beta_peptide_modeling.cc File Reference

#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/conformation/Residue.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/etable/Etable.hh>
#include <core/scoring/ScoringManager.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/ScoreFunctionFactory.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/id/AtomID_Map.hh>
#include <core/id/AtomID.hh>
#include <core/id/DOF_ID.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/kinematics/AtomTree.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/kinematics/tree/Atom.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/Jump.hh>
#include <core/pack/rotamer_set/RotamerCouplings.hh>
#include <core/pack/rotamer_set/RotamerLinks.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/optimization/AtomTreeMinimizer.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <basic/options/option.hh>
#include <basic/options/option_macros.hh>
#include <core/pose/Pose.hh>
#include <core/init/init.hh>
#include <core/import_pose/import_pose.hh>
#include <utility/vector1.hh>
#include <utility/tools/make_vector1.hh>
#include <utility/io/ozstream.hh>
#include <utility/io/izstream.hh>
#include <utility/excn/Exceptions.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/xyzVector.hh>
#include <numeric/xyzMatrix.hh>
#include <numeric/conversions.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <fstream>
#include <iostream>
#include <string>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>

Functions
void	figure_out_fold_tree (pose::Pose &pose)
void	minimize_test ()
void	repack_test ()
void	my_main ()
int	main (int argc, char *argv[])

Function Documentation

void figure_out_fold_tree

(

pose::Pose &

pose

)

References utility::io::oc::cout, demo.D060_Folding::f, and clean_pdb_keep_ligand::nres.

Referenced by minimize_test().

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

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

void minimize_test

(

)

References basic::options::OptionKeys::hotspot::angle, basic::options::OptionKeys::chemical::chemical, basic::options::OptionKeys::constraints::constraints, utility::io::oc::cout, pyrosetta::create_score_function, basic::options::OptionKeys::rna::farna::minimize::deriv_check, numeric::dihedral_radians(), figure_out_fold_tree(), test.T200_Scoring::ii, app.delta_score_per_mutation::mm, in::file::native(), clean_pdb_keep_ligand::nres, basic::options::OptionKeys::optimization::optimization, option, options, clean_pdb_keep_ligand::pdbname, app.surface_docking.surface_docking::pose, numeric::conversions::radians(), PyMOL_demo::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, and app.surface_docking.surface_docking::start_pose.

Referenced by my_main().

void my_main

(

)

References minimize_test(), option, and repack_test().

Referenced by main().

void repack_test

(

)

References utility::io::oc::cerr, basic::options::OptionKeys::chemical::chemical, basic::options::OptionKeys::constraints::constraints, utility::io::oc::cout, pyrosetta::create_score_function, utility::options::OptionKeys::options::exit, basic::options::OptionKeys::frags::j, in::file::native(), clean_pdb_keep_ligand::nres, option, loops::pack, clean_pdb_keep_ligand::pdbname, app.surface_docking.surface_docking::pose, PyMOL_demo::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, and app.surface_docking.surface_docking::start_pose.

Referenced by my_main().