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protocols::antibody2::GraftOneCDRLoop Class Reference

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

#include <GraftOneCDRLoop.hh>

Inheritance diagram for protocols::antibody2::GraftOneCDRLoop:
Inheritance graph
Collaboration diagram for protocols::antibody2::GraftOneCDRLoop:
Collaboration graph

Public Member Functions

 GraftOneCDRLoop ()
 GraftOneCDRLoop (AntibodyCDRNameEnum const &cdr_name, AntibodyInfoOP antibody_info, Ab_TemplateInfoOP ab_t_info)
 ~GraftOneCDRLoop ()
virtual void apply (core::pose::Pose &pose_in)
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
void enable_benchmark_mode (bool setting)
 enable benchmark mode More...
void set_scorefxn (core::scoring::ScoreFunctionOP scorefxn)
 users can pass their own scorefunction for packing after grafting More...
void h3_stem_off (bool setting)
 R2 just graft R2 by copying some stem residues, and remove H3 to do H3 loop modeling later. But the terminal has been changed by this grafting. Therefore, in R3, an option for not copying h3 stem is provided. More...
void set_flank_size (double setting)
 GraftOneCDRLoop (GraftOneCDRLoop const &rhs)
 copy ctor More...
GraftOneCDRLoopoperator= (GraftOneCDRLoop const &rhs)
 assignment operator More...
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
virtual ~Mover ()
virtual MoverSP create ()
virtual void apply (core::io::serialization::PipeMap &pmap)
virtual void parse_state (SerializableState const &state)
virtual void parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)
virtual void save_state (SerializableState &state)
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 Mover (Mover const &other)
Moveroperator= (Mover const &other)
 assignment operator More...
virtual core::Real last_proposal_density_ratio ()
std::string const & type () const
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...
void set_current_tag (std::string const &new_tag)
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 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...
void type (const std::string &type_in)
virtual MoverOP clone () const
 clone has to be overridden only if clone invocation is expected. More...
virtual void parse_my_tag (TagPtr const tag, DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
std::string get_type () const
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...
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 reinitialize_for_each_job () const
 this function informs 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
 this function informs 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
 this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...
void set_current_job (protocols::jobdist::BasicJobCOP job)
jobdist::BasicJobCOP get_current_job () const

Private Member Functions

void set_default ()
void init ()
void finalize_setup ()
void initForEqualOperatorAndCopyConstructor (GraftOneCDRLoop &lhs, GraftOneCDRLoop const &rhs)

Private Attributes

core::Size flank_size_
core::Size stem_copy_size_
AntibodyCDRNameEnum cdr_name_
AntibodyInfoOP ab_info_
Ab_TemplateInfoOP ab_t_info_
bool benchmark_
bool h3_stem_not_graft_
core::scoring::ScoreFunctionCOP scorefxn_

Additional Inherited Members

- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr TagPtr
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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. 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

protocols::antibody2::GraftOneCDRLoop::GraftOneCDRLoop ( )
protocols::antibody2::GraftOneCDRLoop::GraftOneCDRLoop ( AntibodyCDRNameEnum const &  cdr_name,
AntibodyInfoOP  antibody_info,
Ab_TemplateInfoOP  ab_t_info 
protocols::antibody2::GraftOneCDRLoop::~GraftOneCDRLoop ( )
protocols::antibody2::GraftOneCDRLoop::GraftOneCDRLoop ( GraftOneCDRLoop const &  rhs)

Member Function Documentation

void protocols::antibody2::GraftOneCDRLoop::apply ( core::pose::Pose pose_in)
void protocols::antibody2::GraftOneCDRLoop::enable_benchmark_mode ( bool  setting)

enable benchmark mode

References benchmark_.

void protocols::antibody2::GraftOneCDRLoop::finalize_setup ( )
std::string protocols::antibody2::GraftOneCDRLoop::get_name ( ) const

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

Implements protocols::moves::Mover.

void protocols::antibody2::GraftOneCDRLoop::h3_stem_off ( bool  setting)

R2 just graft R2 by copying some stem residues, and remove H3 to do H3 loop modeling later. But the terminal has been changed by this grafting. Therefore, in R3, an option for not copying h3 stem is provided.

References h3_stem_not_graft_.

void protocols::antibody2::GraftOneCDRLoop::init ( void  )
void protocols::antibody2::GraftOneCDRLoop::initForEqualOperatorAndCopyConstructor ( GraftOneCDRLoop lhs,
GraftOneCDRLoop const &  rhs 
GraftOneCDRLoop & protocols::antibody2::GraftOneCDRLoop::operator= ( GraftOneCDRLoop const &  rhs)

assignment operator

References initForEqualOperatorAndCopyConstructor().

void protocols::antibody2::GraftOneCDRLoop::set_default ( )
void protocols::antibody2::GraftOneCDRLoop::set_flank_size ( double  setting)

References flank_size_.

void protocols::antibody2::GraftOneCDRLoop::set_scorefxn ( core::scoring::ScoreFunctionOP  scorefxn)

users can pass their own scorefunction for packing after grafting

References scorefxn_.

Member Data Documentation

AntibodyInfoOP protocols::antibody2::GraftOneCDRLoop::ab_info_
Ab_TemplateInfoOP protocols::antibody2::GraftOneCDRLoop::ab_t_info_
bool protocols::antibody2::GraftOneCDRLoop::benchmark_
AntibodyCDRNameEnum protocols::antibody2::GraftOneCDRLoop::cdr_name_
core::Size protocols::antibody2::GraftOneCDRLoop::flank_size_
bool protocols::antibody2::GraftOneCDRLoop::h3_stem_not_graft_
core::scoring::ScoreFunctionCOP protocols::antibody2::GraftOneCDRLoop::scorefxn_

Referenced by finalize_setup(), and set_scorefxn().

core::Size protocols::antibody2::GraftOneCDRLoop::stem_copy_size_

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