kcluster.cc File Reference

#include <fstream>
#include <iostream>
#include <map>
#include <string>
#include <utility>
#include <boost/format.hpp>
#include <basic/options/option.hh>
#include <basic/options/keys/OptionKeys.hh>
#include <basic/options/keys/cmiles.OptionKeys.gen.hh>
#include <devel/init.hh>
#include <numeric/random/random.hh>
#include <utility/vector1.hh>
#include <core/types.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/import_pose/pose_stream/util.hh>
#include <core/import_pose/pose_stream/MetaPoseInputStream.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/io/silent/SilentStruct.hh>
#include <core/io/silent/SilentStructFactory.hh>
#include <core/pose/Pose.hh>
#include <core/scoring/rms_util.hh>

Classes
class	PairComparator

Functions
double	dist (const vector1< Pose > &models, int i, int j)
	@detail Computes the distance between two structures using gdtmm More...
void	choose_centroids (const int k, const vector1< Pose > &models, vector1< int > *centroids)
void	assign_models (const vector1< Pose > &models, const vector1< int > &centroids, vector1< int > *assignments)
	@detail Assign each model to the nearest cluster center More...
void	write_output_files (const vector1< Pose > &models, const vector1< int > &centroids, const vector1< int > &assignments)
	Generate per-cluster silent files. More...
void	write_distances (const vector1< Pose > &models, const vector1< int > &centroids, const vector1< int > &assignments)
	@detail Writes per-cluster distance distributions to file More...
int	main (int argc, char *argv[])

Detailed Description

Author

Christopher Miles (cmile.nosp@m.s@uw.nosp@m..edu)

Function Documentation

assign_models()

void assign_models	(	const vector1< Pose > &	models,
		const vector1< int > &	centroids,
		vector1< int > *	assignments
	)

@detail Assign each model to the nearest cluster center

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::centroids, dist(), build_jacobian::distance, create_a3b_hbs::i, create_a3b_hbs::j, max(), min_index(), and closure_error::models.

Referenced by main().

choose_centroids()

void choose_centroids	(	const int	k,
		const vector1< Pose > &	models,
		vector1< int > *	centroids
	)

@detail Selects k cluster centers using a simple rule: the next cluster center to be added is as far as possible from the centers chosen so far

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, kmeans_adaptive_kernel_density_bb_dependent_rotlib::centroids, utility::io::oc::cout, dist(), build_jacobian::distance, create_a3b_hbs::i, create_a3b_hbs::j, create_a3b_hbs::k, max(), min(), closure_error::models, and numeric::random::random_range().

Referenced by main().

dist()

double dist	(	const vector1< Pose > &	models,
		int	i,
		int	j
	)

@detail Computes the distance between two structures using gdtmm

References create_a3b_hbs::i, create_a3b_hbs::j, subloop_histogram::key, closure_error::models, and pair.

Referenced by BuriedUnsatPolarsFinder::acc_geom_check(), add_constraints(), add_shell(), pseudoTrace::add_to_C(), pseudoTrace::add_to_N(), ZincMatchFilter::apply(), InteractionDistMinimizer::apply(), xtal_water_bunsat::apply(), PairDistance::apply(), SwapElementsMover1::apply(), protocols::moves::SimpleCstMover::apply(), assign_models(), cal_distance(), cal_score(), calc_base_centroid_rmsd(), calc_dist(), ConstraintStatsMover::calc_native_stats(), ConstraintStatsMover::calc_stats(), calculate_burial(), DistanceMatrix::calculate_distances(), calculate_hASA_by_type_and_attractiveE(), check_oxygen_contact_and_output(), check_redundant(), choose_centroids(), ScoreFragmentSetMover::closability_score(), numeric::AverageLinkClusterer::comparator(), compute_intrinsic_deviation(), compute_motif_score(), concave_hull(), create_starting_template(), createMinimizationConstraint(), decompose(), derive(), detect_neighbors(), distance(), numeric::kdtree::KDPoint::distance(), BuriedUnsatPolarsFinder::don_geom_check(), env_sugar_test(), find_nearest_res(), find_neighbors_directional(), get_csts_from_pose(), get_disulfides_from_aln(), get_gaussian_chain_func(), get_interface_residues(), CrystDesign::get_interface_residues(), CrystFFTDock::get_interfaces_allatom(), get_jump_distance(), get_neighbor_residues(), CrystDesign::get_neighbor_residues(), CrystFFTDock::get_transform_distance(), good_geometry(), numeric::geometry::hashing::SixDCoordinateBinner::halfbin6(), HbondZinc::hbond_constraint(), local_rms(), main(), mathntensor_from_dist(), membrane_center_protein_core(), my_main(), neighborWeight(), ScoreFragmentSetMover::overlap_score(), overlap_score(), pct_features_in_common(), populate_database_with_dummy_data(), read_distances(), DisulfideBondEnergy::rebuildAndDetectDisulfideBond(), residues_too_distant(), setup_rna_base_pair_constraints(), sigmoid(), EnvToolMover::sigmoidish_neighbor(), sigmoidish_neighbor(), MatchSet::sigmoidish_neighbor(), soft_overlap_score(), soften_clash_check(), numeric::kdtree::sq_vec_distance(), std_clash_check(), DisulfideBondEnergy::tabulate(), test(), numeric::kinematic_closure::test_eucDistance(), detail::dragonbox::to_decimal(), vdw_stats(), viewer_main(), protocols::moves::SimpleCstMover::write(), write_ahdist_to_db(), and write_distances().

main()

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

References argv, assign_models(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::centroids, choose_centroids(), test.T009_Exceptions::e, basic::init(), gaussian-sampling::input, closure_error::models, basic::options::OptionKeys::cmiles::kcluster::num_clusters, basic::options::option, beta_nonlocal::pose, write_distances(), and write_output_files().

write_distances()

void write_distances	(	const vector1< Pose > &	models,
		const vector1< int > &	centroids,
		const vector1< int > &	assignments
	)

@detail Writes per-cluster distance distributions to file

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::centroids, dist(), pyrosetta.tests.distributed.test_dask::format, create_a3b_hbs::i, create_a3b_hbs::j, closure_error::models, erraser_single_res_analysis::out, and str().

Referenced by main().

write_output_files()

void write_output_files	(	const vector1< Pose > &	models,
		const vector1< int > &	centroids,
		const vector1< int > &	assignments
	)

Generate per-cluster silent files.

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::centroids, pyrosetta.tests.distributed.test_dask::format, create_a3b_hbs::i, closure_error::models, sfd, basic::options::OptionKeys::in::file::silent, and str().

Referenced by main().