Component that performs a protocol for user-specified variable length remodeling of protein backbone segments. More...

#include <VarLengthBuild.hh>

Inheritance diagram for protocols::forge::components::VarLengthBuild:

Public Types
typedef std::string	String

typedef core::Real	Real

typedef core::Size	Size

typedef core::fragment::ConstantLengthFragSetOP	ConstantLengthFragSetOP

typedef core::fragment::FrameList	FrameList

typedef core::fragment::OrderedFragSetOP	OrderedFragSetOP

typedef core::kinematics::MoveMap	MoveMap

typedef core::pose::Pose	Pose

typedef core::scoring::ScoreFunction	ScoreFunction

typedef core::scoring::ScoreFunctionOP	ScoreFunctionOP

typedef protocols::loops::Loops	Loops

typedef protocols::forge::remodel::RemodelData	RemodelData

typedef protocols::moves::MoverOP	MoverOP

typedef protocols::forge::build::BuildManager	BuildManager

typedef protocols::forge::build::Interval	Interval

typedef protocols::forge::remodel::RemodelConstraintGeneratorOP	RemodelConstraintGeneratorOP

typedef BuildManager::BIOPConstIterator	BIOPConstIterator

typedef BuildManager::Original2Modified	Original2Modified

typedef BuildManager::Positions	Positions

Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP	TagCOP

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
	VarLengthBuild ()
	default constructor More...

	VarLengthBuild (BuildManager const &manager)
	BuildManager constructor. More...

	VarLengthBuild (BuildManager const &manager, RemodelData const &remodel_data)
	BuildManager + RemodelData constructor. More...

	VarLengthBuild (VarLengthBuild const &rval)
	copy constructor More...

	~VarLengthBuild () override
	default destructor More...

MoverOP	clone () const override
	clone this object More...

MoverOP	fresh_instance () const override
	create a new instance of this type of object More...

BuildManager const &	manager () const
	build manager More...

bool	recover_original_on_failure () const
	at the end of apply(), reset the Pose to the original Pose if mover was not successful? (default true) More...

String const &	loop_mover_str () const
	the string id of the loop mover to use (default "RemodelLoopMover") More...

bool	cache_fragments () const
	cache fragments after picking? (default true) More...

VLB_VallMemoryUsage::Enum	vall_memory_usage () const
	option dictating whether to keep VallLibrary in memory or clear it under certain circumstances after picking fragments. (default KEEP_IN_MEMORY) More...

Size	num_fragpick () const
	the number of fragments to pick at each position (default 200) More...

bool	use_fullmer () const
	also use fragments spanning the entire length of a loop? (default false) More...

String const &	original_sequence ()
	full sequence string corresponding to original input pose used to pick sequence biased fragments; if empty, sequence bias is not used when picking fragments More...

String const &	new_secondary_structure_override () const
	full sequence string with length corresponding to the new modified pose used to pick secondary structure biased fragments. More...

String const &	new_sequence_override () const
	full amino acid string with length corresponding to the new modified pose used to pick sequence biased fragments. More...

Real	max_linear_chainbreak () const
	return the highest linear chainbreak score a chainbreak can have and still be considered closed More...

bool	restart_mode () const
	Flag to turn on restart mode, in which VLB assumes that the Pose fed to it during apply() has already been modified by the manager. (default False) More...

void	scorefunction (ScoreFunction const &sfx)
	set ScoreFunction used during build More...

void	scorefunction (ScoreFunctionOP const &sfx)
	set ScoreFunction used during build More...

void	manager (BuildManager const &manager)
	set build manager; also clears any cached fragments More...

void	recover_original_on_failure (bool const flag)
	at the end of apply(), reset the Pose to the original Pose if mover was not successful? More...

void	loop_mover_str (String const &str)
	set the loop mover to use via string More...

void	cache_fragments (bool const flag)
	cache fragments after picking? More...

void	vall_memory_usage (VLB_VallMemoryUsage::Enum const level)
	option dictating whether to keep VallLibrary in memory or clear it under certain circumstances after picking fragments. More...

void	num_fragpick (Size const num)
	the number of fragments to pick at each position (default 200) More...

void	use_fullmer (bool const flag)
	also use fragments spanning the entire length of a loop? More...

void	original_sequence (String const &seq)
	full sequence string corresponding to original input pose used to pick sequence biased fragments; if empty, sequence bias is not used when picking fragments More...

void	new_secondary_structure_override (String const &str)
	full sequence string with length corresponding to the new modified pose used to pick secondary structure biased fragments. More...

void	new_sequence_override (String const &str)
	full amino acid string with length corresponding to the new modified pose used to pick sequence biased fragments. More...

void	max_linear_chainbreak (Real const tol)
	set the highest linear chainbreak score a chainbreak can have and still be considered closed More...

void	loop_mover_fold_tree_constant (bool const flag)

void	restart_mode (bool const flag)
	Flag to turn on restart mode, in which VLB assumes that the Pose fed to it during apply() has already been modified by the manager. (default False) More...

void	ignore_cmdline_enzdes_cstfile (bool const flag)

void	clear_rcgs ()
	get rid of all rcgs More...

void	add_rcg (RemodelConstraintGeneratorOP rcg)
	adding an rcg. this will set the rcg internal vlb backpointer More...

void	clear_setup_movers ()

void	add_setup_mover (moves::MoverOP mover_in)

void	clear_user_provided_movers ()

void	add_user_provided_mover (moves::MoverOP mover_in)

void	clear_fragments ()
	clear any currently cached fragments More...

void	set_abego (utility::vector1< String > const &abego)
	set abego definition for fragments More...

void	apply (Pose &pose) override
	run protocol on given Pose More...

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

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual MoverOP	create ()

MoverCOP	get_self_ptr () const

MoverOP	get_self_ptr ()

MoverCAP	get_self_weak_ptr () const

MoverAP	get_self_weak_ptr ()

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

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...

virtual bool	reinitialize_for_each_job () const
	Inform 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
	Inform 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...

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...

void	set_type (std::string const &setting)
	Set the 'type' string. More...

std::string	get_type () const

void	type (const std::string &type_in)
	Set the 'type' string. More...

std::string const &	type () const
	Get the set 'type' string. More...

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	parse_my_tag (TagCOP tag, basic::datacache::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...

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

virtual void	set_current_tag (std::string const &new_tag)

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...

virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...

virtual core::Real	last_proposal_density_ratio ()

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	mover_provides_citation_info () const
	Does this mover provide information about how to cite it? More...

virtual utility::vector1 < basic::citation_manager::CitationCollectionCOP >	provide_citation_info () const
	Provide the citation. More...

virtual bool	mover_is_unpublished () const
	Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...

virtual utility::vector1 < basic::citation_manager::UnpublishedModuleInfoCOP >	provide_authorship_info_for_unpublished () const
	Provide a list of authors and their e-mail addresses, as strings. More...

Protected Member Functions
virtual bool	centroid_build (Pose &pose)
	run centroid level protocol on given Pose More...

virtual MoverOP	loop_mover_instance (loops::LoopsOP const loops, MoveMap const &false_mm)
	return the appropriate loop mover More...

void	pick_all_fragments (String const &complete_ss, String const &complete_aa, utility::vector1< String > const &complete_abego, Interval const &interval, Size const n_frags)
	pick fragments of size full, 9, 3, 1 More...

FrameList	pick_fragments (String const &complete_ss, String const &complete_aa, utility::vector1< String > const &complete_abego, Interval const &interval, Size const frag_length, Size const n_frags)
	pick fragments of a given length, padding when necessary More...

void	set_starting_non_canonical (Pose &pose)

void	setup_remodel_constraints (Pose &pose)
	telling all rcgs to setup and insert constraints into the pose More...

void	remove_remodel_constraints (Pose &pose)
	telling all rcgs to remove their constraints from the pose 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...

Private Types
typedef protocols::moves::Mover	Super

Private Member Functions
VarLengthBuild &	operator= (VarLengthBuild const &rval)
	disallow copy assignment More...

Private Attributes
BuildManager	manager_
	manages desired build instructions More...

ScoreFunctionOP	sfx_
	the ScoreFunction used during build More...

protocols::forge::remodel::RemodelData	remodel_data_
	, used when constraints are defined through Remodel More...

bool	recover_original_on_failure_
	at the end of apply(), reset the Pose to the original Pose if mover was not successful? (default true) More...

String	loop_mover_str_
	the string ID of the LoopMover used during build (default "RemodelLoopMover" ) More...

bool	cache_fragments_
	cache fragments after picking? (default true) More...

VLB_VallMemoryUsage::Enum	vall_memory_usage_
	option dictating whether to keep VallLibrary in memory or clear it under certain circumstances after picking fragments. (default KEEP_IN_MEMORY) More...

Size	num_fragpick_
	the number of fragments to pick at each position (default 200) More...

bool	use_fullmer_
	also use fragments spanning the entire length of a loop? (default false) More...

String	original_sequence_
	full sequence string corresponding to original input pose used to pick sequence biased fragments; if empty, sequence bias is not used when picking fragments More...

String	new_secondary_structure_override_
	full sequence string with length corresponding to the new modified pose used to pick secondary structure biased fragments. More...

String	new_sequence_override_
	full amino acid string with length corresponding to the new modified pose used to pick sequence biased fragments. More...

Real	max_linear_chainbreak_
	the highest linear chainbreak score a chainbreak can have and still be considered closed More...

bool	fragments_picked_
	internal flag indicating if fragments for all intervals have been picked More...

OrderedFragSetOP	fragfull_
	full-mer to use during fragment insertion More...

ConstantLengthFragSetOP	frag9_
	9-mers to use during fragment insertion More...

ConstantLengthFragSetOP	frag3_
	3-mers to use during fragment insertion More...

ConstantLengthFragSetOP	frag1_
	1-mers to use during fragment insertion More...

utility::vector1< String >	abego_
	abego for picking fragments More...

utility::vector1 < RemodelConstraintGeneratorOP >	rcgs_
	collection of RCGs to manage remodel constraints More...

utility::vector1< moves::MoverOP >	setup_movers_
	collection of movers that get a chance to modify the pose after the new lenght has been setup but before remodeling starts More...

utility::vector1< moves::MoverOP >	user_provided_movers_
	collection of movers that mess with the pose during RemodelLoopMover apply where n is determined by the variable below gets piped straight into RemodelLoopMover, only has an effect if this is the loop mover used More...

Size	user_provided_movers_apply_cycle_
	determines how often the above movers get called in the loop mover, also only has an effect if the RemodelLoopMover is used (default 3) More...

bool	loop_mover_fold_tree_constant_
	tell RemodelLoopMover to keep the foldtree untouched also only has an effect if RemodelLoopmover is used note: will only tell loop mover is this is set to true More...

bool	restart_mode_
	Flag to turn on restart mode, in which VLB assumes that the Pose fed to it during apply() has already been modified by the manager. (default False) More...

bool	ignore_cmdline_enzdes_cstfile_
	flo jan 11 reading an enzdes cstfile in the middle of remodel messes up a remodel run that was started from enzdes More...

Size	repeat_tail_length_

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. More...

Detailed Description

Component that performs a protocol for user-specified variable length remodeling of protein backbone segments.

This bootstrap implementation performs centroid level loop building using 9,3,1-mer fragments and running a LoopMover with the Remodel 'remodel_cen' score function. The default loop mover is the forge RemodelLoopMover. It does not yet handle extensions or continuous replacements. This class is under heavy development, expect many changes to both API and internals.

Member Typedef Documentation

typedef BuildManager::BIOPConstIterator protocols::forge::components::VarLengthBuild::BIOPConstIterator

typedef protocols::forge::build::BuildManager protocols::forge::components::VarLengthBuild::BuildManager

typedef core::fragment::ConstantLengthFragSetOP protocols::forge::components::VarLengthBuild::ConstantLengthFragSetOP

typedef core::fragment::FrameList protocols::forge::components::VarLengthBuild::FrameList

typedef protocols::forge::build::Interval protocols::forge::components::VarLengthBuild::Interval

typedef protocols::loops::Loops protocols::forge::components::VarLengthBuild::Loops

typedef core::kinematics::MoveMap protocols::forge::components::VarLengthBuild::MoveMap

typedef protocols::moves::MoverOP protocols::forge::components::VarLengthBuild::MoverOP

typedef core::fragment::OrderedFragSetOP protocols::forge::components::VarLengthBuild::OrderedFragSetOP

typedef BuildManager::Original2Modified protocols::forge::components::VarLengthBuild::Original2Modified

typedef core::pose::Pose protocols::forge::components::VarLengthBuild::Pose

typedef BuildManager::Positions protocols::forge::components::VarLengthBuild::Positions

typedef core::Real protocols::forge::components::VarLengthBuild::Real

typedef protocols::forge::remodel::RemodelConstraintGeneratorOP protocols::forge::components::VarLengthBuild::RemodelConstraintGeneratorOP

typedef protocols::forge::remodel::RemodelData protocols::forge::components::VarLengthBuild::RemodelData

typedef core::scoring::ScoreFunction protocols::forge::components::VarLengthBuild::ScoreFunction

typedef core::scoring::ScoreFunctionOP protocols::forge::components::VarLengthBuild::ScoreFunctionOP

typedef core::Size protocols::forge::components::VarLengthBuild::Size

typedef std::string protocols::forge::components::VarLengthBuild::String

typedef protocols::moves::Mover protocols::forge::components::VarLengthBuild::Super

private

Constructor & Destructor Documentation

protocols::forge::components::VarLengthBuild::VarLengthBuild ( )

default constructor

protocols::forge::components::VarLengthBuild::VarLengthBuild ( BuildManager const & manager )

BuildManager constructor.

protocols::forge::components::VarLengthBuild::VarLengthBuild	(	BuildManager const &	manager,
		RemodelData const &	remodel_data
	)

BuildManager + RemodelData constructor.

BuildManager + remodelData constructor.

protocols::forge::components::VarLengthBuild::VarLengthBuild ( VarLengthBuild const & rval )

copy constructor

References cache_fragments_, frag1_, frag3_, frag9_, fragfull_, and fragments_picked_.

protocols::forge::components::VarLengthBuild::~VarLengthBuild ( )

overridedefault

default destructor

Member Function Documentation

void protocols::forge::components::VarLengthBuild::add_rcg ( RemodelConstraintGeneratorOP rcg )

adding an rcg. this will set the rcg internal vlb backpointer

References protocols::moves::Mover::get_self_ptr(), and rcgs_.

Referenced by protocols::fldsgn::BluePrintBDR::setup_invrot_tree_in_vlb().

void protocols::forge::components::VarLengthBuild::add_setup_mover ( moves::MoverOP mover_in )

References setup_movers_.

Referenced by protocols::fldsgn::BluePrintBDR::setup_invrot_tree_in_vlb().

void protocols::forge::components::VarLengthBuild::add_user_provided_mover ( moves::MoverOP mover_in )

References user_provided_movers_.

Referenced by protocols::fldsgn::BluePrintBDR::setup_invrot_tree_in_vlb().

void protocols::forge::components::VarLengthBuild::apply ( Pose & pose )

overridevirtual

run protocol on given Pose

Returns: if procedure successful, return Pose with modifications and a sealed fold tree, otherwise return Pose with modifications and the in-progress cut fold tree

Remarks: Before invoking this function it's best to make sure the secondary structure in the Pose is marked via the method that you would prefer, e.g. by Dssp (protocols::jumping::Dssp), by the old Rosetta++ binning method (core::pose::set_ss_from_phipsi) or by external method such as reading in a file.

Implements protocols::moves::Mover.

Referenced by protocols::protein_interface_design::movers::VLB::apply().

bool protocols::forge::components::VarLengthBuild::cache_fragments ( ) const

inline

cache fragments after picking? (default true)

If true, will cache fragments and reuse them upon each apply() call instead of repicking every time.

References cache_fragments_.

void protocols::forge::components::VarLengthBuild::cache_fragments ( bool const flag )

inline

cache fragments after picking?

If true, will cache fragments and reuse them upon each apply() call instead of repicking every time.

References cache_fragments_.

bool protocols::forge::components::VarLengthBuild::centroid_build ( Pose & pose )

protectedvirtual

run centroid level protocol on given Pose

Returns: true if regions modeled within tolerances, false otherwise

Referenced by apply().

void protocols::forge::components::VarLengthBuild::clear_fragments ( )

clear any currently cached fragments

References frag1_, frag3_, frag9_, fragfull_, and fragments_picked_.

Referenced by manager().

void protocols::forge::components::VarLengthBuild::clear_rcgs ( )

get rid of all rcgs

References rcgs_.

void protocols::forge::components::VarLengthBuild::clear_setup_movers ( )

References setup_movers_.

Referenced by protocols::fldsgn::BluePrintBDR::setup_invrot_tree_in_vlb().

void protocols::forge::components::VarLengthBuild::clear_user_provided_movers ( )

References user_provided_movers_.

Referenced by protocols::fldsgn::BluePrintBDR::setup_invrot_tree_in_vlb().

protocols::moves::MoverOP protocols::forge::components::VarLengthBuild::clone ( ) const

overridevirtual

clone this object

Reimplemented from protocols::moves::Mover.

protocols::moves::MoverOP protocols::forge::components::VarLengthBuild::fresh_instance ( ) const

overridevirtual

create a new instance of this type of object

Reimplemented from protocols::moves::Mover.

std::string protocols::forge::components::VarLengthBuild::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

void protocols::forge::components::VarLengthBuild::ignore_cmdline_enzdes_cstfile ( bool const flag )

inline

References ignore_cmdline_enzdes_cstfile_.

void protocols::forge::components::VarLengthBuild::loop_mover_fold_tree_constant ( bool const flag )

inline

References loop_mover_fold_tree_constant_.

Referenced by protocols::fldsgn::BluePrintBDR::setup_invrot_tree_in_vlb().

VarLengthBuild::MoverOP protocols::forge::components::VarLengthBuild::loop_mover_instance	(	loops::LoopsOP const	loops,
		MoveMap const &	false_mm
	)

protectedvirtual

return the appropriate loop mover

Parameters

[in]	loops	The loops to model.
[in]	false_mm	Enforce False settings in this MoveMap. Currently only useful with the RemodelLoopMover.

References frag1_, frag3_, frag9_, fragfull_, loop_mover_fold_tree_constant_, loop_mover_str_, remodel_data_, repeat_tail_length_, sfx_, use_fullmer_, user_provided_movers_, and user_provided_movers_apply_cycle_.

Referenced by centroid_build().

String const& protocols::forge::components::VarLengthBuild::loop_mover_str ( ) const

inline

the string id of the loop mover to use (default "RemodelLoopMover")

Returns: "RemodelLoopMover" for the forge RemodelLoopMover, otherwise a string recognized by create_loop_mover() in the "LoopMoverFactory".

References loop_mover_str_.

void protocols::forge::components::VarLengthBuild::loop_mover_str ( String const & str )

inline

set the loop mover to use via string

use "RemodelLoopMover" for the forge RemodelLoopMover, otherwise set it to a string recognized by create_loop_mover() in the "LoopMoverFactory".

References loop_mover_str_, and protocols::kinmatch::str().

BuildManager const& protocols::forge::components::VarLengthBuild::manager ( ) const

inline

build manager

References manager_.

Referenced by manager(), and setup_remodel_constraints().

void protocols::forge::components::VarLengthBuild::manager ( BuildManager const & manager )

set build manager; also clears any cached fragments

References clear_fragments(), manager(), and manager_.

Real protocols::forge::components::VarLengthBuild::max_linear_chainbreak ( ) const

inline

return the highest linear chainbreak score a chainbreak can have and still be considered closed

Remarks: default 0.07

References max_linear_chainbreak_.

void protocols::forge::components::VarLengthBuild::max_linear_chainbreak ( Real const tol )

inline

set the highest linear chainbreak score a chainbreak can have and still be considered closed

References max_linear_chainbreak_.

String const& protocols::forge::components::VarLengthBuild::new_secondary_structure_override ( ) const

inline

full sequence string with length corresponding to the new modified pose used to pick secondary structure biased fragments.

Remarks: IMPORTANT: This is an override! If this string is filled, it will be used as the string to pick secondary structure biased fragments without modification. All secondary structure settings that might be taken from the original Pose or from the BuildInstructions will be ignored. The length of this string must be equal to the length of the NEW modified pose, otherwise the protocol will stop with error – you can use BuildManager::dummy_modify() to help figure things out.

References new_secondary_structure_override_.

void protocols::forge::components::VarLengthBuild::new_secondary_structure_override ( String const & str )

inline

full sequence string with length corresponding to the new modified pose used to pick secondary structure biased fragments.

Parameters

[in] str String with length equals to the new modified pose. See remarks for help on how to determine this. String is allowed to be empty, in which case it will clear the setting.

Remarks: IMPORTANT: This is an override! If this string is filled, it will be used as the string to pick secondary structure biased fragments without modification. All secondary structure settings that might be taken from the original Pose or from the BuildInstructions will be ignored. The length of this string must be equal to the length of the NEW modified pose, otherwise the protocol will stop with error – you can use BuildManager::dummy_modify() to help figure things out.

References new_secondary_structure_override_, and protocols::kinmatch::str().

String const& protocols::forge::components::VarLengthBuild::new_sequence_override ( ) const

inline

full amino acid string with length corresponding to the new modified pose used to pick sequence biased fragments.

Remarks: IMPORTANT: This is an override! If this string is filled, it will be used as the string to pick sequence biased fragments without modification. All sequence settings that might be taken from the original Pose or from the BuildInstructions will be ignored. The length of this string must be equal to the length of the NEW modified pose, otherwise the protocol will stop with error – you can use BuildManager::dummy_modify() to help figure things out.

References new_sequence_override_.

void protocols::forge::components::VarLengthBuild::new_sequence_override ( String const & str )

inline

full amino acid string with length corresponding to the new modified pose used to pick sequence biased fragments.

Parameters

[in] str String with length equals to the new modified pose. See remarks for help on how to determine this. String is allowed to be empty, in which case it will clear the setting.

Remarks: IMPORTANT: This is an override! If this string is filled, it will be used as the string to pick sequence biased fragments without modification. All sequence settings that might be taken from the original Pose or from the BuildInstructions will be ignored. The length of this string must be equal to the length of the NEW modified pose, otherwise the protocol will stop with error – you can use BuildManager::dummy_modify() to help figure things out.

References new_sequence_override_, and protocols::kinmatch::str().

Size protocols::forge::components::VarLengthBuild::num_fragpick ( ) const

inline

the number of fragments to pick at each position (default 200)

References num_fragpick_.

void protocols::forge::components::VarLengthBuild::num_fragpick ( Size const num )

inline

the number of fragments to pick at each position (default 200)

References num_fragpick_.

VarLengthBuild& protocols::forge::components::VarLengthBuild::operator= ( VarLengthBuild const & rval )

private

disallow copy assignment

Remarks: Mover base class prevents this from working...

String const& protocols::forge::components::VarLengthBuild::original_sequence ( )

inline

full sequence string corresponding to original input pose used to pick sequence biased fragments; if empty, sequence bias is not used when picking fragments

References original_sequence_.

void protocols::forge::components::VarLengthBuild::original_sequence ( String const & seq )

inline

full sequence string corresponding to original input pose used to pick sequence biased fragments; if empty, sequence bias is not used when picking fragments

References original_sequence_.

void protocols::forge::components::VarLengthBuild::pick_all_fragments	(	String const &	complete_ss,
		String const &	complete_aa,
		utility::vector1< String > const &	complete_abego,
		Interval const &	interval,
		Size const	n_frags
	)

protected

pick fragments of size full, 9, 3, 1

Parameters

[in]	complete_ss	The complete secondary structure string, typically from a Pose.
[in]	complete_aa	The complete amino acid string, typically from a Pose; can be empty. If empty, sequence bias is not used to pick fragments.
[in]	complete_abego	The complete abego string, typically from setter, set_abego
[in]	interval	The interval [left, right] to pick fragments from; Pose numbering (i.e. 1-based indexing).
[in]	n_frags	The number of fragments to pick per position.
[in]	complete_ss	The complete secondary structure string, typically from a Pose.
[in]	complete_aa	The complete amino acid string, typically from a Pose; can be empty. If empty, sequence bias is not used to pick fragments.
[in]	interval	The interval [left, right] to pick fragments from; Pose numbering (i.e. 1-based indexing).
[in]	n_frags	The number of fragments to pick per position.

References frag1_, frag3_, frag9_, fragfull_, protocols::forge::build::Interval::length(), pick_fragments(), protocols::forge::methods::smallmer_from_largemer(), and use_fullmer_.

Referenced by centroid_build().

VarLengthBuild::FrameList protocols::forge::components::VarLengthBuild::pick_fragments	(	String const &	complete_ss,
		String const &	complete_aa,
		utility::vector1< String > const &	complete_abego,
		Interval const &	interval,
		Size const	frag_length,
		Size const	n_frags
	)

protected

pick fragments of a given length, padding when necessary

Parameters

[in]	complete_ss	The complete secondary structure string, typically from a Pose.
[in]	complete_aa	The complete amino acid string, typically from a Pose; can be empty. If empty, sequence bias is not used to pick fragments.
[in]	complete_abego	The complete abego string, typically from a setter, set_abego
[in]	interval	The interval [left, right] to pick fragments from; Pose numbering (i.e. 1-based indexing).
[in]	frag_length	The desired length of the fragments
[in]	n_frags	The number of fragments to pick per position.
[in]	complete_ss	The complete secondary structure string, typically from a Pose.
[in]	complete_aa	The complete amino acid string, typically from a Pose; can be empty. If empty, sequence bias is not used to pick fragments.
[in]	interval	The interval [left, right] to pick fragments from; Pose numbering (i.e. 1-based indexing).
[in]	frag_length	The desired length of the fragments
[in]	n_frags	The number of fragments to pick per position.

References protocols::forge::build::Interval::left, protocols::forge::build::Interval::length(), core::fragment::picking_old::vall::pick_fragments(), core::fragment::picking_old::vall::pick_fragments_by_ss(), core::fragment::picking_old::vall::pick_fragments_by_ss_plus_aa(), and protocols::forge::components::TR().

Referenced by pick_all_fragments(), and protocols::denovo_design::components::VLBProtected::pick_fragments_public().

bool protocols::forge::components::VarLengthBuild::recover_original_on_failure ( ) const

inline

at the end of apply(), reset the Pose to the original Pose if mover was not successful? (default true)

References recover_original_on_failure_.

void protocols::forge::components::VarLengthBuild::recover_original_on_failure ( bool const flag )

inline

at the end of apply(), reset the Pose to the original Pose if mover was not successful?

References recover_original_on_failure_.

void protocols::forge::components::VarLengthBuild::remove_remodel_constraints ( Pose & pose )

protected

telling all rcgs to remove their constraints from the pose

References rcgs_.

Referenced by centroid_build().

bool protocols::forge::components::VarLengthBuild::restart_mode ( ) const

inline

Flag to turn on restart mode, in which VLB assumes that the Pose fed to it during apply() has already been modified by the manager. (default False)

Remarks: In restart mode, VLB only runs the manager's dummy modify capability during apply() to get the mapping info.

References restart_mode_.

void protocols::forge::components::VarLengthBuild::restart_mode ( bool const flag )

inline

Flag to turn on restart mode, in which VLB assumes that the Pose fed to it during apply() has already been modified by the manager. (default False)

Remarks: In restart mode, VLB only runs the manager's dummy modify capability during apply() to get the mapping info.

References restart_mode_.

void protocols::forge::components::VarLengthBuild::scorefunction ( ScoreFunction const & sfx )

set ScoreFunction used during build

References core::scoring::ScoreFunction::clone(), and sfx_.

Referenced by protocols::protein_interface_design::movers::VLB::apply().

void protocols::forge::components::VarLengthBuild::scorefunction ( ScoreFunctionOP const & sfx )

set ScoreFunction used during build

References sfx_.

void protocols::forge::components::VarLengthBuild::set_abego ( utility::vector1< String > const & abego )

inline

set abego definition for fragments

References core::scoring::abego, and abego_.

void protocols::forge::components::VarLengthBuild::set_starting_non_canonical ( Pose & pose )

protected

References core::chemical::CENTROID, core::chemical::ResidueTypeFinder::get_all_possible_residue_types(), core::chemical::ResidueTypeFinder::name3(), core::pose::replace_pose_residue_copying_existing_coordinates(), and core::pose::Pose::total_residue().

Referenced by centroid_build().

void protocols::forge::components::VarLengthBuild::setup_remodel_constraints ( Pose & pose )

protected

telling all rcgs to setup and insert constraints into the pose

References manager(), rcgs_, and protocols::forge::components::TR().

Referenced by centroid_build().

bool protocols::forge::components::VarLengthBuild::use_fullmer ( ) const

inline

also use fragments spanning the entire length of a loop? (default false)

References use_fullmer_.

void protocols::forge::components::VarLengthBuild::use_fullmer ( bool const flag )

inline

also use fragments spanning the entire length of a loop?

References use_fullmer_.

VLB_VallMemoryUsage::Enum protocols::forge::components::VarLengthBuild::vall_memory_usage ( ) const

inline

option dictating whether to keep VallLibrary in memory or clear it under certain circumstances after picking fragments. (default KEEP_IN_MEMORY)

References vall_memory_usage_.

void protocols::forge::components::VarLengthBuild::vall_memory_usage ( VLB_VallMemoryUsage::Enum const level )

inline

option dictating whether to keep VallLibrary in memory or clear it under certain circumstances after picking fragments.

References vall_memory_usage_.

Member Data Documentation

utility::vector1< String > protocols::forge::components::VarLengthBuild::abego_

private

abego for picking fragments

Referenced by apply(), centroid_build(), and set_abego().

bool protocols::forge::components::VarLengthBuild::cache_fragments_

private

cache fragments after picking? (default true)

If true, will cache fragments and reuse them upon each apply() call instead of repicking every time.

Referenced by cache_fragments(), centroid_build(), and VarLengthBuild().

ConstantLengthFragSetOP protocols::forge::components::VarLengthBuild::frag1_

private

1-mers to use during fragment insertion

Referenced by centroid_build(), clear_fragments(), loop_mover_instance(), pick_all_fragments(), and VarLengthBuild().

ConstantLengthFragSetOP protocols::forge::components::VarLengthBuild::frag3_

private

3-mers to use during fragment insertion

Referenced by centroid_build(), clear_fragments(), loop_mover_instance(), pick_all_fragments(), and VarLengthBuild().

ConstantLengthFragSetOP protocols::forge::components::VarLengthBuild::frag9_

private

9-mers to use during fragment insertion

Referenced by centroid_build(), clear_fragments(), loop_mover_instance(), pick_all_fragments(), and VarLengthBuild().

OrderedFragSetOP protocols::forge::components::VarLengthBuild::fragfull_

private

full-mer to use during fragment insertion

Referenced by centroid_build(), clear_fragments(), loop_mover_instance(), pick_all_fragments(), and VarLengthBuild().

bool protocols::forge::components::VarLengthBuild::fragments_picked_

private

internal flag indicating if fragments for all intervals have been picked

Referenced by centroid_build(), clear_fragments(), and VarLengthBuild().

bool protocols::forge::components::VarLengthBuild::ignore_cmdline_enzdes_cstfile_

private

flo jan 11 reading an enzdes cstfile in the middle of remodel messes up a remodel run that was started from enzdes

Referenced by centroid_build(), and ignore_cmdline_enzdes_cstfile().

bool protocols::forge::components::VarLengthBuild::loop_mover_fold_tree_constant_

private

tell RemodelLoopMover to keep the foldtree untouched also only has an effect if RemodelLoopmover is used note: will only tell loop mover is this is set to true

Referenced by loop_mover_fold_tree_constant(), and loop_mover_instance().

String protocols::forge::components::VarLengthBuild::loop_mover_str_

private

the string ID of the LoopMover used during build (default "RemodelLoopMover" )

use "RemodelLoopMover" for the forge RemodelLoopMover, otherwise set it to a string recognized by create_loop_mover() in the "LoopMoverFactory".

Referenced by loop_mover_instance(), and loop_mover_str().

BuildManager protocols::forge::components::VarLengthBuild::manager_

private

manages desired build instructions

Referenced by apply(), centroid_build(), and manager().

Real protocols::forge::components::VarLengthBuild::max_linear_chainbreak_

private

the highest linear chainbreak score a chainbreak can have and still be considered closed

Referenced by centroid_build(), and max_linear_chainbreak().

String protocols::forge::components::VarLengthBuild::new_secondary_structure_override_

private

full sequence string with length corresponding to the new modified pose used to pick secondary structure biased fragments.

Remarks: IMPORTANT: This is an override! If this string is filled, it will be used as the string to pick secondary structure biased fragments without modification. All secondary structure settings that might be taken from the original Pose or from the BuildInstructions will be ignored. The length of this string must be equal to the length of the NEW modified pose, otherwise the protocol will stop with error – you can use BuildManager::dummy_modify() to help figure things out.

Referenced by centroid_build(), and new_secondary_structure_override().

String protocols::forge::components::VarLengthBuild::new_sequence_override_

private

full amino acid string with length corresponding to the new modified pose used to pick sequence biased fragments.

Remarks: IMPORTANT: This is an override! If this string is filled, it will be used as the string to pick sequence biased fragments without modification. All sequence settings that might be taken from the original Pose or from the BuildInstructions will be ignored. The length of this string must be equal to the length of the NEW modified pose, otherwise the protocol will stop with error – you can use BuildManager::dummy_modify() to help figure things out.

Referenced by centroid_build(), and new_sequence_override().

Size protocols::forge::components::VarLengthBuild::num_fragpick_

private

the number of fragments to pick at each position (default 200)

Referenced by centroid_build(), and num_fragpick().

String protocols::forge::components::VarLengthBuild::original_sequence_

private

full sequence string corresponding to original input pose used to pick sequence biased fragments; if empty, sequence bias is not used when picking fragments

Referenced by centroid_build(), and original_sequence().

utility::vector1< RemodelConstraintGeneratorOP > protocols::forge::components::VarLengthBuild::rcgs_

private

collection of RCGs to manage remodel constraints

Referenced by add_rcg(), clear_rcgs(), remove_remodel_constraints(), and setup_remodel_constraints().

bool protocols::forge::components::VarLengthBuild::recover_original_on_failure_

private

at the end of apply(), reset the Pose to the original Pose if mover was not successful? (default true)

Referenced by apply(), and recover_original_on_failure().

protocols::forge::remodel::RemodelData protocols::forge::components::VarLengthBuild::remodel_data_

private

, used when constraints are defined through Remodel

Referenced by apply(), centroid_build(), and loop_mover_instance().

Size protocols::forge::components::VarLengthBuild::repeat_tail_length_

private

Referenced by apply(), and loop_mover_instance().

bool protocols::forge::components::VarLengthBuild::restart_mode_

private

Flag to turn on restart mode, in which VLB assumes that the Pose fed to it during apply() has already been modified by the manager. (default False)

Remarks: In restart mode, VLB only runs the manager's dummy modify capability during apply() to get the mapping info.

Referenced by apply(), and restart_mode().

utility::vector1< moves::MoverOP > protocols::forge::components::VarLengthBuild::setup_movers_

private

collection of movers that get a chance to modify the pose after the new lenght has been setup but before remodeling starts

Referenced by add_setup_mover(), apply(), and clear_setup_movers().

ScoreFunctionOP protocols::forge::components::VarLengthBuild::sfx_

private

the ScoreFunction used during build

Referenced by centroid_build(), loop_mover_instance(), and scorefunction().

bool protocols::forge::components::VarLengthBuild::use_fullmer_

private

also use fragments spanning the entire length of a loop? (default false)

Referenced by centroid_build(), loop_mover_instance(), pick_all_fragments(), and use_fullmer().

utility::vector1< moves::MoverOP > protocols::forge::components::VarLengthBuild::user_provided_movers_

private

collection of movers that mess with the pose during RemodelLoopMover apply where n is determined by the variable below gets piped straight into RemodelLoopMover, only has an effect if this is the loop mover used

Referenced by add_user_provided_mover(), clear_user_provided_movers(), and loop_mover_instance().

Size protocols::forge::components::VarLengthBuild::user_provided_movers_apply_cycle_

private

determines how often the above movers get called in the loop mover, also only has an effect if the RemodelLoopMover is used (default 3)

Referenced by loop_mover_instance().

VLB_VallMemoryUsage::Enum protocols::forge::components::VarLengthBuild::vall_memory_usage_

private

option dictating whether to keep VallLibrary in memory or clear it under certain circumstances after picking fragments. (default KEEP_IN_MEMORY)

Referenced by centroid_build(), and vall_memory_usage().

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

src/protocols/forge/components/VarLengthBuild.hh
src/protocols/forge/components/VarLengthBuild.cc

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