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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 <core/scoring/EnergyGraph.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/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/variant_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 <devel/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/pose_metric_calculators/DecomposeAndReweightEnergiesCalculator.hh>
#include <protocols/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

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

static basic::Tracer TR ("apps.public.pepspec")
 
std::string input_seq
 
vector1< pep_coord_cstpep_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 
)
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 
)
Real get_binding_score ( Pose  pose,
Size  pep_chain,
ScoreFunctionOP  full_scorefxn 
)
vector1< std::pair< Size, Size > > get_clash_pairs ( pose::Pose  pose,
vector1< bool is_checked,
scoring::ScoreFunctionOP const &  scorefxn,
Real const  clash_threshold 
)
Size get_n_pep_nbrs ( pose::Pose const &  pose,
vector1< bool > const  is_pep,
Real const  cutoff_cg 
)
bool has_clash ( pose::Pose  pose,
vector1< bool is_checked,
scoring::ScoreFunctionOP const &  scorefxn,
Real const  clash_threshold 
)
void initialize_peptide ( pose::Pose pose)
int main ( int  argc,
char *  argv[] 
)
core::fragment::FragSetCOP make_1mer_frags ( core::Size const  seqpos_start,
core::Size const  seqpos_stop,
std::string const &  seq,
Size const  nfrags 
)
core::fragment::FragSetCOP make_frags ( core::Size const  start,
core::Size const  stop,
std::string const &  seq 
)
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 
)
void* my_main ( void *  )
void packmin_unbound_pep ( pose::Pose pose,
scoring::ScoreFunctionOP  full_scorefxn 
)
Size pep_anchor ( )
Size pep_begin ( )
Size pep_chain ( )

Referenced by print_pep_analysis(), and RunPepSpec().

Size pep_end ( )
Size pep_jump ( )

Referenced by run_pep_prep(), and RunPepSpec().

std::string pep_phipsi_analysis ( pose::Pose  pose)
std::string pep_rmsd_analysis ( pose::Pose  pose)
void perturb_pep_bb ( pose::Pose pose,
kinematics::MoveMapOP  mm_move,
scoring::ScoreFunctionOP  cen_scorefxn,
Size  n_iter 
)
void print_pep_analysis ( std::string  pdb_name,
std::fstream &  out_file,
Pose  pose,
Real  prot_score,
ScoreFunctionOP  full_scorefxn,
bool  dump_pdb 
)
Size prot_anchor ( )
Size prot_begin ( )
Size prot_chain ( )
Size prot_end ( )
void remove_pep_res ( pose::Pose pose,
bool  add_nterm,
bool  add_cterm 
)
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::cluster::energy_based_clustering::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(), 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(), test.Workshop5test::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, erraser_single_res_analysis::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(), demo.D010_Pose_structure::pose, pyrosetta.distributed.io::pose_from_file, 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(), 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)

Variable Documentation

std::string input_seq
vector1< pep_coord_cst > pep_coord_csts

Referenced by RunPepSpec(), and set_pep_csts().

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