Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::antibody::GraftedStemOptimizer Class Reference

Grafts only one CDR onto a framework. More...

#include <GraftedStemOptimizer.hh>

Inheritance diagram for protocols::antibody::GraftedStemOptimizer:
Inheritance graph

Public Member Functions

 GraftedStemOptimizer (CDRNameEnum const &cdr_name, AntibodyInfoOP antibody_info)
 ~GraftedStemOptimizer () override
void apply (core::pose::Pose &pose) override
 Main Method. More...
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
void enable_benchmark_mode (bool const &setting)
 enable benchmark mode More...
void set_scorefxn (core::scoring::ScoreFunctionOP setting)
 users can pass their own scorefunction, foldtree, movemap, and taskfactory More...
void set_deep_optimization (bool const &setting)
 deep optimization will do small_share_ccd More...
core::kinematics::FoldTreeOP get_N_C_stems_foldtree (core::pose::Pose const &pose) const
core::kinematics::FoldTreeOP get_Nstem_foldtree (core::pose::Pose const &pose) const
core::kinematics::FoldTreeOP get_Cstem_foldtree (core::pose::Pose const &pose) const
core::kinematics::MoveMapOP get_stem_movemap (core::pose::Pose const &pose, std::string const &type, bool const &include_nb_sc=false) const
core::pack::task::TaskFactoryOP get_stem_taskfactory (core::pose::Pose &pose, std::string const &type, bool const &include_nb_sc=false) const
void set_stem_size (core::Size const &setting)
 stem that was replaced by the extra reesidues at the end of the loop terminus. Default is "2" More...
 GraftedStemOptimizer (GraftedStemOptimizer const &rhs)
 copy ctor More...
GraftedStemOptimizeroperator= (GraftedStemOptimizer const &rhs)
 assignment operator 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...
virtual MoverOP fresh_instance () const
 Generates a new Mover object freshly created with the default ctor. 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
virtual void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
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...
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...

Private Member Functions

void init ()
void setup_protocol (core::pose::Pose &pose)
void initForEqualOperatorAndCopyConstructor (GraftedStemOptimizer &lhs, GraftedStemOptimizer const &rhs)

Private Attributes

core::Size stem_size_
CDRNameEnum cdr_name_
AntibodyInfoOP ab_info_
bool benchmark_
loops::LoopOP cdr_loop_
core::scoring::ScoreFunctionOP scorefxn_
moves::MonteCarloOP mc_
moves::SequenceMoverOP optimize_stems_
bool deep_optimization_

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

Grafts only one CDR onto a framework.

Constructor & Destructor Documentation

◆ GraftedStemOptimizer() [1/2]

protocols::antibody::GraftedStemOptimizer::GraftedStemOptimizer ( CDRNameEnum const &  cdr_name,
AntibodyInfoOP  antibody_info 

References ab_info_, cdr_name_, and init().

◆ ~GraftedStemOptimizer()

protocols::antibody::GraftedStemOptimizer::~GraftedStemOptimizer ( )

◆ GraftedStemOptimizer() [2/2]

protocols::antibody::GraftedStemOptimizer::GraftedStemOptimizer ( GraftedStemOptimizer const &  rhs)

Member Function Documentation

◆ apply()

void protocols::antibody::GraftedStemOptimizer::apply ( core::pose::Pose )

◆ enable_benchmark_mode()

void protocols::antibody::GraftedStemOptimizer::enable_benchmark_mode ( bool const &  setting)

enable benchmark mode

References benchmark_.

◆ get_Cstem_foldtree()

kinematics::FoldTreeOP protocols::antibody::GraftedStemOptimizer::get_Cstem_foldtree ( core::pose::Pose const &  pose) const

◆ get_N_C_stems_foldtree()

kinematics::FoldTreeOP protocols::antibody::GraftedStemOptimizer::get_N_C_stems_foldtree ( core::pose::Pose const &  pose) const

◆ get_name()

std::string protocols::antibody::GraftedStemOptimizer::get_name ( ) const

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

Implements protocols::moves::Mover.

◆ get_Nstem_foldtree()

kinematics::FoldTreeOP protocols::antibody::GraftedStemOptimizer::get_Nstem_foldtree ( core::pose::Pose const &  pose) const

◆ get_stem_movemap()

kinematics::MoveMapOP protocols::antibody::GraftedStemOptimizer::get_stem_movemap ( core::pose::Pose const &  pose,
std::string const &  type,
bool const &  include_nb_sc = false 
) const

◆ get_stem_taskfactory()

pack::task::TaskFactoryOP protocols::antibody::GraftedStemOptimizer::get_stem_taskfactory ( core::pose::Pose pose,
std::string const &  type,
bool const &  include_nb_sc = false 
) const

◆ init()

void protocols::antibody::GraftedStemOptimizer::init ( void  )

◆ initForEqualOperatorAndCopyConstructor()

void protocols::antibody::GraftedStemOptimizer::initForEqualOperatorAndCopyConstructor ( GraftedStemOptimizer lhs,
GraftedStemOptimizer const &  rhs 

◆ operator=()

GraftedStemOptimizer & protocols::antibody::GraftedStemOptimizer::operator= ( GraftedStemOptimizer const &  rhs)

assignment operator

References initForEqualOperatorAndCopyConstructor().

◆ set_deep_optimization()

void protocols::antibody::GraftedStemOptimizer::set_deep_optimization ( bool const &  setting)

deep optimization will do small_share_ccd

References deep_optimization_.

◆ set_scorefxn()

void protocols::antibody::GraftedStemOptimizer::set_scorefxn ( core::scoring::ScoreFunctionOP  setting)

users can pass their own scorefunction, foldtree, movemap, and taskfactory

LLLLLLLLLLLLLLLLLLL#### L1-3.pdb, H1-3.pdb

..ffffffff@@ @@ffffffffff.. framework.pdb || || grafting \/ ffffffff@##LLLLLLLLLLLLLLLLLLL##@ffffffffff

      _____ set up fold tree  _____
     |     |                 |     |
     |  |  |                 |  |  |


References scorefxn_.

◆ set_stem_size()

void protocols::antibody::GraftedStemOptimizer::set_stem_size ( core::Size const &  setting)

stem that was replaced by the extra reesidues at the end of the loop terminus. Default is "2"

References stem_size_, and TRG().

◆ setup_protocol()

void protocols::antibody::GraftedStemOptimizer::setup_protocol ( core::pose::Pose pose)

Member Data Documentation

◆ ab_info_

AntibodyInfoOP protocols::antibody::GraftedStemOptimizer::ab_info_

◆ benchmark_

bool protocols::antibody::GraftedStemOptimizer::benchmark_

◆ cdr_loop_

loops::LoopOP protocols::antibody::GraftedStemOptimizer::cdr_loop_

◆ cdr_name_

CDRNameEnum protocols::antibody::GraftedStemOptimizer::cdr_name_

◆ deep_optimization_

bool protocols::antibody::GraftedStemOptimizer::deep_optimization_

◆ mc_

moves::MonteCarloOP protocols::antibody::GraftedStemOptimizer::mc_

Referenced by apply(), and init().

◆ optimize_stems_

moves::SequenceMoverOP protocols::antibody::GraftedStemOptimizer::optimize_stems_

Referenced by apply(), init(), and setup_protocol().

◆ scorefxn_

core::scoring::ScoreFunctionOP protocols::antibody::GraftedStemOptimizer::scorefxn_

◆ stem_size_

core::Size protocols::antibody::GraftedStemOptimizer::stem_size_

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