protocols::flxbb Namespace Reference

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

Definition at line 62 of file utility.cc.

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

Definition at line 198 of file LayerDesignOperation.hh.

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

Definition at line 63 of file utility.cc.

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

Definition at line 38 of file DesignTask.fwd.hh.

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

Definition at line 34 of file DesignTask.fwd.hh.

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

Definition at line 28 of file DesignTask.fwd.hh.

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

Definition at line 30 of file DesignTask.fwd.hh.

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

Definition at line 31 of file DesignTask.fwd.hh.

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

Definition at line 27 of file FilterStructs.fwd.hh.

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

Definition at line 28 of file FilterStructs.fwd.hh.

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

Definition at line 24 of file FilterStructs.fwd.hh.

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

Definition at line 22 of file FlxbbDesign.fwd.hh.

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

Definition at line 22 of file InterlockAroma.fwd.hh.

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

Definition at line 22 of file LayerDesignOperation.fwd.hh.

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

Definition at line 61 of file utility.cc.

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

Definition at line 59 of file utility.cc.

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

Definition at line 58 of file utility.cc.

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

Definition at line 60 of file utility.cc.

Function Documentation

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

constraint between N- and C-terminal Ca atoms

Definition at line 155 of file utility.cc.

References core::chemical::ResidueType::atom_index(), core::pose::Pose::residue_type(), 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

Definition at line 66 of file utility.cc.

References core::chemical::ResidueType::atom_index(), core::chemical::ResidueType::is_ligand(), core::chemical::ResidueType::name3(), core::pose::Pose::residue_type(), 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

Definition at line 185 of file utility.cc.

References core::conformation::Residue::atom_index(), core::chemical::ResidueType::atom_index(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::scoring::Strands::SS_strand_end, core::pose::Pose::total_residue(), core::scoring::Strands::total_strands, 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.

Definition at line 263 of file utility.cc.

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

(

)

Definition at line 45 of file FlxbbDesign_main.cc.

References core::scoring::constraints::add_constraints_from_cmdline_to_scorefxn(), core::scoring::constraints::add_fa_constraints_from_cmdline_to_scorefxn(), and core::scoring::getScoreFunction().