protocols::anchored_design Namespace Reference

Classes
class	Anchor
	Anchor class provides for the "anchor" part of a scaffold in anchored interface design. More...
class	AnchoredDesignMover
class	AnchoredPerturbMover
class	AnchoredRefineMover
class	AnchorMoversData
	This data class wraps all the data needed for the AnchoredDesign movers. More...

Typedefs
typedef utility::pointer::shared_ptr< Anchor >	AnchorOP
typedef utility::pointer::shared_ptr< Anchor const >	AnchorCOP
typedef utility::pointer::shared_ptr< AnchoredDesignMover >	AnchoredDesignMoverOP
typedef utility::pointer::shared_ptr< AnchoredPerturbMover >	AnchoredPerturbMoverOP
typedef utility::pointer::shared_ptr< AnchoredRefineMover >	AnchoredRefineMoverOP
typedef utility::pointer::shared_ptr< AnchorMoversData >	AnchorMoversDataOP
typedef utility::pointer::shared_ptr< AnchorMoversData const >	AnchorMoversDataCOP

Functions
std::string const	bad_anchorfile ("YOU_FORGOT_TO_SPECIFY_AN_ANCHOR_FILE")
std::string const	EMPTY_STRING ("")
int const	ANCHOR_TARGET (1)
void	debug_dump_pose (core::pose::Pose const &pose, core::pose::PoseOP posecopy, std::string const &tag, protocols::moves::MoverOP mover)
	a local helper function, not in the header More...
void	dump_cutpoint_info (core::pose::Pose const &pose)
	a local helper function for debugging, not in the header More...
core::Real const	VDW_WEIGHT (2.0)
core::Real const	CHAINBREAK_WEIGHT (10.0)
std::string const	INTERFACE_CALC ("AnchoredDesign_InterfaceNeighborDefinitionCalculator")
std::string const	NEIGHBORHOOD_CALC ("AnchoredDesign_NeighborhoodByDistanceCalculator")

Typedef Documentation

AnchorCOP

typedef utility::pointer::shared_ptr< Anchor const > protocols::anchored_design::AnchorCOP

AnchoredDesignMoverOP

typedef utility::pointer::shared_ptr< AnchoredDesignMover > protocols::anchored_design::AnchoredDesignMoverOP

AnchoredPerturbMoverOP

typedef utility::pointer::shared_ptr< AnchoredPerturbMover > protocols::anchored_design::AnchoredPerturbMoverOP

AnchoredRefineMoverOP

typedef utility::pointer::shared_ptr< AnchoredRefineMover > protocols::anchored_design::AnchoredRefineMoverOP

AnchorMoversDataCOP

typedef utility::pointer::shared_ptr< AnchorMoversData const > protocols::anchored_design::AnchorMoversDataCOP

AnchorMoversDataOP

typedef utility::pointer::shared_ptr< AnchorMoversData > protocols::anchored_design::AnchorMoversDataOP

AnchorOP

typedef utility::pointer::shared_ptr< Anchor > protocols::anchored_design::AnchorOP

Function Documentation

ANCHOR_TARGET()

int const protocols::anchored_design::ANCHOR_TARGET

(

1

)

Referenced by protocols::anchored_design::AnchoredDesignMover::perturb_anchor(), and protocols::anchored_design::AnchoredDesignMover::set_fold_tree_and_cutpoints().

bad_anchorfile()

std::string const protocols::anchored_design::bad_anchorfile

(

"YOU_FORGOT_TO_SPECIFY_AN_ANCHOR_FILE"

)

CHAINBREAK_WEIGHT()

core::Real const protocols::anchored_design::CHAINBREAK_WEIGHT

(

10.

0

)

debug_dump_pose()

void protocols::anchored_design::debug_dump_pose	(	core::pose::Pose const &	pose,
		core::pose::PoseOP	posecopy,
		std::string const &	tag,
		protocols::moves::MoverOP	mover
	)

a local helper function, not in the header

References protocols::jd2::output_intermediate_pose().

Referenced by protocols::anchored_design::AnchoredPerturbMover::apply(), and protocols::anchored_design::AnchoredRefineMover::apply().

dump_cutpoint_info()

void protocols::anchored_design::dump_cutpoint_info

(

core::pose::Pose const &

pose

)

a local helper function for debugging, not in the header

References core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), core::conformation::Residue::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), core::pose::Pose::residue(), core::pose::Pose::size(), and T_shared().

Referenced by protocols::anchored_design::AnchoredPerturbMover::apply(), protocols::anchored_design::AnchoredRefineMover::apply(), and protocols::anchored_design::AnchoredDesignMover::set_fold_tree_and_cutpoints().

EMPTY_STRING()

std::string const protocols::anchored_design::EMPTY_STRING

(

""

)

Referenced by protocols::anchored_design::AnchoredDesignMover::apply(), protocols::anchored_design::AnchorMoversData::autogenerate_frags(), protocols::anchored_design::AnchoredDesignMover::init_on_new_input(), protocols::anchored_design::AnchoredDesignMover::read_options(), protocols::anchored_design::AnchorMoversData::read_options(), protocols::anchored_design::AnchoredDesignMover::reinitialize_for_new_input(), and protocols::anchored_design::AnchorMoversData::set_unset_packertask_factory().

INTERFACE_CALC()

std::string const protocols::anchored_design::INTERFACE_CALC

(

"AnchoredDesign_InterfaceNeighborDefinitionCalculator"

)

NEIGHBORHOOD_CALC()

std::string const protocols::anchored_design::NEIGHBORHOOD_CALC

(

"AnchoredDesign_NeighborhoodByDistanceCalculator"

)

VDW_WEIGHT()

core::Real const protocols::anchored_design::VDW_WEIGHT

(

2.

0

)