pep_prep.cc File Reference

#include <protocols/frags/VallData.hh>
#include <protocols/frags/TorsionFragment.hh>
#include <core/scoring/constraints/CoordinateConstraint.hh>
#include <core/scoring/constraints/ConstraintIO.hh>
#include <core/scoring/func/FlatHarmonicFunc.hh>
#include <protocols/simple_moves/BackboneMover.hh>
#include <protocols/minimization_packing/MinMover.hh>
#include <protocols/moves/MonteCarlo.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/moves/MoverContainer.hh>
#include <protocols/moves/OutputMovers.hh>
#include <protocols/rigid/RigidBodyMover.hh>
#include <protocols/moves/TrialMover.hh>
#include <protocols/minimization_packing/PackRotamersMover.hh>
#include <protocols/minimization_packing/RotamerTrialsMover.hh>
#include <protocols/moves/RepeatMover.hh>
#include <protocols/loops/ccd_closure.hh>
#include <protocols/loops/loops_main.hh>
#include <protocols/viewer/viewers.hh>
#include <core/types.hh>
#include <core/scoring/sasa.hh>
#include <core/chemical/AA.hh>
#include <core/chemical/AtomTypeSet.hh>
#include <core/conformation/Conformation.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueMatcher.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/pack/rotamer_set/RotamerCouplings.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/ResidueTypeSelector.hh>
#include <core/chemical/VariantType.hh>
#include <core/chemical/util.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/EnergyMap.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/etable/Etable.hh>
#include <core/scoring/ScoringManager.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/Ramachandran.hh>
#include <core/pack/dunbrack/RotamerLibrary.hh>
#include <core/pack/dunbrack/RotamerLibraryScratchSpace.hh>
#include <core/scoring/hbonds/HBondSet.hh>
#include <core/scoring/hbonds/hbonds.hh>
#include <core/scoring/etable/count_pair/CountPairFunction.hh>
#include <core/pack/rotamer_trials.hh>
#include <core/pack/pack_rotamers.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/kinematics/RT.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/kinematics/util.hh>
#include <core/id/AtomID_Map.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBPoseMap.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/util.hh>
#include <basic/options/util.hh>
#include <basic/basic.hh>
#include <basic/database/open.hh>
#include <devel/init.hh>
#include <core/import_pose/import_pose.hh>
#include <utility/vector1.hh>
#include <utility/file/FileName.hh>
#include <numeric/conversions.hh>
#include <numeric/xyzVector.hh>
#include <numeric/random/random.hh>
#include <numeric/random/random_permutation.hh>
#include <ObjexxFCL/string.functions.hh>
#include <core/sequence/util.hh>
#include <core/id/SequenceMapping.hh>
#include <core/sequence/Sequence.hh>
#include <core/sequence/SequenceProfile.hh>
#include <core/sequence/SequenceAlignment.hh>
#include <core/sequence/NWAligner.hh>
#include <core/sequence/SWAligner.hh>
#include <core/sequence/L1ScoringScheme.hh>
#include <core/sequence/MatrixScoringScheme.hh>
#include <core/sequence/SimpleScoringScheme.hh>
#include <core/sequence/ScoringScheme.fwd.hh>
#include <core/sequence/ScoringSchemeFactory.hh>
#include <cstdlib>
#include <fstream>
#include <iostream>
#include <string>
#include <sstream>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <basic/options/keys/pepspec.OptionKeys.gen.hh>
#include <basic/options/keys/constraints.OptionKeys.gen.hh>
#include <basic/Tracer.hh>
#include <numeric/NumericTraits.hh>

Classes
struct	pep_coord_cst

Functions
void	print_pep_csts (vector1< Vector > pep_cst_all_vects, vector1< Real > pep_cst_all_tols, vector1< Real > pep_cst_all_sds, vector1< Size > n_pep_cs, vector1< Size > pep_cst_all_indices, vector1< std::string > pep_cst_all_atom_names)
void	set_pep_cst (pose::Pose &pose, Size pep_anchor, pep_coord_cst pep_cst)
void	make_sequence_change (Size const seqpos, chemical::AA const &new_aa, pose::Pose &pose)
bool	has_clash (pose::Pose pose, vector1< bool > check_seqpos, scoring::ScoreFunctionOP const &scorefxn, Real const clash_threshold, bool print_clash)
std::string	pep_rmsd_analysis (pose::Pose pose, Size prot_begin, Size prot_end, Size pep_begin, Size pep_anchor, Size pep_end)
Real	average (vector1< Real > real_vec)
vector1< Real >	shift_angles (vector1< Real > &angles)
void	run_pep_prep ()
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("apps.pilot.chrisk/pep_prep")
vector1< pep_coord_cst >	pep_coord_csts

Function Documentation

average()

Real average

(

vector1< Real >

real_vec

)

References create_a3b_hbs::i.

Referenced by run_pep_prep(), and shift_angles().

has_clash()

bool has_clash	(	pose::Pose	pose,
		vector1< bool >	check_seqpos,
		scoring::ScoreFunctionOP const &	scorefxn,
		Real const	clash_threshold,
		bool	print_clash
	)

References clash(), test.T200_Scoring::emap, utility::graph::Edge::get_node(), is_clash(), create_a3b_hbs::j, utility::graph::Node::lower_edge_list_end(), beta_nonlocal::pose, basic::options::OptionKeys::frags::scoring::scoring, ObjexxFCL::string_of(), TR, and utility::graph::Node::upper_edge_list_end().

Referenced by run_pep_prep().

main()

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

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

make_sequence_change()

void make_sequence_change	(	Size const	seqpos,
		chemical::AA const &	new_aa,
		pose::Pose &	pose
	)

This function will make a sequence mutation while trying to preserve the variants

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

Referenced by gen_pep_bb_sequential(), initialize_peptide(), mutate_random_residue(), pep_scan_analysis(), refine_fa_pep_bb(), run_pep_prep(), and RunPepSpec().

pep_rmsd_analysis()

std::string pep_rmsd_analysis	(	pose::Pose	pose,
		Size	prot_begin,
		Size	prot_end,
		Size	pep_begin,
		Size	pep_anchor,
		Size	pep_end
	)

References create_a3b_hbs::i, in::file::native(), pepspec::native_align(), pepspec::native_pep_anchor(), pepspec::native_pep_chain(), natoms(), num_chains(), option, basic::options::OptionKeys::pepspec::pep_anchor, pep_begin(), pepspec::pep_chain(), pep_end(), beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, prot_begin(), prot_end(), basic::options::OptionKeys::pepspec::rmsd_analysis, sd(), ObjexxFCL::string_of(), superimpose_pose(), and basic::options::OptionKeys::inout::dbms::user.

Referenced by run_pep_prep().

print_pep_csts()

void print_pep_csts	(	vector1< Vector >	pep_cst_all_vects,
		vector1< Real >	pep_cst_all_tols,
		vector1< Real >	pep_cst_all_sds,
		vector1< Size >	n_pep_cs,
		vector1< Size >	pep_cst_all_indices,
		vector1< std::string >	pep_cst_all_atom_names
	)

References basic::options::OptionKeys::cluster::energy_based_clustering::cst_file, create_a3b_hbs::i, out::file::o(), option, erraser_single_res_analysis::out, pepspec::p_homol_csts(), ObjexxFCL::pow(), ObjexxFCL::string_of(), basic::options::OptionKeys::inout::dbms::user, numeric::xyzVector< T >::x(), numeric::xyzVector< T >::y(), and numeric::xyzVector< T >::z().

Referenced by run_pep_prep().

run_pep_prep()

void run_pep_prep

(

)

References orn_macrocycle::ala, align_pose(), pepspec::anchor_type(), basic::options::OptionKeys::pepspec::anchor_type, pep_coord_cst::atom_name, average(), begin, check_clash(), pepspec::clash_cutoff(), pyrosetta::create_score_function, numeric::conversions::degrees(), numeric::xyzVector< T >::distance(), basic::options::OptionKeys::matdes::dock::dump_pdb, end, create_a3b_hbs::f, create_a3b_hbs::first, basic::options::OptionKeys::frags::frags, getline(), has_clash(), pepspec::homol_csts(), create_a3b_hbs::i, create_a3b_hbs::ii, line, make_sequence_change(), vancomycin::min_mover, basic::options::OptionKeys::MonteCarlo::MonteCarlo, pepspec::n_anchor_dock_std_devs(), pepspec::n_append(), basic::options::OptionKeys::pepspec::n_append, pepspec::n_dock_loop(), pepspec::n_peptides(), basic::options::OptionKeys::pepspec::n_peptides, pepspec::n_prepend(), basic::options::OptionKeys::pepspec::n_prepend, pepspec::no_prepack_prot(), create_a3b_hbs::nres, num_chains(), out::file::o(), option, erraser_single_res_analysis::out, demo.D010_Pose_structure::pdb_filename, pepspec::pdb_list(), basic::options::OptionKeys::pepspec::pep_anchor, pep_begin(), pep_end(), pep_jump(), pep_coord_cst::pep_pos, pep_rmsd_analysis(), beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, pepspec::prep_align_prot_to(), pepspec::prep_rot_std_dev(), pepspec::prep_trans_std_dev(), pepspec::prep_use_ref_rotamers(), print_pep_csts(), prot_anchor(), prot_begin(), prot_chain(), prot_end(), numeric::conversions::radians(), numeric::random::random_permutation(), pepspec::ref_pdb_list(), pepspec::remove_input_bb(), residue, numeric::random::rg(), pepspec::rmsd_analysis(), test.T200_Scoring::rsd1, test.T200_Scoring::rsd2, pepspec::run_sequential(), oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, pep_coord_cst::sd, basic::options::OptionKeys::recces::seq1, basic::options::OptionKeys::recces::seq2, pepspec::seq_align(), basic::options::OptionKeys::pepspec::seq_align, basic::options::OptionKeys::relax::sequence, set_pep_cst(), shift_angles(), pepspec::soft_wts(), numeric::square(), challenge::ss, basic::options::start_file(), ObjexxFCL::string_of(), superimpose_pose(), vancomycin::task, pep_coord_cst::tol, TR, numeric::random::uniform(), numeric::random::RandomGenerator::uniform(), pepspec::use_input_bb(), basic::options::OptionKeys::inout::dbms::user, utility_exit_with_message, pep_coord_cst::x, x, numeric::xyzVector< T >::x(), pep_coord_cst::x0, pep_coord_cst::y, predPRE::y, numeric::xyzVector< T >::y(), pep_coord_cst::z, predPRE::z, and numeric::xyzVector< T >::z().

Referenced by main().

set_pep_cst()

void set_pep_cst	(	pose::Pose &	pose,
		Size	pep_anchor,
		pep_coord_cst	pep_cst
	)

References pep_coord_cst::atom_name, basic::options::OptionKeys::chemical::chemical, basic::options::OptionKeys::constraints::constraints, basic::options::OptionKeys::pepspec::pep_anchor, pep_coord_cst::pep_pos, beta_nonlocal::pose, prot_anchor(), pep_coord_cst::sd, pep_coord_cst::tol, pep_coord_cst::x, numeric::xyzVector< T >::x(), pep_coord_cst::x0, pep_coord_cst::y, numeric::xyzVector< T >::y(), pep_coord_cst::z, and numeric::xyzVector< T >::z().

Referenced by run_pep_prep().

shift_angles()

vector1< Real > shift_angles

(

vector1< Real > &

angles

)

References ObjexxFCL::abs(), oop_conformations::angles, average(), create_a3b_hbs::i, pi, and numeric::NumericTraits< T >::pi().

Referenced by run_pep_prep().

Variable Documentation

pep_coord_csts

vector1< pep_coord_cst > pep_coord_csts

TR

basic::Tracer TR("apps.pilot.chrisk/pep_prep") ( "apps.pilot.chrisk/pep_prep"  )

static

Referenced by has_clash(), and run_pep_prep().