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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::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::Sizefind_ligands (Pose const &pose)
 Looks for unknown amino acids in the pose and returns their indices. More...
 

Typedef Documentation

typedef utility::pointer::shared_ptr< CombinedTaskOperation > protocols::flxbb::CombinedTaskOperationOP
typedef utility::pointer::shared_ptr< DesignTask_Layer > protocols::flxbb::DesignTask_LayerOP
typedef utility::pointer::shared_ptr< DesignTask_Normal > protocols::flxbb::DesignTask_NormalOP
typedef utility::pointer::shared_ptr< DesignTask > protocols::flxbb::DesignTaskOP
typedef utility::vector1< DesignTaskOP > protocols::flxbb::DesignTaskSet
typedef utility::pointer::shared_ptr< DesignTaskSet > protocols::flxbb::DesignTaskSetOP
typedef utility::pointer::shared_ptr< FilterStructs_Packstat > protocols::flxbb::FilterStructs_PackstatOP
typedef utility::pointer::shared_ptr< FilterStructs > protocols::flxbb::FilterStructsOP
typedef utility::pointer::shared_ptr< FlxbbDesign > protocols::flxbb::FlxbbDesignOP
typedef utility::pointer::shared_ptr< InterlockAroma > protocols::flxbb::InterlockAromaOP
typedef utility::pointer::shared_ptr< LayerDesignOperation > protocols::flxbb::LayerDesignOperationOP
using protocols::flxbb::String = typedef std::string

Function Documentation

ConstraintOPs protocols::flxbb::constraints_NtoC ( Pose const &  pose,
Real const  coef,
Real const  condist 
)
ConstraintOPs protocols::flxbb::constraints_sheet ( Pose const &  pose,
BluePrintOP const &  blue,
Real const  coef,
Real const  condist = 5.5 
)
ConstraintOPs protocols::flxbb::constraints_sheet ( Pose const &  pose,
Real const  coef,
Real const  condist 
)
utility::vector1< core::Size > protocols::flxbb::find_ligands ( Pose const &  pose)
void protocols::flxbb::FlxbbDesign_main ( )
std::string protocols::flxbb::layer_design_ss_layer_group ( )
std::string protocols::flxbb::layer_design_ss_layer_naming_func ( std::string const &  element_name)
std::string protocols::flxbb::layer_design_ss_layer_or_taskop_group ( )
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

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.

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().

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