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protocols::antibody2::ModelCDRH3 Class Reference

Ab initio modeling of CDR H3 loop. More...

#include <ModelCDRH3.hh>

Inheritance diagram for protocols::antibody2::ModelCDRH3:
Inheritance graph
Collaboration diagram for protocols::antibody2::ModelCDRH3:
Collaboration graph

Public Member Functions

 ModelCDRH3 ()
 default constructor More...
 ModelCDRH3 (AntibodyInfoOP antibody_info)
 constructor with arguments More...
 ModelCDRH3 (AntibodyInfoOP antibody_info, core::scoring::ScoreFunctionCOP lowres_scorefxn)
 constructor with arguments More...
 ~ModelCDRH3 ()
 default destructor More...
void set_default ()
virtual void apply (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_camelid (bool setting)
 enable camelid modeling mode More...
void set_lowres_score_func (core::scoring::ScoreFunctionCOP lowres_scorefxn)
 set scorefunction for low resolution of CDR H3 modeling More...
void set_task_factory (pack::task::TaskFactoryCOP tf)
 set task factory More...
void turn_off_H3_filter ()
void turn_off_cter_insert ()
void set_perturb_type (std::string setting)
void set_bad_nter (bool setting)
- 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 init ()

Private Attributes

bool user_defined_
bool do_cter_insert_
Real cen_cst_
pose::Pose hfr_pose_
Size c_ter_stem_
 Number of ADDITIONAL residues modeled from H3_CTERM. More...
Size max_cycle_
core::scoring::ScoreFunctionOP lowres_scorefxn_
bool benchmark_
 benchmark flag More...
bool loops_flag_
 loop_building in docking More...
bool dle_flag_
 insert fragment in docking More...
bool bad_nter_
bool is_camelid_
 is camelid antibody without light chain More...
antibody2::AntibodyInfoOP ab_info_
pack::task::TaskFactoryOP tf_
H3CterInsertOP h3_cter_insert_mover_
H3PerturbCCDOP h3_perturb_ccd_build_
loops::loop_mover::IndependentLoopMoverOP remodel_mover_
std::string remodel_

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

Ab initio modeling of CDR H3 loop.

Constructor & Destructor Documentation

protocols::antibody2::ModelCDRH3::ModelCDRH3 ( )

default constructor

protocols::antibody2::ModelCDRH3::ModelCDRH3 ( AntibodyInfoOP  antibody_info)

constructor with arguments

References ab_info_, init(), and user_defined_.

protocols::antibody2::ModelCDRH3::ModelCDRH3 ( AntibodyInfoOP  antibody_info,
core::scoring::ScoreFunctionCOP  lowres_scorefxn 

constructor with arguments

References ab_info_, init(), lowres_scorefxn_, and user_defined_.

protocols::antibody2::ModelCDRH3::~ModelCDRH3 ( )

default destructor

Member Function Documentation

void protocols::antibody2::ModelCDRH3::apply ( pose::Pose pose_in)
void protocols::antibody2::ModelCDRH3::enable_benchmark_mode ( bool  setting)

enable benchmark mode

std::string protocols::antibody2::ModelCDRH3::get_name ( ) const

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

Implements protocols::moves::Mover.

void protocols::antibody2::ModelCDRH3::init ( void  )
void protocols::antibody2::ModelCDRH3::set_bad_nter ( bool  setting)
void protocols::antibody2::ModelCDRH3::set_camelid ( bool  setting)

enable camelid modeling mode

void protocols::antibody2::ModelCDRH3::set_default ( )
void protocols::antibody2::ModelCDRH3::set_lowres_score_func ( core::scoring::ScoreFunctionCOP  lowres_scorefxn)

set scorefunction for low resolution of CDR H3 modeling

References lowres_scorefxn_.

void protocols::antibody2::ModelCDRH3::set_perturb_type ( std::string  setting)
void protocols::antibody2::ModelCDRH3::set_task_factory ( pack::task::TaskFactoryCOP  tf)

set task factory

References tf_.

void protocols::antibody2::ModelCDRH3::turn_off_cter_insert ( )
void protocols::antibody2::ModelCDRH3::turn_off_H3_filter ( )

References h3_perturb_ccd_build_.

Member Data Documentation

antibody2::AntibodyInfoOP protocols::antibody2::ModelCDRH3::ab_info_

Referenced by apply(), init(), and ModelCDRH3().

bool protocols::antibody2::ModelCDRH3::bad_nter_

Referenced by apply(), and set_default().

bool protocols::antibody2::ModelCDRH3::benchmark_

benchmark flag

Referenced by set_default().

Size protocols::antibody2::ModelCDRH3::c_ter_stem_

Number of ADDITIONAL residues modeled from H3_CTERM.

These residues range from H:n-2,n-1,n,n+1 of H3

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

Real protocols::antibody2::ModelCDRH3::cen_cst_

Referenced by set_default().

bool protocols::antibody2::ModelCDRH3::dle_flag_

insert fragment in docking

Referenced by set_default().

bool protocols::antibody2::ModelCDRH3::do_cter_insert_

Referenced by apply(), and set_default().

H3CterInsertOP protocols::antibody2::ModelCDRH3::h3_cter_insert_mover_

Referenced by apply(), and init().

H3PerturbCCDOP protocols::antibody2::ModelCDRH3::h3_perturb_ccd_build_

Referenced by apply(), init(), and turn_off_H3_filter().

pose::Pose protocols::antibody2::ModelCDRH3::hfr_pose_

Referenced by apply().

bool protocols::antibody2::ModelCDRH3::is_camelid_

is camelid antibody without light chain

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

bool protocols::antibody2::ModelCDRH3::loops_flag_

loop_building in docking

Referenced by set_default().

core::scoring::ScoreFunctionOP protocols::antibody2::ModelCDRH3::lowres_scorefxn_
Size protocols::antibody2::ModelCDRH3::max_cycle_

Referenced by apply(), and set_default().

std::string protocols::antibody2::ModelCDRH3::remodel_

Referenced by apply(), and set_default().

loops::loop_mover::IndependentLoopMoverOP protocols::antibody2::ModelCDRH3::remodel_mover_

Referenced by apply().

pack::task::TaskFactoryOP protocols::antibody2::ModelCDRH3::tf_

Referenced by set_task_factory().

bool protocols::antibody2::ModelCDRH3::user_defined_

Referenced by ModelCDRH3(), and set_default().

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