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:

[legend]

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 void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. 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< MutationSet >	mutation_sets_

utility::vector1< core::Real >	weights_

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 )

References set_defaults(), and set_mutation_sets().

protocols::task_operations::MutationSetDesignOperation::MutationSetDesignOperation	(	utility::vector1< MutationSet >	mutation_sets,
		utility::vector1< core::Real >	weights
	)

References set_defaults(), and set_mutation_sets().

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

Change a packer task in some way. The input pose is the one to which the input task will be later applied.

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

References core::pack::task::ResidueLevelTask::get_original_residue(), include_native_aa_, mutation_sets_, core::pack::task::PackerTask::nonconst_residue_task(), picking_rounds_, core::pack::task::PackerTask::residue_task(), core::pack::task::ResidueLevelTask::restrict_absent_canonical_aas(), core::scoring::rg, protocols::noesy_assign::round(), sample_index_, core::pose::Pose::size(), and weights_.

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

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

References keyname(), and core::pack::task::operation::task_op_schema_empty().

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

References include_native_aa_, picking_rounds_, and reset_sample_index().

Referenced by MutationSetDesignOperation().

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_.