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

#include <ModelCDRH3.hh>

Inheritance diagram for protocols::antibody2::ModelCDRH3:

Collaboration diagram for protocols::antibody2::ModelCDRH3:

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)

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 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 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 ()

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 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

Ab initio modeling of CDR H3 loop.

Definition at line 48 of file ModelCDRH3.hh.

Constructor & Destructor Documentation

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

default constructor

Definition at line 52 of file ModelCDRH3.cc.

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

constructor with arguments

Definition at line 57 of file ModelCDRH3.cc.

References ab_info_, init(), and user_defined_.

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

constructor with arguments

Definition at line 66 of file ModelCDRH3.cc.

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

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

default destructor

Definition at line 55 of file ModelCDRH3.cc.

Member Function Documentation

void protocols::antibody2::ModelCDRH3::apply ( pose::Pose & pose_in)

virtual

Implements protocols::moves::Mover.

Definition at line 140 of file ModelCDRH3.cc.

References ab_info_, protocols::simple_moves::SwitchResidueTypeSetMover::apply(), protocols::simple_moves::ReturnSidechainMover::apply(), bad_nter_, c_ter_stem_, core::chemical::CENTROID, protocols::loops::LoopMoverFactory::create_loop_mover(), protocols::antibody2::cutpoints_separation(), do_cter_insert_, core::chemical::FA_STANDARD, protocols::loops::LoopMoverFactory::get_instance(), protocols::moves::Mover::get_native_pose(), protocols::antibody2::h3, h3_cter_insert_mover_, h3_perturb_ccd_build_, hfr_pose_, is_camelid_, lowres_scorefxn_, max_cycle_, core::pose::Pose::omega(), core::pose::Pose::pdb_info(), core::import_pose::pose_from_pdb(), core::pose::Pose::psi(), protocols::loops::read_loop_fragments(), remodel_, remodel_mover_, protocols::loops::set_extended_torsions(), core::pose::Pose::set_omega(), core::pose::Pose::set_psi(), protocols::antibody2::simple_one_loop_fold_tree(), protocols::medal::to_centroid(), core::pose::Pose::total_residue(), and protocols::TR().

void protocols::antibody2::ModelCDRH3::enable_benchmark_mode ( bool setting)

inline

enable benchmark mode

Definition at line 68 of file ModelCDRH3.hh.

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

virtual

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

Implements protocols::moves::Mover.

Definition at line 319 of file ModelCDRH3.cc.

void protocols::antibody2::ModelCDRH3::init ( void )

private

Definition at line 79 of file ModelCDRH3.cc.

References ab_info_, c_ter_stem_, protocols::antibody2::Extended, h3_cter_insert_mover_, h3_perturb_ccd_build_, is_camelid_, protocols::antibody2::Kinked, lowres_scorefxn_, and set_default().

Referenced by ModelCDRH3().

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

inline

Definition at line 95 of file ModelCDRH3.hh.

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

inline

enable camelid modeling mode

Definition at line 73 of file ModelCDRH3.hh.

void protocols::antibody2::ModelCDRH3::set_default ( )

Definition at line 96 of file ModelCDRH3.cc.

References core::scoring::atom_pair_constraint, bad_nter_, benchmark_, c_ter_stem_, cen_cst_, core::scoring::chainbreak, core::scoring::ScoreFunctionFactory::create_score_function(), dle_flag_, do_cter_insert_, is_camelid_, loops_flag_, lowres_scorefxn_, max_cycle_, remodel_, and user_defined_.

Referenced by init().

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

set scorefunction for low resolution of CDR H3 modeling

Definition at line 123 of file ModelCDRH3.cc.

References lowres_scorefxn_.

void protocols::antibody2::ModelCDRH3::set_perturb_type ( std::string setting)

inline

Definition at line 91 of file ModelCDRH3.hh.

void protocols::antibody2::ModelCDRH3::set_task_factory ( pack::task::TaskFactoryCOP tf)

set task factory

Definition at line 128 of file ModelCDRH3.cc.

References tf_.

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

inline

Definition at line 86 of file ModelCDRH3.hh.

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

Definition at line 134 of file ModelCDRH3.cc.

References h3_perturb_ccd_build_.

Member Data Documentation

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

private

Definition at line 134 of file ModelCDRH3.hh.

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

bool protocols::antibody2::ModelCDRH3::bad_nter_

private

Definition at line 128 of file ModelCDRH3.hh.

Referenced by apply(), and set_default().

bool protocols::antibody2::ModelCDRH3::benchmark_

private

benchmark flag

Definition at line 120 of file ModelCDRH3.hh.

Referenced by set_default().

Size protocols::antibody2::ModelCDRH3::c_ter_stem_

private

Number of ADDITIONAL residues modeled from H3_CTERM.

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

Definition at line 111 of file ModelCDRH3.hh.

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

Real protocols::antibody2::ModelCDRH3::cen_cst_

private

Definition at line 105 of file ModelCDRH3.hh.

Referenced by set_default().

bool protocols::antibody2::ModelCDRH3::dle_flag_

private

insert fragment in docking

Definition at line 126 of file ModelCDRH3.hh.

Referenced by set_default().

bool protocols::antibody2::ModelCDRH3::do_cter_insert_

private

Definition at line 102 of file ModelCDRH3.hh.

Referenced by apply(), and set_default().

H3CterInsertOP protocols::antibody2::ModelCDRH3::h3_cter_insert_mover_

private

Definition at line 141 of file ModelCDRH3.hh.

Referenced by apply(), and init().

H3PerturbCCDOP protocols::antibody2::ModelCDRH3::h3_perturb_ccd_build_

private

Definition at line 142 of file ModelCDRH3.hh.

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

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

private

Definition at line 106 of file ModelCDRH3.hh.

Referenced by apply().

bool protocols::antibody2::ModelCDRH3::is_camelid_

private

is camelid antibody without light chain

Definition at line 132 of file ModelCDRH3.hh.

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

bool protocols::antibody2::ModelCDRH3::loops_flag_

private

loop_building in docking

Definition at line 123 of file ModelCDRH3.hh.

Referenced by set_default().

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

private

Definition at line 117 of file ModelCDRH3.hh.

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

Size protocols::antibody2::ModelCDRH3::max_cycle_

private

Definition at line 113 of file ModelCDRH3.hh.

Referenced by apply(), and set_default().

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

private

Definition at line 146 of file ModelCDRH3.hh.

Referenced by apply(), and set_default().

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

private

Definition at line 143 of file ModelCDRH3.hh.

Referenced by apply().

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

private

Definition at line 137 of file ModelCDRH3.hh.

Referenced by set_task_factory().

bool protocols::antibody2::ModelCDRH3::user_defined_

private

Definition at line 100 of file ModelCDRH3.hh.

Referenced by ModelCDRH3(), and set_default().

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

src/protocols/antibody2/ModelCDRH3.hh
src/protocols/antibody2/ModelCDRH3.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation