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protocols::task_operations::MutationSetDesignOperation Class Reference

Sample a set of mutations each time packer is generated. A MutationSet is a simple map of resnum:aa. Each apply will sample a set either at random, or with a set of weights. More...

#include <MutationSetDesignOperation.hh>

Inheritance diagram for protocols::task_operations::MutationSetDesignOperation:
Inheritance graph
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Public Member Functions

 MutationSetDesignOperation ()
 
 MutationSetDesignOperation (utility::vector1< MutationSet > mutation_sets)
 
 MutationSetDesignOperation (utility::vector1< MutationSet > mutation_sets, utility::vector1< core::Real > weights)
 
 MutationSetDesignOperation (MutationSetDesignOperation const &src)
 
void apply (core::pose::Pose const &pose, core::pack::task::PackerTask &task) const override
 Change a packer task in some way. The input pose is the one to which the input task will be later applied. More...
 
 ~MutationSetDesignOperation () override
 
void set_mutation_sets (utility::vector1< MutationSet > mutation_sets)
 Set the mutation sets. Each MutationSet is a std::map of resnum:aa Will use a weight of 1 for each. More...
 
void set_mutation_sets (utility::vector1< MutationSet > mutation_sets, utility::vector1< core::Real > mutation_set_weights)
 Set the mutation sets and corresponding weights Each MutationSet is a std::map of resnum:aa. More...
 
void add_mutation_set (MutationSet mutation_set)
 add a mutation set with weight 1. More...
 
void add_mutation_set (MutationSet mutation_set, core::Real weight)
 add a mutation set with a weight. More...
 
void clear_mutation_sets ()
 Clear any stored mutation sets and weights. More...
 
void include_native_aa (bool const &setting)
 Include native amino acid in the allowed_aas list. Default False. More...
 
void set_picking_rounds (core::Size picking_rounds)
 Number of times we sample from our sets. Default 1/apply. The more rounds, the closer the final amino acid set for each position will be to the full profile for that position. If using weights for the residue sets, this would increase variability. More...
 
void set_sample_index (core::Size sample_index)
 Set the class to iterate through the sets instead of sampling from them. More...
 
core::Size get_sample_index () const
 
core::Size get_total_mutation_sets () const
 Get the total number of mutation sets housed. More...
 
void reset_sample_index ()
 Set the sample index back to zero - which means we will sample from all of them according to weights. More...
 
core::pack::task::operation::TaskOperationOP clone () const override
 Create another task operation of the type matching the most-derived version of the class. More...
 
- Public Member Functions inherited from core::pack::task::operation::TaskOperation
 ~TaskOperation () override
 
virtual void parse_tag (TagCOP, DataMap &)
 Used to parse an xml-like tag to load parameters and properties. More...
 
virtual bool task_operation_provides_citation_info () const
 Does this task operation provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool task_operation_is_unpublished () const
 Does this task_operation indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Static Public Member Functions

static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
static std::string keyname ()
 

Private Member Functions

void set_defaults ()
 

Private Attributes

bool include_native_aa_
 
utility::vector1< MutationSetmutation_sets_
 
utility::vector1< core::Realweights_
 
core::Size picking_rounds_
 
core::Size sample_index_
 

Additional Inherited Members

- Public Types inherited from core::pack::task::operation::TaskOperation
typedef utility::tag::TagCOP TagCOP
 
typedef basic::datacache::DataMap DataMap
 
typedef pose::Pose Pose
 

Detailed Description

Sample a set of mutations each time packer is generated. A MutationSet is a simple map of resnum:aa. Each apply will sample a set either at random, or with a set of weights.

Does not enable/disable packing or design by default. Simply controls what the design set will be. Typically each set would be of the same resnums, but this is not necessary. Iterative Sampling can be achieved somewhat by setting the sample index with each pack. Does not touch any resnums not in a sampled mutation set.

Constructor & Destructor Documentation

protocols::task_operations::MutationSetDesignOperation::MutationSetDesignOperation ( )

References set_defaults().

protocols::task_operations::MutationSetDesignOperation::MutationSetDesignOperation ( utility::vector1< MutationSet mutation_sets)
protocols::task_operations::MutationSetDesignOperation::MutationSetDesignOperation ( utility::vector1< MutationSet mutation_sets,
utility::vector1< core::Real weights 
)
protocols::task_operations::MutationSetDesignOperation::MutationSetDesignOperation ( MutationSetDesignOperation const &  src)
default
protocols::task_operations::MutationSetDesignOperation::~MutationSetDesignOperation ( )
overridedefault

Member Function Documentation

void protocols::task_operations::MutationSetDesignOperation::add_mutation_set ( MutationSet  mutation_set)

add a mutation set with weight 1.

References mutation_sets_, and weights_.

void protocols::task_operations::MutationSetDesignOperation::add_mutation_set ( MutationSet  mutation_set,
core::Real  weight 
)

add a mutation set with a weight.

References mutation_sets_, and weights_.

void protocols::task_operations::MutationSetDesignOperation::apply ( core::pose::Pose const &  ,
core::pack::task::PackerTask  
) const
overridevirtual
void protocols::task_operations::MutationSetDesignOperation::clear_mutation_sets ( )

Clear any stored mutation sets and weights.

References mutation_sets_, and weights_.

TaskOperationOP protocols::task_operations::MutationSetDesignOperation::clone ( ) const
overridevirtual

Create another task operation of the type matching the most-derived version of the class.

Implements core::pack::task::operation::TaskOperation.

core::Size protocols::task_operations::MutationSetDesignOperation::get_sample_index ( ) const

References sample_index_.

core::Size protocols::task_operations::MutationSetDesignOperation::get_total_mutation_sets ( ) const

Get the total number of mutation sets housed.

References mutation_sets_.

void protocols::task_operations::MutationSetDesignOperation::include_native_aa ( bool const &  setting)

Include native amino acid in the allowed_aas list. Default False.

References include_native_aa_.

Referenced by protocols::antibody::task_operations::AddCDRProfileSetsOperation::apply().

static std::string protocols::task_operations::MutationSetDesignOperation::keyname ( )
inlinestatic

Referenced by provide_xml_schema().

void protocols::task_operations::MutationSetDesignOperation::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::task_operations::MutationSetDesignOperation::reset_sample_index ( )

Set the sample index back to zero - which means we will sample from all of them according to weights.

References sample_index_.

Referenced by set_defaults().

void protocols::task_operations::MutationSetDesignOperation::set_defaults ( )
private
void protocols::task_operations::MutationSetDesignOperation::set_mutation_sets ( utility::vector1< MutationSet mutation_sets)

Set the mutation sets. Each MutationSet is a std::map of resnum:aa Will use a weight of 1 for each.

References mutation_sets_, and weights_.

Referenced by protocols::antibody::task_operations::AddCDRProfileSetsOperation::apply(), and MutationSetDesignOperation().

void protocols::task_operations::MutationSetDesignOperation::set_mutation_sets ( utility::vector1< MutationSet mutation_sets,
utility::vector1< core::Real mutation_set_weights 
)

Set the mutation sets and corresponding weights Each MutationSet is a std::map of resnum:aa.

References mutation_sets_, and weights_.

void protocols::task_operations::MutationSetDesignOperation::set_picking_rounds ( core::Size  picking_rounds)

Number of times we sample from our sets. Default 1/apply. The more rounds, the closer the final amino acid set for each position will be to the full profile for that position. If using weights for the residue sets, this would increase variability.

References picking_rounds_.

Referenced by protocols::antibody::task_operations::AddCDRProfileSetsOperation::apply().

void protocols::task_operations::MutationSetDesignOperation::set_sample_index ( core::Size  sample_index)

Set the class to iterate through the sets instead of sampling from them.

Get the sampling number if using iterative mode. Starts at zero, resets with size of mutation set. Used to sample particular indexes, since we can't do this iteratively due to const apply. 1 through n Set to 0 in order to sample from the weights.

References sample_index_.

Member Data Documentation

bool protocols::task_operations::MutationSetDesignOperation::include_native_aa_
private
utility::vector1< MutationSet > protocols::task_operations::MutationSetDesignOperation::mutation_sets_
private
core::Size protocols::task_operations::MutationSetDesignOperation::picking_rounds_
private
core::Size protocols::task_operations::MutationSetDesignOperation::sample_index_
private
utility::vector1< core::Real > protocols::task_operations::MutationSetDesignOperation::weights_
private

The documentation for this class was generated from the following files: