rotamer_repack.cc File Reference

#include <devel/init.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/util.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/chemical/util.hh>
#include <core/conformation/Residue.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/import_pose/import_pose.hh>
#include <core/io/silent/SilentStruct.hh>
#include <core/io/silent/ScoreFileSilentStruct.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/scoring/types.hh>
#include <core/scoring/ScoringManager.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoreType.hh>
#include <core/scoring/hbonds/HBondSet.hh>
#include <core/scoring/hbonds/hbonds.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/EnergyMap.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/scoring/etable/Etable.hh>
#include <core/scoring/etable/EtableEnergy.hh>
#include <core/scoring/etable/count_pair/CountPairAll.hh>
#include <core/scoring/etable/count_pair/CountPairFactory.hh>
#include <core/pack/dunbrack/RotamericSingleResidueDunbrackLibrary.hh>
#include <core/pack/dunbrack/RotamericSingleResidueDunbrackLibrary.tmpl.hh>
#include <core/pack/dunbrack/RotamerLibraryScratchSpace.hh>
#include <core/pack/dunbrack/RotamerLibrary.hh>
#include <core/scoring/electron_density/util.hh>
#include <utility/tools/make_vector1.hh>
#include <utility/tools/make_map.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/rtmin.hh>
#include <basic/options/option.hh>
#include <basic/options/util.hh>
#include <basic/Tracer.hh>
#include <protocols/viewer/viewers.hh>
#include <protocols/minimization_packing/PackRotamersMover.hh>
#include <protocols/minimization_packing/RotamerTrialsMover.hh>
#include <protocols/minimization_packing/RotamerTrialsMinMover.hh>
#include <protocols/minimization_packing/MinMover.hh>
#include <protocols/simple_moves/sidechain_moves/SidechainMover.hh>
#include <protocols/moves/MonteCarlo.hh>
#include <protocols/electron_density/util.hh>
#include <basic/options/keys/packing.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/rot_anl.OptionKeys.gen.hh>
#include <basic/options/keys/corrections.OptionKeys.gen.hh>
#include <basic/options/keys/edensity.OptionKeys.gen.hh>

Namespaces
	basic
	Tags used to tag messeges sent by MPI functions used to decide whether a slave is requesting a new job id or flagging as job as being a bad input.
	basic::options
	basic::options::OptionKeys

Functions
std::map< std::string, utility::vector1< std::string > >	sc_rmsd_AtomIDs (utility::tools::make_map(std::string(" DA"), utility::tools::make_vector1(std::string("N6"), std::string("C5"), std::string("N7")), std::string(" DC"), utility::tools::make_vector1(std::string("N4"), std::string("C4"), std::string("C5")), std::string(" DG"), utility::tools::make_vector1(std::string("O6"), std::string("C5"), std::string("N7")), std::string(" DT"), utility::tools::make_vector1(std::string("O4"), std::string("C5"), std::string("C7")), std::string("GLY"), utility::tools::make_vector1(std::string("N"), std::string("CA"), std::string("C")), std::string("ALA"), utility::tools::make_vector1(std::string("CB"), std::string("CA"), std::string("N")), std::string("CYS"), utility::tools::make_vector1(std::string("SG"), std::string("CB"), std::string("CA")), std::string("ASP"), utility::tools::make_vector1(std::string("OD1"), std::string("CG"), std::string("OD2")), std::string("GLU"), utility::tools::make_vector1(std::string("OE1"), std::string("CD"), std::string("OE2")), std::string("PHE"), utility::tools::make_vector1(std::string("CE1"), std::string("CZ"), std::string("CE2")), std::string("HIS"), utility::tools::make_vector1(std::string("ND1"), std::string("CE1"), std::string("NE2")), std::string("ILE"), utility::tools::make_vector1(std::string("CD1"), std::string("CG1"), std::string("CG2")), std::string("LYS"), utility::tools::make_vector1(std::string("NZ"), std::string("CE"), std::string("CD")), std::string("LEU"), utility::tools::make_vector1(std::string("CG"), std::string("CD1"), std::string("CD2")), std::string("MET"), utility::tools::make_vector1(std::string("CG"), std::string("SD"), std::string("CE")), std::string("ASN"), utility::tools::make_vector1(std::string("OD1"), std::string("CG"), std::string("ND2")), std::string("GLN"), utility::tools::make_vector1(std::string("OE1"), std::string("CD"), std::string("NE2")), std::string("PRO"), utility::tools::make_vector1(std::string("CG"), std::string("CD"), std::string("NV")), std::string("ARG"), utility::tools::make_vector1(std::string("NH1"), std::string("CZ"), std::string("NH2")), std::string("SER"), utility::tools::make_vector1(std::string("OG"), std::string("CB"), std::string("CA")), std::string("THR"), utility::tools::make_vector1(std::string("OG1"), std::string("CB"), std::string("CG2")), std::string("VAL"), utility::tools::make_vector1(std::string("CG1"), std::string("CB"), std::string("CG2")), std::string("TRP"), utility::tools::make_vector1(std::string("NE1"), std::string("CZ2"), std::string("CE3")), std::string("TYR"), utility::tools::make_vector1(std::string("OH"), std::string("CE1"), std::string("CE2"))))
void	set_pose_occ_and_bfac (Pose &pose, Pose const native_pose)
Real	get_atom_lk_energy_by_residue_no_count_pair (scoring::ScoreFunctionOP scorefxn, conformation::Residue const &rsd1, Size const atom1, conformation::Residue const &rsd2)
Real	get_atom_lk_energy (pose::Pose const pose, scoring::ScoreFunctionOP scorefxn, Size const seqpos, Size const iatom)
Real	get_atom_lk_burial (pose::Pose const pose, scoring::ScoreFunctionOP scorefxn, Size const seqpos, Size const iatom)
Real	get_res_avg_lk_burial (pose::Pose const pose, scoring::ScoreFunctionOP scorefxn, Size const seqpos, bool incl_bb, bool incl_sc)
Real	get_res_hbond_bb_score_raw (pose::Pose const pose, Size const seqpos)
Size	get_n_bb_hbonds (Pose const pose, Size const seqpos)
Size	get_n_sc_hbonds (Pose const pose, Size const seqpos)
Real	get_sc_bfactor (Pose const native_pose, Size const seqpos)
Real	get_sc_rmsd (Pose const pose, Pose const native_pose, Size const seqpos)
Real	get_sc_automorphic_rmsd (Pose pose, Pose ref_pose, Size const seqpos)
Real	get_three_atom_sc_rmsd (Pose const pose, Pose const native_pose, Size const seqpos)
void	split_fa_dun (Pose const pose, Size const seqpos, Real &fa_dun_rot, Real &fa_dun_dev, pack::dunbrack::RotVector &rotvec)
std::string	get_aa_torsion_string (Pose const pose, Size const seqpos)
std::string	res_lvl_analysis (Pose pose, Pose const native_pose, Size const seqpos, ScoreFunctionOP scorefxn, ScoreFunctionOP scorefxn_edens, bool const do_sc_rmsd)
void	get_res_data_ss (io::silent::SilentStructOP &ss, Pose pose, Pose const native_pose, Size const seqpos, ScoreFunctionOP scorefxn, ScoreFunctionOP scorefxn_edens, bool const do_sc_rmsd)
void	minimize_all_sidechains (Pose &pose, scoring::ScoreFunctionOP const scorefxn, bool const min_dna)
void	minimize_sidechain (Pose &pose, scoring::ScoreFunctionOP const scorefxn, Size const seqpos)
core::pack::task::PackerTaskOP	single_res_task (Pose pose, Size const seqpos, bool const no_incl_curr, bool design)
void	scmove_residue (Pose &pose, scoring::ScoreFunctionOP const scorefxn, Size const seqpos, bool const no_incl_curr)
void	rottrial_residue (Pose &pose, scoring::ScoreFunctionOP const scorefxn, Size const seqpos, bool const no_incl_curr, bool const design)
void	rottrialmin_residue (Pose &pose, scoring::ScoreFunctionOP const scorefxn, Size const seqpos, bool const design)
void	RotamerAnalysis ()
void *	my_main (void *)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TRnat ("rot_anl.nat")
static basic::Tracer	TRmin ("rot_anl.min")
static basic::Tracer	TRrtmin ("rot_anl.rtmin")
static basic::Tracer	TRscmove ("rot_anl.scmove")

Function Documentation

get_aa_torsion_string()

std::string get_aa_torsion_string	(	Pose const	pose,
		Size const	seqpos
	)

References beta_nonlocal::pose, and ObjexxFCL::string_of().

Referenced by res_lvl_analysis().

get_atom_lk_burial()

Real get_atom_lk_burial	(	pose::Pose const	pose,
		scoring::ScoreFunctionOP	scorefxn,
		Size const	seqpos,
		Size const	iatom
	)

References get_atom_lk_energy(), beta_nonlocal::pose, and oop_conformations::scorefxn.

Referenced by get_res_avg_lk_burial().

get_atom_lk_energy()

Real get_atom_lk_energy	(	pose::Pose const	pose,
		scoring::ScoreFunctionOP	scorefxn,
		Size const	seqpos,
		Size const	iatom
	)

References utility::graph::Node::const_edge_list_end(), get_atom_lk_energy_by_residue_no_count_pair(), utility::graph::Edge::get_node(), create_a3b_hbs::j, beta_nonlocal::pose, and oop_conformations::scorefxn.

Referenced by get_atom_lk_burial().

get_atom_lk_energy_by_residue_no_count_pair()

Real get_atom_lk_energy_by_residue_no_count_pair	(	scoring::ScoreFunctionOP	scorefxn,
		conformation::Residue const &	rsd1,
		Size const	atom1,
		conformation::Residue const &	rsd2
	)

References numeric::xyzVector< T >::distance_squared(), test.T009_Exceptions::e, ObjexxFCL::FArray3D< T >::index(), test.G201_Module_Structure::l1, test.T200_Scoring::rsd1, test.T200_Scoring::rsd2, and oop_conformations::scorefxn.

Referenced by get_atom_lk_energy().

get_n_bb_hbonds()

Size get_n_bb_hbonds	(	Pose const	pose,
		Size const	seqpos
	)

References create_a3b_hbs::i, and beta_nonlocal::pose.

Referenced by get_res_data_ss().

get_n_sc_hbonds()

Size get_n_sc_hbonds	(	Pose const	pose,
		Size const	seqpos
	)

References create_a3b_hbs::i, and beta_nonlocal::pose.

Referenced by get_res_data_ss(), and res_lvl_analysis().

get_res_avg_lk_burial()

Real get_res_avg_lk_burial	(	pose::Pose const	pose,
		scoring::ScoreFunctionOP	scorefxn,
		Size const	seqpos,
		bool	incl_bb,
		bool	incl_sc
	)

References get_atom_lk_burial(), beta_nonlocal::pose, and oop_conformations::scorefxn.

Referenced by get_res_data_ss(), and res_lvl_analysis().

get_res_data_ss()

void get_res_data_ss	(	io::silent::SilentStructOP &	ss,
		Pose	pose,
		Pose const	native_pose,
		Size const	seqpos,
		ScoreFunctionOP	scorefxn,
		ScoreFunctionOP	scorefxn_edens,
		bool const	do_sc_rmsd
	)

References get_n_bb_hbonds(), get_n_sc_hbonds(), get_res_avg_lk_burial(), get_res_hbond_bb_score_raw(), get_sc_automorphic_rmsd(), get_sc_bfactor(), create_a3b_hbs::ii, edensity::mapfile(), docking::native_pose, option, beta_nonlocal::pose, ObjexxFCL::pow(), oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, split_fa_dun(), challenge::ss, basic::options::OptionKeys::inout::dbms::user, value, and weights().

Referenced by RotamerAnalysis().

get_res_hbond_bb_score_raw()

Real get_res_hbond_bb_score_raw	(	pose::Pose const	pose,
		Size const	seqpos
	)

References beta_nonlocal::pose, and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by get_res_data_ss().

get_sc_automorphic_rmsd()

Real get_sc_automorphic_rmsd	(	Pose	pose,
		Pose	ref_pose,
		Size const	seqpos
	)

References beta_nonlocal::pose, ObjexxFCL::string_of(), and utility_exit_with_message.

Referenced by get_res_data_ss(), and res_lvl_analysis().

get_sc_bfactor()

Real get_sc_bfactor	(	Pose const	native_pose,
		Size const	seqpos
	)

References count, create_a3b_hbs::ii, and docking::native_pose.

Referenced by get_res_data_ss(), and res_lvl_analysis().

get_sc_rmsd()

Real get_sc_rmsd	(	Pose const	pose,
		Pose const	native_pose,
		Size const	seqpos
	)

References count, create_a3b_hbs::ii, docking::native_pose, beta_nonlocal::pose, ObjexxFCL::string_of(), and utility_exit_with_message.

get_three_atom_sc_rmsd()

Real get_three_atom_sc_rmsd	(	Pose const	pose,
		Pose const	native_pose,
		Size const	seqpos
	)

References count, create_a3b_hbs::ii, docking::native_pose, beta_nonlocal::pose, sc_rmsd_AtomIDs(), ObjexxFCL::string_of(), and utility_exit_with_message.

main()

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

References argv, test.T009_Exceptions::e, basic::init(), my_main(), and viewer_main().

minimize_all_sidechains()

void minimize_all_sidechains	(	Pose &	pose,
		scoring::ScoreFunctionOP const	scorefxn,
		bool const	min_dna
	)

References create_a3b_hbs::i, vancomycin::min_mover, beta_nonlocal::mm, beta_nonlocal::pose, and oop_conformations::scorefxn.

minimize_sidechain()

void minimize_sidechain	(	Pose &	pose,
		scoring::ScoreFunctionOP const	scorefxn,
		Size const	seqpos
	)

References vancomycin::min_mover, beta_nonlocal::mm, beta_nonlocal::pose, and oop_conformations::scorefxn.

Referenced by RotamerAnalysis(), and scmove_residue().

my_main()

void* my_main

(

void *

)

References utility::options::OptionKeys::options::exit, and RotamerAnalysis().

Referenced by main().

res_lvl_analysis()

std::string res_lvl_analysis	(	Pose	pose,
		Pose const	native_pose,
		Size const	seqpos,
		ScoreFunctionOP	scorefxn,
		ScoreFunctionOP	scorefxn_edens,
		bool const	do_sc_rmsd
	)

References get_aa_torsion_string(), get_n_sc_hbonds(), get_res_avg_lk_burial(), get_sc_automorphic_rmsd(), get_sc_bfactor(), edensity::mapfile(), docking::native_pose, option, beta_nonlocal::pose, oop_conformations::scorefxn, split_fa_dun(), ObjexxFCL::string_of(), and basic::options::OptionKeys::inout::dbms::user.

RotamerAnalysis()

void RotamerAnalysis

(

)

References revert_app::design, rot_anl::design(), rot_anl::dump_pdb(), get_res_data_ss(), edensity::mapfile(), rot_anl::min(), minimize_sidechain(), in::file::native(), docking::native_pose, option, demo.D050_Packer_task::packer_task(), predPRE::pdbname, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, rot_anl::repack(), packing::resfile(), rottrial_residue(), rottrialmin_residue(), rot_anl::rtmin(), rot_anl::scmove(), scmove_residue(), oop_conformations::scorefxn, set_pose_occ_and_bfac(), sfd, challenge::ss, basic::options::start_file(), ObjexxFCL::string_of(), rot_anl::tag(), tag, and basic::options::OptionKeys::inout::dbms::user.

Referenced by my_main().

rottrial_residue()

void rottrial_residue	(	Pose &	pose,
		scoring::ScoreFunctionOP const	scorefxn,
		Size const	seqpos,
		bool const	no_incl_curr,
		bool const	design
	)

References revert_app::design, demo.D050_Packer_task::packer_task(), beta_nonlocal::pose, oop_conformations::scorefxn, and single_res_task().

Referenced by RotamerAnalysis().

rottrialmin_residue()

void rottrialmin_residue	(	Pose &	pose,
		scoring::ScoreFunctionOP const	scorefxn,
		Size const	seqpos,
		bool const	design
	)

References revert_app::design, demo.D050_Packer_task::packer_task(), beta_nonlocal::pose, create_a3b_hbs::score, oop_conformations::scorefxn, and single_res_task().

Referenced by RotamerAnalysis().

sc_rmsd_AtomIDs()

std::map< std::string, utility::vector1< std::string > > sc_rmsd_AtomIDs

(

utility::tools::make_map(std::string(" DA"), utility::tools::make_vector1(std::string("N6"), std::string("C5"), std::string("N7")), std::string(" DC"), utility::tools::make_vector1(std::string("N4"), std::string("C4"), std::string("C5")), std::string(" DG"), utility::tools::make_vector1(std::string("O6"), std::string("C5"), std::string("N7")), std::string(" DT"), utility::tools::make_vector1(std::string("O4"), std::string("C5"), std::string("C7")), std::string("GLY"), utility::tools::make_vector1(std::string("N"), std::string("CA"), std::string("C")), std::string("ALA"), utility::tools::make_vector1(std::string("CB"), std::string("CA"), std::string("N")), std::string("CYS"), utility::tools::make_vector1(std::string("SG"), std::string("CB"), std::string("CA")), std::string("ASP"), utility::tools::make_vector1(std::string("OD1"), std::string("CG"), std::string("OD2")), std::string("GLU"), utility::tools::make_vector1(std::string("OE1"), std::string("CD"), std::string("OE2")), std::string("PHE"), utility::tools::make_vector1(std::string("CE1"), std::string("CZ"), std::string("CE2")), std::string("HIS"), utility::tools::make_vector1(std::string("ND1"), std::string("CE1"), std::string("NE2")), std::string("ILE"), utility::tools::make_vector1(std::string("CD1"), std::string("CG1"), std::string("CG2")), std::string("LYS"), utility::tools::make_vector1(std::string("NZ"), std::string("CE"), std::string("CD")), std::string("LEU"), utility::tools::make_vector1(std::string("CG"), std::string("CD1"), std::string("CD2")), std::string("MET"), utility::tools::make_vector1(std::string("CG"), std::string("SD"), std::string("CE")), std::string("ASN"), utility::tools::make_vector1(std::string("OD1"), std::string("CG"), std::string("ND2")), std::string("GLN"), utility::tools::make_vector1(std::string("OE1"), std::string("CD"), std::string("NE2")), std::string("PRO"), utility::tools::make_vector1(std::string("CG"), std::string("CD"), std::string("NV")), std::string("ARG"), utility::tools::make_vector1(std::string("NH1"), std::string("CZ"), std::string("NH2")), std::string("SER"), utility::tools::make_vector1(std::string("OG"), std::string("CB"), std::string("CA")), std::string("THR"), utility::tools::make_vector1(std::string("OG1"), std::string("CB"), std::string("CG2")), std::string("VAL"), utility::tools::make_vector1(std::string("CG1"), std::string("CB"), std::string("CG2")), std::string("TRP"), utility::tools::make_vector1(std::string("NE1"), std::string("CZ2"), std::string("CE3")), std::string("TYR"), utility::tools::make_vector1(std::string("OH"), std::string("CE1"), std::string("CE2")))

)

Referenced by get_three_atom_sc_rmsd().

scmove_residue()

void scmove_residue	(	Pose &	pose,
		scoring::ScoreFunctionOP const	scorefxn,
		Size const	seqpos,
		bool const	no_incl_curr
	)

References create_a3b_hbs::i, mc, minimize_sidechain(), basic::options::OptionKeys::MonteCarlo::MonteCarlo, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, basic::options::OptionKeys::dna::specificity::nloop, rot_anl::nloop_scmove(), option, demo.D050_Packer_task::packer_task(), beta_nonlocal::pose, ObjexxFCL::pow(), oop_conformations::scorefxn, and single_res_task().

Referenced by RotamerAnalysis().

set_pose_occ_and_bfac()

void set_pose_occ_and_bfac	(	Pose &	pose,
		Pose const	native_pose
	)

References create_a3b_hbs::ii, docking::native_pose, beta_nonlocal::pose, ObjexxFCL::string_of(), and utility_exit_with_message.

Referenced by RotamerAnalysis().

single_res_task()

core::pack::task::PackerTaskOP single_res_task	(	Pose	pose,
		Size const	seqpos,
		bool const	no_incl_curr,
		bool	design
	)

References revert_app::design, demo.D050_Packer_task::packer_task(), and beta_nonlocal::pose.

Referenced by rottrial_residue(), rottrialmin_residue(), and scmove_residue().

split_fa_dun()

void split_fa_dun	(	Pose const	pose,
		Size const	seqpos,
		Real &	fa_dun_rot,
		Real &	fa_dun_dev,
		pack::dunbrack::RotVector &	rotvec
	)

References ObjexxFCL::abs(), corrections::correct(), corrections::score::dun10(), option, beta_nonlocal::pose, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::out::path::scratch, and basic::options::OptionKeys::inout::dbms::user.

Referenced by get_res_data_ss(), and res_lvl_analysis().

Variable Documentation

TRmin

basic::Tracer TRmin("rot_anl.min") ( "rot_anl.min"  )

static

TRnat

basic::Tracer TRnat("rot_anl.nat") ( "rot_anl.nat"  )

static

TRrtmin

basic::Tracer TRrtmin("rot_anl.rtmin") ( "rot_anl.rtmin"  )

static

TRscmove

basic::Tracer TRscmove("rot_anl.scmove") ( "rot_anl.scmove"  )

static