#include <GraftCDRLoopsProtocol.hh>

Inheritance diagram for protocols::antibody2::GraftCDRLoopsProtocol:

Collaboration diagram for protocols::antibody2::GraftCDRLoopsProtocol:

Public Types
typedef std::map< std::string, bool >	GraftMap

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

Public Member Functions
	GraftCDRLoopsProtocol ()

	~GraftCDRLoopsProtocol ()

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...

virtual void	apply (core::pose::Pose &pose)

void	set_graft_l1 (bool graft_l1)

void	set_graft_l2 (bool graft_l2)

void	set_graft_l3 (bool graft_l3)

void	set_graft_h1 (bool graft_h1)

void	set_graft_h2 (bool graft_h2)

void	set_graft_h3 (bool graft_h3)

void	set_h3_stem_graft (bool h3_stem_graft)

void	set_packonly_after_graft (bool setting)

void	set_camelid (bool camelid)

void	set_camelid_constraints (bool camelid_constraints)

void	set_benchmark (bool benchmark)

void	set_cst_weight (core::Real cst_weight)

void	set_sc_min (bool scmin)

void	set_rt_min (bool rtmin)

virtual std::string	get_name () const
	Each derived class must specify its name. The class name. More...

void	display_constraint_residues (core::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)

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

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	finalize_setup (core::pose::Pose &pose)

void	init ()

void	setup_objects ()

void	init_from_options ()

Friends
std::ostream &	operator<< (std::ostream &out, const GraftCDRLoopsProtocol &ab_m_2)

Additional Inherited Members
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 38 of file GraftCDRLoopsProtocol.hh.

Member Typedef Documentation

typedef std::map< std::string, bool > protocols::antibody2::GraftCDRLoopsProtocol::GraftMap

Definition at line 40 of file GraftCDRLoopsProtocol.hh.

Constructor & Destructor Documentation

protocols::antibody2::GraftCDRLoopsProtocol::GraftCDRLoopsProtocol ( )

Definition at line 71 of file GraftCDRLoopsProtocol.cc.

References init().

Referenced by clone().

protocols::antibody2::GraftCDRLoopsProtocol::~GraftCDRLoopsProtocol ( )

Definition at line 76 of file GraftCDRLoopsProtocol.cc.

Member Function Documentation

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

virtual

Implements protocols::moves::Mover.

Definition at line 300 of file GraftCDRLoopsProtocol.cc.

References ab_info_, protocols::antibody2::align_to_native(), camelid_constraints_, protocols::nonlocal::current_job(), display_constraint_residues(), finalize_setup(), protocols::jd2::JobDistributor::get_instance(), protocols::moves::Mover::get_native_pose(), graft_sequence_, core::pose::Pose::secstruct(), core::pose::Pose::set_secstruct(), core::pose::set_ss_from_phipsi(), core::pose::Pose::total_residue(), and protocols::TR().

protocols::moves::MoverOP protocols::antibody2::GraftCDRLoopsProtocol::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 79 of file GraftCDRLoopsProtocol.cc.

References GraftCDRLoopsProtocol().

void protocols::antibody2::GraftCDRLoopsProtocol::display_constraint_residues ( core::pose::Pose & pose)

Definition at line 369 of file GraftCDRLoopsProtocol.cc.

References ab_info_, protocols::antibody2::Extended, protocols::antibody2::h3, core::conformation::Residue::name3(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), and protocols::TR().

Referenced by apply().

void protocols::antibody2::GraftCDRLoopsProtocol::finalize_setup ( core::pose::Pose & pose)

private

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

virtual

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

Implements protocols::moves::Mover.

Definition at line 362 of file GraftCDRLoopsProtocol.cc.

void protocols::antibody2::GraftCDRLoopsProtocol::init ( void )

private

Definition at line 85 of file GraftCDRLoopsProtocol.cc.

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

Referenced by GraftCDRLoopsProtocol().

void protocols::antibody2::GraftCDRLoopsProtocol::init_from_options ( )

private

Definition at line 143 of file GraftCDRLoopsProtocol.cc.

References camelid_, graft_l1_, graft_l2_, graft_l3_, core::import_pose::pose_from_pdb(), set_benchmark(), set_camelid(), set_camelid_constraints(), set_cst_weight(), set_graft_h1(), set_graft_h2(), set_graft_h3(), set_graft_l1(), set_graft_l2(), set_graft_l3(), set_h3_stem_graft(), protocols::moves::Mover::set_native_pose(), set_packonly_after_graft(), and protocols::TR().

Referenced by init().

void protocols::antibody2::GraftCDRLoopsProtocol::register_options ( )

static

Associates relevant options with the AntibodyModeler class.

Definition at line 119 of file GraftCDRLoopsProtocol.cc.

Referenced by init().

void protocols::antibody2::GraftCDRLoopsProtocol::set_benchmark ( bool benchmark)

inline

Definition at line 87 of file GraftCDRLoopsProtocol.hh.

Referenced by init_from_options().

void protocols::antibody2::GraftCDRLoopsProtocol::set_camelid ( bool camelid)

inline

Definition at line 81 of file GraftCDRLoopsProtocol.hh.

Referenced by init_from_options().

void protocols::antibody2::GraftCDRLoopsProtocol::set_camelid_constraints ( bool camelid_constraints)

inline

Definition at line 84 of file GraftCDRLoopsProtocol.hh.

Referenced by init_from_options().

void protocols::antibody2::GraftCDRLoopsProtocol::set_cst_weight ( core::Real cst_weight)

inline

Definition at line 90 of file GraftCDRLoopsProtocol.hh.

Referenced by init_from_options().

void protocols::antibody2::GraftCDRLoopsProtocol::set_default ( )

Assigns default values to primitive members.

Definition at line 97 of file GraftCDRLoopsProtocol.cc.

References benchmark_, camelid_, camelid_constraints_, cst_weight_, graft_h1_, graft_h2_, graft_h3_, graft_l1_, graft_l2_, graft_l3_, h3_no_stem_graft_, packonly_after_graft_, rt_min_, sc_min_, and protocols::TR().

Referenced by init().

void protocols::antibody2::GraftCDRLoopsProtocol::set_graft_h1 ( bool graft_h1)

inline

Definition at line 66 of file GraftCDRLoopsProtocol.hh.

Referenced by init_from_options().

void protocols::antibody2::GraftCDRLoopsProtocol::set_graft_h2 ( bool graft_h2)

inline

Definition at line 69 of file GraftCDRLoopsProtocol.hh.

Referenced by init_from_options().

void protocols::antibody2::GraftCDRLoopsProtocol::set_graft_h3 ( bool graft_h3)

inline

Definition at line 72 of file GraftCDRLoopsProtocol.hh.

Referenced by init_from_options().

void protocols::antibody2::GraftCDRLoopsProtocol::set_graft_l1 ( bool graft_l1)

inline

Definition at line 57 of file GraftCDRLoopsProtocol.hh.

Referenced by init_from_options().

void protocols::antibody2::GraftCDRLoopsProtocol::set_graft_l2 ( bool graft_l2)

inline

Definition at line 60 of file GraftCDRLoopsProtocol.hh.

Referenced by init_from_options().

void protocols::antibody2::GraftCDRLoopsProtocol::set_graft_l3 ( bool graft_l3)

inline

Definition at line 63 of file GraftCDRLoopsProtocol.hh.

Referenced by init_from_options().

void protocols::antibody2::GraftCDRLoopsProtocol::set_h3_stem_graft ( bool h3_stem_graft)

inline

Definition at line 75 of file GraftCDRLoopsProtocol.hh.

Referenced by init_from_options().

void protocols::antibody2::GraftCDRLoopsProtocol::set_packonly_after_graft ( bool setting)

inline

Definition at line 78 of file GraftCDRLoopsProtocol.hh.

Referenced by init_from_options().

void protocols::antibody2::GraftCDRLoopsProtocol::set_rt_min ( bool rtmin)

inline

Definition at line 96 of file GraftCDRLoopsProtocol.hh.

void protocols::antibody2::GraftCDRLoopsProtocol::set_sc_min ( bool scmin)

inline

Definition at line 93 of file GraftCDRLoopsProtocol.hh.

void protocols::antibody2::GraftCDRLoopsProtocol::setup_objects ( )

private

Definition at line 203 of file GraftCDRLoopsProtocol.cc.

References ab_info_, ab_t_info_, core::scoring::atom_pair_constraint, core::scoring::chainbreak, core::scoring::ScoreFunctionFactory::create_score_function(), graft_sequence_, core::scoring::overlap_chainbreak, scorefxn_pack_, and tf_.

Referenced by init().

void protocols::antibody2::GraftCDRLoopsProtocol::show ( std::ostream & out = std::cout)

Show the complete setup of the docking protocol

Definition at line 405 of file GraftCDRLoopsProtocol.cc.

Friends And Related Function Documentation

std::ostream& operator<<	(	std::ostream &	out,
		const GraftCDRLoopsProtocol &	ab_m_2
	)

friend

Definition at line 409 of file GraftCDRLoopsProtocol.cc.

Member Data Documentation

AntibodyInfoOP protocols::antibody2::GraftCDRLoopsProtocol::ab_info_

private

Definition at line 132 of file GraftCDRLoopsProtocol.hh.

Referenced by apply(), display_constraint_residues(), finalize_setup(), and setup_objects().

Ab_TemplateInfoOP protocols::antibody2::GraftCDRLoopsProtocol::ab_t_info_

private

Definition at line 133 of file GraftCDRLoopsProtocol.hh.

Referenced by finalize_setup(), and setup_objects().

bool protocols::antibody2::GraftCDRLoopsProtocol::benchmark_

private

Definition at line 127 of file GraftCDRLoopsProtocol.hh.

Referenced by finalize_setup(), and set_default().

bool protocols::antibody2::GraftCDRLoopsProtocol::camelid_

private

Definition at line 123 of file GraftCDRLoopsProtocol.hh.

Referenced by finalize_setup(), init_from_options(), protocols::antibody2::operator<<(), and set_default().

bool protocols::antibody2::GraftCDRLoopsProtocol::camelid_constraints_

private

Definition at line 124 of file GraftCDRLoopsProtocol.hh.

Referenced by apply(), and set_default().

core::Real protocols::antibody2::GraftCDRLoopsProtocol::cst_weight_

private

Definition at line 129 of file GraftCDRLoopsProtocol.hh.

Referenced by finalize_setup(), and set_default().

bool protocols::antibody2::GraftCDRLoopsProtocol::graft_h1_

private

Definition at line 120 of file GraftCDRLoopsProtocol.hh.

Referenced by finalize_setup(), protocols::antibody2::operator<<(), and set_default().

bool protocols::antibody2::GraftCDRLoopsProtocol::graft_h2_

private

Definition at line 120 of file GraftCDRLoopsProtocol.hh.

Referenced by finalize_setup(), protocols::antibody2::operator<<(), and set_default().

bool protocols::antibody2::GraftCDRLoopsProtocol::graft_h3_

private

Definition at line 120 of file GraftCDRLoopsProtocol.hh.

Referenced by finalize_setup(), protocols::antibody2::operator<<(), and set_default().

bool protocols::antibody2::GraftCDRLoopsProtocol::graft_l1_

private

Definition at line 119 of file GraftCDRLoopsProtocol.hh.

Referenced by finalize_setup(), init_from_options(), protocols::antibody2::operator<<(), and set_default().

bool protocols::antibody2::GraftCDRLoopsProtocol::graft_l2_

private

Definition at line 119 of file GraftCDRLoopsProtocol.hh.

Referenced by finalize_setup(), init_from_options(), protocols::antibody2::operator<<(), and set_default().

bool protocols::antibody2::GraftCDRLoopsProtocol::graft_l3_

private

Definition at line 119 of file GraftCDRLoopsProtocol.hh.

Referenced by finalize_setup(), init_from_options(), protocols::antibody2::operator<<(), and set_default().

protocols::moves::SequenceMoverOP protocols::antibody2::GraftCDRLoopsProtocol::graft_sequence_

private

Definition at line 137 of file GraftCDRLoopsProtocol.hh.

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

bool protocols::antibody2::GraftCDRLoopsProtocol::h3_no_stem_graft_

private

Definition at line 121 of file GraftCDRLoopsProtocol.hh.

Referenced by finalize_setup(), and set_default().

bool protocols::antibody2::GraftCDRLoopsProtocol::packonly_after_graft_

private

Definition at line 122 of file GraftCDRLoopsProtocol.hh.

Referenced by finalize_setup(), and set_default().

bool protocols::antibody2::GraftCDRLoopsProtocol::rt_min_

private

Definition at line 126 of file GraftCDRLoopsProtocol.hh.

Referenced by finalize_setup(), and set_default().

bool protocols::antibody2::GraftCDRLoopsProtocol::sc_min_

private

Definition at line 125 of file GraftCDRLoopsProtocol.hh.

Referenced by finalize_setup(), and set_default().

core::scoring::ScoreFunctionOP protocols::antibody2::GraftCDRLoopsProtocol::scorefxn_pack_

private

Definition at line 130 of file GraftCDRLoopsProtocol.hh.

Referenced by setup_objects().

pack::task::TaskFactoryOP protocols::antibody2::GraftCDRLoopsProtocol::tf_

private

Definition at line 135 of file GraftCDRLoopsProtocol.hh.

Referenced by finalize_setup(), and setup_objects().

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

src/protocols/antibody2/GraftCDRLoopsProtocol.hh
src/protocols/antibody2/GraftCDRLoopsProtocol.cc

Private Attributes
bool	graft_l1_

bool	graft_l2_

bool	graft_l3_

bool	graft_h1_

bool	graft_h2_

bool	graft_h3_

bool	h3_no_stem_graft_

bool	packonly_after_graft_

bool	camelid_

bool	camelid_constraints_

bool	sc_min_

bool	rt_min_

bool	benchmark_

core::Real	cst_weight_

core::scoring::ScoreFunctionOP	scorefxn_pack_

AntibodyInfoOP	ab_info_

Ab_TemplateInfoOP	ab_t_info_

pack::task::TaskFactoryOP	tf_

protocols::moves::SequenceMoverOP	graft_sequence_

Public Types

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation