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/ScoreFunctionFactory.hh>
#include <core/scoring/constraints/CoordinateConstraint.hh>
#include <core/scoring/constraints/DihedralConstraint.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/id/AtomID.hh>
#include <core/kinematics/AtomTree.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/kinematics/tree/Atom.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/pack/rotamer_set/RotamerLinks.hh>
#include <core/pack/pack_rotamers.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/palette/CustomBaseTypePackerPalette.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 <devel/init.hh>
#include <core/import_pose/import_pose.hh>
#include <utility/vector1.hh>
#include <utility/excn/Exceptions.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/xyzVector.hh>
#include <numeric/conversions.hh>
#include <iostream>
#include <string>
#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

figure_out_fold_tree()

void figure_out_fold_tree

(

pose::Pose &

pose

)

References utility::io::oc::cout, create_a3b_hbs::f, create_a3b_hbs::i, kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, create_a3b_hbs::nres, and beta_nonlocal::pose.

Referenced by minimize_test().

main()

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

References argv, test.T009_Exceptions::e, basic::init(), my_main(), and NEW_OPT.

minimize_test()

void minimize_test

(

)

References basic::options::OptionKeys::hotspot::angle, basic::options::OptionKeys::constraints::constraints, utility::io::oc::cout, pyrosetta::create_score_function, basic::options::OptionKeys::rna::denovo::minimize::deriv_check, numeric::dihedral_radians(), figure_out_fold_tree(), create_a3b_hbs::i, create_a3b_hbs::ii, beta_nonlocal::mm, in::file::native(), create_a3b_hbs::nres, option, options, predPRE::pdbname, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, numeric::conversions::radians(), oop_conformations::scorefxn, and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by main(), and my_main().

my_main()

void my_main

(

)

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

Referenced by main().

repack_test()

void repack_test

(

)

References utility::io::oc::cerr, basic::options::OptionKeys::constraints::constraints, utility::io::oc::cout, pyrosetta::create_score_function, utility::options::OptionKeys::options::exit, create_a3b_hbs::i, create_a3b_hbs::j, create_a3b_hbs::k, in::file::native(), create_a3b_hbs::nres, option, vancomycin::pack, predPRE::pdbname, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, oop_conformations::scorefxn, and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by my_main().