Rosetta Protocols  2014.35
Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::antibody::LHRepulsiveRampLegacy Class Reference

#include <LHRepulsiveRampLegacy.hh>

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)
virtual protocols::moves::MoverOP clone () const
 Return a clone of the Mover object. More...
 ~LHRepulsiveRampLegacy ()
 default destructor More...
void set_default ()
void set_dock_score_func (scoring::ScoreFunctionCOP dock_scorefxn)
void set_pack_score_func (scoring::ScoreFunctionCOP pack_scorefxn)
virtual void apply (core::pose::Pose &pose)
 ramping up the fullatom repulsive weight slowly to allow the partners to relieve clashes and make way for each other More...
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
void set_task_factory (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 ~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
void set_type (std::string const &setting)
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 (TagCOP tag, basic::datacache::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
 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...
void set_current_job (protocols::jobdist::BasicJobCOP job)
jobdist::BasicJobCOP get_current_job () const
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...

Private Member Functions

void init (loops::Loops loops_in, bool camelid)
void setup_objects ()
void finalize_setup (pose::Pose &pose)
void snugfit_MC_min (pose::Pose &pose, core::scoring::ScoreFunctionOP temp_scorefxn)
void repulsive_ramp (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_
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_
scoring::ScoreFunctionOP dock_scorefxn_
scoring::ScoreFunctionOP pack_scorefxn_
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::stringStrings
- 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

Referenced by clone().

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

constructor with arguments

References init(), and user_defined_.

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

default destructor

Member Function Documentation

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

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


Detailed: 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
[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 )
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
Aroop 07/13/2010
Last Modified: 07/13/2010

Implements protocols::moves::Mover.

References core::pose::add_variant_type_to_pose_residue(), all_loops_, protocols::loops::Loops::begin(), benchmark_, core::scoring::ScoreFunction::clone(), CUTPOINT_LOWER, CUTPOINT_UPPER, dock_scorefxn_, protocols::loops::Loops::end(), 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

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.

References LHRepulsiveRampLegacy().

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

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 

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

Referenced by LHRepulsiveRampLegacy().

void protocols::antibody::LHRepulsiveRampLegacy::repulsive_ramp ( pose::Pose pose_in,
loops::Loops  loops_in 
void protocols::antibody::LHRepulsiveRampLegacy::set_default ( )
void protocols::antibody::LHRepulsiveRampLegacy::set_dock_score_func ( scoring::ScoreFunctionCOP  dock_scorefxn)
void protocols::antibody::LHRepulsiveRampLegacy::set_pack_score_func ( scoring::ScoreFunctionCOP  pack_scorefxn)
core::Real protocols::antibody::LHRepulsiveRampLegacy::set_rot_mag ( core::Real  rot_mag)
void protocols::antibody::LHRepulsiveRampLegacy::set_task_factory ( pack::task::TaskFactoryCOP  tf)

References tf_.

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

Member Data Documentation

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

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

bool protocols::antibody::LHRepulsiveRampLegacy::benchmark_

Referenced by apply(), and set_default().

kinematics::MoveMapOP protocols::antibody::LHRepulsiveRampLegacy::cdr_dock_map_

Referenced by finalize_setup(), and snugfit_MC_min().

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

Referenced by init().

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

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

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

Referenced by set_default(), and snugfit_MC_min().

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

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

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

Referenced by apply(), and set_default().

core::Real protocols::antibody::LHRepulsiveRampLegacy::rot_mag_

Referenced by set_default(), and snugfit_MC_min().

core::Real protocols::antibody::LHRepulsiveRampLegacy::temperature_

Referenced by set_default(), and snugfit_MC_min().

pack::task::TaskFactoryOP protocols::antibody::LHRepulsiveRampLegacy::tf_
core::Real protocols::antibody::LHRepulsiveRampLegacy::trans_mag_

Referenced by set_default(), and snugfit_MC_min().

bool protocols::antibody::LHRepulsiveRampLegacy::user_defined_

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