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

Functions
void	FlxbbDesign_main ()
template<class T >
LayerDesignOperation::LayerDefinitions	makeMap (T const &map_initializer)
std::string	print_string_vector (utility::vector1< std::string > const &vect)
	Utility function to convert a string vector into a comma-separated list of strings. More...
std::string	layer_design_ss_layer_naming_func (std::string const &element_name)
std::string	layer_design_ss_layer_group ()
std::string	layer_design_ss_layer_or_taskop_group ()
std::string	unique_chars (std::string const &orig)
	returns a string containing sorted, unique residue one-letter codes More...
utility::vector1< std::string >	unique_strs (utility::vector1< std::string > const &orig, utility::vector1< std::string > const &orig2)
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< core::Size >	find_ligands (Pose const &pose)
	Looks for unknown amino acids in the pose and returns their indices. More...

Typedef Documentation

BluePrintOP

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

CombinedTaskOperationOP

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

ConstraintOPs

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

DesignTask_LayerOP

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

DesignTask_NormalOP

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

DesignTaskOP

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

DesignTaskSet

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

DesignTaskSetOP

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

FilterStructs_PackstatOP

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

FilterStructs_TotalChargeOP

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

FilterStructsOP

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

FlxbbDesignOP

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

InterlockAromaOP

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

LayerDesignOperationOP

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

Pose

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

Real

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

Size

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

String

using protocols::flxbb::String = typedef std::string

Function Documentation

constraints_NtoC()

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(), core::pose::Pose::residue_type(), core::pose::Pose::size(), and protocols::TR().

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

constraints_sheet() [1/2]

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(), core::chemical::ResidueType::is_ligand(), core::chemical::ResidueTypeBase::name3(), core::pose::Pose::residue_type(), core::pose::Pose::secstruct(), core::pose::Pose::size(), and protocols::TR().

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

constraints_sheet() [2/2]

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(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::size(), core::scoring::Strands::SS_strand_end, core::scoring::Strands::total_strands, protocols::TR(), and core::conformation::Residue::xyz().

find_ligands()

utility::vector1< core::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::size(), and protocols::TR().

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

FlxbbDesign_main()

void protocols::flxbb::FlxbbDesign_main

(

)

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

layer_design_ss_layer_group()

std::string protocols::flxbb::layer_design_ss_layer_group

(

)

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

layer_design_ss_layer_naming_func()

std::string protocols::flxbb::layer_design_ss_layer_naming_func

(

std::string const &

element_name

)

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

layer_design_ss_layer_or_taskop_group()

std::string protocols::flxbb::layer_design_ss_layer_or_taskop_group

(

)

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

makeMap()

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

print_string_vector()

std::string protocols::flxbb::print_string_vector

(

utility::vector1< std::string > const &

vect

)

Utility function to convert a string vector into a comma-separated list of strings.

unique_chars()

std::string protocols::flxbb::unique_chars

(

std::string const &

orig

)

returns a string containing sorted, unique residue one-letter codes

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

unique_strs()

utility::vector1< std::string > protocols::flxbb::unique_strs	(	utility::vector1< std::string > const &	orig,
		utility::vector1< std::string > const &	orig2
	)