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protocols::antibody2::AntibodyModelerProtocol Class Reference

#include <AntibodyModelerProtocol.hh>

Inheritance diagram for protocols::antibody2::AntibodyModelerProtocol:
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Collaboration diagram for protocols::antibody2::AntibodyModelerProtocol:
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Public Member Functions

 AntibodyModelerProtocol ()
 
 ~AntibodyModelerProtocol ()
 
virtual protocols::moves::MoverOP clone () const
 clone has to be overridden only if clone invocation is expected. More...
 
void set_default ()
 Assigns default values to primitive members. More...
 
void sync_objects_with_flags ()
 Instantiates non-primitive members based on the value of the primitive members. More...
 
virtual void apply (pose::Pose &pose)
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
void set_BenchMark (bool setting)
 
void set_ModelH3 (bool setting)
 
void set_SnugFit (bool setting)
 
void set_refine_h3 (bool setting)
 
void set_H3Filter (bool setting)
 
void set_CterInsert (bool setting)
 
void set_sc_min (bool setting)
 
void set_rt_min (bool setting)
 
void set_flank_residue_min (bool setting)
 
void set_perturb_type (std::string remodel)
 
void set_refine_type (std::string refine)
 
void set_H3Filter_Tolerance (core::Size const number)
 
void set_cst_weight (core::Real const cst_weight)
 
void set_use_constraints (bool const use_csts)
 
void set_constrain_cter (bool const setting)
 
void set_constrain_vlvh_qq (bool const setting)
 
void set_flank_residue_size (core::Real const flank_residue_size)
 
void set_middle_pack_min (bool middle_pack_min)
 
void set_bad_nter (bool setting)
 
void display_constraint_residues (pose::Pose &pose)
 
void show (std::ostream &out=std::cout)
 
- 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 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
 

Static Public Member Functions

static void register_options ()
 Associates relevant options with the AntibodyModeler class. More...
 
- 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...
 

Private Member Functions

void init_from_options ()
 Assigns user specified values to primitive members using command line options. More...
 
void finalize_setup (core::pose::Pose &pose)
 Performs the portion of setup of non-primitive members that requires a pose - called on apply. More...
 
void init ()
 Sets up the instance of AntibodyModeler and initializes all members based on values passed in at construction or via the command line. More...
 
void setup_objects ()
 

Private Attributes

bool model_h3_
 
bool snugfit_
 
bool refine_h3_
 
bool h3_filter_
 
bool cter_insert_
 
bool LH_repulsive_ramp_
 
bool sc_min_
 
bool rt_min_
 
bool camelid_
 
bool camelid_constraints_
 
bool flank_residue_min_
 
bool flank_residue_size_
 
bool middle_pack_min_
 
std::string h3_perturb_type_
 
std::string h3_refine_type_
 
core::Real cen_cst_
 
core::Real high_cst_
 
bool bad_nter_
 
bool use_csts_
 
bool constrain_vlvh_qq_
 
bool constrain_cter_
 
bool benchmark_
 
bool user_defined_
 
bool flags_and_objects_are_in_sync_
 
core::Size h3_filter_tolerance_
 
core::Real cst_weight_
 
core::scoring::ScoreFunctionOP loop_scorefxn_highres_
 
core::scoring::ScoreFunctionOP loop_scorefxn_centroid_
 
core::scoring::ScoreFunctionOP dock_scorefxn_highres_
 
core::scoring::ScoreFunctionOP pack_scorefxn_
 
protocols::simple_moves::ConstraintSetMoverOP cdr_constraint_
 
AntibodyInfoOP ab_info_
 

Friends

std::ostream & operator<< (std::ostream &out, const AntibodyModelerProtocol &ab_m)
 

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
protocols::filters::Filters_map 
Filters_map
 
typedef std::list< std::string > Strings
 
- 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...
 

Constructor & Destructor Documentation

protocols::antibody2::AntibodyModelerProtocol::AntibodyModelerProtocol ( )

References init(), and user_defined_.

Referenced by clone().

protocols::antibody2::AntibodyModelerProtocol::~AntibodyModelerProtocol ( )

Member Function Documentation

void protocols::antibody2::AntibodyModelerProtocol::apply ( pose::Pose pose)
virtual
protocols::moves::MoverOP protocols::antibody2::AntibodyModelerProtocol::clone ( ) const
virtual

clone has to be overridden only if clone invocation is expected.

clone is meant to return an OP'ed deep copy of this object. 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.

Reimplemented from protocols::moves::Mover.

References AntibodyModelerProtocol().

void protocols::antibody2::AntibodyModelerProtocol::display_constraint_residues ( pose::Pose pose)
void protocols::antibody2::AntibodyModelerProtocol::finalize_setup ( core::pose::Pose pose)
private
std::string protocols::antibody2::AntibodyModelerProtocol::get_name ( ) const
virtual

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

Implements protocols::moves::Mover.

void protocols::antibody2::AntibodyModelerProtocol::init ( void  )
private

Sets up the instance of AntibodyModeler and initializes all members based on values passed in at construction or via the command line.

References init_from_options(), set_default(), and setup_objects().

Referenced by AntibodyModelerProtocol().

void protocols::antibody2::AntibodyModelerProtocol::init_from_options ( )
private
void protocols::antibody2::AntibodyModelerProtocol::register_options ( )
static

Associates relevant options with the AntibodyModeler class.

void protocols::antibody2::AntibodyModelerProtocol::set_bad_nter ( bool  setting)
inline

Referenced by init_from_options().

void protocols::antibody2::AntibodyModelerProtocol::set_BenchMark ( bool  setting)
inline

Referenced by init_from_options().

void protocols::antibody2::AntibodyModelerProtocol::set_constrain_cter ( bool const  setting)
inline

Referenced by init_from_options().

void protocols::antibody2::AntibodyModelerProtocol::set_constrain_vlvh_qq ( bool const  setting)
inline

Referenced by init_from_options().

void protocols::antibody2::AntibodyModelerProtocol::set_cst_weight ( core::Real const  cst_weight)
inline

Referenced by init_from_options().

void protocols::antibody2::AntibodyModelerProtocol::set_CterInsert ( bool  setting)
inline

Referenced by init_from_options().

void protocols::antibody2::AntibodyModelerProtocol::set_default ( )
void protocols::antibody2::AntibodyModelerProtocol::set_flank_residue_min ( bool  setting)
inline

Referenced by init_from_options().

void protocols::antibody2::AntibodyModelerProtocol::set_flank_residue_size ( core::Real const  flank_residue_size)
inline
void protocols::antibody2::AntibodyModelerProtocol::set_H3Filter ( bool  setting)
inline

Referenced by init_from_options().

void protocols::antibody2::AntibodyModelerProtocol::set_H3Filter_Tolerance ( core::Size const  number)
inline

Referenced by init_from_options().

void protocols::antibody2::AntibodyModelerProtocol::set_middle_pack_min ( bool  middle_pack_min)
inline
void protocols::antibody2::AntibodyModelerProtocol::set_ModelH3 ( bool  setting)
inline

Referenced by init_from_options().

void protocols::antibody2::AntibodyModelerProtocol::set_perturb_type ( std::string  remodel)
inline

Referenced by init_from_options().

void protocols::antibody2::AntibodyModelerProtocol::set_refine_h3 ( bool  setting)
inline

Referenced by init_from_options().

void protocols::antibody2::AntibodyModelerProtocol::set_refine_type ( std::string  refine)
inline

Referenced by init_from_options().

void protocols::antibody2::AntibodyModelerProtocol::set_rt_min ( bool  setting)
inline

Referenced by init_from_options().

void protocols::antibody2::AntibodyModelerProtocol::set_sc_min ( bool  setting)
inline

Referenced by init_from_options().

void protocols::antibody2::AntibodyModelerProtocol::set_SnugFit ( bool  setting)
inline

Referenced by init_from_options().

void protocols::antibody2::AntibodyModelerProtocol::set_use_constraints ( bool const  use_csts)
inline

Referenced by init_from_options().

void protocols::antibody2::AntibodyModelerProtocol::setup_objects ( )
private
void protocols::antibody2::AntibodyModelerProtocol::show ( std::ostream &  out = std::cout)

Show the complete setup of the antibody modeler protocol

References flags_and_objects_are_in_sync_, and sync_objects_with_flags().

void protocols::antibody2::AntibodyModelerProtocol::sync_objects_with_flags ( )

Instantiates non-primitive members based on the value of the primitive members.

References flags_and_objects_are_in_sync_.

Referenced by apply(), setup_objects(), and show().

Friends And Related Function Documentation

std::ostream& operator<< ( std::ostream &  out,
const AntibodyModelerProtocol ab_m 
)
friend

Member Data Documentation

AntibodyInfoOP protocols::antibody2::AntibodyModelerProtocol::ab_info_
private
bool protocols::antibody2::AntibodyModelerProtocol::bad_nter_
private

Referenced by apply(), and set_default().

bool protocols::antibody2::AntibodyModelerProtocol::benchmark_
private

Referenced by set_default().

bool protocols::antibody2::AntibodyModelerProtocol::camelid_
private
bool protocols::antibody2::AntibodyModelerProtocol::camelid_constraints_
private

Referenced by apply(), and set_default().

protocols::simple_moves::ConstraintSetMoverOP protocols::antibody2::AntibodyModelerProtocol::cdr_constraint_
private

Referenced by finalize_setup(), and set_default().

core::Real protocols::antibody2::AntibodyModelerProtocol::cen_cst_
private

Referenced by set_default().

bool protocols::antibody2::AntibodyModelerProtocol::constrain_cter_
private

Referenced by set_default(), and setup_objects().

bool protocols::antibody2::AntibodyModelerProtocol::constrain_vlvh_qq_
private

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

core::Real protocols::antibody2::AntibodyModelerProtocol::cst_weight_
private
bool protocols::antibody2::AntibodyModelerProtocol::cter_insert_
private
core::scoring::ScoreFunctionOP protocols::antibody2::AntibodyModelerProtocol::dock_scorefxn_highres_
private

Referenced by apply(), and setup_objects().

bool protocols::antibody2::AntibodyModelerProtocol::flags_and_objects_are_in_sync_
private
bool protocols::antibody2::AntibodyModelerProtocol::flank_residue_min_
private

Referenced by apply(), and set_default().

bool protocols::antibody2::AntibodyModelerProtocol::flank_residue_size_
private

Referenced by apply(), and set_default().

bool protocols::antibody2::AntibodyModelerProtocol::h3_filter_
private
core::Size protocols::antibody2::AntibodyModelerProtocol::h3_filter_tolerance_
private
std::string protocols::antibody2::AntibodyModelerProtocol::h3_perturb_type_
private
std::string protocols::antibody2::AntibodyModelerProtocol::h3_refine_type_
private
core::Real protocols::antibody2::AntibodyModelerProtocol::high_cst_
private

Referenced by set_default().

bool protocols::antibody2::AntibodyModelerProtocol::LH_repulsive_ramp_
private
core::scoring::ScoreFunctionOP protocols::antibody2::AntibodyModelerProtocol::loop_scorefxn_centroid_
private

Referenced by apply(), and setup_objects().

core::scoring::ScoreFunctionOP protocols::antibody2::AntibodyModelerProtocol::loop_scorefxn_highres_
private

Referenced by apply(), and setup_objects().

bool protocols::antibody2::AntibodyModelerProtocol::middle_pack_min_
private

Referenced by set_default().

bool protocols::antibody2::AntibodyModelerProtocol::model_h3_
private
core::scoring::ScoreFunctionOP protocols::antibody2::AntibodyModelerProtocol::pack_scorefxn_
private

Referenced by apply(), and setup_objects().

bool protocols::antibody2::AntibodyModelerProtocol::refine_h3_
private
bool protocols::antibody2::AntibodyModelerProtocol::rt_min_
private

Referenced by apply(), and set_default().

bool protocols::antibody2::AntibodyModelerProtocol::sc_min_
private

Referenced by apply(), and set_default().

bool protocols::antibody2::AntibodyModelerProtocol::snugfit_
private
bool protocols::antibody2::AntibodyModelerProtocol::use_csts_
private

Referenced by set_default(), and setup_objects().

bool protocols::antibody2::AntibodyModelerProtocol::user_defined_
private

Referenced by AntibodyModelerProtocol().


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