protocols::flxbb Namespace Reference

Classes
class	CombinedTaskOperation
class	DesignTask
class	DesignTask_Layer
class	DesignTask_Normal
class	FilterStructs
class	FilterStructs_Packstat
class	FilterStructs_TotalCharge
class	FlxbbDesign
class	FlxbbDesignCreator
class	FlxbbDesignPack
class	InterlockAroma
class	InterlockAromaCreator
class	LayerDesignOperation
class	LayerDesignOperationCreator

Typedefs
typedef utility::pointer::owning_ptr < DesignTask >	DesignTaskOP
typedef utility::vector1 < DesignTaskOP >	DesignTaskSet
typedef utility::pointer::owning_ptr < DesignTaskSet >	DesignTaskSetOP
typedef utility::pointer::owning_ptr < DesignTask_Normal >	DesignTask_NormalOP
typedef utility::pointer::owning_ptr < DesignTask_Layer >	DesignTask_LayerOP
typedef utility::pointer::owning_ptr < FilterStructs >	FilterStructsOP
typedef utility::pointer::owning_ptr < FilterStructs_Packstat >	FilterStructs_PackstatOP
typedef utility::pointer::owning_ptr < FilterStructs_TotalCharge >	FilterStructs_TotalChargeOP
typedef utility::pointer::owning_ptr < FlxbbDesign >	FlxbbDesignOP
typedef utility::pointer::owning_ptr < InterlockAroma >	InterlockAromaOP
typedef utility::pointer::owning_ptr < LayerDesignOperation >	LayerDesignOperationOP
typedef utility::pointer::owning_ptr < CombinedTaskOperation >	CombinedTaskOperationOP
typedef core::Size	Size
typedef core::Real	Real
typedef std::string	String
typedef core::pose::Pose	Pose
typedef protocols::jd2::parser::BluePrintOP	BluePrintOP
typedef core::scoring::constraints::ConstraintOPs	ConstraintOPs

Functions
void	FlxbbDesign_main ()
template<class T >
LayerDesignOperation::LayerDefinitions	makeMap (T const &map_initializer)
ConstraintOPs	constraints_sheet (Pose const &pose, BluePrintOP const &blue, Real const coef, Real const condist=5.5)
	constrain hydrogen bonds in beta sheet ( not used ) More...
ConstraintOPs	constraints_NtoC (Pose const &pose, Real const coef, Real const condist=11.0)
	constraint between N- and C-terminal Ca atoms More...
ConstraintOPs	constraints_sheet (Pose const &pose, Real const coef, Real const condist=5.5)
	constrain between Ca atoms in beta sheet More...
utility::vector1< Size >	find_ligands (Pose const &pose)
	Looks for unknown amino acids in the pose and returns their indices. More...

Typedef Documentation

typedef protocols::jd2::parser::BluePrintOP protocols::flxbb::BluePrintOP

typedef utility::pointer::owning_ptr< CombinedTaskOperation > protocols::flxbb::CombinedTaskOperationOP

typedef core::scoring::constraints::ConstraintOPs protocols::flxbb::ConstraintOPs

typedef utility::pointer::owning_ptr< DesignTask_Layer > protocols::flxbb::DesignTask_LayerOP

typedef utility::pointer::owning_ptr< DesignTask_Normal > protocols::flxbb::DesignTask_NormalOP

typedef utility::pointer::owning_ptr< DesignTask > protocols::flxbb::DesignTaskOP

typedef utility::vector1< DesignTaskOP > protocols::flxbb::DesignTaskSet

typedef utility::pointer::owning_ptr< DesignTaskSet > protocols::flxbb::DesignTaskSetOP

typedef utility::pointer::owning_ptr< FilterStructs_Packstat > protocols::flxbb::FilterStructs_PackstatOP

typedef utility::pointer::owning_ptr< FilterStructs_TotalCharge > protocols::flxbb::FilterStructs_TotalChargeOP

typedef utility::pointer::owning_ptr< FilterStructs > protocols::flxbb::FilterStructsOP

typedef utility::pointer::owning_ptr< FlxbbDesign > protocols::flxbb::FlxbbDesignOP

typedef utility::pointer::owning_ptr< InterlockAroma > protocols::flxbb::InterlockAromaOP

typedef utility::pointer::owning_ptr< LayerDesignOperation > protocols::flxbb::LayerDesignOperationOP

typedef core::pose::Pose protocols::flxbb::Pose

typedef core::Real protocols::flxbb::Real

typedef core::Size protocols::flxbb::Size

typedef std::string protocols::flxbb::String

Function Documentation

ConstraintOPs protocols::flxbb::constraints_NtoC	(	Pose const &	pose,
		Real const	coef,
		Real const	condist
	)

constraint between N- and C-terminal Ca atoms

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

Referenced by protocols::flxbb::FlxbbDesign::apply(), protocols::flxbb::FlxbbDesign::read_options(), and protocols::flxbb::FlxbbDesign::register_options().

ConstraintOPs protocols::flxbb::constraints_sheet	(	Pose const &	pose,
		BluePrintOP const &	blue,
		Real const	coef,
		Real const	condist = 5.5
	)

constrain hydrogen bonds in beta sheet ( not used )

constrain between Ca atoms in beta sheet, which are specified in blueprint file

References core::chemical::ResidueType::atom_index(), basic::options::OptionKeys::flxbb::constraints_sheet_include_cacb_pseudotorsion, core::chemical::ResidueType::is_ligand(), core::chemical::ResidueType::name3(), nres, basic::options::option, core::pose::Pose::residue_type(), runtime_assert, tag, core::pose::Pose::total_residue(), and protocols::TR.

Referenced by protocols::flxbb::FlxbbDesign::apply(), protocols::flxbb::FlxbbDesign::read_options(), and protocols::flxbb::FlxbbDesign::register_options().

ConstraintOPs protocols::flxbb::constraints_sheet	(	Pose const &	pose,
		Real const	coef,
		Real const	condist
	)

constrain between Ca atoms in beta sheet

References core::conformation::Residue::atom_index(), core::chemical::ResidueType::atom_index(), protocols::simple_filters::dssp(), nres, core::pose::Pose::residue(), core::pose::Pose::residue_type(), ss, tag, core::pose::Pose::total_residue(), and protocols::TR.

utility::vector1< Size > protocols::flxbb::find_ligands

(

Pose const &

pose

)

Looks for unknown amino acids in the pose and returns their indices.

References core::conformation::Residue::is_protein(), core::conformation::Residue::name3(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and protocols::TR.

Referenced by protocols::flxbb::LayerDesignOperation::apply().

void protocols::flxbb::FlxbbDesign_main

(

)

References basic::options::OptionKeys::in::file::fullatom, core::scoring::get_score_function(), basic::options::option, and protocol.

template<class T >

LayerDesignOperation::LayerDefinitions protocols::flxbb::makeMap

(

T const &

map_initializer

)

Indirection to get around c++11 flexibility in initializing maps. Used in set_default_layer_residues below. Idea stolen from this thread on github: https://github.com/ethz-asl/libpointmatcher/issues/13

Referenced by protocols::flxbb::LayerDesignOperation::set_default_layer_residues().