::pose::Pose &pose)
void	repack_cluster (const core::pose::Pose &p, core::pose::Pose repacked, core::scoring::ScoreFunctionOP score_fxn, std::set< core::Size > cluster, const std::string cluster_acc, std::string p_name, utility::io::ozstream &outfile)
bool	passes_quality_check (const core::pose::Pose &p, core::Size i, core::Size &num_neighbors)
void	find_clusters (core::pose::Pose &p, core::pack::task::PackerTask &input_packer_task, std::map< std::set< core::Size >, std::string > &filtered_clusters)
int	main (int argc, char *argv[])

Variables
const core::Size	buried_threshold = 14
const core::Size	neighbor_dist = 8
const core::Real	repack_sphere_radius = 8
const core::Size	rot_trials_iterations = 10
const core::Size	env_quality_check_dist = 6
const core::Size	backrub_iterations = 10
static basic::Tracer	TR ("apps.pilot.amelie.detect_tight_clusters")
	detect_tight_clusters

Function Documentation

compare_chi1_2_angles()

void compare_chi1_2_angles	(	const core::pose::Pose &	native_p,
		const core::pose::Pose &	repacked_p,
		const std::set< core::Size > &	cluster,
		utility::vector1< int > &	chi_dev_lst,
		utility::vector1< std::string > &	chi_dev_details
	)

References begin, basic::options::OptionKeys::msd::debug, end, create_a3b_hbs::i, make_comparison::measured, option, runtime_assert, utility::to_string(), and TR.

Referenced by repack_cluster().

derive_MoveMap_from_cluster_lst()

core::kinematics::MoveMapOP derive_MoveMap_from_cluster_lst	(	core::pose::Pose const &	pose,
		utility::vector1< bool > const &	is_flexible,
		bool	allow_bb_move = false
	)

References create_a3b_hbs::i, basic::options::OptionKeys::in::file::movemap, and beta_nonlocal::pose.

Referenced by repack_cluster(), and sidechain_fastrelax().

detect_neighbors()

void detect_neighbors	(	const core::pose::Pose &	p,
		const core::Size	pos,
		const core::Real	radius,
		std::map< core::Size, bool > &	neighbor_map
	)

References a, compute_difference::b, dist(), create_a3b_hbs::i, natoms(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, make_symmdef_file_denovo::pos, and basic::options::OptionKeys::cluster::radius.

Referenced by repack_cluster().

find_clusters()

void find_clusters	(	core::pose::Pose &	p,
		core::pack::task::PackerTask &	input_packer_task,
		std::map< std::set< core::Size >, std::string > &	filtered_clusters
	)

References begin, buried_threshold, basic::options::OptionKeys::msd::debug, build_jacobian::distance, end, detail::find(), create_a3b_hbs::i, create_a3b_hbs::ii, create_a3b_hbs::j, beta_nonlocal::jj, create_a3b_hbs::k, kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, basic::options::OptionKeys::frags::contacts::neighbors, basic::options::option, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, passes_quality_check(), utility::to_string(), and TR.

Referenced by main().

main()

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

References out::path::all(), argv, basic::options::OptionKeys::backrub::backrub, basic::options::OptionKeys::carbohydrates::glycan_sampler::cartmin, basic::options::OptionKeys::msd::debug, test.T009_Exceptions::e, find_clusters(), basic::init(), basic::options::OptionKeys::min_pack, in::file::native(), NEW_OPT, OPT, basic::options::option, option, lactamize::outfile, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, closure_error::path, out::path::pdb(), pdbs, pyrosetta.distributed.io::pose_from_file, repack_cluster(), packing::resfile(), in::file::s(), beta_nonlocal::score_fxn, sidechain_fastrelax(), subloop_histogram::size, utility::to_string(), TR, and basic::options::OptionKeys::inout::dbms::user.

OPT_1GRP_KEY() [1/5]

OPT_1GRP_KEY	(	Boolean	,
		detect_tight_clusters	,
		generate_output_structures
	)

OPT_1GRP_KEY() [2/5]

require_renumbered_structures OPT_1GRP_KEY	(	Boolean	,
		detect_tight_clusters	,
		repack_8A_sphere
	)

OPT_1GRP_KEY() [3/5]

require_renumbered_structures chi_deviation_thresholds detect_interchain_clusters heavy_atom_dist OPT_1GRP_KEY	(	Real	,
		detect_tight_clusters	,
		b_factor_threshold
	)

OPT_1GRP_KEY() [4/5]

require_renumbered_structures chi_deviation_thresholds OPT_1GRP_KEY	(	Real	,
		detect_tight_clusters	,
		backrub_sc_prob
	)

OPT_1GRP_KEY() [5/5]

require_renumbered_structures chi_deviation_thresholds detect_interchain_clusters OPT_1GRP_KEY	(	Real	,
		detect_tight_clusters	,
		min_num_neighbors
	)

passes_quality_check()

bool passes_quality_check	(	const core::pose::Pose &	p,
		core::Size	i,
		core::Size &	num_neighbors
	)

References basic::options::OptionKeys::msd::debug, numeric::xyzVector< T >::distance(), env_quality_check_dist, create_a3b_hbs::i, create_a3b_hbs::ii, beta_nonlocal::jj, natoms(), neighbor_dist, basic::options::option, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, make_symmdef_file_denovo::pos, and TR.

Referenced by find_clusters().

repack_cluster()

void repack_cluster	(	const core::pose::Pose &	p,
		core::pose::Pose	repacked,
		core::scoring::ScoreFunctionOP	score_fxn,
		std::set< core::Size >	cluster,
		const std::string	cluster_acc,
		std::string	p_name,
		utility::io::ozstream &	outfile
	)

References utility::vectorL< L, T, A >::at(), basic::options::OptionKeys::backrub::backrub, backrub_iterations, basic::options::OptionKeys::carbohydrates::glycan_sampler::cartmin, compare_chi1_2_angles(), pyrosetta::create_score_function, basic::options::OptionKeys::msd::debug, derive_MoveMap_from_cluster_lst(), detect_neighbors(), test.T009_Exceptions::e, basic::Tracer::flush(), create_a3b_hbs::i, create_a3b_hbs::j, mc, vancomycin::min_mover, basic::options::OptionKeys::min_pack, beta_nonlocal::mm, basic::options::OptionKeys::MonteCarlo::MonteCarlo, basic::options::option, option, lactamize::outfile, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, make_symmdef_file_denovo::pos, repack_sphere_radius, numeric::random::rg(), rot_trials_iterations, test.T500_Packing::rotamer_trials, basic::options::OptionKeys::rot_anl::rtmin, runtime_assert, beta_nonlocal::score_fxn, sidechain_fastrelax(), score::soft_wts(), utility::to_string(), TR, numeric::random::RandomGenerator::uniform(), and basic::options::OptionKeys::inout::dbms::user.

Referenced by main().

sidechain_fastrelax()

void sidechain_fastrelax	(	core::scoring::ScoreFunctionOP	scorefxn,
		utility::vector1< bool > const &	is_flexible,
		bool const	cartesian_min,
		core::pose::Pose &	pose
	)

References peptidomimetic_ensembles::cartesian_min, derive_MoveMap_from_cluster_lst(), basic::options::OptionKeys::abinitio::fastrelax, basic::options::OptionKeys::in::file::movemap, beta_nonlocal::pose, and oop_conformations::scorefxn.

Referenced by main(), and repack_cluster().

sort_min()

require_renumbered_structures chi_deviation_thresholds detect_interchain_clusters heavy_atom_dist external_cluster bool sort_min	(	const std::pair< core::Size, core::Real > &	left,
		const std::pair< core::Size, core::Real > &	right
	)

References basic::options::OptionKeys::ufv::left, and basic::options::OptionKeys::ufv::right.

Variable Documentation

backrub_iterations

const core::Size backrub_iterations = 10

Referenced by HbondZinc::hbond_constraint(), and repack_cluster().

buried_threshold

const core::Size buried_threshold = 14

Referenced by find_clusters().

detect_tight_clusters

require_renumbered_structures chi_deviation_thresholds detect_interchain_clusters heavy_atom_dist detect_tight_clusters

env_quality_check_dist

const core::Size env_quality_check_dist = 6

Referenced by passes_quality_check().

neighbor_dist

const core::Size neighbor_dist = 8

Referenced by passes_quality_check().

repack_sphere_radius

const core::Real repack_sphere_radius = 8

Referenced by design_cluster(), and repack_cluster().

rot_trials_iterations

const core::Size rot_trials_iterations = 10

Referenced by repack_cluster().

TR

basic::Tracer TR("apps.pilot.amelie.detect_tight_clusters") ( "apps.pilot.amelie.detect_tight_clusters"  )

static

Referenced by compare_chi1_2_angles(), find_clusters(), main(), passes_quality_check(), and repack_cluster().