pepspec.cc File Reference

#include <protocols/frags/VallData.hh>
#include <protocols/frags/TorsionFragment.hh>
#include <core/fragment/ConstantLengthFragSet.hh>
#include <core/fragment/FragSet.hh>
#include <core/fragment/Frame.hh>
#include <core/fragment/picking_old/vall/util.hh>
#include <core/fragment/picking_old/FragmentLibraryManager.hh>
#include <core/scoring/LREnergyContainer.hh>
#include <core/scoring/methods/Methods.hh>
#include <core/scoring/ScoreType.hh>
#include <protocols/simple_moves/BackboneMover.hh>
#include <protocols/simple_moves/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/simple_moves/PackRotamersMover.hh>
#include <protocols/simple_moves/RotamerTrialsMover.hh>
#include <protocols/moves/RepeatMover.hh>
#include <protocols/simple_moves/FragmentMover.hh>
#include <protocols/viewer/viewers.hh>
#include <core/types.hh>
#include <core/scoring/sasa.hh>
#include <core/chemical/AtomTypeSet.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/conformation/ResidueFactory.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/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/scoring/hbonds/HBondSet.hh>
#include <core/scoring/hbonds/hbonds.hh>
#include <core/scoring/etable/count_pair/CountPairFactory.hh>
#include <core/scoring/etable/count_pair/CountPairAll.hh>
#include <core/scoring/etable/count_pair/CountPairFunction.hh>
#include <core/scoring/etable/EtableEnergy.hh>
#include <core/scoring/etable/BaseEtableEnergy.tmpl.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 <protocols/toolbox/IGEdgeReweighters.hh>
#include <core/pack/task/IGEdgeReweightContainer.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/kinematics/util.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/pose/PDBPoseMap.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/metrics/CalculatorFactory.hh>
#include <basic/options/util.hh>
#include <basic/basic.hh>
#include <basic/MetricValue.hh>
#include <basic/database/open.hh>
#include <protocols/init/init.hh>
#include <utility/vector1.hh>
#include <utility/file/file_sys_util.hh>
#include <numeric/xyzVector.hh>
#include <numeric/random/random.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/func/FlatHarmonicFunc.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/constraints/CoordinateConstraint.hh>
#include <core/scoring/constraints/ConstraintIO.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/score.OptionKeys.gen.hh>
#include <basic/options/keys/pepspec.OptionKeys.gen.hh>
#include <basic/options/keys/constraints.OptionKeys.gen.hh>
#include <protocols/toolbox/pose_metric_calculators/DecomposeAndReweightEnergiesCalculator.hh>
#include <protocols/toolbox/pose_metric_calculators/ResidueDecompositionByChainCalculator.hh>
#include <core/pose/metrics/simple_calculators/InterfaceNeighborDefinitionCalculator.hh>
#include <core/pose/metrics/simple_calculators/InterfaceSasaDefinitionCalculator.hh>
#include <core/pose/metrics/simple_calculators/InterfaceDeltaEnergeticsCalculator.hh>
#include <core/import_pose/import_pose.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/util/SwitchResidueTypeSet.hh>
#include <utility/excn/Exceptions.hh>

Classes
struct	pep_coord_cst
class	myMC

Functions
static THREAD_LOCAL basic::Tracer	TR ("apps.public.pepspec")
Size	prot_chain (0)
Size	prot_begin (0)
Size	prot_anchor (0)
Size	prot_end (0)
Size	pep_jump (2)
Size	pep_chain (0)
Size	pep_begin (0)
Size	pep_anchor (0)
Size	pep_end (0)
Size	aa2index (chemical::AA aa)
Size	get_n_pep_nbrs (pose::Pose const &pose, vector1< bool > const is_pep, Real const cutoff_cg)
void	make_sequence_change (Size const seqpos, AA const &new_aa, pose::Pose &pose)
bool	has_clash (pose::Pose pose, vector1< bool > is_checked, scoring::ScoreFunctionOP const &scorefxn, Real const clash_threshold)
vector1< std::pair< Size, Size > >	get_clash_pairs (pose::Pose pose, vector1< bool > is_checked, scoring::ScoreFunctionOP const &scorefxn, Real const clash_threshold)
std::string	pep_rmsd_analysis (pose::Pose pose)
std::string	pep_phipsi_analysis (pose::Pose pose)
void	add_termini (pose::Pose &pose)
void	add_pep_res (pose::Pose &pose, bool add_nterm, bool add_cterm)
void	remove_pep_res (pose::Pose &pose, bool add_nterm, bool add_cterm)
void	initialize_peptide (pose::Pose &pose)
void	set_pep_csts (pose::Pose &pose)
core::fragment::FragSetCOP	make_frags (core::Size const start, core::Size const stop, std::string const &seq)
	helper code for fragments generation, copied from S.M.Lewis More...
core::fragment::FragSetCOP	make_1mer_frags (core::Size const seqpos_start, core::Size const seqpos_stop, std::string const &seq, Size const nfrags)
void	gen_pep_bb_sequential (pose::Pose &pose, scoring::ScoreFunctionOP cen_scorefxn)
void	perturb_pep_bb (pose::Pose &pose, kinematics::MoveMapOP mm_move, scoring::ScoreFunctionOP cen_scorefxn, Size n_iter)
void	mutate_random_residue (Pose &pose, vector1< bool > is_mutable, ScoreFunctionOP soft_scorefxn, ScoreFunctionOP full_scorefxn)
void	packmin_unbound_pep (pose::Pose &pose, scoring::ScoreFunctionOP full_scorefxn)
Real	get_binding_score (Pose pose, Size pep_chain, ScoreFunctionOP full_scorefxn)
void	print_pep_analysis (std::string pdb_name, std::fstream &out_file, Pose pose, Real prot_score, ScoreFunctionOP full_scorefxn, bool dump_pdb)
void	RunPepSpec ()
void *	my_main (void *)
int	main (int argc, char *argv[])

Variables
std::string	input_seq
vector1< pep_coord_cst >	pep_coord_csts

Function Documentation

Size aa2index

(

chemical::AA

aa

)

References ObjexxFCL::index().

void add_pep_res	(	pose::Pose &	pose,
		bool	add_nterm,
		bool	add_cterm
	)

References add_termini(), pep_anchor(), pep_begin(), and pep_end().

void add_termini

(

pose::Pose &

pose

)

References pep_begin(), and pep_end().

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

void gen_pep_bb_sequential	(	pose::Pose &	pose,
		scoring::ScoreFunctionOP	cen_scorefxn
	)

References basic::options::OptionKeys::pepspec::cg_res_type, pepspec::cg_res_type(), basic::options::OptionKeys::chemical::chemical, basic::options::OptionKeys::pepspec::clash_cutoff, pepspec::clash_cutoff(), basic::options::OptionKeys::constraints::cst_weight, test.Workshop4test::fragset, pepspec::gen_pep_bb_sequential(), get_clash_pairs(), has_clash(), pepspec::homol_csts(), test.T200_Scoring::ii, pepspec::input_seq(), input_seq, make_1mer_frags(), make_sequence_change(), max(), basic::options::OptionKeys::score::saxs::min_score, basic::options::OptionKeys::MonteCarlo::MonteCarlo, basic::options::OptionKeys::pepspec::n_append, pepspec::n_append(), basic::options::OptionKeys::pepspec::n_build_loop, pepspec::n_build_loop(), basic::options::OptionKeys::pepspec::n_prepend, pepspec::n_prepend(), pepspec::no_cen_rottrials(), option, pep_anchor(), pep_begin(), pep_end(), app.surface_docking.surface_docking::pose, prot_begin(), prot_end(), app.delta_score_per_mutation::res, numeric::random::rg(), basic::options::OptionKeys::frags::scoring::scoring, set_pep_csts(), numeric::random::RandomGenerator::uniform(), pepspec::use_input_bb(), basic::options::OptionKeys::inout::dbms::user, and basic::options::OptionKeys::remodel::vdw.

Referenced by RunPepSpec().

Real get_binding_score	(	Pose	pose,
		Size	pep_chain,
		ScoreFunctionOP	full_scorefxn
	)

References packmin_unbound_pep(), and app.surface_docking.surface_docking::pose.

Referenced by print_pep_analysis(), and RunPepSpec().

vector1< std::pair< Size, Size > > get_clash_pairs	(	pose::Pose	pose,
		vector1< bool >	is_checked,
		scoring::ScoreFunctionOP const &	scorefxn,
		Real const	clash_threshold
	)

References basic::options::OptionKeys::chemical::chemical, test.T200_Scoring::emap, basic::options::OptionKeys::frags::j, app.surface_docking.surface_docking::pose, and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by gen_pep_bb_sequential().

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

References test.T200_Scoring::ii, basic::options::OptionKeys::frags::j, test.T200_Scoring::rsd1, and test.T200_Scoring::rsd2.

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

References basic::options::OptionKeys::chemical::chemical, test.T200_Scoring::emap, app.surface_docking.surface_docking::pose, and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by gen_pep_bb_sequential().

void initialize_peptide

(

pose::Pose &

pose

)

References basic::options::OptionKeys::pepspec::cg_res_type, pepspec::cg_res_type(), pepspec::input_seq(), make_sequence_change(), pepspec::no_design(), option, pep_anchor(), pep_begin(), pep_end(), app.surface_docking.surface_docking::pose, prot_anchor(), prot_chain(), pepspec::remove_input_bb(), app.delta_score_per_mutation::res, test.T200_Scoring::rsd1, test.T200_Scoring::rsd2, app.surface_docking.surface_docking::start_pose, pepspec::use_input_bb(), and basic::options::OptionKeys::inout::dbms::user.

Referenced by RunPepSpec().

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

References utility::io::oc::cout, basic::init(), utility::excn::EXCN_Base::msg(), my_main(), options, and TR().

core::fragment::FragSetCOP make_1mer_frags	(	core::Size const	seqpos_start,
		core::Size const	seqpos_stop,
		std::string const &	seq,
		Size const	nfrags
	)

References test.Workshop4test::fragset, numeric::kinematic_closure::frame(), pepspec::input_seq(), basic::options::OptionKeys::frags::j, basic::options::OptionKeys::in::file::list, option, numeric::random::rg(), pepspec::ss_type(), numeric::random::uniform(), and basic::options::OptionKeys::inout::dbms::user.

Referenced by gen_pep_bb_sequential().

core::fragment::FragSetCOP make_frags	(	core::Size const	start,
		core::Size const	stop,
		std::string const &	seq
	)

helper code for fragments generation, copied from S.M.Lewis

References test.Workshop4test::fragset, numeric::kinematic_closure::frame(), basic::options::OptionKeys::frags::j, and basic::options::OptionKeys::in::file::list.

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

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

References TR().

Referenced by gen_pep_bb_sequential(), initialize_peptide(), mutate_random_residue(), and RunPepSpec().

void mutate_random_residue	(	Pose &	pose,
		vector1< bool >	is_mutable,
		ScoreFunctionOP	soft_scorefxn,
		ScoreFunctionOP	full_scorefxn
	)

References make_sequence_change(), app.delta_score_per_mutation::min_mover, pep_anchor(), numeric::random::rg(), numeric::random::uniform(), and numeric::random::RandomGenerator::uniform().

Referenced by RunPepSpec().

void* my_main

(

void *

)

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

Referenced by main().

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

References app.delta_score_per_mutation::min_mover, app.delta_score_per_mutation::mm, loops::pack, app.surface_docking.surface_docking::pose, and app.delta_score_per_mutation::task.

Referenced by get_binding_score(), and RunPepSpec().

Size pep_anchor

(

0

)

Referenced by add_pep_res(), gen_pep_bb_sequential(), initialize_peptide(), mutate_random_residue(), pep_phipsi_analysis(), pep_rmsd_analysis(), remove_pep_res(), run_pep_prep(), RunPepSpec(), and set_pep_csts().

Size pep_begin

(

0

)

Referenced by add_pep_res(), add_termini(), gen_pep_bb_sequential(), initialize_peptide(), pep_phipsi_analysis(), pep_rmsd_analysis(), print_pep_analysis(), remove_pep_res(), run_pep_prep(), RunPepSpec(), and set_pep_csts().

Size pep_chain

(

0

)

Referenced by print_pep_analysis(), and RunPepSpec().

Size pep_end

(

0

)

Referenced by add_pep_res(), add_termini(), HbsDesignMover::apply(), PeptoidDesignMover::apply(), OopDesignMover::apply(), gen_pep_bb_sequential(), initialize_peptide(), pep_phipsi_analysis(), pep_rmsd_analysis(), print_pep_analysis(), remove_pep_res(), run_pep_prep(), RunPepSpec(), set_pep_csts(), and DougsDockDesignMinimizeMagicMover::setup_pert_foldtree().

Size pep_jump

(

2

)

Referenced by run_pep_prep(), and RunPepSpec().

std::string pep_phipsi_analysis

(

pose::Pose

pose

)

References ObjexxFCL::abs(), in::file::native(), pepspec::native_pep_anchor(), pepspec::native_pep_chain(), basic::options::OptionKeys::AnchoredDesign::filters::omega, option, pepspec::pep_anchor(), pep_anchor(), pep_begin(), pepspec::pep_chain(), pep_end(), ObjexxFCL::string_of(), and basic::options::OptionKeys::inout::dbms::user.

std::string pep_rmsd_analysis

(

pose::Pose

pose

)

References pyrosetta::get_score_function, in::file::native(), pepspec::native_align(), pepspec::native_pep_anchor(), pepspec::native_pep_chain(), option, pepspec::pep_anchor(), pep_anchor(), pep_begin(), pepspec::pep_chain(), pep_end(), prot_begin(), prot_end(), basic::options::OptionKeys::pepspec::rmsd_analysis, ObjexxFCL::string_of(), and basic::options::OptionKeys::inout::dbms::user.

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 app.surface_docking.surface_docking::pose.

Referenced by RunPepSpec().

void print_pep_analysis	(	std::string	pdb_name,
		std::fstream &	out_file,
		Pose	pose,
		Real	prot_score,
		ScoreFunctionOP	full_scorefxn,
		bool	dump_pdb
	)

References pepspec::binding_score(), pepspec::calc_sasa(), basic::options::OptionKeys::constraints::cst_weight, get_binding_score(), pepspec::homol_csts(), option, pep_begin(), pep_chain(), pep_end(), app.surface_docking.surface_docking::pose, ObjexxFCL::string_of(), pepspec::upweight_interface(), basic::options::OptionKeys::inout::dbms::user, and basic::MetricValue< T >::value().

Referenced by RunPepSpec().

Size prot_anchor

(

0

)

Referenced by initialize_peptide(), run_pep_prep(), RunPepSpec(), set_pep_cst(), and set_pep_csts().

Size prot_begin

(

0

)

Referenced by gen_pep_bb_sequential(), pep_rmsd_analysis(), run_pep_prep(), and RunPepSpec().

Size prot_chain

(

0

)

Referenced by initialize_peptide(), run_pep_prep(), and RunPepSpec().

Size prot_end

(

0

)

Referenced by gen_pep_bb_sequential(), pep_rmsd_analysis(), run_pep_prep(), and RunPepSpec().

void remove_pep_res	(	pose::Pose &	pose,
		bool	add_nterm,
		bool	add_cterm
	)

References add_termini(), pep_anchor(), pep_begin(), and pep_end().

void RunPepSpec

(

)

References pepspec::add_buffer_res(), add_termini(), pep_coord_cst::atom_name, pepspec::binding_score(), pepspec::cen_wts(), utility::file::create_directory(), pyrosetta::create_score_function, basic::options::OptionKeys::constraints::cst_file, basic::options::OptionKeys::constraints::cst_weight, basic::options::OptionKeys::cp::cutoff, pepspec::diversify_lvl(), pepspec::diversify_pep_seqs(), pepspec::dump_cg_bb(), demo.D060_Folding::f, gen_pep_bb_sequential(), get_binding_score(), pyrosetta::get_score_function, ObjexxFCL::getline(), pepspec::homol_csts(), test.T200_Scoring::ii, initialize_peptide(), pepspec::input_seq(), input_seq, pepspec::interface_cutoff(), basic::options::OptionKeys::frags::j, make_sequence_change(), app.delta_score_per_mutation::min_mover, basic::options::OptionKeys::MonteCarlo::MonteCarlo, mutate_random_residue(), basic::options::OptionKeys::pepspec::n_append, pepspec::n_append(), pepspec::n_build_loop(), basic::options::OptionKeys::pepspec::n_cgrelax_loop, pepspec::n_cgrelax_loop(), basic::options::OptionKeys::pepspec::n_peptides, pepspec::n_peptides(), basic::options::OptionKeys::pepspec::n_prepend, pepspec::n_prepend(), pepspec::no_cen(), pepspec::no_design(), out::file::o(), option, basic::options::OptionKeys::canonical_sampling::out::out, packmin_unbound_pep(), demo.D010_Pose_structure::pdb_filename, pepspec::pdb_list(), pepspec::pep_anchor(), pep_anchor(), pep_begin(), pepspec::pep_chain(), pep_chain(), pep_coord_csts, pep_end(), pep_jump(), pep_coord_cst::pep_pos, perturb_pep_bb(), app.surface_docking.surface_docking::pose, print_pep_analysis(), prot_anchor(), prot_begin(), prot_chain(), prot_end(), myMC::recover_low(), clean_pdb_keep_ligand::resnum, numeric::random::rg(), myMC::roll(), test.T200_Scoring::rsd1, test.T200_Scoring::rsd2, pepspec::run_sequential(), basic::options::OptionKeys::pepspec::save_all_pdbs, pepspec::save_all_pdbs(), basic::options::OptionKeys::pepspec::save_low_pdbs, pepspec::save_low_pdbs(), pep_coord_cst::sd, set_pep_csts(), pepspec::soft_wts(), basic::options::start_file(), app.surface_docking.surface_docking::start_pose, ObjexxFCL::string_of(), pep_coord_cst::tol, TR(), numeric::random::RandomGenerator::uniform(), pepspec::upweight_interface(), pepspec::use_input_bb(), basic::options::OptionKeys::inout::dbms::user, utility_exit_with_message, basic::options::OptionKeys::remodel::vdw, score::weights(), pep_coord_cst::x, pep_coord_cst::x0, pep_coord_cst::y, and pep_coord_cst::z.

Referenced by my_main().

void set_pep_csts

(

pose::Pose &

pose

)

References pep_coord_cst::atom_name, basic::options::OptionKeys::constraints::constraints, option, pepspec::p_homol_csts(), pep_anchor(), pep_begin(), pep_coord_csts, pep_end(), pep_coord_cst::pep_pos, prot_anchor(), numeric::random::rg(), pep_coord_cst::sd, pep_coord_cst::tol, numeric::random::uniform(), pep_coord_cst::x, pep_coord_cst::x0, pep_coord_cst::y, and pep_coord_cst::z.

Referenced by gen_pep_bb_sequential(), and RunPepSpec().

static THREAD_LOCAL basic::Tracer TR ( "apps.public.pepspec"  )

static

Referenced by main(), make_sequence_change(), and RunPepSpec().

Variable Documentation

std::string input_seq

Referenced by add_rosetta_options_11(), gen_pep_bb_sequential(), and RunPepSpec().

vector1< pep_coord_cst > pep_coord_csts

Referenced by RunPepSpec(), and set_pep_csts().