Rosetta
Functions
gcc185_test.cc File Reference
#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/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/viewer/viewers.hh>
#include <core/types.hh>
#include <core/scoring/sasa.hh>
#include <core/util/prof.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/util.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/scoring/etable/Etable.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/Ramachandran.hh>
#include <core/scoring/dunbrack/RotamerLibrary.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/kinematics/FoldTree.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/id/AtomID_Map.hh>
#include <core/id/AtomID_Map.Pose.hh>
#include <core/id/AtomID.hh>
#include <core/id/DOF_ID.hh>
#include <core/kinematics/AtomTree.hh>
#include <core/kinematics/Jump.hh>
#include <core/mm/MMTorsionLibrary.hh>
#include <core/mm/MMTorsionLibrary.fwd.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <core/options/option.hh>
#include <core/options/after_opts.hh>
#include <core/options/keys/OptionKeys.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/options/util.hh>
#include <core/util/basic.hh>
#include <core/io/database/open.hh>
#include <devel/init.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/scoring/constraints/CoordinateConstraint.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/constraints/AngleConstraint.hh>
#include <core/scoring/constraints/DihedralConstraint.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <utility/vector1.hh>
#include <numeric/xyzVector.hh>
#include <numeric/random/random.hh>
#include <numeric/conversions.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <fstream>
#include <iostream>
#include <string>
#include <core/util/Tracer.hh>

Functions

Real rhiju_pack (pose::Pose &pose, scoring::ScoreFunctionOP &scorefxn)
 
Real soft_pack (pose::Pose &pose)
 
Real hard_pack (pose::Pose &pose)
 
void hard_minimize (pose::Pose &pose)
 
void get_subpose (pose::Pose &pose, pose::Pose &subpose, Size const start1, Size const end1, Size const start2, Size const end2)
 
void find_closest_points (pose::Pose &pose, Size const start1, Size const end1, Size const start2, Size const end2, Size &closest_i, Size &closest_j)
 
void get_useful_fold_trees_for_gcc185 (pose::Pose &pose, kinematics::FoldTree &f_minimize, kinematics::FoldTree &f_repack)
 
void get_ddG (pose::Pose &pose, std::string const pdb)
 
void repack_minimize_test ()
 
int main (int argc, char *argv[])
 

Function Documentation

◆ find_closest_points()

void find_closest_points ( pose::Pose &  pose,
Size const  start1,
Size const  end1,
Size const  start2,
Size const  end2,
Size &  closest_i,
Size &  closest_j 
)

References create_a3b_hbs::i, create_a3b_hbs::j, and beta_nonlocal::pose.

Referenced by get_useful_fold_trees_for_gcc185().

◆ get_ddG()

void get_ddG ( pose::Pose &  pose,
std::string const  pdb 
)

References utility::io::oc::cout, basic::options::OptionKeys::matdes::dock::dump_pdb, hard_pack(), kic_runner::pdb, beta_nonlocal::pose, test.T008_Serialization::pose1, and test.T008_Serialization::pose2.

Referenced by repack_minimize_test().

◆ get_subpose()

void get_subpose ( pose::Pose &  pose,
pose::Pose &  subpose,
Size const  start1,
Size const  end1,
Size const  start2,
Size const  end2 
)

References utility::io::oc::cout, create_a3b_hbs::f, create_a3b_hbs::i, create_a3b_hbs::nres, beta_nonlocal::pose, and basic::options::OptionKeys::frags::scoring::scoring.

◆ get_useful_fold_trees_for_gcc185()

void get_useful_fold_trees_for_gcc185 ( pose::Pose &  pose,
kinematics::FoldTree &  f_minimize,
kinematics::FoldTree &  f_repack 
)

References find_closest_points(), create_a3b_hbs::i, create_a3b_hbs::j, create_a3b_hbs::nres, and beta_nonlocal::pose.

Referenced by repack_minimize_test().

◆ hard_minimize()

void hard_minimize ( pose::Pose &  pose)

References basic::options::OptionKeys::constraints::constraints, utility::io::oc::cout, basic::options::OptionKeys::rna::denovo::minimize::deriv_check, create_a3b_hbs::i, create_a3b_hbs::ii, beta_nonlocal::mm, create_a3b_hbs::nres, options, beta_nonlocal::pose, oop_conformations::scorefxn, and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by repack_minimize_test().

◆ hard_pack()

Real hard_pack ( pose::Pose &  pose)

References beta_nonlocal::pose, rhiju_pack(), oop_conformations::scorefxn, and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by get_ddG().

◆ main()

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

References argv, test.T009_Exceptions::e, utility::options::OptionKeys::options::exit, basic::init(), and repack_minimize_test().

◆ repack_minimize_test()

void repack_minimize_test ( )

References basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, basic::options::OptionKeys::matdes::dock::dump_pdb, get_ddG(), get_useful_fold_trees_for_gcc185(), hard_minimize(), create_a3b_hbs::nres, option, kic_runner::pdb, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, docking::s, basic::options::OptionKeys::frags::scoring::scoring, and soft_pack().

Referenced by main().

◆ rhiju_pack()

Real rhiju_pack ( pose::Pose &  pose,
scoring::ScoreFunctionOP &  scorefxn 
)

References utility::io::oc::cout, create_a3b_hbs::nres, beta_nonlocal::pose, oop_conformations::scorefxn, and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by hard_pack(), and soft_pack().

◆ soft_pack()

Real soft_pack ( pose::Pose &  pose)

References pyrosetta::create_score_function, beta_nonlocal::pose, rhiju_pack(), oop_conformations::scorefxn, and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by repack_minimize_test().

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