Rosetta
Functions | Variables
dna_spec_test.cc File Reference
#include <devel/dna/protocols.hh>
#include <devel/dna/ProteinDNA_Relax.hh>
#include <devel/dna/util.hh>
#include <protocols/loops/loops_main.hh>
#include <protocols/loops/Loops.hh>
#include <protocols/loops/LoopMover_CCD.hh>
#include <utility/excn/Exceptions.hh>
#include <protocols/viewer/viewers.hh>
#include <core/scoring/EnergiesCacheableDataType.hh>
#include <core/scoring/LREnergyContainer.hh>
#include <core/scoring/dna/setup.hh>
#include <core/scoring/dna/base_geometry.hh>
#include <core/scoring/dna/BasePartner.hh>
#include <core/scoring/dna/DNA_BasePotential.hh>
#include <core/pack/dunbrack/RotamerLibrary.hh>
#include <core/scoring/func/Func.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/constraints/CoordinateConstraint.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/ScoringManager.hh>
#include <core/scoring/AtomVDW.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/hbonds/hbonds.hh>
#include <core/scoring/hbonds/hbonds_geom.hh>
#include <core/scoring/hbonds/HBondSet.hh>
#include <core/scoring/hbonds/HBondDatabase.hh>
#include <core/energy_methods/FA_ElecEnergy.hh>
#include <core/scoring/etable/EtableEnergy.hh>
#include <core/scoring/etable/count_pair/CountPairFunction.hh>
#include <core/scoring/etable/count_pair/CountPairFactory.hh>
#include <core/types.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/VariantType.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/AtomTypeSet.hh>
#include <core/chemical/AA.hh>
#include <core/conformation/util.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueMatcher.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/rotamer_set/RotamerCouplings.hh>
#include <core/pack/rotamer_set/WaterAnchorInfo.hh>
#include <core/pack/rotamer_set/WaterPackingInfo.hh>
#include <core/pack/rotamer_set/WaterPackingInfo.fwd.hh>
#include <core/kinematics/FoldTree.hh>
#include <protocols/viewer/visualize.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/id/AtomID_Map.hh>
#include <core/id/AtomID_Map.Pose.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/PDBPoseMap.hh>
#include <core/pose/datacache/CacheableDataType.hh>
#include <core/scoring/Energies.hh>
#include <basic/options/util.hh>
#include <basic/datacache/BasicDataCache.hh>
#include <basic/prof.hh>
#include <core/id/SequenceMapping.hh>
#include <core/sequence/util.hh>
#include <devel/init.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <utility/vector1.hh>
#include <numeric/xyzVector.hh>
#include <numeric/xyzMatrix.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/random/random.hh>
#include <ObjexxFCL/string.functions.hh>
#include <fstream>
#include <iostream>
#include <string>
#include <set>
#include <cstdlib>
#include <sstream>
#include <basic/Tracer.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/dna.OptionKeys.gen.hh>
#include <basic/options/keys/phil.OptionKeys.gen.hh>
#include <basic/options/keys/packing.OptionKeys.gen.hh>
#include <core/chemical/AtomType.hh>
#include <core/import_pose/import_pose.hh>
#include <core/pose/util.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <protocols/frags/TorsionFragment.fwd.hh>
#include <core/util/SwitchResidueTypeSet.hh>
#include <ObjexxFCL/format.hh>

Functions

void show_allowed_residue_types (pack::task::PackerTask const &task, Size const seqpos)
 
void setup_atom_number (pose::Pose const &pose, id::AtomID_Map< int > &atom_number)
 
void read_list_file (std::string const &filename, utility::vector1< std::string > &l)
 
void extract_pdb_id (std::string const file, std::string &pdb_id)
 
void retrieve_residue_pair_energies (scoring::Energies const &energies, Size pos1, Size pos2, bool &are_they_neighbors, scoring::EnergyMap &emap)
 
void show_clashes (pose::Pose &pose, scoring::ScoreFunction const &scorefxn, Real const clash_threshold)
 
void dump_clash_pdb (pose::Pose &pose, scoring::ScoreFunction const &scorefxn, Real const clash_threshold, std::string const &filename)
 
void show_pairing_info (pose::Pose const &pose, Size const seqpos)
 
void show_rasmol_hbonds (scoring::hbonds::HBondSet const &hbond_set, id::AtomID_Map< int > const &atom_number, std::ostream &out)
 
void show_residue_hbonds (pose::Pose const &pose, Size const seqpos)
 
void wriggle_test (pose::Pose const &start_pose, Size const seqpos)
 
void dump_hbond_pdb (pose::Pose &pose, std::string const &filename)
 
void show_residue_residue_clashes (conformation::Residue const &rsd1, conformation::Residue const &rsd2, scoring::ScoreFunction const &scorefxn, Real const threshold, std::string const &output_tag)
 
void show_protein_DNA_interactions (pose::Pose &pose, scoring::ScoreFunction const &scorefxn)
 
void find_dna_rotamers (std::ofstream &pdb_lib, std::ofstream &dihedral_lib)
 
void get_base_pucker (conformation::Residue const &rsd, std::pair< std::string, std::string > &pucker)
 
void rescore_test ()
 
void intra_dna_stats ()
 
void kono_sarai_stats ()
 
std::string atom_line (std::string const &atom_name, std::string const &rsd_name, Vector const &xyz, int &counter)
 
void kono_sarai_zscore ()
 
void phosphate_stats ()
 
void spec_test (pose::Pose const &start_pose, scoring::ScoreFunction const &scorefxn, utility::vector1< Size > const &pos_list, std::string const &output_tag)
 
void idealize_tf_pose (pose::Pose &pose)
 
void zif268_test ()
 
void bzip_test ()
 
void endo_test ()
 
void cst_test ()
 
void tf_specificity_test (std::string const &tf_name, std::string wts_tag, std::string const &output_tag, Real const Wfa_elec, Real const Wdna_bp, Real const Wdna_bs)
 
void tf_specificity_test ()
 
void dna_specificity_test (std::string const &filename, int const motif_begin, int const motif_size, std::string wts_tag, std::string const &output_tag, Real const Wfa_elec, Real const Wdna_bp, Real const Wdna_bs)
 
void dna_nbr_radii_test ()
 
void loop_modeling_test ()
 
void luxr_setup ()
 
void luxr_test ()
 
void atom_vdw_test ()
 
void dna_specificity_test ()
 
void dump_dna_kinemage ()
 
void read_write ()
 
void analyze_interface_test ()
 
void water_test ()
 
void water_test_fixed_O ()
 
void interface_repack_test ()
 
void not1_test ()
 
void design_test ()
 
void compare_dna_energies ()
 
void compare_energies ()
 
void zf_test ()
 
void hbond_stats ()
 
void dna_dr_test ()
 
vector1< Size > find_dna_chainbreaks (pose::Pose const &pose)
 
void cleanup_dna_chains (pose::Pose &pose)
 
void dna_chain_check ()
 
vector1< Size > parse_pdb_pos (pose::Pose const &pose, utility::options::StringVectorOptionKey const &key)
 
vector1< Size > parse_pdb_pos (pose::Pose const &pose)
 
void not1_loop_test ()
 
void * my_main (void *)
 
int main (int argc, char *argv[])
 

Variables

static basic::Tracer ti ("demo.phil.dna_spec_test", basic::t_info)
 
static basic::Tracer tt ("demo.phil.dna_spec_test", basic::t_trace)
 

Function Documentation

◆ analyze_interface_test()

void analyze_interface_test ( )

References basic::options::OptionKeys::matdes::dock::dump_pdb, test.T200_Scoring::hbond_set, create_a3b_hbs::i, basic::options::OptionKeys::dna::specificity::moving_jump, option, erraser_single_res_analysis::out, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, setup_atom_number(), basic::options::OptionKeys::out::sf, show_rasmol_hbonds(), and basic::options::start_file().

Referenced by my_main().

◆ atom_line()

std::string atom_line ( std::string const &  atom_name,
std::string const &  rsd_name,
Vector const &  xyz,
int &  counter 
)

References demo.D060_Folding::counter, ObjexxFCL::format::F(), test.T110_numeric::I, and basic::options::OptionKeys::in::file::xyz.

Referenced by phosphate_stats().

◆ atom_vdw_test()

void atom_vdw_test ( )

References basic::options::OptionKeys::constraints::constraints, utility::io::oc::cout, basic::options::OptionKeys::matdes::dock::dump_pdb, utility::options::OptionKeys::options::exit, ObjexxFCL::format::F(), create_a3b_hbs::i, create_a3b_hbs::ii, create_a3b_hbs::j, beta_nonlocal::jj, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, create_a3b_hbs::nres, erraser_single_res_analysis::out, beta_nonlocal::pose, test.T200_Scoring::rsd1, test.T200_Scoring::rsd2, basic::options::OptionKeys::frags::scoring::scoring, and basic::options::start_files().

Referenced by my_main().

◆ bzip_test()

void bzip_test ( )

References pyrosetta::create_score_function, test.T220_AtomAtomPairEnergies::fa_elec, lactamize::filename, create_a3b_hbs::j, basic::options::OptionKeys::dna::specificity::motif_begin, basic::options::OptionKeys::dna::specificity::motif_size, option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, read_list_file(), oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::start_file(), basic::options::OptionKeys::dna::specificity::Wdna_bp, basic::options::OptionKeys::dna::specificity::Wdna_bs, basic::options::OptionKeys::dna::specificity::weights_tag, basic::options::OptionKeys::dna::specificity::weights_tag_list, and basic::options::OptionKeys::dna::specificity::Wfa_elec.

Referenced by my_main().

◆ cleanup_dna_chains()

void cleanup_dna_chains ( pose::Pose &  pose)

References basic::options::OptionKeys::dna::dna, end, detail::find(), find_dna_chainbreaks(), create_a3b_hbs::i, create_a3b_hbs::nres, beta_nonlocal::pose, tt, and utility_exit_with_message.

Referenced by dna_chain_check().

◆ compare_dna_energies()

void compare_dna_energies ( )

References utility::io::oc::cout, pyrosetta::create_score_function, basic::options::OptionKeys::dna::dna, test.T200_Scoring::emap, ObjexxFCL::format::F(), create_a3b_hbs::i, test.T110_numeric::I, create_a3b_hbs::j, create_a3b_hbs::nres, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, retrieve_residue_pair_energies(), test.T200_Scoring::rsd1, test.T200_Scoring::rsd2, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::start_file(), and weights().

Referenced by my_main().

◆ compare_energies()

void compare_energies ( )

References utility::io::oc::cout, basic::options::OptionKeys::dna::dna, test.T200_Scoring::emap, ObjexxFCL::format::F(), create_a3b_hbs::i, test.T110_numeric::I, create_a3b_hbs::j, create_a3b_hbs::nres, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, retrieve_residue_pair_energies(), oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::start_file(), and weights().

Referenced by my_main().

◆ cst_test()

void cst_test ( )

References idealize_tf_pose(), beta_nonlocal::pose, and pyrosetta.distributed.io::pose_from_file.

Referenced by my_main().

◆ design_test()

void design_test ( )

References utility::io::oc::cout, pyrosetta::create_score_function, basic::options::OptionKeys::dna::dna, out::file::o(), option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::prof_reset(), basic::prof_show(), basic::options::OptionKeys::dna::specificity::score_function, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::start_file(), vancomycin::task, and basic::options::OptionKeys::inout::dbms::user.

Referenced by my_main().

◆ dna_chain_check()

void dna_chain_check ( )

References cleanup_dna_chains(), utility::io::oc::cout, basic::options::OptionKeys::dna::dna, test.T200_Scoring::emap, ObjexxFCL::format::F(), evaluate_beta_mutants::file, create_a3b_hbs::i, test.T110_numeric::I, create_a3b_hbs::j, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, create_a3b_hbs::nres, num_chains(), options, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, retrieve_residue_pair_energies(), test.T200_Scoring::rsd1, test.T200_Scoring::rsd2, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::start_files(), and tt.

Referenced by my_main().

◆ dna_dr_test()

void dna_dr_test ( )

References beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, and tt.

Referenced by my_main().

◆ dna_nbr_radii_test()

void dna_nbr_radii_test ( )

References basic::options::OptionKeys::constraints::constraints, utility::io::oc::cout, numeric::xyzVector< T >::distance(), basic::options::OptionKeys::frags::frags, create_a3b_hbs::i, create_a3b_hbs::j, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, kic_runner::pdb, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::frags::scoring::scoring, and basic::options::start_files().

Referenced by my_main().

◆ dna_specificity_test() [1/2]

void dna_specificity_test ( )

References utility::io::oc::cout, dna_specificity_test(), create_a3b_hbs::i, create_a3b_hbs::j, basic::options::OptionKeys::dna::specificity::motif_begin, basic::options::OptionKeys::dna::specificity::motif_size, option, out::output_tag(), read_list_file(), basic::options::start_files(), ObjexxFCL::string_of(), basic::options::OptionKeys::dna::specificity::Wdna_bp, basic::options::OptionKeys::dna::specificity::Wdna_bs, basic::options::OptionKeys::dna::specificity::weights_tag, basic::options::OptionKeys::dna::specificity::weights_tag_list, and basic::options::OptionKeys::dna::specificity::Wfa_elec.

◆ dna_specificity_test() [2/2]

void dna_specificity_test ( std::string const &  filename,
int const  motif_begin,
int const  motif_size,
std::string  wts_tag,
std::string const &  output_tag,
Real const  Wfa_elec,
Real const  Wdna_bp,
Real const  Wdna_bs 
)

References utility::io::oc::cout, pyrosetta::create_score_function, test.T220_AtomAtomPairEnergies::fa_elec, basic::options::OptionKeys::dna::specificity::fast, lactamize::filename, basic::options::OptionKeys::dna::specificity::min_type, basic::options::OptionKeys::dna::specificity::minimize_tolerance, basic::options::OptionKeys::dna::specificity::motif_begin, basic::options::OptionKeys::dna::specificity::motif_size, basic::options::OptionKeys::dna::specificity::nloop, option, drrafter_rna::output_tag, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::dna::specificity::post_minimize, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::dna::specificity::soft_rep, basic::options::OptionKeys::dna::specificity::Wdna_bp, basic::options::OptionKeys::dna::specificity::Wdna_bs, and basic::options::OptionKeys::dna::specificity::Wfa_elec.

Referenced by dna_specificity_test().

◆ dump_clash_pdb()

void dump_clash_pdb ( pose::Pose &  pose,
scoring::ScoreFunction const &  scorefxn,
Real const  clash_threshold,
std::string const &  filename 
)

Dump a pdb file with b-factor = total (weighted) repulsive energy per atom and with monitors between clashing atoms above clash_threshold

References clash_score(), test.T200_Scoring::emap, lactamize::filename, utility::graph::Edge::get_node(), create_a3b_hbs::i, create_a3b_hbs::ii, basic::options::initialize(), create_a3b_hbs::j, beta_nonlocal::jj, erraser_single_res_analysis::out, beta_nonlocal::pose, test.T200_Scoring::rsd1, test.T200_Scoring::rsd2, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, setup_atom_number(), utility::graph::Node::upper_edge_list_end(), and basic::options::OptionKeys::sc::weight.

Referenced by not1_test().

◆ dump_dna_kinemage()

void dump_dna_kinemage ( )

References utility::options::OptionKeys::options::exit, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, and basic::options::start_file().

◆ dump_hbond_pdb()

void dump_hbond_pdb ( pose::Pose &  pose,
std::string const &  filename 
)

References spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::D, basic::options::OptionKeys::matdes::dock::dump_pdb, lactamize::filename, test.T200_Scoring::hbond_set, erraser_single_res_analysis::out, PHI, beta_nonlocal::pose, setup_atom_number(), show_rasmol_hbonds(), and THETA.

Referenced by not1_test(), show_protein_DNA_interactions(), water_test(), and water_test_fixed_O().

◆ endo_test()

void endo_test ( )

References pyrosetta::create_score_function, basic::options::OptionKeys::matdes::dock::dump_pdb, test.T220_AtomAtomPairEnergies::fa_elec, lactamize::filename, create_a3b_hbs::i, create_a3b_hbs::j, basic::options::OptionKeys::dna::specificity::min_type, basic::options::OptionKeys::dna::specificity::minimize_tolerance, basic::options::OptionKeys::dna::specificity::motif_begin, basic::options::OptionKeys::dna::specificity::motif_size, basic::options::OptionKeys::dna::specificity::nloop, option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::dna::specificity::post_minimize, read_list_file(), oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::start_file(), basic::options::OptionKeys::dna::specificity::Wdna_bp, basic::options::OptionKeys::dna::specificity::Wdna_bs, basic::options::OptionKeys::dna::specificity::weights_tag, basic::options::OptionKeys::dna::specificity::weights_tag_list, and basic::options::OptionKeys::dna::specificity::Wfa_elec.

Referenced by my_main().

◆ extract_pdb_id()

void extract_pdb_id ( std::string const  file,
std::string &  pdb_id 
)

References evaluate_beta_mutants::file, and erraser_single_res_analysis::pdb_id.

Referenced by rescore_test(), and zf_test().

◆ find_dna_chainbreaks()

vector1< Size > find_dna_chainbreaks ( pose::Pose const &  pose)

References create_a3b_hbs::i, beta_nonlocal::pose, test.T200_Scoring::rsd1, test.T200_Scoring::rsd2, and revert_app::threshold.

Referenced by cleanup_dna_chains().

◆ find_dna_rotamers()

void find_dna_rotamers ( std::ofstream &  pdb_lib,
std::ofstream &  dihedral_lib 
)

References basic::options::OptionKeys::dna::dna, basic::options::OptionKeys::matdes::dock::dump_pdb, ObjexxFCL::format::F(), create_a3b_hbs::i, test.T110_numeric::I, basic::options::initialize(), create_a3b_hbs::j, basic::options::OptionKeys::cm::nn, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::frags::scoring::scoring, and basic::options::start_files().

Referenced by my_main().

◆ get_base_pucker()

void get_base_pucker ( conformation::Residue const &  rsd,
std::pair< std::string, std::string > &  pucker 
)

References ObjexxFCL::abs(), atoms, measure_params::cross(), measure_params::dot(), numeric::xyzVector< T >::dot(), create_a3b_hbs::i, create_a3b_hbs::ii, and run_backbone::names.

Referenced by intra_dna_stats().

◆ hbond_stats()

void hbond_stats ( )

References numeric::arccos(), utility::io::oc::cout, numeric::conversions::degrees(), numeric::xyzVector< T >::distance_squared(), measure_params::dot(), ObjexxFCL::format::F(), evaluate_beta_mutants::file, create_a3b_hbs::i, create_a3b_hbs::ii, create_a3b_hbs::j, beta_nonlocal::jj, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, create_a3b_hbs::nres, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, test.T200_Scoring::rsd1, test.T200_Scoring::rsd2, basic::options::start_files(), and tt.

Referenced by my_main().

◆ idealize_tf_pose()

void idealize_tf_pose ( pose::Pose &  pose)

References basic::options::OptionKeys::constraints::constraints, demo.D060_Folding::counter, utility::io::oc::cout, basic::options::OptionKeys::matdes::dock::dump_pdb, utility::options::OptionKeys::options::exit, create_a3b_hbs::f, ObjexxFCL::format::F(), detail::find(), create_a3b_hbs::i, test.T110_numeric::I, create_a3b_hbs::ii, create_a3b_hbs::j, beta_nonlocal::jj, ObjexxFCL::lead_zero_string_of(), beta_nonlocal::mm, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, create_a3b_hbs::nres, out::nstruct(), option, options, beta_nonlocal::pose, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, and numeric::random::uniform().

Referenced by cst_test().

◆ interface_repack_test()

void interface_repack_test ( )

References utility::io::oc::cout, create_a3b_hbs::i, interface, create_a3b_hbs::j, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, basic::options::OptionKeys::dna::specificity::nloop, create_a3b_hbs::nres, option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::dna::specificity::score_function, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::start_files(), vancomycin::task, and basic::options::OptionKeys::inout::dbms::user.

◆ intra_dna_stats()

void intra_dna_stats ( )

void motif_scan() {

vector1< string > const files( basic::options::start_files() );

for ( Size m=1; m<= files.size(); ++m ) { string const & file( files[m] );

pose::Pose pose; core::import_pose::pose_from_file( pose, file , core::import_pose::PDB_file);

read the motif positions

} Collect stats on intra-dna interactions for the purposes of parametrizing DNA reference energies

fa_atr, rep, sol hbond fa_elec

References utility::io::oc::cout, basic::options::OptionKeys::dna::dna, basic::options::OptionKeys::matdes::dock::dump_pdb, ObjexxFCL::format::E(), test.T200_Scoring::emap, ObjexxFCL::format::F(), test.T220_AtomAtomPairEnergies::fa_elec, get_base_pucker(), create_a3b_hbs::i, test.T110_numeric::I, ObjexxFCL::lead_zero_string_of(), basic::options::OptionKeys::cm::nn, options, p2, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, retrieve_residue_pair_energies(), test.T200_Scoring::rsd1, test.T200_Scoring::rsd2, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, show_residue_residue_clashes(), basic::options::start_files(), and tag.

Referenced by my_main().

◆ kono_sarai_stats()

void kono_sarai_stats ( )

References utility::io::oc::cout, basic::options::OptionKeys::dna::dna, measure_params::dot(), ObjexxFCL::format::F(), create_a3b_hbs::i, test.T110_numeric::I, create_a3b_hbs::j, basic::options::OptionKeys::cm::nn, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, enumerate_junctions::q, test.T200_Scoring::rsd2, basic::options::OptionKeys::frags::scoring::scoring, basic::options::start_files(), x, xx, predPRE::y, yy, predPRE::z, and test.T110_numeric::zz.

Referenced by my_main().

◆ kono_sarai_zscore()

void kono_sarai_zscore ( )

References utility::io::oc::cout, basic::options::OptionKeys::dna::dna, measure_params::dot(), ObjexxFCL::format::F(), create_a3b_hbs::i, create_a3b_hbs::j, create_a3b_hbs::k, basic::options::OptionKeys::cm::nn, erraser_single_res_analysis::out, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, enumerate_junctions::q, test.T200_Scoring::rsd2, basic::options::OptionKeys::frags::scoring::scoring, basic::options::start_files(), x, xx, predPRE::y, yy, predPRE::z, and test.T110_numeric::zz.

Referenced by my_main().

◆ loop_modeling_test()

void loop_modeling_test ( )

References basic::options::OptionKeys::constraints::constraints, utility::io::oc::cout, numeric::xyzVector< T >::distance(), basic::options::OptionKeys::matdes::dock::dump_pdb, test.T009_Exceptions::e, basic::options::OptionKeys::frags::frags, create_a3b_hbs::i, test.T110_numeric::I, create_a3b_hbs::j, demo.D080_Loop_modeling::loop_begin, basic::options::OptionKeys::cluster::loops, kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, offset, option, kic_runner::pdb, make_symmdef_file_denovo::pos, beta_nonlocal::pose, basic::prof_reset(), basic::prof_show(), basic::options::OptionKeys::frags::scoring::scoring, basic::options::start_file(), and utility_exit_with_message.

Referenced by my_main().

◆ luxr_setup()

void luxr_setup ( )

References utility::io::oc::cout, basic::options::OptionKeys::dna::dna, basic::options::OptionKeys::matdes::dock::dump_pdb, utility::options::OptionKeys::options::exit, create_a3b_hbs::f, create_a3b_hbs::i, create_a3b_hbs::ii, create_a3b_hbs::j, beta_nonlocal::jj, kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, create_a3b_hbs::nres, out::file::o(), option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::start_file(), and utility_exit_with_message.

Referenced by my_main().

◆ luxr_test()

void luxr_test ( )

References basic::options::OptionKeys::dna::dna, test.T220_AtomAtomPairEnergies::fa_elec, lactamize::filename, ObjexxFCL::lead_zero_string_of(), basic::options::OptionKeys::dna::specificity::motif_begin, basic::options::OptionKeys::dna::specificity::motif_size, basic::options::OptionKeys::dna::specificity::moving_jump, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, local::nstruct, out::nstruct(), option, out::output_tag(), beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::prof_reset(), basic::prof_show(), basic::options::OptionKeys::dna::specificity::randomize_motif, basic::options::OptionKeys::dna::specificity::score_function, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::start_file(), tt, basic::options::OptionKeys::inout::dbms::user, utility_exit_with_message, basic::options::OptionKeys::dna::specificity::Wdna_bp, basic::options::OptionKeys::dna::specificity::Wdna_bs, and basic::options::OptionKeys::dna::specificity::Wfa_elec.

Referenced by my_main().

◆ 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 analyze_interface_test(), atom_vdw_test(), bzip_test(), compare_dna_energies(), compare_energies(), cst_test(), design_test(), dna_chain_check(), dna_dr_test(), dna_nbr_radii_test(), endo_test(), utility::options::OptionKeys::options::exit, find_dna_rotamers(), hbond_stats(), intra_dna_stats(), kono_sarai_stats(), kono_sarai_zscore(), loop_modeling_test(), luxr_setup(), luxr_test(), SmotifHasher::mode, not1_loop_test(), not1_test(), option, phosphate_stats(), read_write(), rescore_test(), tf_specificity_test(), utility_exit_with_message, value, water_test(), zf_test(), and zif268_test().

Referenced by main().

◆ not1_loop_test()

void not1_loop_test ( )

References utility::io::oc::cout, loops::cutpoint, create_a3b_hbs::f, lactamize::filename, create_a3b_hbs::i, create_a3b_hbs::j, ObjexxFCL::lead_zero_string_of(), demo.D080_Loop_modeling::loop_begin, pivot_selection::loop_end, basic::options::OptionKeys::cluster::loops, basic::options::OptionKeys::dna::specificity::methylate, local::nstruct, option, options, drrafter_rna::output_tag, parse_pdb_pos(), beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::dna::specificity::score_function, oop_conformations::scorefxn, basic::options::start_file(), tt, and basic::options::OptionKeys::inout::dbms::user.

Referenced by my_main().

◆ not1_test()

void not1_test ( )

References utility::io::oc::cout, basic::options::OptionKeys::dna::dna, dump_clash_pdb(), dump_hbond_pdb(), utility::options::OptionKeys::options::exit, test.T220_AtomAtomPairEnergies::fa_elec, test.T200_Scoring::hbond_set, create_a3b_hbs::i, beta_nonlocal::mm, basic::options::OptionKeys::dna::specificity::motif_begin, option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, test.T500_Packing::rotamer_trials, test.T200_Scoring::rsd1, test.T200_Scoring::rsd2, basic::options::OptionKeys::dna::specificity::score_function, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, show_residue_hbonds(), basic::options::start_file(), ObjexxFCL::string_of(), vancomycin::task, basic::options::OptionKeys::inout::dbms::user, basic::options::OptionKeys::dna::specificity::Wdna_bp, basic::options::OptionKeys::dna::specificity::Wdna_bs, and basic::options::OptionKeys::dna::specificity::Wfa_elec.

Referenced by my_main().

◆ parse_pdb_pos() [1/2]

vector1< Size > parse_pdb_pos ( pose::Pose const &  pose)

References parse_pdb_pos(), basic::options::OptionKeys::dna::specificity::pdb_pos, and beta_nonlocal::pose.

◆ parse_pdb_pos() [2/2]

vector1< Size > parse_pdb_pos ( pose::Pose const &  pose,
utility::options::StringVectorOptionKey const &  key 
)

References predPRE::chain, create_a3b_hbs::i, ObjexxFCL::int_of(), subloop_histogram::key, option, make_symmdef_file_denovo::pos, and beta_nonlocal::pose.

Referenced by not1_loop_test(), and parse_pdb_pos().

◆ phosphate_stats()

void phosphate_stats ( )

References atom_line(), demo.D060_Folding::counter, numeric::xyzVector< T >::distance(), basic::options::OptionKeys::dna::dna, create_a3b_hbs::i, create_a3b_hbs::j, beta_nonlocal::jj, basic::options::OptionKeys::cm::nn, erraser_single_res_analysis::out, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, test.T200_Scoring::rsd2, basic::options::OptionKeys::frags::scoring::scoring, basic::options::start_files(), and stub().

Referenced by my_main().

◆ read_list_file()

void read_list_file ( std::string const &  filename,
utility::vector1< std::string > &  l 
)

References utility::io::oc::cout, data, lactamize::filename, getline(), extract_by_sidechain_sasa_score::l, line, and utility_exit_with_message.

Referenced by bzip_test(), dna_specificity_test(), endo_test(), rescore_test(), tf_specificity_test(), zf_test(), and zif268_test().

◆ read_write()

void read_write ( )

References out::file::o(), option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, and basic::options::start_file().

Referenced by my_main().

◆ rescore_test()

void rescore_test ( )

References pyrosetta::create_score_function, test.T200_Scoring::emap, extract_pdb_id(), ObjexxFCL::format::F(), evaluate_beta_mutants::file, create_a3b_hbs::i, create_a3b_hbs::j, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, option, erraser_single_res_analysis::pdb_id, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, read_list_file(), res, erraser_analysis::res2, retrieve_residue_pair_energies(), oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::start_files(), predPRE::t, tag, weights(), basic::options::OptionKeys::dna::specificity::weights_tag, and basic::options::OptionKeys::dna::specificity::weights_tag_list.

Referenced by my_main().

◆ retrieve_residue_pair_energies()

void retrieve_residue_pair_energies ( scoring::Energies const &  energies,
Size  pos1,
Size  pos2,
bool &  are_they_neighbors,
scoring::EnergyMap &  emap 
)

References utility::graph::Node::const_upper_edge_list_end(), test.T200_Scoring::emap, utility::graph::Edge::get_node(), and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by compare_dna_energies(), compare_energies(), dna_chain_check(), intra_dna_stats(), and rescore_test().

◆ setup_atom_number()

void setup_atom_number ( pose::Pose const &  pose,
id::AtomID_Map< int > &  atom_number 
)

References create_a3b_hbs::i, basic::options::initialize(), create_a3b_hbs::j, and beta_nonlocal::pose.

Referenced by analyze_interface_test(), dump_clash_pdb(), and dump_hbond_pdb().

◆ show_allowed_residue_types()

void show_allowed_residue_types ( pack::task::PackerTask const &  task,
Size const  seqpos 
)

References utility::io::oc::cout, and vancomycin::task.

Referenced by water_test().

◆ show_clashes()

void show_clashes ( pose::Pose &  pose,
scoring::ScoreFunction const &  scorefxn,
Real const  clash_threshold 
)

References clash(), utility::io::oc::cout, ObjexxFCL::format::F(), utility::graph::Edge::get_node(), create_a3b_hbs::i, test.T110_numeric::I, create_a3b_hbs::j, beta_nonlocal::pose, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, and utility::graph::Node::upper_edge_list_end().

Referenced by spec_test().

◆ show_pairing_info()

void show_pairing_info ( pose::Pose const &  pose,
Size const  seqpos 
)

References utility::io::oc::cout, basic::options::OptionKeys::dna::dna, ObjexxFCL::format::F(), beta_nonlocal::pose, and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by spec_test().

◆ show_protein_DNA_interactions()

void show_protein_DNA_interactions ( pose::Pose &  pose,
scoring::ScoreFunction const &  scorefxn 
)

References utility::io::oc::cout, dump_hbond_pdb(), test.T200_Scoring::emap, ObjexxFCL::format::F(), test.T200_Scoring::hbond_set, create_a3b_hbs::i, test.T110_numeric::I, beta_nonlocal::pose, oop_conformations::scorefxn, and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by spec_test().

◆ show_rasmol_hbonds()

void show_rasmol_hbonds ( scoring::hbonds::HBondSet const &  hbond_set,
id::AtomID_Map< int > const &  atom_number,
std::ostream &  out 
)

References test.T200_Scoring::hbond_set, and create_a3b_hbs::i.

Referenced by analyze_interface_test(), and dump_hbond_pdb().

◆ show_residue_hbonds()

void show_residue_hbonds ( pose::Pose const &  pose,
Size const  seqpos 
)

References utility::io::oc::cout, ObjexxFCL::format::F(), test.T200_Scoring::hbond_set, create_a3b_hbs::i, test.T110_numeric::I, and beta_nonlocal::pose.

Referenced by not1_test().

◆ show_residue_residue_clashes()

void show_residue_residue_clashes ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
scoring::ScoreFunction const &  scorefxn,
Real const  threshold,
std::string const &  output_tag 
)

References utility::io::oc::cout, test.T200_Scoring::emap, ObjexxFCL::format::F(), test.T110_numeric::I, create_a3b_hbs::ii, beta_nonlocal::jj, drrafter_rna::output_tag, test.T200_Scoring::rsd1, test.T200_Scoring::rsd2, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, revert_app::threshold, and basic::options::OptionKeys::sc::weight.

Referenced by intra_dna_stats().

◆ spec_test()

void spec_test ( pose::Pose const &  start_pose,
scoring::ScoreFunction const &  scorefxn,
utility::vector1< Size > const &  pos_list,
std::string const &  output_tag 
)

References utility::io::oc::cout, revert_app::design, basic::options::OptionKeys::dna::dna, basic::options::OptionKeys::matdes::dock::dump_pdb, test.T200_Scoring::emap, utility::options::OptionKeys::options::exit, ObjexxFCL::format::F(), create_a3b_hbs::i, test.T110_numeric::I, create_a3b_hbs::ii, interface, beta_nonlocal::mm, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, basic::options::OptionKeys::dna::specificity::nloop, basic::options::OptionKeys::cm::nn, create_a3b_hbs::nres, drrafter_rna::output_tag, make_symmdef_file_denovo::pos, beta_nonlocal::pose, basic::prof_reset(), basic::prof_show(), create_a3b_hbs::r, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, beta_sc_scan::seq, show_clashes(), show_pairing_info(), show_protein_DNA_interactions(), vancomycin::task, and ObjexxFCL::uppercased().

Referenced by tf_specificity_test().

◆ tf_specificity_test() [1/2]

void tf_specificity_test ( )

References create_a3b_hbs::i, create_a3b_hbs::j, option, out::output_tag(), read_list_file(), basic::options::start_files(), tf_specificity_test(), basic::options::OptionKeys::dna::specificity::Wdna_bp, basic::options::OptionKeys::dna::specificity::Wdna_bs, basic::options::OptionKeys::dna::specificity::weights_tag, basic::options::OptionKeys::dna::specificity::weights_tag_list, and basic::options::OptionKeys::dna::specificity::Wfa_elec.

◆ tf_specificity_test() [2/2]

void tf_specificity_test ( std::string const &  tf_name,
std::string  wts_tag,
std::string const &  output_tag,
Real const  Wfa_elec,
Real const  Wdna_bp,
Real const  Wdna_bs 
)

References ObjexxFCL::abs(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, chain_begin(), chains, utility::io::oc::cout, pyrosetta::create_score_function, data, basic::options::OptionKeys::dna::dna, basic::options::OptionKeys::matdes::dock::dump_pdb, test.T009_Exceptions::e, create_a3b_hbs::f, test.T220_AtomAtomPairEnergies::fa_elec, lactamize::filename, getline(), create_a3b_hbs::i, create_a3b_hbs::ii, create_a3b_hbs::j, beta_nonlocal::jj, create_a3b_hbs::k, extract_by_sidechain_sasa_score::l, line, basic::options::OptionKeys::dna::specificity::min_type, basic::options::OptionKeys::dna::specificity::minimize_tolerance, basic::options::OptionKeys::dna::specificity::nloop, option, erraser_single_res_analysis::out, drrafter_rna::output_tag, kic_runner::pdb, make_symmdef_file_denovo::pos, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::dna::specificity::post_minimize, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, beta_sc_scan::seq, basic::options::OptionKeys::dna::specificity::soft_rep, spec_test(), tag, basic::options::OptionKeys::dna::specificity::Wdna_bp, basic::options::OptionKeys::dna::specificity::Wdna_bs, basic::options::OptionKeys::dna::specificity::Wfa_elec, and wriggle_test().

Referenced by my_main(), and tf_specificity_test().

◆ water_test()

void water_test ( )

References atoms, dump_hbond_pdb(), packing::ex1::ex1(), packing::exdna::exdna(), create_a3b_hbs::i, create_a3b_hbs::ii, create_a3b_hbs::j, packing::ex1::level(), packing::exdna::level(), beta_nonlocal::mm, basic::options::OptionKeys::dna::specificity::nstep_water, option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::dna::specificity::score_function, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, show_allowed_residue_types(), basic::options::start_file(), vancomycin::task, and basic::options::OptionKeys::inout::dbms::user.

Referenced by my_main().

◆ water_test_fixed_O()

void water_test_fixed_O ( )

References dump_hbond_pdb(), create_a3b_hbs::i, create_a3b_hbs::ii, create_a3b_hbs::j, beta_nonlocal::mm, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, test.T200_Scoring::rsd2, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::start_file(), vancomycin::task, and basic::options::OptionKeys::in::file::xyz.

◆ wriggle_test()

void wriggle_test ( pose::Pose const &  start_pose,
Size const  seqpos 
)

References ObjexxFCL::abs(), atoms, utility::io::oc::cout, numeric::xyzVector< T >::cross(), numeric::xyzVector< T >::dot(), basic::options::OptionKeys::matdes::dock::dump_pdb, test.T009_Exceptions::e, ObjexxFCL::format::F(), create_a3b_hbs::i, test.G201_Module_Structure::l1, ObjexxFCL::lead_zero_string_of(), beta_nonlocal::pose, create_a3b_hbs::r, tag, numeric::random::uniform(), oop_scan::v1, and oop_scan::v2.

Referenced by tf_specificity_test().

◆ zf_test()

void zf_test ( )

References predPRE::chain, utility::io::oc::cout, pyrosetta::create_score_function, data, basic::options::OptionKeys::dna::dna, extract_pdb_id(), test.T220_AtomAtomPairEnergies::fa_elec, basic::options::OptionKeys::dna::specificity::fast, evaluate_beta_mutants::file, lactamize::filename, getline(), create_a3b_hbs::j, extract_by_sidechain_sasa_score::l, line, basic::options::OptionKeys::dna::specificity::motif_size, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, name, option, out::output_tag(), erraser_single_res_analysis::pdb_id, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, read_list_file(), oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::start_files(), utility_exit_with_message, basic::options::OptionKeys::dna::specificity::Wdna_bp, basic::options::OptionKeys::dna::specificity::Wdna_bs, basic::options::OptionKeys::dna::specificity::weights_tag, basic::options::OptionKeys::dna::specificity::weights_tag_list, and basic::options::OptionKeys::dna::specificity::Wfa_elec.

Referenced by my_main().

◆ zif268_test()

void zif268_test ( )

References utility::io::oc::cout, pyrosetta::create_score_function, basic::options::OptionKeys::dna::dna, basic::options::OptionKeys::matdes::dock::dump_pdb, test.T220_AtomAtomPairEnergies::fa_elec, basic::options::OptionKeys::dna::specificity::fast, lactamize::filename, create_a3b_hbs::i, interface, create_a3b_hbs::j, basic::options::OptionKeys::dna::specificity::motif_begin, basic::options::OptionKeys::dna::specificity::motif_size, create_a3b_hbs::nres, option, out::output_tag(), beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, read_list_file(), oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::dna::specificity::Wdna_bp, basic::options::OptionKeys::dna::specificity::Wdna_bs, basic::options::OptionKeys::dna::specificity::weights_tag, basic::options::OptionKeys::dna::specificity::weights_tag_list, and basic::options::OptionKeys::dna::specificity::Wfa_elec.

Referenced by my_main().

Variable Documentation

◆ ti

basic::Tracer ti("demo.phil.dna_spec_test", basic::t_info) ( "demo.phil.dna_spec_test"  ,
basic::t_info   
)
static

◆ tt

basic::Tracer tt("demo.phil.dna_spec_test", basic::t_trace) ( "demo.phil.dna_spec_test"  ,
basic::t_trace   
)
static

Referenced by cleanup_dna_chains(), dna_chain_check(), dna_dr_test(), hbond_stats(), luxr_test(), and not1_loop_test().

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