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protocols::forge::components::VarLengthBuild Class Reference

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:
Inheritance graph
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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 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...
 
core::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 (core::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)
 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 Stringsinfo ()
 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, core::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, core::Size const frag_length, core::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

VarLengthBuildoperator= (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...
 
core::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< Stringabego_
 abego for picking fragments More...
 
utility::vector1
< RemodelConstraintGeneratorOP
rcgs_
 collection of RCGs to manage remodel constraints More...
 
utility::vector1< moves::MoverOPsetup_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::MoverOPuser_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...
 
core::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...
 
core::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

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

References abego_, core::pose::add_variant_type_to_pose_residue(), protocols::symmetry::SetupForSymmetryMover::apply(), protocols::forge::build::BuildManager::begin(), protocols::forge::remodel::RemodelData::blueprint, centroid_build(), core::chemical::CENTROID_t, core::pose::Pose::conformation(), core::conformation::ResidueFactory::create_residue(), core::conformation::Conformation::delete_residue_slow(), protocols::forge::build::BuildManager::empty(), core::sequence::end, protocols::moves::FAIL_DO_NOT_RETRY, core::pose::Pose::fold_tree(), protocols::forge::methods::fold_tree_from_pose(), protocols::moves::Mover::get_last_move_status(), core::conformation::Conformation::insert_ideal_geometry_at_polymer_bond(), protocols::forge::build::BuildManager::intervals_containing_undefined_positions(), protocols::forge::methods::intervals_to_loops(), core::pose::Pose::is_centroid(), core::pose::symmetry::is_symmetric(), manager_, protocols::forge::build::BuildManager::modify(), protocols::moves::MS_SUCCESS, core::pose::Pose::omega(), protocols::forge::build::BuildManager::original2modified(), core::pose::Pose::phi(), core::pose::Pose::psi(), recover_original_on_failure_, remodel_data_, protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), repeat_tail_length_, core::pose::replace_pose_residue_copying_existing_coordinates(), core::pose::Pose::residue_type(), core::conformation::Conformation::residue_typeset_mode(), restart_mode_, protocols::forge::methods::restore_residues(), core::kinematics::FoldTree::root(), core::conformation::Conformation::safely_append_polymer_residue_after_seqpos(), core::pose::symmetry::sealed_symmetric_fold_tree(), protocols::forge::remodel::RemodelData::sequence, protocols::moves::Mover::set_last_move_status(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), protocols::forge::remodel::RemodelLoopMover::set_repeat_tail_length(), setup_movers_, core::pose::Pose::size(), core::util::switch_to_residue_type_set(), protocols::forge::components::TR(), and core::chemical::UPPER_TERMINUS_VARIANT.

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

References protocols::cluster::calibur::aa, abego_, protocols::forge::components::VLB_VallMemoryUsage::ALWAYS_CLEAR, core::scoring::atom_pair_constraint, protocols::forge::remodel::RemodelData::blueprint, core::pack::dunbrack::c, cache_fragments_, core::scoring::Energies::clear(), protocols::forge::components::VLB_VallMemoryUsage::CLEAR_IF_CACHING_FRAGMENTS, protocols::forge::methods::count_cutpoints(), core::scoring::dihedral_constraint, protocols::forge::remodel::RemodelData::dssp_updated_ss, core::pose::Pose::energies(), core::pose::datacache::ENZDES_OBSERVER, protocols::forge::methods::find_cutpoint(), frag1_, frag3_, frag9_, fragfull_, fragments_picked_, protocols::toolbox::match_enzdes_util::get_enzdes_observer(), ignore_cmdline_enzdes_cstfile_, protocols::forge::build::BuildManager::intervals_containing_undefined_positions(), protocols::forge::components::VLB_VallMemoryUsage::KEEP_IN_MEMORY, protocols::forge::build::Interval::left, protocols::forge::methods::linear_chainbreak(), core::scoring::linear_chainbreak, loop_mover_instance(), manager_, max_linear_chainbreak_, protocols::forge::build::BuildManager::movemap(), core::conformation::Residue::name1(), protocols::forge::build::BuildManager::new_positions(), new_secondary_structure_override_, new_sequence_override_, num_fragpick_, core::pose::Pose::observer_cache(), protocols::forge::build::BuildManager::original2modified(), original_sequence_, pick_all_fragments(), remodel_data_, remove_remodel_constraints(), core::pose::Pose::residue(), protocols::forge::build::Interval::right, core::pose::Pose::secstruct(), core::pose::datacache::ObserverCache::set(), set_starting_non_canonical(), setup_remodel_constraints(), sfx_, core::pose::Pose::size(), protocols::forge::components::TR(), use_fullmer_, and vall_memory_usage_.

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 ( )
void protocols::forge::components::VarLengthBuild::clear_user_provided_movers ( )
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
void protocols::forge::components::VarLengthBuild::loop_mover_fold_tree_constant ( bool const  flag)
inline
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]loopsThe loops to model.
[in]false_mmEnforce 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]strString 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]strString 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().

core::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 ( core::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,
core::Size const  n_frags 
)
protected

pick fragments of size full, 9, 3, 1

Parameters
[in]complete_ssThe complete secondary structure string, typically from a Pose.
[in]complete_aaThe complete amino acid string, typically from a Pose; can be empty. If empty, sequence bias is not used to pick fragments.
[in]complete_abegoThe complete abego string, typically from setter, set_abego
[in]intervalThe interval [left, right] to pick fragments from; Pose numbering (i.e. 1-based indexing).
[in]n_fragsThe number of fragments to pick per position.
[in]complete_ssThe complete secondary structure string, typically from a Pose.
[in]complete_aaThe complete amino acid string, typically from a Pose; can be empty. If empty, sequence bias is not used to pick fragments.
[in]intervalThe interval [left, right] to pick fragments from; Pose numbering (i.e. 1-based indexing).
[in]n_fragsThe 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,
core::Size const  frag_length,
core::Size const  n_frags 
)
protected

pick fragments of a given length, padding when necessary

Parameters
[in]complete_ssThe complete secondary structure string, typically from a Pose.
[in]complete_aaThe complete amino acid string, typically from a Pose; can be empty. If empty, sequence bias is not used to pick fragments.
[in]complete_abegoThe complete abego string, typically from a setter, set_abego
[in]intervalThe interval [left, right] to pick fragments from; Pose numbering (i.e. 1-based indexing).
[in]frag_lengthThe desired length of the fragments
[in]n_fragsThe number of fragments to pick per position.
[in]complete_ssThe complete secondary structure string, typically from a Pose.
[in]complete_aaThe complete amino acid string, typically from a Pose; can be empty. If empty, sequence bias is not used to pick fragments.
[in]intervalThe interval [left, right] to pick fragments from; Pose numbering (i.e. 1-based indexing).
[in]frag_lengthThe desired length of the fragments
[in]n_fragsThe 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
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().

core::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().

core::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().

core::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: