apps::public1::scenarios::chemically_conjugated_docking Namespace Reference

Functions
utility::vector1< core::Size >	add_extra_bodies (core::pose::Pose &pose, basic::Tracer &TR)
	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, basic::Tracer &TR)
void	ubq_ras_distance (core::pose::Pose const &pose, basic::Tracer &, protocols::jd2::JobOP job_me)
void	ubq_ras_rotation_angle (core::pose::Pose const &pose, basic::Tracer &TR, protocols::jd2::JobOP job_me, core::Size const GTPase_target, bool const ubiquitin)
void	create_extra_output (core::pose::Pose const &pose, basic::Tracer &TR, bool const ubiquitin, core::Size const GTPase_target)

Function Documentation

utility::vector1< core::Size > apps::public1::scenarios::chemically_conjugated_docking::add_extra_bodies ( core::pose::Pose &  pose, basic::Tracer &  TR  )

inline

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 basic::options::OptionKeys::cutoutdomain::end, basic::options::OptionKeys::chemically_conjugated_docking::extra_bodies, basic::options::option, pyrosetta.io::poses_from_files(), and basic::options::OptionKeys::inout::dbms::user.

Referenced by UBQ_GTPase_disulfide_Mover::init_on_new_input(), and UBQ_E2Mover::init_on_new_input().

void apps::public1::scenarios::chemically_conjugated_docking::create_extra_output ( core::pose::Pose const &  pose, basic::Tracer &  TR, bool const  ubiquitin, core::Size const  GTPase_target  )

inline

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 UBQ_GTPase_disulfide_Mover::analyze_and_filter().

void apps::public1::scenarios::chemically_conjugated_docking::pack_extra_bodies ( utility::vector1< core::Size > const &  extra_bodies_chains, core::pose::Pose const &  pose, std::set< core::Size > &  region, basic::Tracer &  TR  )

inline

References basic::options::OptionKeys::run::chain, basic::options::OptionKeys::cutoutdomain::end, and basic::options::OptionKeys::cutoutdomain::start.

Referenced by UBQ_GTPase_disulfide_Mover::init_on_new_input(), and UBQ_E2Mover::init_on_new_input().

void apps::public1::scenarios::chemically_conjugated_docking::ubq_ras_distance ( core::pose::Pose const &  pose, basic::Tracer &  , protocols::jd2::JobOP  job_me  )

inline

do ubiquitin-ras pair distance measurement and reporting

References utility::FixedSizeLexicographicalIterator< S >::at_end(), utility::FixedSizeLexicographicalIterator< S >::begin(), distance(), and test.Workshop3test::ras.

Referenced by create_extra_output().

void apps::public1::scenarios::chemically_conjugated_docking::ubq_ras_rotation_angle ( core::pose::Pose const &  pose, basic::Tracer &  TR, protocols::jd2::JobOP  job_me, core::Size const  GTPase_target, bool const  ubiquitin  )

inline

References numeric::angle_of(), numeric::conversions::degrees(), and numeric::dihedral_degrees().

Referenced by create_extra_output().