Classes
class	UBQ_GTPaseMover
	A mover typically used for binding ubiquitin to a substrate protein. More...

class	UBQ_GTPaseMoverCreator

Typedefs
typedef utility::pointer::shared_ptr< UBQ_GTPaseMover >	UBQ_GTPaseMoverOP

typedef utility::pointer::shared_ptr< UBQ_GTPaseMover const >	UBQ_GTPaseMoverCOP

Functions
utility::vector1< core::Size >	add_extra_bodies (core::pose::Pose &pose)
	The purpose of this code is to allow for static extra things in the system; for its original incarnations, to allow for a RING domain to occlude its site on E2 and a GAP (+MG +GDP) to occlude ras. More...

void	pack_extra_bodies (utility::vector1< core::Size > const &extra_bodies_chains, core::pose::Pose const &pose, std::set< core::Size > &region)

void	ubq_ras_distance (core::pose::Pose &pose)

void	ubq_ras_rotation_angle (core::pose::Pose const &pose, protocols::jd2::JobOP job_me, core::Size const GTPase_target, bool const ubiquitin)

void	create_extra_output (core::pose::Pose &pose, bool const ubiquitin, core::Size const GTPase_target)

std::ostream &	operator<< (std::ostream &os, UBQ_GTPaseMover const &mover)
	private methods /// More...

Typedef Documentation

◆ UBQ_GTPaseMoverCOP

typedef utility::pointer::shared_ptr< UBQ_GTPaseMover const > protocols::chemically_conjugated_docking::UBQ_GTPaseMoverCOP

◆ UBQ_GTPaseMoverOP

typedef utility::pointer::shared_ptr< UBQ_GTPaseMover > protocols::chemically_conjugated_docking::UBQ_GTPaseMoverOP

Function Documentation

◆ add_extra_bodies()

utility::vector1< core::Size > protocols::chemically_conjugated_docking::add_extra_bodies ( core::pose::Pose & pose )

The purpose of this code is to allow for static extra things in the system; for its original incarnations, to allow for a RING domain to occlude its site on E2 and a GAP (+MG +GDP) to occlude ras.

extra bodies/////////////////////////////////////////////////

References core::conformation::Conformation::append_polymer_residue_after_seqpos(), core::conformation::Conformation::append_residue_by_jump(), core::conformation::Residue::atom_name(), core::pose::Pose::conformation(), core::pose::Pose::fold_tree(), core::conformation::Conformation::num_chains(), core::import_pose::PDB_file, core::import_pose::poses_from_files(), core::pose::Pose::residue(), core::kinematics::FoldTree::root(), core::pose::Pose::size(), and protocols::TR().

Referenced by protocols::chemically_conjugated_docking::UBQ_GTPaseMover::initialize().

◆ create_extra_output()

void protocols::chemically_conjugated_docking::create_extra_output	(	core::pose::Pose &	pose,
		bool const	ubiquitin,
		core::Size const	GTPase_target
	)

This function is specific to the original system for which this code was written - if you are not trying to duplicate the initial results you should remove it!

References ubq_ras_distance(), and ubq_ras_rotation_angle().

Referenced by protocols::chemically_conjugated_docking::UBQ_GTPaseMover::analyze_and_filter().

◆ operator<<()

std::ostream & protocols::chemically_conjugated_docking::operator<<	(	std::ostream &	os,
		UBQ_GTPaseMover const &	mover
	)

private methods ///

References protocols::chemically_conjugated_docking::UBQ_GTPaseMover::show().

◆ pack_extra_bodies()

void protocols::chemically_conjugated_docking::pack_extra_bodies	(	utility::vector1< core::Size > const &	extra_bodies_chains,
		core::pose::Pose const &	pose,
		std::set< core::Size > &	region
	)

References core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::conformation::Conformation::chain_endings(), core::pose::Pose::conformation(), core::sequence::end, protocols::loops::start, protocols::loops::stop, and protocols::TR().

Referenced by protocols::chemically_conjugated_docking::UBQ_GTPaseMover::initialize().

◆ ubq_ras_distance()

void protocols::chemically_conjugated_docking::ubq_ras_distance ( core::pose::Pose & pose )

do ubiquitin-ras pair distance measurement and reporting

References core::chemical::ResidueType::atom_index(), core::kinematics::distance(), core::pose::Pose::residue_type(), core::pose::setPoseExtraScore(), and core::pose::Pose::xyz().

Referenced by create_extra_output().

◆ ubq_ras_rotation_angle()

void protocols::chemically_conjugated_docking::ubq_ras_rotation_angle	(	core::pose::Pose const &	pose,
		protocols::jd2::JobOP	job_me,
		core::Size const	GTPase_target,
		bool const	ubiquitin
	)

References core::chemical::ResidueType::atom_index(), core::pose::Pose::residue_type(), protocols::TR(), and core::pose::Pose::xyz().