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protocols::antibody::design::MutateFrameworkForCluster Class Reference

Mutates framework positions to what is needed for a particular cluster if that cluster has needed mutations. More...

#include <MutateFrameworkForCluster.hh>

Inheritance diagram for protocols::antibody::design::MutateFrameworkForCluster:
Inheritance graph
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Public Member Functions

 MutateFrameworkForCluster ()
 Constructor for RosettaScripts only. More...
 
 MutateFrameworkForCluster (AntibodyInfoCOP ab_info)
 
 MutateFrameworkForCluster (MutateFrameworkForCluster const &src)
 
 ~MutateFrameworkForCluster () override
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
moves::MoverOP fresh_instance () const override
 Generates a new Mover object freshly created with the default ctor. More...
 
void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data) override
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
void set_cdr_only (CDRNameEnum const &cdr)
 
void set_cdrs (utility::vector1< bool > const &cdrs)
 
void set_pack_shell (core::Real const pack_shell)
 Set the distance for the packing shell. More...
 
void set_scorefxn (core::scoring::ScoreFunctionCOP scorefxn)
 
void set_custom_data (std::map< clusters::CDRClusterEnum, utility::vector1< MutantPosition > > const &mutant_info)
 Set custom data instead of loading it from the database. More...
 
std::map
< clusters::CDRClusterEnum,
utility::vector1
< MutantPosition > > 
get_data ()
 Get data used to do the design. More...
 
bool has_framework_dependant_clusters (core::pose::Pose const &pose)
 
bool has_framework_dependant_cluster (core::pose::Pose const &pose, CDRNameEnum const cdr)
 
utility::vector1
< clusters::CDRClusterEnum
framework_dependant_clusters ()
 Get all framework dependant clusters in list. More...
 
utility::vector1< boolframework_dependant_positions (core::pose::Pose const &pose)
 Get all framework positions that would be required by clusters regardless of whether that cluster is in the pose. More...
 
utility::vector1< boolframework_dependant_positions (core::pose::Pose const &pose, clusters::CDRClusterEnum const cluster)
 Get all framework positions that would be required by a cluster regardless of whether that cluster is in the pose. More...
 
utility::vector1< boolframework_dependant_mutations (core::pose::Pose const &pose, clusters::CDRClusterEnum const cluster, core::Size const resnum)
 Get all framework mutations for a particular framework dependent position, regardless of whether that cluster is in the pose. More...
 
void provide_citation_info (basic::citation_manager::CitationCollectionList &) const override
 Provide the citation. 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 MoverOP clone () const
 Return a clone of the Mover object. 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 void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. 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...
 

Private Member Functions

void set_defaults ()
 
void load_data ()
 

Private Attributes

AntibodyInfoCOP ab_info_
 
bool regenerate_abinfo_ = false
 
core::scoring::ScoreFunctionCOP scorefxn_
 
std::map
< clusters::CDRClusterEnum,
utility::vector1
< MutantPosition > > 
mutant_info_
 
utility::vector1< boolcdrs_
 
core::Real pack_shell_
 

Additional Inherited Members

- 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
 
- 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...
 
- 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

Mutates framework positions to what is needed for a particular cluster if that cluster has needed mutations.

Will use clusters from pose data cache if there, otherwise, will use clusters set from AntibodyInfo.

Use set_cdr or set_cdrs to limit to a particular CDR or set of CDRs.

Constructor & Destructor Documentation

protocols::antibody::design::MutateFrameworkForCluster::MutateFrameworkForCluster ( )

Constructor for RosettaScripts only.

References load_data(), and set_defaults().

protocols::antibody::design::MutateFrameworkForCluster::MutateFrameworkForCluster ( AntibodyInfoCOP  ab_info)

References load_data(), and set_defaults().

protocols::antibody::design::MutateFrameworkForCluster::MutateFrameworkForCluster ( MutateFrameworkForCluster const &  src)
default
protocols::antibody::design::MutateFrameworkForCluster::~MutateFrameworkForCluster ( )
overridedefault

Member Function Documentation

void protocols::antibody::design::MutateFrameworkForCluster::apply ( core::pose::Pose )
overridevirtual
utility::vector1< CDRClusterEnum > protocols::antibody::design::MutateFrameworkForCluster::framework_dependant_clusters ( )

Get all framework dependant clusters in list.

References mutant_info_.

Referenced by apply().

utility::vector1< bool > protocols::antibody::design::MutateFrameworkForCluster::framework_dependant_mutations ( core::pose::Pose const &  pose,
clusters::CDRClusterEnum const  cluster,
core::Size const  resnum 
)

Get all framework mutations for a particular framework dependent position, regardless of whether that cluster is in the pose.

References ab_info_, protocols::antibody::design::get_resnum_from_single_string_w_landmark(), and mutant_info_.

utility::vector1< bool > protocols::antibody::design::MutateFrameworkForCluster::framework_dependant_positions ( core::pose::Pose const &  pose)

Get all framework positions that would be required by clusters regardless of whether that cluster is in the pose.

References ab_info_, protocols::antibody::design::get_resnum_from_single_string_w_landmark(), mutant_info_, and core::pose::Pose::size().

utility::vector1< bool > protocols::antibody::design::MutateFrameworkForCluster::framework_dependant_positions ( core::pose::Pose const &  pose,
clusters::CDRClusterEnum const  cluster 
)

Get all framework positions that would be required by a cluster regardless of whether that cluster is in the pose.

References ab_info_, protocols::antibody::design::get_resnum_from_single_string_w_landmark(), mutant_info_, and core::pose::Pose::size().

protocols::moves::MoverOP protocols::antibody::design::MutateFrameworkForCluster::fresh_instance ( ) const
overridevirtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

std::map< clusters::CDRClusterEnum, utility::vector1< MutantPosition > > protocols::antibody::design::MutateFrameworkForCluster::get_data ( )

Get data used to do the design.

References mutant_info_.

std::string protocols::antibody::design::MutateFrameworkForCluster::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

Referenced by provide_citation_info().

bool protocols::antibody::design::MutateFrameworkForCluster::has_framework_dependant_cluster ( core::pose::Pose const &  pose,
CDRNameEnum const  cdr 
)
bool protocols::antibody::design::MutateFrameworkForCluster::has_framework_dependant_clusters ( core::pose::Pose const &  pose)
void protocols::antibody::design::MutateFrameworkForCluster::load_data ( )
private
void protocols::antibody::design::MutateFrameworkForCluster::parse_my_tag ( TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

References cdrs_, protocols::antibody::get_cdr_bool_from_tag(), pack_shell_, core::scoring::parse_score_function(), regenerate_abinfo_, and scorefxn_.

void protocols::antibody::design::MutateFrameworkForCluster::provide_citation_info ( basic::citation_manager::CitationCollectionList &  citations) const
overridevirtual

Provide the citation.

Reimplemented from protocols::moves::Mover.

References get_name().

void protocols::antibody::design::MutateFrameworkForCluster::set_cdr_only ( CDRNameEnum const &  cdr)

References cdrs_.

void protocols::antibody::design::MutateFrameworkForCluster::set_cdrs ( utility::vector1< bool > const &  cdrs)

References cdrs_.

void protocols::antibody::design::MutateFrameworkForCluster::set_custom_data ( std::map< clusters::CDRClusterEnum, utility::vector1< MutantPosition > > const &  mutant_info)

Set custom data instead of loading it from the database.

References mutant_info_.

void protocols::antibody::design::MutateFrameworkForCluster::set_defaults ( )
private
void protocols::antibody::design::MutateFrameworkForCluster::set_pack_shell ( core::Real const  pack_shell)

Set the distance for the packing shell.

References pack_shell_.

void protocols::antibody::design::MutateFrameworkForCluster::set_scorefxn ( core::scoring::ScoreFunctionCOP  scorefxn)

References scorefxn_.

Member Data Documentation

AntibodyInfoCOP protocols::antibody::design::MutateFrameworkForCluster::ab_info_
private
utility::vector1<bool> protocols::antibody::design::MutateFrameworkForCluster::cdrs_
private
std::map<clusters::CDRClusterEnum, utility::vector1<MutantPosition> > protocols::antibody::design::MutateFrameworkForCluster::mutant_info_
private
core::Real protocols::antibody::design::MutateFrameworkForCluster::pack_shell_
private
bool protocols::antibody::design::MutateFrameworkForCluster::regenerate_abinfo_ = false
private

Referenced by apply(), and parse_my_tag().

core::scoring::ScoreFunctionCOP protocols::antibody::design::MutateFrameworkForCluster::scorefxn_
private

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