domain_assemble.cc File Reference

#include <math.h>
#include <fstream>
#include <core/pose/Pose.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/util.hh>
#include <core/pose/init_id_map.hh>
#include <core/id/AtomID.hh>
#include <core/id/AtomID_Map.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/AtomTree.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/kinematics/RT.hh>
#include <core/kinematics/Stub.hh>
#include <core/kinematics/tree/Atom.hh>
#include <core/chemical/util.hh>
#include <numeric/random/random.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/Conformation.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/AtomTypeSet.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/import_pose/import_pose.hh>
#include <core/import_pose/pose_stream/util.hh>
#include <core/import_pose/pose_stream/PoseInputStream.hh>
#include <core/import_pose/pose_stream/MetaPoseInputStream.hh>
#include <core/io/silent/SilentStruct.hh>
#include <core/io/silent/ScoreFileSilentStruct.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/util/SwitchResidueTypeSet.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/HBondOptions.hh>
#include <core/scoring/hbonds/hbonds.hh>
#include <core/scoring/hbonds/constants.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/sasa.hh>
#include <numeric/xyzVector.hh>
#include <numeric/xyzMatrix.hh>
#include <utility/tools/make_vector1.hh>
#include <utility/tools/make_map.hh>
#include <utility/string_util.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 <core/optimization/MinimizerOptions.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <basic/options/option.hh>
#include <basic/options/util.hh>
#include <basic/options/after_opts.hh>
#include <basic/options/keys/OptionKeys.hh>
#include <basic/options/option_macros.hh>
#include <basic/Tracer.hh>
#include <devel/init.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/moves/MonteCarlo.hh>
#include <core/scoring/dssp/Dssp.hh>
#include <core/pose/metrics/CalculatorFactory.hh>
#include <protocols/pose_metric_calculators/MetricValueGetter.hh>
#include <basic/MetricValue.hh>
#include <core/pose/metrics/simple_calculators/SasaCalculatorLegacy.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
	chrisk

Functions
RT	get_atomatom_rt (pose::Pose const &pose, Size seqpos1, string atom1, Size seqpos2, string atom2)
void	find_backbone_rts_in_pose (Pose const &pose, kinematics::RT const &rt, Real const rt_tol, Size const seqsep_tol, Size const term_tol, bool loops_only, vector1< std::pair< Size, Size > > &cutpairs)
Real	calc_nonlocal_segment_bb_rmsd (Pose const &pose1, vector1< Size > const seqpos1s, Pose &pose2, vector1< Size > const seqpos2s)
void	find_nonlocal_segment_alignments_in_pose (Pose &pose, Pose const &src_pose, vector1< Size > const src_nonlocal_segment, Real const rmsd_tol, Size const seqsep_tol, Size const term_tol, bool loops_only, vector1< vector1< Size > > &aln_nonlocal_segments)
void	find_cutpair_alignments_in_pose (Pose &pose, Pose const &src_pose, std::pair< Size, Size > const src_cutpair, Real const rmsd_tol, Size const seqsep_tol, Size const term_tol, bool loops_only, vector1< std::pair< Size, Size > > &aln_cutpairs)
void	setup_secstruct_dssp (pose::Pose &pose)
void	copy_segment_bb (Pose &pose, Size length, Pose const &src_pose, Size pose_start, Size src_pose_start)
Jump	get_rsdrsd_jump (Pose pose, Size const seqpos1, Size const seqpos2)
void	trim_pose_termini (Pose &pose, Size const nterm, Size const cterm)
void	append_pose_by_jump (Pose &src_pose, Size const src_seqpos, Pose const &ap_pose, Size const ap_seqpos)
void	build_pose_by_jumps_from_domains (vector1< Pose > domain_poses, vector1< std::pair< Size, Size > > const &domain_cutpairs, Pose &construct_pose)
void	find_rsd_nbrs (Pose const &pose, vector1< bool > const &is_incl, Real const nbr_radius, vector1< bool > &is_nbr)
void	dump_insert_pdb_and_remodel_blueprint (Pose const &cutpose, std::pair< Size, Size > const cut_cutpair, Pose inpose, std::pair< Size, Size > const in_cutpair, Real design_link_nbr_radius, Real repack_link_nbr_radius, Size n_add_linker)
void	go (pose::Pose cutpose)
void	load_coords ()
void *	my_main (void *)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("chrisk")
basic::options::StringOptionKey	chrisk::tag ("chrisk:tag")
basic::options::StringOptionKey	chrisk::insert_pdb ("chrisk:insert_pdb")
basic::options::RealOptionKey	chrisk::rt_tol ("chrisk:rt_tol")
basic::options::RealOptionKey	chrisk::rmsd_tol ("chrisk:rmsd_tol")
basic::options::IntegerOptionKey	chrisk::seqsep_tol ("chrisk:seqsep_tol")
basic::options::IntegerOptionKey	chrisk::term_tol ("chrisk:term_tol")
basic::options::IntegerOptionKey	chrisk::trim_tol ("chrisk:trim_tol")
basic::options::IntegerOptionKey	chrisk::nterm_in ("chrisk:nterm_in")
basic::options::IntegerOptionKey	chrisk::cterm_in ("chrisk:cterm_in")
basic::options::BooleanOptionKey	chrisk::loops_only ("chrisk:loops_only")
basic::options::RealOptionKey	chrisk::design_radius ("chrisk:design_radius")
basic::options::RealOptionKey	chrisk::repack_radius ("chrisk:repack_radius")
basic::options::IntegerOptionKey	chrisk::n_add_linker ("chrisk:n_add_linker")

Function Documentation

append_pose_by_jump()

void append_pose_by_jump	(	Pose &	src_pose,
		Size const	src_seqpos,
		Pose const &	ap_pose,
		Size const	ap_seqpos
	)

Referenced by build_pose_by_jumps_from_domains().

build_pose_by_jumps_from_domains()

void build_pose_by_jumps_from_domains	(	vector1< Pose >	domain_poses,
		vector1< std::pair< Size, Size > > const &	domain_cutpairs,
		Pose &	construct_pose
	)

References append_pose_by_jump(), create_a3b_hbs::first, and trim_pose_termini().

calc_nonlocal_segment_bb_rmsd()

Real calc_nonlocal_segment_bb_rmsd	(	Pose const &	pose1,
		vector1< Size > const	seqpos1s,
		Pose &	pose2,
		vector1< Size > const	seqpos2s
	)

References test.T008_Serialization::pose1, test.T008_Serialization::pose2, and superimpose_pose().

Referenced by find_nonlocal_segment_alignments_in_pose().

copy_segment_bb()

void copy_segment_bb	(	Pose &	pose,
		Size	length,
		Pose const &	src_pose,
		Size	pose_start,
		Size	src_pose_start
	)

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

dump_insert_pdb_and_remodel_blueprint()

void dump_insert_pdb_and_remodel_blueprint	(	Pose const &	cutpose,
		std::pair< Size, Size > const	cut_cutpair,
		Pose	inpose,
		std::pair< Size, Size > const	in_cutpair,
		Real	design_link_nbr_radius,
		Real	repack_link_nbr_radius,
		Size	n_add_linker
	)

References aa, find_rsd_nbrs(), chrisk::n_add_linker, option, erraser_single_res_analysis::out, oop_conformations::scorefxn, challenge::ss, chrisk::tag, tag, utility::to_string(), and trim_pose_termini().

Referenced by go().

find_backbone_rts_in_pose()

void find_backbone_rts_in_pose	(	Pose const &	pose,
		kinematics::RT const &	rt,
		Real const	rt_tol,
		Size const	seqsep_tol,
		Size const	term_tol,
		bool	loops_only,
		vector1< std::pair< Size, Size > > &	cutpairs
	)

References get_atomatom_rt(), create_a3b_hbs::i, create_a3b_hbs::j, chrisk::loops_only, beta_nonlocal::pose, chrisk::rt_tol, chrisk::seqsep_tol, chrisk::term_tol, and TR.

find_cutpair_alignments_in_pose()

void find_cutpair_alignments_in_pose	(	Pose &	pose,
		Pose const &	src_pose,
		std::pair< Size, Size > const	src_cutpair,
		Real const	rmsd_tol,
		Size const	seqsep_tol,
		Size const	term_tol,
		bool	loops_only,
		vector1< std::pair< Size, Size > > &	aln_cutpairs
	)

References find_nonlocal_segment_alignments_in_pose(), chrisk::loops_only, beta_nonlocal::pose, chrisk::rmsd_tol, chrisk::seqsep_tol, and chrisk::term_tol.

Referenced by go().

find_nonlocal_segment_alignments_in_pose()

void find_nonlocal_segment_alignments_in_pose	(	Pose &	pose,
		Pose const &	src_pose,
		vector1< Size > const	src_nonlocal_segment,
		Real const	rmsd_tol,
		Size const	seqsep_tol,
		Size const	term_tol,
		bool	loops_only,
		vector1< vector1< Size > > &	aln_nonlocal_segments
	)

References calc_nonlocal_segment_bb_rmsd(), create_a3b_hbs::i, create_a3b_hbs::j, chrisk::loops_only, beta_nonlocal::pose, chrisk::rmsd_tol, chrisk::seqsep_tol, chrisk::term_tol, and TR.

Referenced by find_cutpair_alignments_in_pose().

find_rsd_nbrs()

void find_rsd_nbrs	(	Pose const &	pose,
		vector1< bool > const &	is_incl,
		Real const	nbr_radius,
		vector1< bool > &	is_nbr
	)

References beta_nonlocal::pose, test.T200_Scoring::rsd1, and test.T200_Scoring::rsd2.

Referenced by dump_insert_pdb_and_remodel_blueprint().

get_atomatom_rt()

RT get_atomatom_rt	(	pose::Pose const &	pose,
		Size	seqpos1,
		string	atom1,
		Size	seqpos2,
		string	atom2
	)

References beta_nonlocal::pose, test.T200_Scoring::rsd1, and test.T200_Scoring::rsd2.

Referenced by find_backbone_rts_in_pose().

get_rsdrsd_jump()

Jump get_rsdrsd_jump	(	Pose	pose,
		Size const	seqpos1,
		Size const	seqpos2
	)

References test.T020_Pose_Bindings::ft, and beta_nonlocal::pose.

go()

void go

(

pose::Pose

cutpose

)

References chrisk::cterm_in, chrisk::design_radius, dump_insert_pdb_and_remodel_blueprint(), find_cutpair_alignments_in_pose(), chrisk::insert_pdb, chrisk::loops_only, chrisk::n_add_linker, chrisk::nterm_in, option, pyrosetta.distributed.io::pose_from_file, chrisk::repack_radius, chrisk::rmsd_tol, chrisk::rt_tol, oop_conformations::scorefxn, chrisk::seqsep_tol, setup_secstruct_dssp(), superimpose_pose(), chrisk::term_tol, utility::to_string(), chrisk::trim_tol, and basic::options::OptionKeys::inout::dbms::user.

Referenced by load_coords().

load_coords()

void load_coords

(

)

References go(), gaussian-sampling::input, option, beta_nonlocal::pose, and in::file::residue_type_set().

Referenced by my_main().

main()

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

References argv, chrisk::cterm_in, chrisk::design_radius, basic::init(), chrisk::insert_pdb, chrisk::loops_only, my_main(), chrisk::n_add_linker, chrisk::nterm_in, option, chrisk::repack_radius, chrisk::rmsd_tol, chrisk::rt_tol, chrisk::seqsep_tol, chrisk::tag, chrisk::term_tol, chrisk::trim_tol, and viewer_main().

my_main()

void* my_main

(

void *

)

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

Referenced by main().

setup_secstruct_dssp()

void setup_secstruct_dssp

(

pose::Pose &

pose

)

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

Referenced by go().

trim_pose_termini()

void trim_pose_termini	(	Pose &	pose,
		Size const	nterm,
		Size const	cterm
	)

References beta_nonlocal::pose.

Referenced by build_pose_by_jumps_from_domains(), and dump_insert_pdb_and_remodel_blueprint().

Variable Documentation

TR

basic::Tracer TR("chrisk") ( "chrisk"  )

static

Referenced by find_backbone_rts_in_pose(), and find_nonlocal_segment_alignments_in_pose().