mike_linker_test.cc File Reference

#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/conformation/Conformation.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/operation/TaskOperation.fwd.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/constraints/AngleConstraint.hh>
#include <core/scoring/constraints/ConstraintSet.fwd.hh>
#include <core/scoring/constraints/DihedralConstraint.hh>
#include <core/scoring/func/CircularHarmonicFunc.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/MoveMap.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <protocols/jd2/Job.hh>
#include <protocols/ncbb/util.hh>
#include <protocols/moves/MoverContainer.hh>
#include <protocols/moves/RepeatMover.hh>
#include <protocols/moves/TrialMover.hh>
#include <protocols/moves/MonteCarlo.hh>
#include <protocols/minimization_packing/MinMover.hh>
#include <protocols/minimization_packing/RotamerTrialsMover.hh>
#include <protocols/simple_moves/BackboneMover.hh>
#include <protocols/ncbb/hbs/HbsPatcher.hh>
#include <protocols/simple_moves/chiral/ChiralMover.hh>
#include <numeric/random/random.hh>
#include <devel/init.hh>
#include <basic/options/util.hh>
#include <basic/options/option.hh>
#include <basic/Tracer.hh>
#include <utility/pointer/owning_ptr.hh>
#include <utility/vector1.hh>
#include <string>
#include <sstream>
#include <numeric/NumericTraits.hh>
#include <basic/options/keys/OptionKeys.hh>

Classes
class	MikeLinkerMover
class	TorsionVectorMover

Namespaces
	azide_link_creator

Typedefs
using	MikeLinkerMoverOP = utility::pointer::shared_ptr< MikeLinkerMover >
using	MikeLinkerMoverCOP = utility::pointer::shared_ptr< const MikeLinkerMover >
using	TorsionVectorMoverOP = utility::pointer::shared_ptr< TorsionVectorMover >
using	TorsionVectorMoverCOP = utility::pointer::shared_ptr< const TorsionVectorMover >

Functions
int	main (int argc, char *argv[])
void	enforce_atoms_coplanar (utility::vector1< id::AtomID > atoms, core::pose::Pose &pose)
void	enforce_triazole_distance (utility::vector1< id::AtomID > atoms, core::pose::Pose &pose)
void	add_triazole_constraints (core::pose::Pose &pose, Size az1, Size az2, Size linker)
utility::vector1< utility::vector1< AtomID > >	get_linker_dihedrals (Pose pose, Size resi)
core::kinematics::FoldTree	double_unlinked_fold_tree (core::pose::Pose pose, core::Size r1, core::Size r2)
core::kinematics::FoldTree	double_linked_fold_tree (core::pose::Pose pose, core::Size r1, core::Size r2)

Variables
static basic::Tracer	TR ("MikeLinkerMover")
IntegerOptionKey const	azide_link_creator::lys_one ("azide_link_creator::lys_one")
IntegerOptionKey const	azide_link_creator::lys_two ("azide_link_creator::lys_two")
StringVectorOptionKey const	azide_link_creator::lys_one_pdb ("azide_link_creator::lys_one_pdb")
StringVectorOptionKey const	azide_link_creator::lys_two_pdb ("azide_link_creator::lys_two_pdb")
BooleanOptionKey const	azide_link_creator::min_all ("azide_link_creator::min_all")

Typedef Documentation

MikeLinkerMoverCOP

using MikeLinkerMoverCOP = utility::pointer::shared_ptr<const MikeLinkerMover>

MikeLinkerMoverOP

using MikeLinkerMoverOP = utility::pointer::shared_ptr<MikeLinkerMover>

TorsionVectorMoverCOP

using TorsionVectorMoverCOP = utility::pointer::shared_ptr<const TorsionVectorMover>

TorsionVectorMoverOP

using TorsionVectorMoverOP = utility::pointer::shared_ptr<TorsionVectorMover>

Function Documentation

add_triazole_constraints()

void add_triazole_constraints	(	core::pose::Pose &	pose,
		Size	az1,
		Size	az2,
		Size	linker
	)

References CE1, CE2, enforce_atoms_coplanar(), enforce_triazole_distance(), func, beta_nonlocal::pose, basic::options::OptionKeys::motifs::r1, basic::options::OptionKeys::motifs::r2, and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by MikeLinkerMover::apply().

double_linked_fold_tree()

core::kinematics::FoldTree double_linked_fold_tree	(	core::pose::Pose	pose,
		core::Size	r1,
		core::Size	r2
	)

References create_a3b_hbs::f, beta_nonlocal::pose, basic::options::OptionKeys::motifs::r1, basic::options::OptionKeys::motifs::r2, and TR.

Referenced by MikeLinkerMover::apply().

double_unlinked_fold_tree()

core::kinematics::FoldTree double_unlinked_fold_tree	(	core::pose::Pose	pose,
		core::Size	r1,
		core::Size	r2
	)

References create_a3b_hbs::f, beta_nonlocal::pose, basic::options::OptionKeys::motifs::r1, basic::options::OptionKeys::motifs::r2, and TR.

enforce_atoms_coplanar()

void enforce_atoms_coplanar	(	utility::vector1< id::AtomID >	atoms,
		core::pose::Pose &	pose
	)

References docking::a1, atoms, func, create_a3b_hbs::i, beta_nonlocal::pose, basic::options::OptionKeys::frags::scoring::scoring, and TR.

Referenced by add_triazole_constraints().

enforce_triazole_distance()

void enforce_triazole_distance	(	utility::vector1< id::AtomID >	atoms,
		core::pose::Pose &	pose
	)

References atoms, func, create_a3b_hbs::i, beta_nonlocal::pose, and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by add_triazole_constraints().

get_linker_dihedrals()

utility::vector1< utility::vector1< AtomID > > get_linker_dihedrals	(	Pose	pose,
		Size	resi
	)

References beta_nonlocal::pose, and pna::resi.

Referenced by MikeLinkerMover::apply().

main()

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

References argv, test.T009_Exceptions::e, basic::init(), azide_link_creator::lys_one, azide_link_creator::lys_one_pdb, azide_link_creator::lys_two, azide_link_creator::lys_two_pdb, azide_link_creator::min_all, and option.

Variable Documentation

TR

basic::Tracer TR("MikeLinkerMover") ( "MikeLinkerMover"  )

static

Referenced by MikeLinkerMover::apply(), double_linked_fold_tree(), double_unlinked_fold_tree(), and enforce_atoms_coplanar().