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protocols::antibody::LHRepulsiveRampLegacy Class Reference

#include <LHRepulsiveRampLegacy.hh>

Inheritance diagram for protocols::antibody::LHRepulsiveRampLegacy:
Inheritance graph
[legend]

Public Member Functions

 LHRepulsiveRampLegacy ()
 default constructor More...
 
 LHRepulsiveRampLegacy (loops::Loops loops_in)
 constructor with arguments More...
 
 LHRepulsiveRampLegacy (AntibodyInfoOP antibody_in)
 
 LHRepulsiveRampLegacy (AntibodyInfoOP antibody_in, bool camelid)
 
 LHRepulsiveRampLegacy (loops::Loops loops_in, core::scoring::ScoreFunctionCOP dock_scorefxn, core::scoring::ScoreFunctionCOP pack_scorefxn)
 
 LHRepulsiveRampLegacy (AntibodyInfoOP antibody_in, core::scoring::ScoreFunctionCOP dock_scorefxn, core::scoring::ScoreFunctionCOP pack_scorefxn)
 
protocols::moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
 
 ~LHRepulsiveRampLegacy () override
 default destructor More...
 
void set_default ()
 
void set_dock_score_func (core::scoring::ScoreFunctionCOP dock_scorefxn)
 
void set_pack_score_func (core::scoring::ScoreFunctionCOP pack_scorefxn)
 
void apply (core::pose::Pose &pose) override
 ramping up the fullatom repulsive weight slowly to allow the partners to relieve clashes and make way for each other More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void set_task_factory (core::pack::task::TaskFactoryCOP tf)
 
core::Real set_rot_mag (core::Real rot_mag)
 
core::Real set_trans_mag (core::Real trans_mag)
 
- 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 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 bool mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Private Member Functions

void init (loops::Loops loops_in, bool camelid)
 
void setup_objects ()
 
void finalize_setup (core::pose::Pose &pose)
 
void snugfit_MC_min (core::pose::Pose &pose, core::scoring::ScoreFunctionOP temp_scorefxn)
 
void repulsive_ramp (core::pose::Pose &pose_in, loops::Loops loops_in)
 

Private Attributes

AntibodyInfoOP ab_info_
 
bool user_defined_
 
bool benchmark_
 
bool is_camelid_
 
loops::Loops all_loops_
 
core::Size nres_
 
core::kinematics::MoveMapOP cdr_dock_map_
 
core::Size rep_ramp_cycles_
 
std::string min_type_
 
core::Real rot_mag_
 
core::Real trans_mag_
 
core::Real temperature_
 
core::Real min_threshold_
 
core::Size num_repeats_
 
core::scoring::ScoreFunctionOP dock_scorefxn_
 
core::scoring::ScoreFunctionOP pack_scorefxn_
 
core::pack::task::TaskFactoryOP tf_
 

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...
 

Constructor & Destructor Documentation

protocols::antibody::LHRepulsiveRampLegacy::LHRepulsiveRampLegacy ( )

default constructor

protocols::antibody::LHRepulsiveRampLegacy::LHRepulsiveRampLegacy ( loops::Loops  loops_in)

constructor with arguments

References init(), and user_defined_.

protocols::antibody::LHRepulsiveRampLegacy::LHRepulsiveRampLegacy ( AntibodyInfoOP  antibody_in)

References init(), and user_defined_.

protocols::antibody::LHRepulsiveRampLegacy::LHRepulsiveRampLegacy ( AntibodyInfoOP  antibody_in,
bool  camelid 
)

References init(), and user_defined_.

protocols::antibody::LHRepulsiveRampLegacy::LHRepulsiveRampLegacy ( loops::Loops  loops_in,
core::scoring::ScoreFunctionCOP  dock_scorefxn,
core::scoring::ScoreFunctionCOP  pack_scorefxn 
)
protocols::antibody::LHRepulsiveRampLegacy::LHRepulsiveRampLegacy ( AntibodyInfoOP  antibody_in,
core::scoring::ScoreFunctionCOP  dock_scorefxn,
core::scoring::ScoreFunctionCOP  pack_scorefxn 
)
protocols::antibody::LHRepulsiveRampLegacy::~LHRepulsiveRampLegacy ( )
overridedefault

default destructor

Member Function Documentation

void protocols::antibody::LHRepulsiveRampLegacy::apply ( core::pose::Pose pose)
overridevirtual

ramping up the fullatom repulsive weight slowly to allow the partners to relieve clashes and make way for each other

This routine is specially targetted to the coupled optimization of docking partners and the loop region. The loop modelling & all previous steps involve mainly centroid mode .On switching on fullatom mode, one is bound to end up with clashes.To relieve the clashes, it is essential to slowly dial up the repulsive weight instead of turning it on to the maximum value in one single step

Parameters
[in]inputpose which is assumed to have a docking fold tree
Global Read: fa_rep : fullatom repulsive weight
Global Write: fa_rep ( It is reset to the original value at the end )
Remarks
A particular portion is commented out,which can be uncommented if one uses a low resolution homology model. Check details in the beginning of the commented out region
References:
Author
Aroop 07/13/2010

Implements protocols::moves::Mover.

References core::pose::add_variant_type_to_pose_residue(), all_loops_, benchmark_, core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, dock_scorefxn_, core::scoring::fa_rep, finalize_setup(), min_threshold_, num_repeats_, protocols::loops::remove_cutpoint_variants(), rep_ramp_cycles_, snugfit_MC_min(), and protocols::antibody::TR().

protocols::moves::MoverOP protocols::antibody::LHRepulsiveRampLegacy::clone ( ) const
overridevirtual

Return a clone of the Mover object.

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.

void protocols::antibody::LHRepulsiveRampLegacy::finalize_setup ( core::pose::Pose pose)
private
std::string protocols::antibody::LHRepulsiveRampLegacy::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

void protocols::antibody::LHRepulsiveRampLegacy::init ( loops::Loops  loops_in,
bool  camelid 
)
private

References all_loops_, is_camelid_, set_default(), and tf_.

Referenced by LHRepulsiveRampLegacy().

void protocols::antibody::LHRepulsiveRampLegacy::repulsive_ramp ( core::pose::Pose pose_in,
loops::Loops  loops_in 
)
private
void protocols::antibody::LHRepulsiveRampLegacy::set_default ( )
void protocols::antibody::LHRepulsiveRampLegacy::set_dock_score_func ( core::scoring::ScoreFunctionCOP  dock_scorefxn)
inline

References dock_scorefxn_.

void protocols::antibody::LHRepulsiveRampLegacy::set_pack_score_func ( core::scoring::ScoreFunctionCOP  pack_scorefxn)
inline

References pack_scorefxn_.

core::Real protocols::antibody::LHRepulsiveRampLegacy::set_rot_mag ( core::Real  rot_mag)
inline

References rot_mag_.

void protocols::antibody::LHRepulsiveRampLegacy::set_task_factory ( core::pack::task::TaskFactoryCOP  tf)

References tf_.

core::Real protocols::antibody::LHRepulsiveRampLegacy::set_trans_mag ( core::Real  trans_mag)
inline

References trans_mag_.

void protocols::antibody::LHRepulsiveRampLegacy::setup_objects ( )
private
void protocols::antibody::LHRepulsiveRampLegacy::snugfit_MC_min ( core::pose::Pose pose,
core::scoring::ScoreFunctionOP  temp_scorefxn 
)
private

Member Data Documentation

AntibodyInfoOP protocols::antibody::LHRepulsiveRampLegacy::ab_info_
private
loops::Loops protocols::antibody::LHRepulsiveRampLegacy::all_loops_
private

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

bool protocols::antibody::LHRepulsiveRampLegacy::benchmark_
private

Referenced by apply(), and set_default().

core::kinematics::MoveMapOP protocols::antibody::LHRepulsiveRampLegacy::cdr_dock_map_
private

Referenced by finalize_setup(), and snugfit_MC_min().

core::scoring::ScoreFunctionOP protocols::antibody::LHRepulsiveRampLegacy::dock_scorefxn_
private
bool protocols::antibody::LHRepulsiveRampLegacy::is_camelid_
private

Referenced by init().

core::Real protocols::antibody::LHRepulsiveRampLegacy::min_threshold_
private

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

std::string protocols::antibody::LHRepulsiveRampLegacy::min_type_
private

Referenced by set_default(), and snugfit_MC_min().

core::Size protocols::antibody::LHRepulsiveRampLegacy::nres_
private
core::Size protocols::antibody::LHRepulsiveRampLegacy::num_repeats_
private

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

core::scoring::ScoreFunctionOP protocols::antibody::LHRepulsiveRampLegacy::pack_scorefxn_
private
core::Size protocols::antibody::LHRepulsiveRampLegacy::rep_ramp_cycles_
private

Referenced by apply(), and set_default().

core::Real protocols::antibody::LHRepulsiveRampLegacy::rot_mag_
private
core::Real protocols::antibody::LHRepulsiveRampLegacy::temperature_
private

Referenced by set_default(), and snugfit_MC_min().

core::pack::task::TaskFactoryOP protocols::antibody::LHRepulsiveRampLegacy::tf_
private
core::Real protocols::antibody::LHRepulsiveRampLegacy::trans_mag_
private
bool protocols::antibody::LHRepulsiveRampLegacy::user_defined_
private

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