#include <FlexPepDockingAbInitio.hh>

Inheritance diagram for protocols::flexpep_docking::FlexPepDockingAbInitio:

Collaboration diagram for protocols::flexpep_docking::FlexPepDockingAbInitio:

Public Member Functions
	FlexPepDockingAbInitio (FlexPepDockingFlags flags_in, core::scoring::ScoreFunctionOP scorefxn_in, core::kinematics::MoveMapOP movemap_in, Size const rb_jump_in=1)
	constructor for low resolution flexpible peptide docking More...

	~FlexPepDockingAbInitio ()

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

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

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	setup_for_apply (core::pose::Pose &pose)
	initial setup for apply More...

void	to_centroid (core::pose::Pose &pose) const

void	to_allatom (core::pose::Pose &pose, core::pose::Pose &referencePose) const

void	torsions_monte_carlo (core::pose::Pose &pose, const int cycles, double &acceptance_rate)

void	loopclosure_monte_carlo (core::pose::Pose &pose)

void	rigidbody_monte_carlo (core::pose::Pose &pose, const int cycles, const float trans_magnitude, const float rot_magnitude, double &acceptance_rate)

void	convertPSERtoASP (core::pose::Pose &pose, std::set< int > &pSer_positions)

void	convertPSERtoGLU (core::pose::Pose &pose, std::set< int > &pSer_positions)

void	restorePSER (core::pose::Pose &pose, std::set< int > const &pSer_positions)

Private Attributes
FlexPepDockingFlags	flags_

core::scoring::ScoreFunctionOP	scorefxn_

core::kinematics::MoveMapOP	movemap_

Size	rb_jump_
	the jump number across which to do rigid_body transformations More...

bool	view_
	whether or not to initialize the viewer (for opengl) More...

moves::MonteCarloOP	mc_

protocols::simple_moves::MinMoverOP	minimizer_

protocols::comparative_modeling::LoopRelaxMoverOP	loop_relax_mover_

core::fragment::ConstantLengthFragSetOP	fragset3mer_

core::fragment::ConstantLengthFragSetOP	fragset9mer_

core::fragment::ConstantLengthFragSetOP	fragset5mer_

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 43 of file FlexPepDockingAbInitio.hh.

Constructor & Destructor Documentation

FlexPepDockingAbInitio::FlexPepDockingAbInitio	(	FlexPepDockingFlags	flags_in,
		core::scoring::ScoreFunctionOP	scorefxn_in,
		core::kinematics::MoveMapOP	movemap_in,
		Size const	rb_jump_in = `1`
	)

constructor for low resolution flexpible peptide docking

Definition at line 77 of file FlexPepDockingAbInitio.cc.

References protocols::loops::read_loop_fragments().

FlexPepDockingAbInitio::~FlexPepDockingAbInitio ( )

Definition at line 135 of file FlexPepDockingAbInitio.cc.

Member Function Documentation

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

virtual

Implements protocols::moves::Mover.

Definition at line 318 of file FlexPepDockingAbInitio.cc.

References protocols::medal::to_centroid(), and protocols::TR().

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::apply().

void FlexPepDockingAbInitio::convertPSERtoASP	(	core::pose::Pose &	pose,
		std::set< int > &	pSer_positions
	)

private

Definition at line 377 of file FlexPepDockingAbInitio.cc.

References core::conformation::ResidueFactory::create_residue(), core::chemical::FA_STANDARD, core::chemical::ChemicalManager::get_instance(), core::chemical::ResidueType::has_variant_type(), core::chemical::ResidueType::name3(), core::chemical::PHOSPHORYLATION, core::pose::Pose::replace_residue(), core::pose::Pose::residue_type(), core::pose::Pose::total_residue(), and protocols::TR().

void FlexPepDockingAbInitio::convertPSERtoGLU	(	core::pose::Pose &	pose,
		std::set< int > &	pSer_positions
	)

private

Definition at line 398 of file FlexPepDockingAbInitio.cc.

References core::conformation::ResidueFactory::create_residue(), core::chemical::FA_STANDARD, core::chemical::ChemicalManager::get_instance(), core::chemical::ResidueType::has_variant_type(), core::chemical::ResidueType::name3(), core::chemical::PHOSPHORYLATION, core::pose::Pose::replace_residue(), core::pose::Pose::residue_type(), core::pose::Pose::total_residue(), and protocols::TR().

std::string FlexPepDockingAbInitio::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

Definition at line 371 of file FlexPepDockingAbInitio.cc.

void FlexPepDockingAbInitio::loopclosure_monte_carlo ( core::pose::Pose & pose)

private

Definition at line 263 of file FlexPepDockingAbInitio.cc.

void FlexPepDockingAbInitio::restorePSER	(	core::pose::Pose &	pose,
		std::set< int > const &	pSer_positions
	)

private

Definition at line 418 of file FlexPepDockingAbInitio.cc.

References core::pose::add_variant_type_to_pose_residue(), core::chemical::CENTROID, core::conformation::ResidueFactory::create_residue(), core::chemical::ChemicalManager::get_instance(), core::chemical::PHOSPHORYLATION, and core::pose::Pose::replace_residue().

void FlexPepDockingAbInitio::rigidbody_monte_carlo	(	core::pose::Pose &	pose,
		const int	cycles,
		const float	trans_magnitude,
		const float	rot_magnitude,
		double &	acceptance_rate
	)

private

Definition at line 287 of file FlexPepDockingAbInitio.cc.

References protocols::moves::accept_reject.

void FlexPepDockingAbInitio::setup_for_apply ( core::pose::Pose & pose)

private

initial setup for apply

Definition at line 142 of file FlexPepDockingAbInitio.cc.

References mc_, minimizer_, movemap_, and scorefxn_.

void FlexPepDockingAbInitio::to_allatom	(	core::pose::Pose &	pose,
		core::pose::Pose &	referencePose
	)		const

private

Definition at line 174 of file FlexPepDockingAbInitio.cc.

References core::pose::Pose::is_fullatom().

void FlexPepDockingAbInitio::to_centroid ( core::pose::Pose & pose) const

private

Definition at line 158 of file FlexPepDockingAbInitio.cc.

References protocols::simple_moves::SwitchResidueTypeSetMover::apply(), core::chemical::CENTROID, core::pose::Pose::is_fullatom(), and protocols::TR().

void FlexPepDockingAbInitio::torsions_monte_carlo	(	core::pose::Pose &	pose,
		const int	cycles,
		double &	acceptance_rate
	)

private

Definition at line 188 of file FlexPepDockingAbInitio.cc.

References protocols::moves::accept_reject, and protocols::simple_moves::BackboneMover::angle_max().

Member Data Documentation

FlexPepDockingFlags protocols::flexpep_docking::FlexPepDockingAbInitio::flags_

private

Definition at line 136 of file FlexPepDockingAbInitio.hh.

core::fragment::ConstantLengthFragSetOP protocols::flexpep_docking::FlexPepDockingAbInitio::fragset3mer_

private

Definition at line 158 of file FlexPepDockingAbInitio.hh.

core::fragment::ConstantLengthFragSetOP protocols::flexpep_docking::FlexPepDockingAbInitio::fragset5mer_

private

Definition at line 160 of file FlexPepDockingAbInitio.hh.

core::fragment::ConstantLengthFragSetOP protocols::flexpep_docking::FlexPepDockingAbInitio::fragset9mer_

private

Definition at line 159 of file FlexPepDockingAbInitio.hh.

protocols::comparative_modeling::LoopRelaxMoverOP protocols::flexpep_docking::FlexPepDockingAbInitio::loop_relax_mover_

private

Definition at line 155 of file FlexPepDockingAbInitio.hh.

moves::MonteCarloOP protocols::flexpep_docking::FlexPepDockingAbInitio::mc_

private

Definition at line 150 of file FlexPepDockingAbInitio.hh.

Referenced by setup_for_apply().

protocols::simple_moves::MinMoverOP protocols::flexpep_docking::FlexPepDockingAbInitio::minimizer_

private

Definition at line 152 of file FlexPepDockingAbInitio.hh.

Referenced by setup_for_apply().

core::kinematics::MoveMapOP protocols::flexpep_docking::FlexPepDockingAbInitio::movemap_

private

Definition at line 142 of file FlexPepDockingAbInitio.hh.

Referenced by setup_for_apply().

Size protocols::flexpep_docking::FlexPepDockingAbInitio::rb_jump_

private

the jump number across which to do rigid_body transformations

Definition at line 145 of file FlexPepDockingAbInitio.hh.

core::scoring::ScoreFunctionOP protocols::flexpep_docking::FlexPepDockingAbInitio::scorefxn_

private

Definition at line 139 of file FlexPepDockingAbInitio.hh.

Referenced by setup_for_apply().

bool protocols::flexpep_docking::FlexPepDockingAbInitio::view_

private

whether or not to initialize the viewer (for opengl)

Definition at line 148 of file FlexPepDockingAbInitio.hh.

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

src/protocols/flexpep_docking/FlexPepDockingAbInitio.hh
src/protocols/flexpep_docking/FlexPepDockingAbInitio.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation