design_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/protein_interface_design/design_utils.hh>
#include <utility/vector1.hh>
#include <utility/io/ozstream.hh>
#include <utility/excn/Exceptions.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, design_tight_clusters, generate_output_structures) OPT_1GRP_KEY(Boolean
require_renumbered_structures	OPT_1GRP_KEY (Real, design_tight_clusters, repack_radius) OPT_1GRP_KEY(Integer
require_renumbered_structures num_cycles	OPT_1GRP_KEY (Real, design_tight_clusters, favor_native) OPT_1GRP_KEY(IntegerVector
require_renumbered_structures num_cycles chi_deviation_thresholds	OPT_1GRP_KEY (Real, design_tight_clusters, backrub_sc_prob) OPT_1GRP_KEY(StringVector
require_renumbered_structures num_cycles chi_deviation_thresholds 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_residues_and_chi1_2_angles (const core::pose::Pose &native_p, const core::pose::Pose &repacked_p, const std::set< core::Size > &cluster, utility::vector1< std::string > &mutations, 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)
	use fastrelax to optimize packing More...
void	repack_step (core::pose::Pose &repacked, const core::pack::task::PackerTaskOP repack_packer_task, const core::scoring::ScoreFunctionOP score_fxn, utility::vector1< bool > allow_repacked)
	as some of our packing functions cannot do design (fastrelax, backrub with restrictions) we need to have the option to do packing independent of / interleaved with design More...
void	design_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)
int	main (int argc, char *argv[])

Variables
const core::Size	rot_trials_iterations = 10
static basic::Tracer	TR ("apps.pilot.amelie.design_tight_clusters")
	design_tight_clusters

Function Documentation

compare_residues_and_chi1_2_angles()

void compare_residues_and_chi1_2_angles	(	const core::pose::Pose &	native_p,
		const core::pose::Pose &	repacked_p,
		const std::set< core::Size > &	cluster,
		utility::vector1< std::string > &	mutations,
		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 design_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_step(), and sidechain_fastrelax().

design_cluster()

void design_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(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, basic::options::OptionKeys::carbohydrates::glycan_sampler::cartmin, compare_residues_and_chi1_2_angles(), basic::options::OptionKeys::msd::debug, detect_neighbors(), test.T009_Exceptions::e, basic::options::OptionKeys::msd::favor_native, create_a3b_hbs::i, create_a3b_hbs::j, basic::options::option, option, lactamize::outfile, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, make_symmdef_file_denovo::pos, chrisk::repack_radius, repack_sphere_radius, repack_step(), runtime_assert, beta_nonlocal::score_fxn, utility::to_string(), TR, and basic::options::OptionKeys::inout::dbms::user.

Referenced by main().

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 design_cluster().

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, design_cluster(), test.T009_Exceptions::e, basic::options::OptionKeys::msd::favor_native, 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, chrisk::repack_radius, 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() [1/4]

OPT_1GRP_KEY	(	Boolean	,
		design_tight_clusters	,
		generate_output_structures
	)

OPT_1GRP_KEY() [2/4]

require_renumbered_structures num_cycles chi_deviation_thresholds OPT_1GRP_KEY	(	Real	,
		design_tight_clusters	,
		backrub_sc_prob
	)

OPT_1GRP_KEY() [3/4]

require_renumbered_structures num_cycles OPT_1GRP_KEY	(	Real	,
		design_tight_clusters	,
		favor_native
	)

OPT_1GRP_KEY() [4/4]

require_renumbered_structures OPT_1GRP_KEY	(	Real	,
		design_tight_clusters	,
		repack_radius
	)

repack_step()

void repack_step	(	core::pose::Pose &	repacked,
		const core::pack::task::PackerTaskOP	repack_packer_task,
		const core::scoring::ScoreFunctionOP	score_fxn,
		utility::vector1< bool >	allow_repacked
	)

as some of our packing functions cannot do design (fastrelax, backrub with restrictions) we need to have the option to do packing independent of / interleaved with design

assumption: the packer_task has already been set up correctly and knows which residues may be designed and which should only be packed

References basic::options::OptionKeys::backrub::backrub, basic::options::OptionKeys::carbohydrates::glycan_sampler::cartmin, pyrosetta::create_score_function, derive_MoveMap_from_cluster_lst(), vancomycin::min_mover, basic::options::OptionKeys::min_pack, beta_nonlocal::mm, option, rot_trials_iterations, test.T500_Packing::rotamer_trials, basic::options::OptionKeys::rot_anl::rtmin, beta_nonlocal::score_fxn, sidechain_fastrelax(), score::soft_wts(), and basic::options::OptionKeys::inout::dbms::user.

Referenced by design_cluster(), and main().

sidechain_fastrelax()

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

use fastrelax to optimize packing

note that fastrelax doesn't seem to allow design, so we'll need separate design and packing steps for this

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_step().

sort_min()

require_renumbered_structures num_cycles chi_deviation_thresholds 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

design_tight_clusters

require_renumbered_structures num_cycles chi_deviation_thresholds design_tight_clusters

rot_trials_iterations

const core::Size rot_trials_iterations = 10

Referenced by repack_step().

TR

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

static

Referenced by compare_residues_and_chi1_2_angles(), design_cluster(), and main().