#include <LHRepulsiveRampLegacy.hh>

Inheritance diagram for protocols::antibody2::LHRepulsiveRampLegacy:

Collaboration diagram for protocols::antibody2::LHRepulsiveRampLegacy:

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

Mover &	operator= (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 Strings &	info ()
	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 (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)

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

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

Definition at line 44 of file LHRepulsiveRampLegacy.hh.

Constructor & Destructor Documentation

protocols::antibody2::LHRepulsiveRampLegacy::LHRepulsiveRampLegacy ( )

default constructor

Definition at line 97 of file LHRepulsiveRampLegacy.cc.

Referenced by clone().

protocols::antibody2::LHRepulsiveRampLegacy::LHRepulsiveRampLegacy ( loops::Loops loops_in)

constructor with arguments

Definition at line 103 of file LHRepulsiveRampLegacy.cc.

References init(), and user_defined_.

protocols::antibody2::LHRepulsiveRampLegacy::LHRepulsiveRampLegacy ( AntibodyInfoOP antibody_in)

Definition at line 110 of file LHRepulsiveRampLegacy.cc.

References init(), and user_defined_.

protocols::antibody2::LHRepulsiveRampLegacy::LHRepulsiveRampLegacy	(	AntibodyInfoOP	antibody_in,
		bool	camelid
	)

Definition at line 116 of file LHRepulsiveRampLegacy.cc.

References init(), and user_defined_.

protocols::antibody2::LHRepulsiveRampLegacy::LHRepulsiveRampLegacy	(	loops::Loops	loops_in,
		core::scoring::ScoreFunctionCOP	dock_scorefxn,
		core::scoring::ScoreFunctionCOP	pack_scorefxn
	)

Definition at line 123 of file LHRepulsiveRampLegacy.cc.

References dock_scorefxn_, init(), pack_scorefxn_, and user_defined_.

protocols::antibody2::LHRepulsiveRampLegacy::LHRepulsiveRampLegacy	(	AntibodyInfoOP	antibody_in,
		core::scoring::ScoreFunctionCOP	dock_scorefxn,
		core::scoring::ScoreFunctionCOP	pack_scorefxn
	)

Definition at line 133 of file LHRepulsiveRampLegacy.cc.

References dock_scorefxn_, init(), pack_scorefxn_, and user_defined_.

protocols::antibody2::LHRepulsiveRampLegacy::~LHRepulsiveRampLegacy ( )

default destructor

Definition at line 145 of file LHRepulsiveRampLegacy.cc.

Member Function Documentation

void protocols::antibody2::LHRepulsiveRampLegacy::apply ( core::pose::Pose & pose)

virtual

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

repulsive_ramp

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

Parameters

[in] input pose 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:

Authors: Aroop 07/13/2010

Last Modified: 07/13/2010

Implements protocols::moves::Mover.

Definition at line 277 of file LHRepulsiveRampLegacy.cc.

References core::pose::add_variant_type_to_pose_residue(), all_loops_, protocols::loops::Loops::begin(), benchmark_, core::chemical::CUTPOINT_LOWER, core::chemical::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::TR().

protocols::moves::MoverOP protocols::antibody2::LHRepulsiveRampLegacy::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.

Definition at line 148 of file LHRepulsiveRampLegacy.cc.

References LHRepulsiveRampLegacy().

void protocols::antibody2::LHRepulsiveRampLegacy::finalize_setup ( pose::Pose & pose)

private

Definition at line 198 of file LHRepulsiveRampLegacy.cc.

References all_loops_, cdr_dock_map_, protocols::loops::Loops::num_loop(), protocols::loops::select_loop_residues(), protocols::antibody2::setup_packer_task(), tf_, core::pose::Pose::total_residue(), and protocols::TR().

Referenced by apply().

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

virtual

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

Implements protocols::moves::Mover.

Definition at line 191 of file LHRepulsiveRampLegacy.cc.

void protocols::antibody2::LHRepulsiveRampLegacy::init	(	loops::Loops	loops_in,
		bool	camelid
	)

private

Definition at line 156 of file LHRepulsiveRampLegacy.cc.

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

Referenced by LHRepulsiveRampLegacy().

void protocols::antibody2::LHRepulsiveRampLegacy::repulsive_ramp	(	pose::Pose &	pose_in,
		loops::Loops	loops_in
	)

private

void protocols::antibody2::LHRepulsiveRampLegacy::set_default ( )

Definition at line 168 of file LHRepulsiveRampLegacy.cc.

References benchmark_, core::scoring::chainbreak, core::scoring::ScoreFunctionFactory::create_score_function(), dock_scorefxn_, min_threshold_, min_type_, num_repeats_, core::scoring::overlap_chainbreak, pack_scorefxn_, rep_ramp_cycles_, rot_mag_, temperature_, trans_mag_, and user_defined_.

Referenced by init().

void protocols::antibody2::LHRepulsiveRampLegacy::set_dock_score_func ( scoring::ScoreFunctionCOP dock_scorefxn)

inline

Definition at line 74 of file LHRepulsiveRampLegacy.hh.

void protocols::antibody2::LHRepulsiveRampLegacy::set_pack_score_func ( scoring::ScoreFunctionCOP pack_scorefxn)

inline

Definition at line 78 of file LHRepulsiveRampLegacy.hh.

core::Real protocols::antibody2::LHRepulsiveRampLegacy::set_rot_mag ( core::Real rot_mag)

inline

Definition at line 89 of file LHRepulsiveRampLegacy.hh.

void protocols::antibody2::LHRepulsiveRampLegacy::set_task_factory ( pack::task::TaskFactoryCOP tf)

Definition at line 367 of file LHRepulsiveRampLegacy.cc.

References tf_.

core::Real protocols::antibody2::LHRepulsiveRampLegacy::set_trans_mag ( core::Real trans_mag)

inline

Definition at line 90 of file LHRepulsiveRampLegacy.hh.

void protocols::antibody2::LHRepulsiveRampLegacy::setup_objects ( )

private

void protocols::antibody2::LHRepulsiveRampLegacy::snugfit_MC_min	(	pose::Pose &	pose,
		core::scoring::ScoreFunctionOP	temp_scorefxn
	)

private

Definition at line 329 of file LHRepulsiveRampLegacy.cc.

References cdr_dock_map_, min_threshold_, min_type_, num_repeats_, pack_scorefxn_, protocols::rigid::partner_downstream, rot_mag_, temperature_, tf_, and trans_mag_.

Referenced by apply().

Member Data Documentation

AntibodyInfoOP protocols::antibody2::LHRepulsiveRampLegacy::ab_info_

private

Definition at line 96 of file LHRepulsiveRampLegacy.hh.

loops::Loops protocols::antibody2::LHRepulsiveRampLegacy::all_loops_

private

Definition at line 101 of file LHRepulsiveRampLegacy.hh.

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

bool protocols::antibody2::LHRepulsiveRampLegacy::benchmark_

private

Definition at line 99 of file LHRepulsiveRampLegacy.hh.

Referenced by apply(), and set_default().

kinematics::MoveMapOP protocols::antibody2::LHRepulsiveRampLegacy::cdr_dock_map_

private

Definition at line 103 of file LHRepulsiveRampLegacy.hh.

Referenced by finalize_setup(), and snugfit_MC_min().

scoring::ScoreFunctionOP protocols::antibody2::LHRepulsiveRampLegacy::dock_scorefxn_

private

Definition at line 113 of file LHRepulsiveRampLegacy.hh.

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

bool protocols::antibody2::LHRepulsiveRampLegacy::is_camelid_

private

Definition at line 100 of file LHRepulsiveRampLegacy.hh.

Referenced by init().

core::Real protocols::antibody2::LHRepulsiveRampLegacy::min_threshold_

private

Definition at line 109 of file LHRepulsiveRampLegacy.hh.

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

std::string protocols::antibody2::LHRepulsiveRampLegacy::min_type_

private

Definition at line 105 of file LHRepulsiveRampLegacy.hh.

Referenced by set_default(), and snugfit_MC_min().

core::Size protocols::antibody2::LHRepulsiveRampLegacy::nres_

private

Definition at line 102 of file LHRepulsiveRampLegacy.hh.

core::Size protocols::antibody2::LHRepulsiveRampLegacy::num_repeats_

private

Definition at line 110 of file LHRepulsiveRampLegacy.hh.

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

scoring::ScoreFunctionOP protocols::antibody2::LHRepulsiveRampLegacy::pack_scorefxn_

private

Definition at line 114 of file LHRepulsiveRampLegacy.hh.

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

core::Size protocols::antibody2::LHRepulsiveRampLegacy::rep_ramp_cycles_

private

Definition at line 104 of file LHRepulsiveRampLegacy.hh.

Referenced by apply(), and set_default().

core::Real protocols::antibody2::LHRepulsiveRampLegacy::rot_mag_

private

Definition at line 106 of file LHRepulsiveRampLegacy.hh.

Referenced by set_default(), and snugfit_MC_min().

core::Real protocols::antibody2::LHRepulsiveRampLegacy::temperature_

private

Definition at line 108 of file LHRepulsiveRampLegacy.hh.

Referenced by set_default(), and snugfit_MC_min().

pack::task::TaskFactoryOP protocols::antibody2::LHRepulsiveRampLegacy::tf_

private

Definition at line 131 of file LHRepulsiveRampLegacy.hh.

Referenced by finalize_setup(), init(), set_task_factory(), and snugfit_MC_min().

core::Real protocols::antibody2::LHRepulsiveRampLegacy::trans_mag_

private

Definition at line 107 of file LHRepulsiveRampLegacy.hh.

Referenced by set_default(), and snugfit_MC_min().

bool protocols::antibody2::LHRepulsiveRampLegacy::user_defined_

private

Definition at line 98 of file LHRepulsiveRampLegacy.hh.

Referenced by LHRepulsiveRampLegacy(), and set_default().

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

src/protocols/antibody2/LHRepulsiveRampLegacy.hh
src/protocols/antibody2/LHRepulsiveRampLegacy.cc

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_

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation