tj_util.hh File Reference

#include <utility/string_util.hh>
#include <utility/file/FileName.hh>
#include <utility/file/file_sys_util.hh>
#include <core/chemical/AtomType.hh>
#include <core/chemical/util.hh>
#include <core/chemical/ResidueTypeSet.fwd.hh>
#include <core/conformation/Residue.functions.hh>
#include <core/conformation/Residue.fwd.hh>
#include <core/id/AtomID.hh>
#include <core/id/AtomID_Map.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/import_pose/import_pose.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/pose/init_id_map.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/sequence/util.hh>
#include <core/sequence/SequenceAlignment.hh>
#include <core/scoring/sasa.hh>
#include <core/scoring/ScoreType.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/rms_util.tmpl.hh>
#include <core/pack/optimizeH.hh>
#include <core/pack/pack_missing_sidechains.hh>
#include <protocols/comparative_modeling/util.hh>
#include <protocols/comparative_modeling/coord_util.hh>
#include <protocols/comparative_modeling/PartialThreadingMover.hh>
#include <protocols/loops/Loop.hh>
#include <protocols/loops/Loops.hh>
#include <protocols/loops/util.hh>
#include <protocols/star/Extender.hh>
#include <basic/options/option.hh>
#include <basic/options/util.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/cm.OptionKeys.gen.hh>
#include <basic/Tracer.hh>
#include <map>
#include <iosfwd>
#include <sstream>

Functions
vector1< SequenceAlignment >	input_alignments ()
	inputs the sequence alignments and keeps them ordered the way they were in the alingment.filt file. More...
map< string, SequenceAlignment >	input_alignmentsMapped (bool mapToPdbid)
	inputs the sequence alignments and maps them to to either pdbid or alignment file name. More...
std::map< std::string, core::pose::Pose >	poses_from_cmd_line (utility::vector1< std::string > const &fn_list)
std::map< std::string, core::pose::Pose >	poses_from_cmd_line_noPDBtag (utility::vector1< std::string > const &fn_list)
void	add_side_chains_partialthread (Pose pose)
	@add side chains onto partial threads More...
map< string, Pose >	generate_partial_threads (map< string, SequenceAlignment > alnData, map< string, Pose > templateData, string query_sequence, bool add_sidechains)
	creates a partial thread for an input list of alignments More...
map< string, const protocols::loops::Loops >	get_unalignedLoopsMapped (map< string, SequenceAlignment > alnDataMapped, Size numResidues)
	get all unaligned loops from set of alignments More...
vector1< bool >	calculate_surface_exposure (Pose pose)
	calculates burial More...
void	superimpose_pose_using_aln (Pose &mod_pose, Pose const &ref_pose, SequenceAlignment aln, Size firstAln)
	superimposes aligned residues More...
utility::vector1< core::pose::PoseOP >	input_subset_poses (Size n)
	inputs the first N poses More...
core::pose::PoseOP	get_central_pose (utility::vector1< core::pose::PoseOP > pose_vector)
void	get_disordered_regions (core::pose::PoseOP centralPose, utility::vector1< core::pose::PoseOP > pose_vector, Real threshold)

Variables
static basic::Tracer	tr2 ("brunette.tj_util")

Function Documentation

add_side_chains_partialthread()

void add_side_chains_partialthread

(

Pose

pose

)

@add side chains onto partial threads

References basic::Tracer::Debug, create_a3b_hbs::ii, basic::options::OptionKeys::packing::pack_missing_sidechains, beta_nonlocal::pose, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, and tr2.

Referenced by generate_partial_threads().

calculate_surface_exposure()

vector1<bool> calculate_surface_exposure

(

Pose

pose

)

calculates burial

References create_a3b_hbs::ii, beta_nonlocal::pose, and bur_nodon_tyr::probe_radius.

Referenced by main().

generate_partial_threads()

map<string,Pose> generate_partial_threads	(	map< string, SequenceAlignment >	alnData,
		map< string, Pose >	templateData,
		string	query_sequence,
		bool	add_sidechains
	)

creates a partial thread for an input list of alignments

References add_side_chains_partialthread(), basic::options::OptionKeys::chemical::chemical, and subloop_histogram::iterator.

Referenced by main().

get_central_pose()

core::pose::PoseOP get_central_pose

(

utility::vector1< core::pose::PoseOP >

pose_vector

)

References create_a3b_hbs::ii, beta_nonlocal::jj, and basic::options::OptionKeys::frags::scoring::scoring.

get_disordered_regions()

void get_disordered_regions	(	core::pose::PoseOP	centralPose,
		utility::vector1< core::pose::PoseOP >	pose_vector,
		Real	threshold
	)

References utility::io::oc::cout, create_a3b_hbs::ii, beta_nonlocal::jj, and basic::options::OptionKeys::frags::scoring::scoring.

get_unalignedLoopsMapped()

map<string, const protocols::loops::Loops> get_unalignedLoopsMapped	(	map< string, SequenceAlignment >	alnDataMapped,
		Size	numResidues
	)

get all unaligned loops from set of alignments

References subloop_histogram::iterator, and basic::options::OptionKeys::abinitio::star::star.

Referenced by main().

input_alignments()

vector1<SequenceAlignment> input_alignments

(

)

inputs the sequence alignments and keeps them ordered the way they were in the alingment.filt file.

References in::file::alignment(), cm::aln_format(), option, and basic::options::OptionKeys::relax::sequence.

Referenced by main().

input_alignmentsMapped()

map<string,SequenceAlignment> input_alignmentsMapped

(

bool

mapToPdbid

)

inputs the sequence alignments and maps them to to either pdbid or alignment file name.

References in::file::alignment(), cm::aln_format(), utility::file_basename(), create_a3b_hbs::ii, subloop_histogram::iterator, beta_nonlocal::jj, option, and basic::options::OptionKeys::mp::transform::transform.

input_subset_poses()

utility::vector1< core::pose::PoseOP > input_subset_poses

(

Size

n

)

inputs the first N poses

References basic::options::OptionKeys::chemical::chemical, count, gaussian-sampling::input, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::n.

poses_from_cmd_line()

std::map< std::string, core::pose::Pose > poses_from_cmd_line

(

utility::vector1< std::string > const &

fn_list

)

References basic::options::OptionKeys::chemical::chemical, end, utility::file_basename(), utility::file::file_exists(), file_exists(), beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, and basic::options::OptionKeys::mp::assembly::poses.

poses_from_cmd_line_noPDBtag()

std::map< std::string, core::pose::Pose > poses_from_cmd_line_noPDBtag

(

utility::vector1< std::string > const &

fn_list

)

References basic::options::OptionKeys::chemical::chemical, end, utility::file_basename(), utility::file::file_exists(), file_exists(), beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::mp::assembly::poses, and basic::options::OptionKeys::mp::transform::transform.

Referenced by main().

superimpose_pose_using_aln()

void superimpose_pose_using_aln	(	Pose &	mod_pose,
		Pose const &	ref_pose,
		SequenceAlignment	aln,
		Size	firstAln
	)

superimposes aligned residues

References aln, create_a3b_hbs::ii, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::relax::sequence, and superimpose_pose().

Referenced by region_density_score(), and region_rmsd_structures_aligned().

Variable Documentation

tr2

basic::Tracer tr2("brunette.tj_util") ( "brunette.tj_util"  )

static

Referenced by add_side_chains_partialthread().