Rosetta Protocols  2014.35
Classes | Typedefs | Enumerations | Functions
protocols::antibody::design Namespace Reference

Classes

class  AntibodyDatabaseManager
 Class responsible for loading information from the AntibodyDatabase. More...
 
class  AntibodyDesignModeler
 Class that runs the modeling for AntibodyDesign protocols. Could be moved to antibody. More...
 
class  AntibodyDesignMover
 Main AntibodyDesignMover, tieing together individual movers and classes. Main mover for application. More...
 
class  AntibodyGraftDesignMover
 This class designs antibodies by grafting, using cluster information and constraints to help. It represents the first step in The Rosetta Antibody Designer, but can be used outside of the application. The Antibody Database that this class uses will be available online (Too large for the rosetta_database) Till then, email me for access to the github repository. More...
 
class  AntibodySeqDesignMover
 Designs antibody CDR structures using a variety of different methods. Main methods involve using cluster-based sequence probability statistics and conservative design strategies to limit unknown structural effects caused by aggressive design. Uses North_AHO numbering and cluster-based design. Part of Rosetta Antibody Designer. More...
 
struct  CDRDesignInstructions
 
struct  CDRGraftInstructions
 This struct gives antibody designers complete control either through this classes interface or an instruction file. More...
 
class  ConservativeDesignOperation
 A TaskOperation that sets the allowed amino acids of designable residues to the native amino acid's conservative mutations. More...
 
class  DesignInstructionsParser
 Lightweight class for parsing design instructions. More...
 
class  ResidueProbDesignOperation
 A TaskOperation that allows amino acids at designable positions through a set of aa probabilities. More...
 
struct  SamplingWeights
 

Typedefs

typedef std::map< CDRNameEnum,
CDRGraftInstructions
GraftInstructions
 
typedef std::map< CDRNameEnum,
CDRDesignInstructions
DesignInstructions
 
typedef std::map< CDRNameEnum,
vector1< PoseOP > > 
CDRSet
 
typedef std::map< CDRNameEnum,
vector1< CDRClusterEnum > > 
CDRClusterMap
 
typedef std::map< CDRNameEnum,
vector1< std::string > > 
PDBMap
 
typedef
utility::pointer::owning_ptr
< AntibodyDatabaseManager
AntibodyDatabaseManagerOP
 
typedef
utility::pointer::owning_ptr
< AntibodyDatabaseManager
const > 
AntibodyDatabaseManagerCOP
 
typedef std::map
< core::chemical::AA,
core::Real
AAProbabilities
 
typedef
utility::pointer::owning_ptr
< AntibodyDesignModeler
AntibodyDesignModelerOP
 
typedef
utility::pointer::owning_ptr
< AntibodyDesignModeler const > 
AntibodyDesignModelerCOP
 
typedef
utility::pointer::owning_ptr
< AntibodyDesignMover
AntibodyDesignMoverOP
 
typedef
utility::pointer::owning_ptr
< AntibodyDesignMover const > 
AntibodyDesignMoverCOP
 
typedef
utility::pointer::owning_ptr
< AntibodyGraftDesignMover
AntibodyGraftDesignMoverOP
 
typedef
utility::pointer::owning_ptr
< AntibodyGraftDesignMover
const > 
AntibodyGraftDesignMoverCOP
 
typedef
utility::pointer::owning_ptr
< AntibodySeqDesignMover
AntibodySeqDesignMoverOP
 
typedef
utility::pointer::owning_ptr
< AntibodySeqDesignMover const > 
AntibodySeqDesignMoverCOP
 
typedef
utility::pointer::owning_ptr
< ConservativeDesignOperation
ConservativeDesignOperationOP
 
typedef
utility::pointer::owning_ptr
< ConservativeDesignOperation
const > 
ConservativeDesignOperationCOP
 
typedef std::map< Size,
AAProbabilities
PerResidueAAProbSet
 
typedef
utility::pointer::owning_ptr
< ResidueProbDesignOperation
ResidueProbDesignOperationOP
 
typedef
utility::pointer::owning_ptr
< ResidueProbDesignOperation
const > 
ResidueProbDesignOperationCOP
 

Enumerations

enum  MinTypeEnum {
  relax = 1, centroid_relax, minimize, repack,
  no_min, MinTypeEnum_total = no_min
}
 
enum  DesignTypeEnum {
  relaxed_design = 1, docked_design, fixbb, flxbb,
  DesignTypeEnum_total = flxbb
}
 

Functions

void get_all_graft_permutations (vector1< core::Size > &total_cdr_set, vector1< vector1< core::Size > > &all_permutations, vector1< core::Size >current_index, core::Size const cdr_num)
 Gets all possible graft permutations. More...
 
DesignTypeEnum design_type_from_string (std::string const design_type)
 
std::string design_type_to_string (DesignTypeEnum const design_type)
 

Typedef Documentation

Enumeration Type Documentation

Enumerator
relaxed_design 
docked_design 
fixbb 
flxbb 
DesignTypeEnum_total 
Enumerator
relax 
centroid_relax 
minimize 
repack 
no_min 
MinTypeEnum_total 

Function Documentation

DesignTypeEnum protocols::antibody::design::design_type_from_string ( std::string const  design_type)
std::string protocols::antibody::design::design_type_to_string ( DesignTypeEnum const  design_type)
void protocols::antibody::design::get_all_graft_permutations ( vector1< core::Size > &  total_cdr_set,
vector1< vector1< core::Size > > &  all_permutations,
vector1< core::Size current_index,
core::Size const  cdr_num 
)

Gets all possible graft permutations.

all_permutations is a list of vectors corresponding to cdrs_to_design vector. Essentially, each inner index describes a position in the cdr_set. Indexes correspond to CDRNameEnum, and whose values correspond to the cdr_set index. If the value is 0, it means no cdr in set. Example: <1, 0, 1, 1, 1, 1>. This is a possible combination to try graft, the second CDR, H2 is not part of the combination.

Referenced by protocols::antibody::design::AntibodyGraftDesignMover::get_cdr_set_index_list().