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protocols::dna::DnaInterfaceMultiStateDesign Class Reference

wraps DNA-interface specific considerations around the general multistate design / genetic algorithm framework More...

#include <DnaInterfaceMultiStateDesign.hh>

Inheritance diagram for protocols::dna::DnaInterfaceMultiStateDesign:
Inheritance graph
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Public Types

typedef multistate_design::PosType PosType
 
typedef
core::pack::task::PackerTaskCOP 
PackerTaskCOP
 
typedef
genetic_algorithm::GeneticAlgorithmOP 
GeneticAlgorithmOP
 
- Public Types inherited from protocols::minimization_packing::PackRotamersMover
typedef
core::pack::interaction_graph::AnnealableGraphBaseOP 
AnnealableGraphBaseOP
 
typedef
core::pack::interaction_graph::AnnealableGraphBaseCOP 
AnnealableGraphBaseCOP
 
typedef
core::pack::rotamer_set::RotamerSetsOP 
RotamerSetsOP
 
typedef
core::pack::rotamer_set::RotamerSetsCOP 
RotamerSetsCOP
 
typedef
core::pack::task::PackerTaskCOP 
PackerTaskCOP
 
typedef
core::pack::task::TaskFactoryCOP 
TaskFactoryCOP
 
typedef
core::scoring::ScoreFunctionCOP 
ScoreFunctionCOP
 
- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP TagCOP
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef std::list< std::string > Strings
 

Public Member Functions

 DnaInterfaceMultiStateDesign ()
 
 ~DnaInterfaceMultiStateDesign () override
 
void apply (Pose &) override
 Main Method. More...
 
void copy_dna_chains (DnaChainsOP)
 
void copy_targeted_dna (DnaDesignDefOPs const &)
 
void output_results (Pose &)
 
void parse_my_tag (TagCOP, basic::datacache::DataMap &) override
 parse XML (specifically in the context of the parser/scripting scheme) More...
 
moves::MoverOP fresh_instance () const override
 required in the context of the parser/scripting scheme More...
 
moves::MoverOP clone () const override
 required in the context of the parser/scripting scheme More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
- Public Member Functions inherited from protocols::minimization_packing::PackRotamersMover
 PackRotamersMover ()
 default constructor; reads the nloop_ value from the global options system. More...
 
 PackRotamersMover (utility::options::OptionCollection const &options)
 constructor that reads from the (possibly local) options collection object More...
 
 PackRotamersMover (std::string const &)
 constructor with typename; reads the nloop_ value from the global options system. More...
 
 PackRotamersMover (ScoreFunctionCOP scorefxn, PackerTaskCOP task=nullptr, core::Size nloop=1)
 Constructs a PackRotamersMover with PackerTask <task> evaluated using <scorefxn> More...
 
 ~PackRotamersMover () override
 
 PackRotamersMover (PackRotamersMover const &other)
 
void apply (Pose &pose) override
 Performs side-chain packing based on the input PackerTask using the input ScoreFunction. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void show (std::ostream &output=std::cout) const override
 Outputs details about the Mover, including current settings. More...
 
bool task_is_valid (Pose const &pose) const
 when the PackerTask was not generated locally, verify compatibility with pose More...
 
void parse_my_tag (TagCOP, basic::datacache::DataMap &) override
 parse XML (specifically in the context of the parser/scripting scheme) More...
 
virtual void parse_score_function (TagCOP, basic::datacache::DataMap const &)
 parse "scorefxn" XML option (can be employed virtually by derived Packing movers) More...
 
virtual void parse_task_operations (TagCOP, basic::datacache::DataMap const &)
 parse "task_operations" XML option (can be employed virtually by derived Packing movers) More...
 
void initialize_task_factory_with_operations (std::list< core::pack::task::operation::TaskOperationCOP > const &)
 
protocols::moves::MoverOP fresh_instance () const override
 required in the context of the parser/scripting scheme More...
 
protocols::moves::MoverOP clone () const override
 required in the context of the parser/scripting scheme More...
 
void score_function (ScoreFunctionCOP sf)
 Sets the ScoreFunction to <sf> More...
 
virtual void task_factory (TaskFactoryCOP tf)
 Sets the TaskFactory to <tf> More...
 
void task (PackerTaskCOP t)
 Sets the PackerTask to <t> More...
 
void nloop (core::Size nloop_in)
 
ScoreFunctionCOP score_function () const
 Returns the ScoreFunction. More...
 
PackerTaskCOP task () const
 Returns the PackerTask. More...
 
core::Size nloop () const
 
TaskFactoryCOP task_factory () const
 Returns the TaskFactory. More...
 
RotamerSetsCOP rotamer_sets () const
 Returns the RotamerSets object being used for packing. More...
 
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
 
virtual MoverOP create ()
 
MoverCOP get_self_ptr () const
 
MoverOP get_self_ptr ()
 
MoverCAP get_self_weak_ptr () const
 
MoverAP get_self_weak_ptr ()
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
virtual void test_move (Pose &pose)
 : Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...
 
virtual bool reinitialize_for_each_job () const
 Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...
 
virtual bool reinitialize_for_new_input () const
 Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...
 
MoverStatus get_last_move_status () const
 end parser interface, start Job Distributor interface///////////// More...
 
void reset_status ()
 resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...
 
virtual core::pose::PoseOP get_additional_output ()
 Mechanism by which a mover may return multiple output poses from a single input pose. More...
 
void set_type (std::string const &setting)
 Set the 'type' string. More...
 
std::string get_type () const
 
void type (const std::string &type_in)
 Set the 'type' string. More...
 
std::string const & type () const
 Get the set 'type' string. More...
 
virtual void set_input_pose (PoseCOP pose)
 setter for poses contained for rms More...
 
virtual void set_native_pose (PoseCOP pose)
 setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...
 
PoseCOP get_input_pose () const
 
PoseCOP get_native_pose () const
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 
virtual void set_current_tag (std::string const &new_tag)
 
std::string get_current_tag () const
 A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...
 
virtual core::Real last_proposal_density_ratio ()
 
virtual void clear_info ()
 Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...
 
virtual Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 
virtual bool mover_provides_citation_info () const
 Does this mover 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 mover_is_unpublished () const
 Does this mover 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 std::string mover_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
- Static Public Member Functions inherited from protocols::minimization_packing::PackRotamersMover
static std::string mover_name ()
 
static
utility::tag::XMLSchemaComplexTypeGeneratorOP 
complex_type_generator_for_pack_rotamers_mover (utility::tag::XMLSchemaDefinition &xsd)
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
static void list_options_read (utility::options::OptionKeyList &opts)
 
- Static Public Member Functions inherited from protocols::moves::Mover
static std::string name ()
 
static void register_options ()
 Overload this static method if you access options within the mover. More...
 

Private Member Functions

void initialize (Pose &)
 
void run ()
 
void add_dna_states (Pose const &, PackerTaskCOP)
 

Private Attributes

GeneticAlgorithmOP gen_alg_
 
multistate_design::MultiStatePackerOP multistate_packer_
 
DnaChainsOP dna_chains_
 
DnaDesignDefOPs targeted_dna_
 
core::Size generations_
 
core::Size pop_size_
 
core::Size num_packs_
 
core::Size pop_from_ss_
 
core::Size numresults_
 
core::Real fraction_by_recombination_
 
core::Real mutate_rate_
 
core::Real boltz_temp_
 
core::Real anchor_offset_
 
std::string checkpoint_prefix_
 
core::Size checkpoint_interval_
 
bool checkpoint_gz_
 
bool checkpoint_rename_
 

Additional Inherited Members

- Protected Member Functions inherited from protocols::minimization_packing::PackRotamersMover
virtual void setup (Pose &pose)
 get rotamers, energies. Also performs lazy initialization of ScoreFunction, PackerTask. More...
 
virtual core::PackerEnergy run (Pose &pose, utility::vector0< int > rot_to_pack=utility::vector0< int >()) const
 
virtual void cleanup (core::pose::Pose &pose)
 Clean up cached pose and mover data after the fact. More...
 
virtual void note_packertask_settings (Pose const &)
 note PackerTask's packable and designable residues as string info More...
 
- Protected Member Functions inherited from protocols::moves::Mover
void set_last_move_status (MoverStatus status)
 nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...
 

Detailed Description

wraps DNA-interface specific considerations around the general multistate design / genetic algorithm framework

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::dna::DnaInterfaceMultiStateDesign::DnaInterfaceMultiStateDesign ( )
protocols::dna::DnaInterfaceMultiStateDesign::~DnaInterfaceMultiStateDesign ( )
overridedefault

Member Function Documentation

void protocols::dna::DnaInterfaceMultiStateDesign::add_dna_states ( Pose const &  pose,
PackerTaskCOP  ptask 
)
private
void protocols::dna::DnaInterfaceMultiStateDesign::apply ( Pose )
overridevirtual

Main Method.

Implements protocols::moves::Mover.

References initialize(), output_results(), and run().

moves::MoverOP protocols::dna::DnaInterfaceMultiStateDesign::clone ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

void protocols::dna::DnaInterfaceMultiStateDesign::copy_dna_chains ( DnaChainsOP  dna_chains)

References dna_chains_.

void protocols::dna::DnaInterfaceMultiStateDesign::copy_targeted_dna ( DnaDesignDefOPs const &  defs)

References targeted_dna_.

moves::MoverOP protocols::dna::DnaInterfaceMultiStateDesign::fresh_instance ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

std::string protocols::dna::DnaInterfaceMultiStateDesign::get_name ( ) const
overridevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

References mover_name().

void protocols::dna::DnaInterfaceMultiStateDesign::initialize ( Pose pose)
private
std::string protocols::dna::DnaInterfaceMultiStateDesign::mover_name ( )
static
void protocols::dna::DnaInterfaceMultiStateDesign::output_results ( Pose pose)
void protocols::dna::DnaInterfaceMultiStateDesign::parse_my_tag ( TagCOP  tag,
basic::datacache::DataMap &  datamap 
)
overridevirtual
void protocols::dna::DnaInterfaceMultiStateDesign::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::dna::DnaInterfaceMultiStateDesign::run ( )
private

References gen_alg_, and protocols::dna::TR().

Referenced by apply().

Member Data Documentation

core::Real protocols::dna::DnaInterfaceMultiStateDesign::anchor_offset_
private

Referenced by initialize(), and parse_my_tag().

core::Real protocols::dna::DnaInterfaceMultiStateDesign::boltz_temp_
private

Referenced by initialize(), and parse_my_tag().

bool protocols::dna::DnaInterfaceMultiStateDesign::checkpoint_gz_
private

Referenced by initialize(), and parse_my_tag().

core::Size protocols::dna::DnaInterfaceMultiStateDesign::checkpoint_interval_
private

Referenced by initialize(), and parse_my_tag().

std::string protocols::dna::DnaInterfaceMultiStateDesign::checkpoint_prefix_
private

Referenced by initialize(), and parse_my_tag().

bool protocols::dna::DnaInterfaceMultiStateDesign::checkpoint_rename_
private

Referenced by initialize(), and parse_my_tag().

DnaChainsOP protocols::dna::DnaInterfaceMultiStateDesign::dna_chains_
private
core::Real protocols::dna::DnaInterfaceMultiStateDesign::fraction_by_recombination_
private

Referenced by initialize(), and parse_my_tag().

GeneticAlgorithmOP protocols::dna::DnaInterfaceMultiStateDesign::gen_alg_
private

Referenced by initialize(), output_results(), and run().

core::Size protocols::dna::DnaInterfaceMultiStateDesign::generations_
private

Referenced by initialize(), and parse_my_tag().

multistate_design::MultiStatePackerOP protocols::dna::DnaInterfaceMultiStateDesign::multistate_packer_
private
core::Real protocols::dna::DnaInterfaceMultiStateDesign::mutate_rate_
private

Referenced by initialize(), and parse_my_tag().

core::Size protocols::dna::DnaInterfaceMultiStateDesign::num_packs_
private

Referenced by initialize(), and parse_my_tag().

core::Size protocols::dna::DnaInterfaceMultiStateDesign::numresults_
private

Referenced by output_results(), and parse_my_tag().

core::Size protocols::dna::DnaInterfaceMultiStateDesign::pop_from_ss_
private

Referenced by initialize(), and parse_my_tag().

core::Size protocols::dna::DnaInterfaceMultiStateDesign::pop_size_
private

Referenced by initialize(), and parse_my_tag().

DnaDesignDefOPs protocols::dna::DnaInterfaceMultiStateDesign::targeted_dna_
private

Referenced by copy_targeted_dna(), and initialize().


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