pep_spec.cc File Reference

#include <protocols/frags/VallData.hh>
#include <protocols/frags/TorsionFragment.hh>
#include <core/scoring/dna/setup.hh>
#include <core/scoring/dna/base_geometry.hh>
#include <core/scoring/dna/BasePartner.hh>
#include <core/scoring/GenBornPotential.hh>
#include <core/scoring/LREnergyContainer.hh>
#include <core/scoring/methods/Methods.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/id/SequenceMapping.hh>
#include <core/chemical/AtomTypeSet.hh>
#include <core/chemical/MMAtomTypeSet.hh>
#include <core/chemical/AA.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueMatcher.hh>
#include <core/pack/rotamer_set/RotamerCouplings.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/ResidueTypeSelector.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/chemical/VariantType.hh>
#include <core/chemical/ChemicalManager.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/TaskOperation.hh>
#include <core/kinematics/FoldTree.hh>
#include <protocols/viewer/visualize.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/kinematics/util.hh>
#include <core/id/AtomID_Map.hh>
#include <core/mm/MMTorsionLibrary.hh>
#include <core/mm/MMTorsionLibrary.fwd.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/pose/PDBPoseMap.hh>
#include <core/pose/PDBInfo.hh>
#include <basic/options/util.hh>
#include <basic/basic.hh>
#include <basic/database/open.hh>
#include <devel/init.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <utility/vector1.hh>
#include <utility/file/file_sys_util.hh>
#include <numeric/xyzVector.hh>
#include <numeric/random/random.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <core/scoring/constraints/DihedralConstraint.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/scoring/func/PeriodicFunc.hh>
#include <core/scoring/constraints/DOF_Constraint.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/constraints/ConstraintIO.hh>
#include <core/fragment/picking/FragmentLibraryManager.hh>
#include <core/fragment/picking/vall/VallLibrarian.hh>
#include <core/fragment/picking/vall/gen/LengthGen.hh>
#include <core/fragment/picking/vall/scores/VallFragmentScore.hh>
#include <cstdlib>
#include <fstream>
#include <iostream>
#include <string>
#include <basic/Tracer.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/pep_spec.OptionKeys.gen.hh>
#include <basic/options/keys/constraints.OptionKeys.gen.hh>
#include <core/import_pose/import_pose.hh>
#include <core/util/SwitchResidueTypeSet.hh>

Functions
Size	aa2index (chemical::AA aa)
Size	get_n_pep_nbrs (pose::Pose const &pose, vector1< bool > const is_pep, Real const cutoff_cg)
void	dump_efactor_pdb (pose::Pose &pose, core::scoring::ScoreFunctionOP const scorefxn, std::string const &tag)
void	gen_fold_tree_for_nbr_segments (pose::Pose &pose, FoldTree &ftree, vector1< bool > const &is_ligand, vector1< bool > const &is_skipped, Real const &nbr_cutoff, vector1< bool > &is_nbr)
bool	has_clash (pose::Pose pose, vector1< bool > is_checked, scoring::ScoreFunctionOP const &scorefxn, Real const clash_threshold)
std::string	pep_rmsd_analysis (pose::Pose pose, Size prot_begin, Size prot_end, Size pep_begin, Size pep_anchor, Size pep_end)
std::string	pep_phipsi_analysis (pose::Pose pose, Size pep_begin, Size pep_anchor, Size pep_end)
void	add_termini (pose::Pose &pose, Size &pep_begin, Size &pep_end)
void	add_pep_res (pose::Pose &pose, Size prot_anchor, Size &pep_begin, Size &pep_anchor, Size &pep_end, bool add_nterm, bool add_cterm)
void	remove_pep_res (pose::Pose &pose, Size prot_anchor, Size &pep_begin, Size &pep_anchor, Size &pep_end, bool add_nterm, bool add_cterm)
void	gen_pep_bb_frag (pose::Pose &pose, Size pep_begin, Size pep_anchor, Size pep_end, scoring::ScoreFunctionOP cen_scorefxn, protocols::frags::TorsionFragmentLibrary lib)
void	gen_pep_bb_frag_old (pose::Pose &pose, Size pep_begin, Size pep_anchor, Size pep_end, scoring::ScoreFunctionOP cen_scorefxn, protocols::frags::TorsionFragmentLibrary lib)
void	gen_pep_bb_rama (pose::Pose &pose, Size pep_begin, Size pep_end, scoring::ScoreFunctionOP cen_scorefxn)
void	perturb_pep_bb (pose::Pose &pose, kinematics::MoveMapOP mm_move, scoring::ScoreFunctionOP cen_scorefxn, Size n_iter)
void	refine_fa_pep_bb (Pose &pose, Size pep_anchor, vector1< bool > is_pep, vector1< bool > is_pep_nbr, scoring::ScoreFunctionOP full_scorefxn)
void	packmin_unbound_pep (pose::Pose &pose, scoring::ScoreFunctionOP full_scorefxn, scoring::ScoreFunctionOP soft_scorefxn)
void	RunPepSpec ()
void *	my_main (void *)
int	main (int argc, char *argv[])

Function Documentation

aa2index()

Size aa2index

(

chemical::AA

aa

)

References aa, enumerate_junctions::default, and ObjexxFCL::index().

Referenced by gen_pep_bb_frag().

add_pep_res()

void add_pep_res	(	pose::Pose &	pose,
		Size	prot_anchor,
		Size &	pep_begin,
		Size &	pep_anchor,
		Size &	pep_end,
		bool	add_nterm,
		bool	add_cterm
	)

References add_termini(), basic::options::OptionKeys::pepspec::pep_anchor, pep_begin(), pep_end(), and beta_nonlocal::pose.

Referenced by RunPepSpec().

add_termini()

void add_termini	(	pose::Pose &	pose,
		Size &	pep_begin,
		Size &	pep_end
	)

References pep_begin(), pep_end(), and beta_nonlocal::pose.

Referenced by add_pep_res(), remove_pep_res(), and RunPepSpec().

dump_efactor_pdb()

void dump_efactor_pdb	(	pose::Pose &	pose,
		core::scoring::ScoreFunctionOP const	scorefxn,
		std::string const &	tag
	)

References val2thr::atom, predPRE::chain, chains, ObjexxFCL::format::F(), lactamize::filename, create_a3b_hbs::i, test.T110_numeric::I, create_a3b_hbs::j, create_a3b_hbs::nres, basic::options::option, erraser_single_res_analysis::out, basic::options::OptionKeys::out::file::output_virtual, beta_nonlocal::pose, oop_conformations::scorefxn, and tag.

Referenced by RunPepSpec().

gen_fold_tree_for_nbr_segments()

void gen_fold_tree_for_nbr_segments	(	pose::Pose &	pose,
		FoldTree &	ftree,
		vector1< bool > const &	is_ligand,
		vector1< bool > const &	is_skipped,
		Real const &	nbr_cutoff,
		vector1< bool > &	is_nbr
	)

References utility::io::oc::cout, create_a3b_hbs::i, create_a3b_hbs::ii, create_a3b_hbs::j, beta_nonlocal::jj, create_a3b_hbs::nres, beta_nonlocal::pose, test.T200_Scoring::rsd1, test.T200_Scoring::rsd2, and ObjexxFCL::string_of().

Referenced by RunPepSpec().

gen_pep_bb_frag()

void gen_pep_bb_frag	(	pose::Pose &	pose,
		Size	pep_begin,
		Size	pep_anchor,
		Size	pep_end,
		scoring::ScoreFunctionOP	cen_scorefxn,
		protocols::frags::TorsionFragmentLibrary	lib
	)

References aa2index(), create_a3b_hbs::best_score, basic::options::OptionKeys::MonteCarlo::MonteCarlo, basic::options::OptionKeys::pepspec::n_build_loop, basic::options::OptionKeys::ddg::nfrags, option, basic::options::OptionKeys::pepspec::pep_anchor, pep_begin(), pep_end(), make_symmdef_file_denovo::pos, beta_nonlocal::pose, numeric::random::rg(), subloop_histogram::size, pna::test_score, and numeric::random::uniform().

Referenced by RunPepSpec().

gen_pep_bb_frag_old()

void gen_pep_bb_frag_old	(	pose::Pose &	pose,
		Size	pep_begin,
		Size	pep_anchor,
		Size	pep_end,
		scoring::ScoreFunctionOP	cen_scorefxn,
		protocols::frags::TorsionFragmentLibrary	lib
	)

References create_a3b_hbs::best_score, basic::options::OptionKeys::MonteCarlo::MonteCarlo, basic::options::OptionKeys::pepspec::n_build_loop, basic::options::OptionKeys::ddg::nfrags, option, pep_begin(), pep_end(), make_symmdef_file_denovo::pos, beta_nonlocal::pose, numeric::random::rg(), subloop_histogram::size, and numeric::random::uniform().

gen_pep_bb_rama()

void gen_pep_bb_rama	(	pose::Pose &	pose,
		Size	pep_begin,
		Size	pep_end,
		scoring::ScoreFunctionOP	cen_scorefxn
	)

References aa, basic::options::OptionKeys::MonteCarlo::MonteCarlo, basic::options::OptionKeys::pepspec::n_build_loop, option, pep_begin(), pep_end(), make_symmdef_file_denovo::pos, beta_nonlocal::pose, numeric::random::rg(), numeric::random::uniform(), and numeric::random::RandomGenerator::uniform().

Referenced by RunPepSpec().

get_n_pep_nbrs()

Size get_n_pep_nbrs	(	pose::Pose const &	pose,
		vector1< bool > const	is_pep,
		Real const	cutoff_cg
	)

References create_a3b_hbs::i, create_a3b_hbs::ii, create_a3b_hbs::j, beta_nonlocal::jj, beta_nonlocal::pose, test.T200_Scoring::rsd1, and test.T200_Scoring::rsd2.

has_clash()

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

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, and utility::graph::Node::upper_edge_list_end().

Referenced by refine_fa_pep_bb().

main()

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

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

my_main()

void* my_main

(

void *

)

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

Referenced by main().

packmin_unbound_pep()

void packmin_unbound_pep	(	pose::Pose &	pose,
		scoring::ScoreFunctionOP	full_scorefxn,
		scoring::ScoreFunctionOP	soft_scorefxn
	)

References vancomycin::min_mover, beta_nonlocal::mm, option, vancomycin::pack, beta_nonlocal::pose, and vancomycin::task.

Referenced by RunPepSpec().

pep_phipsi_analysis()

std::string pep_phipsi_analysis	(	pose::Pose	pose,
		Size	pep_begin,
		Size	pep_anchor,
		Size	pep_end
	)

References ObjexxFCL::abs(), basic::options::OptionKeys::AnchoredDesign::filters::omega, option, basic::options::OptionKeys::pepspec::pep_anchor, pep_begin(), basic::options::OptionKeys::pepspec::pep_chain, pep_end(), oop_conformations::phi, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, oop_conformations::psi, ObjexxFCL::string_of(), and basic::options::OptionKeys::inout::dbms::user.

Referenced by 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 pyrosetta::create_score_function, create_a3b_hbs::i, num_chains(), option, basic::options::OptionKeys::pepspec::pep_anchor, pep_begin(), basic::options::OptionKeys::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 RunPepSpec().

perturb_pep_bb()

void perturb_pep_bb	(	pose::Pose &	pose,
		kinematics::MoveMapOP	mm_move,
		scoring::ScoreFunctionOP	cen_scorefxn,
		Size	n_iter
	)

References basic::options::OptionKeys::MonteCarlo::MonteCarlo, and beta_nonlocal::pose.

Referenced by RunPepSpec().

refine_fa_pep_bb()

void refine_fa_pep_bb	(	Pose &	pose,
		Size	pep_anchor,
		vector1< bool >	is_pep,
		vector1< bool >	is_pep_nbr,
		scoring::ScoreFunctionOP	full_scorefxn
	)

References has_clash(), make_sequence_change(), beta_nonlocal::mm, basic::options::OptionKeys::MonteCarlo::MonteCarlo, option, basic::options::OptionKeys::pepspec::pep_anchor, beta_nonlocal::pose, and basic::options::OptionKeys::remodel::rama.

Referenced by RunPepSpec().

remove_pep_res()

void remove_pep_res	(	pose::Pose &	pose,
		Size	prot_anchor,
		Size &	pep_begin,
		Size &	pep_anchor,
		Size &	pep_end,
		bool	add_nterm,
		bool	add_cterm
	)

References add_termini(), basic::options::OptionKeys::pepspec::pep_anchor, pep_begin(), pep_end(), and beta_nonlocal::pose.

Referenced by RunPepSpec().

RunPepSpec()

void RunPepSpec

(

)

References aa, basic::options::OptionKeys::pepspec::add_buffer_res, add_pep_res(), add_termini(), basic::options::OptionKeys::pepspec::cen_wts, basic::options::OptionKeys::constraints::constraints, utility::io::oc::cout, utility::file::create_directory(), pyrosetta::create_score_function, basic::options::OptionKeys::constraints::cst_weight, extract_by_sidechain_sasa_score::cutoff, basic::options::OptionKeys::pepspec::dump_cg_bb, dump_efactor_pdb(), create_a3b_hbs::f, gen_fold_tree_for_nbr_segments(), gen_pep_bb_frag(), gen_pep_bb_rama(), getline(), create_a3b_hbs::i, create_a3b_hbs::ii, input_seq, basic::options::OptionKeys::pepspec::interface_cutoff, create_a3b_hbs::j, beta_nonlocal::jj, make_sequence_change(), vancomycin::min_mover, basic::options::OptionKeys::pepspec::n_append, basic::options::OptionKeys::pepspec::n_cgrelax_loop, basic::options::OptionKeys::pepspec::n_peptides, basic::options::OptionKeys::pepspec::n_prepend, num_chains(), out::file::o(), option, erraser_single_res_analysis::out, packmin_unbound_pep(), demo.D010_Pose_structure::pdb_filename, bur_nodon_tyr::pdb_list, basic::options::OptionKeys::pepspec::pep_anchor, pep_begin(), basic::options::OptionKeys::pepspec::pep_chain, pep_end(), pep_jump(), pep_phipsi_analysis(), pep_rmsd_analysis(), perturb_pep_bb(), beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, prot_anchor(), prot_begin(), prot_chain(), prot_end(), refine_fa_pep_bb(), remove_pep_res(), predPRE::resnum, numeric::random::rg(), basic::options::OptionKeys::pepspec::rmsd_analysis, test.T200_Scoring::rsd1, test.T200_Scoring::rsd2, test.Workshop5test::shear_mover, basic::options::OptionKeys::pepspec::soft_wts, basic::options::start_file(), ObjexxFCL::string_of(), numeric::random::uniform(), basic::options::OptionKeys::inout::dbms::user, utility_exit_with_message, and basic::options::OptionKeys::in::file::vall.

Referenced by my_main().