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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 
)

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, 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 
)

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