protocols::protein_interface_design::movers::Splice Class Reference

designs alanine residues in place of the residue identities at the interface. Retains interface glycines and prolines. More...

#include <Splice.hh>

Inheritance diagram for protocols::protein_interface_design::movers::Splice:

Collaboration diagram for protocols::protein_interface_design::movers::Splice:

Public Types
typedef core::pose::Pose	Pose
typedef utility::vector1 < ResidueBBDofs > ::const_iterator	dbase_const_iterator
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
	Splice ()
void	apply (Pose &pose)
virtual std::string	get_name () const
	Each derived class must specify its name. The class name. More...
protocols::moves::MoverOP	clone () const
	clone has to be overridden only if clone invocation is expected. More...
protocols::moves::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	parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
virtual	~Splice ()
void	from_res (core::Size const f)
core::Size	from_res () const
void	to_res (core::Size const t)
core::Size	to_res () const
std::string	source_pdb () const
void	source_pdb (std::string const s)
void	ccd (bool const c)
bool	ccd () const
void	scorefxn (core::scoring::ScoreFunctionOP sf)
core::scoring::ScoreFunctionOP	scorefxn () const
core::Real	rms_cutoff () const
void	rms_cutoff (core::Real const r)
void	res_move (core::Size const r)
core::Size	res_move () const
void	randomize_cut (bool const r)
bool	randomize_cut () const
void	cut_secondarystruc (bool const r)
bool	cut_secondarystruc () const
core::pack::task::TaskFactoryOP	task_factory () const
void	task_factory (core::pack::task::TaskFactoryOP tf)
core::pack::task::TaskFactoryOP	design_task_factory () const
void	design_task_factory (core::pack::task::TaskFactoryOP tf)
std::string	torsion_database_fname () const
void	torsion_database_fname (std::string const d)
core::Size	database_entry () const
void	database_entry (core::Size const d)
void	read_torsion_database ()
utility::vector1< ResidueBBDofs >	torsion_database () const
void	torsion_database (utility::vector1< ResidueBBDofs > const d)
std::string	template_file () const
void	template_file (std::string const s)
void	poly_ala (bool const p)
bool	poly_ala () const
void	equal_length (bool const e)
bool	equal_length () const
void	fold_tree (core::pose::Pose &pose, core::Size const start, core::Size const stop, core::Size const cut) const
	set the fold tree around start/stop/cut sites. presently makes a simple fold tree, but at one point may be a more complicated function to include two poses More...
bool	design () const
void	design (bool const d)
void	delta_lengths (utility::vector1< int > const dl)
utility::vector1< int >	delta_lengths ()
bool	dbase_iterate () const
void	dbase_iterate (bool const d)
utility::vector1< core::Size > ::const_iterator	dbase_begin () const
utility::vector1< core::Size > ::const_iterator	dbase_end () const
core::Size	find_dbase_entry (core::pose::Pose const &pose)
	controls which dbase entry will be used. Three options: 1. specific one according to user instruction; 2. randomized out of a subset of the dbase with fitting sequence lengths (if user specified 0); 3. iterating over dbase subset More...
core::Size	locked_res () const
void	locked_res (core::Size const r)
void	locked_res_id (char const c)
char	locked_res_id () const
std::string	checkpointing_file () const
void	checkpointing_file (std::string const cf)
void	load_from_checkpoint ()
void	save_to_checkpoint () const
std::string	loop_dbase_file_name () const
void	loop_dbase_file_name (std::string const f)
void	loop_pdb_source (std::string const l)
std::string	loop_pdb_source () const
protocols::filters::FilterOP	splice_filter () const
void	splice_filter (protocols::filters::FilterOP f)
void	database_pdb_entry (std::string const s)
std::string	database_pdb_entry () const
void	read_splice_segments (std::string const segment_type, std::string const segment_name, std::string const file_name)
core::sequence::SequenceProfileOP	generate_sequence_profile ()
void	load_pdb_segments_from_pose_comments (core::pose::Pose const &p)
void	modify_pdb_segments_with_current_segment (std::string const pdb_name)
void	add_sequence_constraints (core::pose::Pose &pose)
void	profile_weight_away_from_interface (core::Real const p)
core::Real	profile_weight_away_from_interface () const
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)
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...
void	set_current_job (protocols::jobdist::BasicJobCOP job)
jobdist::BasicJobCOP	get_current_job () const

Private Member Functions
void	save_values ()
void	retrieve_values ()

Private Attributes
core::Size	from_res_
core::Size	to_res_
core::Size	saved_from_res_
core::Size	saved_to_res_
std::string	source_pdb_
bool	ccd_
core::scoring::ScoreFunctionOP	scorefxn_
core::Real	rms_cutoff_
core::Size	res_move_
bool	randomize_cut_
bool	cut_secondarystruc_
core::pack::task::TaskFactoryOP	task_factory_
core::pack::task::TaskFactoryOP	design_task_factory_
std::string	torsion_database_fname_
core::Size	database_entry_
std::string	database_pdb_entry_
utility::vector1< ResidueBBDofs >	torsion_database_
std::string	template_file_
bool	poly_ala_
bool	equal_length_
	dflt true; thread ala residues in each position other than Gly/Pro or conserved in the source pdb. If false, keeps the input sequence (except Gly/Pro, which are replaced) More...
core::pose::PoseOP	template_pose_
core::pose::PoseOP	start_pose_
core::kinematics::FoldTreeOP	saved_fold_tree_
bool	design_
utility::vector1< int >	delta_lengths_
bool	dbase_iterate_
bool	first_pass_
utility::vector1< core::Size >	dbase_subset_
utility::vector1< core::Size > ::const_iterator	current_dbase_entry_
utility::pointer::owning_ptr < protocols::moves::DataMapObj < bool > >	end_dbase_subset_
utility::pointer::owning_ptr < protocols::moves::DataMapObj < utility::vector1< core::Size > > >	locked_res_
char	locked_res_id_
std::string	checkpointing_file_
std::string	loop_dbase_file_name_
std::string	loop_pdb_source_
utility::pointer::owning_ptr < protocols::moves::DataMapObj < std::string > >	mover_tag_
protocols::filters::FilterOP	splice_filter_
	dflt NULL; to communicate the current Splice mover's loop origin to the GenericMC More...
bool	use_sequence_profiles_
	sequence profiles More...
std::string	segment_type_
std::map< std::string, SpliceSegmentOP >	splice_segments_
std::map< std::string, std::string >	pdb_segments_
core::Real	profile_weight_away_from_interface_

Additional Inherited Members
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

designs alanine residues in place of the residue identities at the interface. Retains interface glycines and prolines.

Member Typedef Documentation

typedef utility::vector1< ResidueBBDofs >::const_iterator protocols::protein_interface_design::movers::Splice::dbase_const_iterator

typedef core::pose::Pose protocols::protein_interface_design::movers::Splice::Pose

Constructor & Destructor Documentation

protocols::protein_interface_design::movers::Splice::Splice

(

)

References dbase_subset_, delta_lengths_, end_dbase_subset_, pdb_segments_, splice_segments_, and torsion_database_.

protocols::protein_interface_design::movers::Splice::~Splice ( )

virtual

Member Function Documentation

void protocols::protein_interface_design::movers::Splice::add_sequence_constraints

(

core::pose::Pose &

pose)

References core::pose::Pose::add_constraint(), core::pack::dunbrack::c, core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), core::pose::Pose::constraint_set(), protocols::protein_interface_design::movers::find_residues_on_chain1_outside_interface(), core::pose::Pose::remove_constraint(), and core::scoring::res_type_constraint.

void protocols::protein_interface_design::movers::Splice::apply ( Pose &  pose)

virtual

Implements protocols::moves::Mover.

References core::chemical::aa_from_name(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::apply(), protocols::simple_moves::PackRotamersMover::apply(), protocols::protein_interface_design::movers::ResidueBBDofs::clear(), core::io::serialization::clone(), core::pose::Pose::conformation(), protocols::protein_interface_design::movers::copy_stretch(), protocols::toolbox::task_operations::DesignAroundOperation::design_shell(), core::conformation::Conformation::detect_disulfides(), core::chemical::DISULFIDE, core::scoring::dssp::Dssp::dssp_reduced(), protocols::moves::FAIL_DO_NOT_RETRY, protocols::moves::FAIL_RETRY, protocols::rosetta_scripts::find_nearest_res(), core::pose::Pose::fold_tree(), core::scoring::dssp::Dssp::get_dssp_secstruct(), core::conformation::Residue::has_variant_type(), protocols::toolbox::task_operations::DesignAroundOperation::include_residue(), protocols::protein_interface_design::movers::LoopLengthChange::loop_start(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::move_map(), protocols::moves::MS_SUCCESS, core::conformation::Residue::name1(), core::conformation::Residue::name3(), core::conformation::Conformation::num_chains(), protocols::protein_interface_design::movers::BBDofs::omega(), core::scoring::omega, core::pose::Pose::omega(), core::chemical::oneletter_code_from_aa(), protocols::protein_interface_design::movers::BBDofs::phi(), protocols::swa::phi(), core::pose::Pose::phi(), core::import_pose::pose_from_pdb(), protocols::protein_interface_design::movers::BBDofs::psi(), protocols::swa::psi(), core::pose::Pose::psi(), protocols::protein_interface_design::movers::BBDofs::resid(), core::pose::Pose::residue(), protocols::rosetta_scripts::residue_packer_states(), protocols::protein_interface_design::movers::BBDofs::resn(), protocols::protein_interface_design::movers::AddChainBreak::resnum(), core::scoring::rms, core::kinematics::MoveMap::set_chi(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::set_task_factory(), protocols::toolbox::task_operations::ThreadSequenceOperation::target_sequence(), protocols::protein_interface_design::filters::Torsion::task_factory(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::temp_final(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::temp_initial(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

void protocols::protein_interface_design::movers::Splice::ccd ( bool const  c)

inline

References core::pack::dunbrack::c, and ccd_.

bool protocols::protein_interface_design::movers::Splice::ccd ( ) const

inline

References ccd_.

std::string protocols::protein_interface_design::movers::Splice::checkpointing_file

(

)

const

void protocols::protein_interface_design::movers::Splice::checkpointing_file

(

std::string const

cf)

protocols::moves::MoverOP protocols::protein_interface_design::movers::Splice::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.

void protocols::protein_interface_design::movers::Splice::cut_secondarystruc ( bool const  r)

inline

References cut_secondarystruc_.

bool protocols::protein_interface_design::movers::Splice::cut_secondarystruc ( ) const

inline

References cut_secondarystruc_.

core::Size protocols::protein_interface_design::movers::Splice::database_entry ( ) const

inline

References database_entry_.

void protocols::protein_interface_design::movers::Splice::database_entry ( core::Size const  d)

inline

References database_entry_.

void protocols::protein_interface_design::movers::Splice::database_pdb_entry ( std::string const  s)

inline

References database_pdb_entry_.

std::string protocols::protein_interface_design::movers::Splice::database_pdb_entry ( ) const

inline

References database_pdb_entry_.

utility::vector1< core::Size >::const_iterator protocols::protein_interface_design::movers::Splice::dbase_begin

(

)

const

utility::vector1< core::Size >::const_iterator protocols::protein_interface_design::movers::Splice::dbase_end

(

)

const

bool protocols::protein_interface_design::movers::Splice::dbase_iterate ( ) const

inline

References dbase_iterate_.

void protocols::protein_interface_design::movers::Splice::dbase_iterate ( bool const  d)

inline

References dbase_iterate_.

void protocols::protein_interface_design::movers::Splice::delta_lengths ( utility::vector1< int > const  dl)

inline

References delta_lengths_.

utility::vector1< int > protocols::protein_interface_design::movers::Splice::delta_lengths ( )

inline

References delta_lengths_.

bool protocols::protein_interface_design::movers::Splice::design ( ) const

inline

References design_.

void protocols::protein_interface_design::movers::Splice::design ( bool const  d)

inline

References design_.

core::pack::task::TaskFactoryOP protocols::protein_interface_design::movers::Splice::design_task_factory

(

)

const

void protocols::protein_interface_design::movers::Splice::design_task_factory

(

core::pack::task::TaskFactoryOP

tf)

void protocols::protein_interface_design::movers::Splice::equal_length ( bool const  e)

inline

References equal_length_.

bool protocols::protein_interface_design::movers::Splice::equal_length ( ) const

inline

References equal_length_.

core::Size protocols::protein_interface_design::movers::Splice::find_dbase_entry

(

core::pose::Pose const &

pose)

controls which dbase entry will be used. Three options: 1. specific one according to user instruction; 2. randomized out of a subset of the dbase with fitting sequence lengths (if user specified 0); 3. iterating over dbase subset

References protocols::rosetta_scripts::find_nearest_res(), protocols::protein_interface_design::movers::RG(), protocols::protein_interface_design::movers::ResidueBBDofs::size(), protocols::protein_interface_design::movers::ResidueBBDofs::start_loop(), and protocols::protein_interface_design::movers::ResidueBBDofs::stop_loop().

void protocols::protein_interface_design::movers::Splice::fold_tree	(	core::pose::Pose &	pose,
		core::Size const	start,
		core::Size const	stop,
		core::Size const	cut
	)		const

set the fold tree around start/stop/cut sites. presently makes a simple fold tree, but at one point may be a more complicated function to include two poses

References core::kinematics::FoldTree::add_edge(), core::kinematics::FoldTree::clear(), core::pose::Pose::conformation(), core::chemical::DISULFIDE, core::pose::Pose::fold_tree(), core::conformation::Residue::has_variant_type(), core::conformation::Residue::name3(), protocols::protein_interface_design::optimal_connection_point(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

protocols::moves::MoverOP protocols::protein_interface_design::movers::Splice::fresh_instance ( ) const

inlinevirtual

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).

fresh_instance is meant to return a new object of this class, created with the default constructor. 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. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

void protocols::protein_interface_design::movers::Splice::from_res ( core::Size const  f)

inline

References from_res_.

core::Size protocols::protein_interface_design::movers::Splice::from_res ( ) const

inline

References from_res_.

core::sequence::SequenceProfileOP protocols::protein_interface_design::movers::Splice::generate_sequence_profile

(

)

References protocols::protein_interface_design::movers::concatenate_profiles().

std::string protocols::protein_interface_design::movers::Splice::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

References protocols::protein_interface_design::movers::SpliceCreator::mover_name().

void protocols::protein_interface_design::movers::Splice::load_from_checkpoint

(

)

The checkpointing file has the following structure: the first line contains an ordered list of the dbase_subset_ for splice to iterate over the loop database. The second line contains the last element tested (the loop-entry number in the database; not the iterator to it!) and the third line contains the best element tested (again, the loop number from the database, not the iterator!). To recover from a checkpoint the following reads the dbase_subset_ then, if this is a first_pass_ the best entry becomes current, and if it is not a first_pass then the current entry is current.

void protocols::protein_interface_design::movers::Splice::load_pdb_segments_from_pose_comments

(

core::pose::Pose const &

p)

References core::pose::get_all_comments().

core::Size protocols::protein_interface_design::movers::Splice::locked_res

(

)

const

void protocols::protein_interface_design::movers::Splice::locked_res

(

core::Size const

r)

void protocols::protein_interface_design::movers::Splice::locked_res_id

(

char const

c)

References core::pack::dunbrack::c.

char protocols::protein_interface_design::movers::Splice::locked_res_id

(

)

const

std::string protocols::protein_interface_design::movers::Splice::loop_dbase_file_name

(

)

const

void protocols::protein_interface_design::movers::Splice::loop_dbase_file_name

(

std::string const

f)

void protocols::protein_interface_design::movers::Splice::loop_pdb_source

(

std::string const

l)

std::string protocols::protein_interface_design::movers::Splice::loop_pdb_source

(

)

const

void protocols::protein_interface_design::movers::Splice::modify_pdb_segments_with_current_segment

(

std::string const

pdb_name)

void protocols::protein_interface_design::movers::Splice::parse_my_tag ( utility::tag::TagPtr const  tag, protocols::moves::DataMap &  data, protocols::filters::Filters_map const &  filters, protocols::moves::Movers_map const &  movers, core::pose::Pose const &  pose  )

virtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.

Reimplemented from protocols::moves::Mover.

References protocols::moves::DataMap::add(), protocols::moves::DataMap::get(), protocols::moves::get_set_from_datamap(), protocols::moves::DataMap::has(), core::conformation::Residue::name1(), protocols::rosetta_scripts::parse_filter(), core::pose::parse_resnum(), protocols::rosetta_scripts::parse_score_function(), protocols::rosetta_scripts::parse_task_operations(), core::import_pose::pose_from_pdb(), and core::pose::Pose::residue().

void protocols::protein_interface_design::movers::Splice::poly_ala ( bool const  p)

inline

References poly_ala_.

bool protocols::protein_interface_design::movers::Splice::poly_ala ( ) const

inline

References poly_ala_.

void protocols::protein_interface_design::movers::Splice::profile_weight_away_from_interface

(

core::Real const

p)

core::Real protocols::protein_interface_design::movers::Splice::profile_weight_away_from_interface

(

)

const

void protocols::protein_interface_design::movers::Splice::randomize_cut ( bool const  r)

inline

References randomize_cut_.

bool protocols::protein_interface_design::movers::Splice::randomize_cut ( ) const

inline

References randomize_cut_.

void protocols::protein_interface_design::movers::Splice::read_splice_segments	(	std::string const	segment_type,
		std::string const	segment_name,
		std::string const	file_name
	)

sequence profiles Splice changes the backbone of the current pose and the following methods deal with dynamically constructing a sequence profile for the current backbone choices.

void protocols::protein_interface_design::movers::Splice::read_torsion_database

(

)

the torsion dbase should have the following structure: each line represents a single loop. Each four values represent <phi> <psi> <omega> <3-let resid>; the last entry in a line represents <loop start>=""> <loop stop>=""> <cut site>=""> cut; where cut signifies that this is the loop designator

References protocols::protein_interface_design::movers::ResidueBBDofs::clear(), protocols::protein_interface_design::movers::ResidueBBDofs::cut_site(), core::scoring::omega, protocols::swa::phi(), protocols::swa::psi(), protocols::protein_interface_design::movers::ResidueBBDofs::push_back(), protocols::protein_interface_design::movers::ResidueBBDofs::source_pdb(), protocols::protein_interface_design::movers::ResidueBBDofs::start_loop(), and protocols::protein_interface_design::movers::ResidueBBDofs::stop_loop().

void protocols::protein_interface_design::movers::Splice::res_move ( core::Size const  r)

inline

References res_move_.

core::Size protocols::protein_interface_design::movers::Splice::res_move ( ) const

inline

References res_move_.

void protocols::protein_interface_design::movers::Splice::retrieve_values ( )

private

core::Real protocols::protein_interface_design::movers::Splice::rms_cutoff ( ) const

inline

References rms_cutoff_.

void protocols::protein_interface_design::movers::Splice::rms_cutoff ( core::Real const  r)

inline

References rms_cutoff_.

void protocols::protein_interface_design::movers::Splice::save_to_checkpoint

(

)

const

void protocols::protein_interface_design::movers::Splice::save_values ( )

private

splice apply might change the from_res/to_res internals since they sometimes refer to the template file. If that happens, we want the values to revert to their original values before the end of the apply function (so retrieve_values) below must be called before return.

void protocols::protein_interface_design::movers::Splice::scorefxn

(

core::scoring::ScoreFunctionOP

sf)

core::scoring::ScoreFunctionOP protocols::protein_interface_design::movers::Splice::scorefxn

(

)

const

std::string protocols::protein_interface_design::movers::Splice::source_pdb ( ) const

inline

References source_pdb_.

void protocols::protein_interface_design::movers::Splice::source_pdb ( std::string const  s)

inline

References source_pdb_.

protocols::filters::FilterOP protocols::protein_interface_design::movers::Splice::splice_filter

(

)

const

void protocols::protein_interface_design::movers::Splice::splice_filter

(

protocols::filters::FilterOP

f)

core::pack::task::TaskFactoryOP protocols::protein_interface_design::movers::Splice::task_factory

(

)

const

void protocols::protein_interface_design::movers::Splice::task_factory

(

core::pack::task::TaskFactoryOP

tf)

std::string protocols::protein_interface_design::movers::Splice::template_file ( ) const

inline

References template_file_.

void protocols::protein_interface_design::movers::Splice::template_file ( std::string const  s)

inline

References template_file_.

void protocols::protein_interface_design::movers::Splice::to_res ( core::Size const  t)

inline

References core::scoring::hbonds::t(), and to_res_.

core::Size protocols::protein_interface_design::movers::Splice::to_res ( ) const

inline

References to_res_.

utility::vector1< ResidueBBDofs > protocols::protein_interface_design::movers::Splice::torsion_database ( ) const

inline

References torsion_database_.

void protocols::protein_interface_design::movers::Splice::torsion_database ( utility::vector1< ResidueBBDofs > const  d)

inline

References torsion_database_.

std::string protocols::protein_interface_design::movers::Splice::torsion_database_fname ( ) const

inline

References torsion_database_fname_.

void protocols::protein_interface_design::movers::Splice::torsion_database_fname ( std::string const  d)

inline

References torsion_database_fname_.

Member Data Documentation

bool protocols::protein_interface_design::movers::Splice::ccd_

private

Referenced by ccd().

std::string protocols::protein_interface_design::movers::Splice::checkpointing_file_

private

utility::vector1< core::Size >::const_iterator protocols::protein_interface_design::movers::Splice::current_dbase_entry_

private

bool protocols::protein_interface_design::movers::Splice::cut_secondarystruc_

private

Referenced by cut_secondarystruc().

core::Size protocols::protein_interface_design::movers::Splice::database_entry_

private

Referenced by database_entry().

std::string protocols::protein_interface_design::movers::Splice::database_pdb_entry_

private

Referenced by database_pdb_entry().

bool protocols::protein_interface_design::movers::Splice::dbase_iterate_

private

Referenced by dbase_iterate().

utility::vector1< core::Size > protocols::protein_interface_design::movers::Splice::dbase_subset_

private

Referenced by Splice().

utility::vector1< int > protocols::protein_interface_design::movers::Splice::delta_lengths_

private

Referenced by delta_lengths(), and Splice().

bool protocols::protein_interface_design::movers::Splice::design_

private

Referenced by design().

core::pack::task::TaskFactoryOP protocols::protein_interface_design::movers::Splice::design_task_factory_

private

utility::pointer::owning_ptr< protocols::moves::DataMapObj< bool > > protocols::protein_interface_design::movers::Splice::end_dbase_subset_

private

Referenced by Splice().

bool protocols::protein_interface_design::movers::Splice::equal_length_

private

dflt true; thread ala residues in each position other than Gly/Pro or conserved in the source pdb. If false, keeps the input sequence (except Gly/Pro, which are replaced)

Referenced by equal_length().

bool protocols::protein_interface_design::movers::Splice::first_pass_

private

core::Size protocols::protein_interface_design::movers::Splice::from_res_

private

Referenced by from_res().

utility::pointer::owning_ptr< protocols::moves::DataMapObj < utility::vector1< core::Size > > > protocols::protein_interface_design::movers::Splice::locked_res_

private

char protocols::protein_interface_design::movers::Splice::locked_res_id_

private

std::string protocols::protein_interface_design::movers::Splice::loop_dbase_file_name_

private

std::string protocols::protein_interface_design::movers::Splice::loop_pdb_source_

private

utility::pointer::owning_ptr< protocols::moves::DataMapObj< std::string > > protocols::protein_interface_design::movers::Splice::mover_tag_

private

std::map< std::string, std::string > protocols::protein_interface_design::movers::Splice::pdb_segments_

private

Referenced by Splice().

bool protocols::protein_interface_design::movers::Splice::poly_ala_

private

Referenced by poly_ala().

core::Real protocols::protein_interface_design::movers::Splice::profile_weight_away_from_interface_

private

bool protocols::protein_interface_design::movers::Splice::randomize_cut_

private

Referenced by randomize_cut().

core::Size protocols::protein_interface_design::movers::Splice::res_move_

private

Referenced by res_move().

core::Real protocols::protein_interface_design::movers::Splice::rms_cutoff_

private

Referenced by rms_cutoff().

core::kinematics::FoldTreeOP protocols::protein_interface_design::movers::Splice::saved_fold_tree_

private

core::Size protocols::protein_interface_design::movers::Splice::saved_from_res_

private

core::Size protocols::protein_interface_design::movers::Splice::saved_to_res_

private

core::scoring::ScoreFunctionOP protocols::protein_interface_design::movers::Splice::scorefxn_

private

std::string protocols::protein_interface_design::movers::Splice::segment_type_

private

std::string protocols::protein_interface_design::movers::Splice::source_pdb_

private

Referenced by source_pdb().

protocols::filters::FilterOP protocols::protein_interface_design::movers::Splice::splice_filter_

private

dflt NULL; to communicate the current Splice mover's loop origin to the GenericMC

std::map< std::string, SpliceSegmentOP > protocols::protein_interface_design::movers::Splice::splice_segments_

private

Referenced by Splice().

core::pose::PoseOP protocols::protein_interface_design::movers::Splice::start_pose_

private

core::pack::task::TaskFactoryOP protocols::protein_interface_design::movers::Splice::task_factory_

private

std::string protocols::protein_interface_design::movers::Splice::template_file_

private

Referenced by template_file().

core::pose::PoseOP protocols::protein_interface_design::movers::Splice::template_pose_

private

core::Size protocols::protein_interface_design::movers::Splice::to_res_

private

Referenced by to_res().

utility::vector1< ResidueBBDofs > protocols::protein_interface_design::movers::Splice::torsion_database_

private

Referenced by Splice(), and torsion_database().

std::string protocols::protein_interface_design::movers::Splice::torsion_database_fname_

private

Referenced by torsion_database_fname().

bool protocols::protein_interface_design::movers::Splice::use_sequence_profiles_

private

sequence profiles

---

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

• src/protocols/protein_interface_design/movers/Splice.hh
• src/protocols/protein_interface_design/movers/Splice.cc