Component that performs a protocol for user-specified variable length remodeling of protein backbone segments. More...
#include <VarLengthBuild.hh>
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 Strings & | info () |
| non-const accessor More... | |
| virtual Strings const & | info () const |
| const accessor More... | |
| virtual void | provide_citation_info (basic::citation_manager::CitationCollectionList &) const |
| Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. 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 | |
| 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_ |
| @remodelData, 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< 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... | |
| 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
◆ BIOPConstIterator
| typedef BuildManager::BIOPConstIterator protocols::forge::components::VarLengthBuild::BIOPConstIterator |
◆ BuildManager
| typedef protocols::forge::build::BuildManager protocols::forge::components::VarLengthBuild::BuildManager |
◆ ConstantLengthFragSetOP
| typedef core::fragment::ConstantLengthFragSetOP protocols::forge::components::VarLengthBuild::ConstantLengthFragSetOP |
◆ FrameList
◆ Interval
◆ Loops
◆ MoveMap
◆ MoverOP
◆ OrderedFragSetOP
| typedef core::fragment::OrderedFragSetOP protocols::forge::components::VarLengthBuild::OrderedFragSetOP |
◆ Original2Modified
| typedef BuildManager::Original2Modified protocols::forge::components::VarLengthBuild::Original2Modified |
◆ Pose
◆ Positions
◆ Real
◆ RemodelConstraintGeneratorOP
| typedef protocols::forge::remodel::RemodelConstraintGeneratorOP protocols::forge::components::VarLengthBuild::RemodelConstraintGeneratorOP |
◆ RemodelData
| typedef protocols::forge::remodel::RemodelData protocols::forge::components::VarLengthBuild::RemodelData |
◆ ScoreFunction
◆ ScoreFunctionOP
| typedef core::scoring::ScoreFunctionOP protocols::forge::components::VarLengthBuild::ScoreFunctionOP |
◆ Size
◆ String
| typedef std::string protocols::forge::components::VarLengthBuild::String |
◆ Super
Constructor & Destructor Documentation
◆ VarLengthBuild() [1/4]
| protocols::forge::components::VarLengthBuild::VarLengthBuild | ( | ) |
default constructor
◆ VarLengthBuild() [2/4]
| protocols::forge::components::VarLengthBuild::VarLengthBuild | ( | BuildManager const & | manager | ) |
BuildManager constructor.
◆ VarLengthBuild() [3/4]
| protocols::forge::components::VarLengthBuild::VarLengthBuild | ( | BuildManager const & | manager, |
| RemodelData const & | remodel_data | ||
| ) |
BuildManager + RemodelData constructor.
BuildManager + remodelData constructor.
◆ VarLengthBuild() [4/4]
| protocols::forge::components::VarLengthBuild::VarLengthBuild | ( | VarLengthBuild const & | rval | ) |
copy constructor
References cache_fragments_, frag1_, frag3_, frag9_, fragfull_, and fragments_picked_.
◆ ~VarLengthBuild()
|
overridedefault |
default destructor
Member Function Documentation
◆ add_rcg()
| 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().
◆ add_setup_mover()
| 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().
◆ add_user_provided_mover()
| 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().
◆ apply()
|
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, core::chemical::modifications::FAIL_DO_NOT_RETRY, 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::pdb_info(), 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().
◆ cache_fragments() [1/2]
|
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_.
◆ cache_fragments() [2/2]
|
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_.
◆ centroid_build()
|
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, 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, core::scoring::linear_chainbreak, protocols::forge::methods::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().
◆ clear_fragments()
| void protocols::forge::components::VarLengthBuild::clear_fragments | ( | ) |
◆ clear_rcgs()
| void protocols::forge::components::VarLengthBuild::clear_rcgs | ( | ) |
get rid of all rcgs
References rcgs_.
◆ clear_setup_movers()
| void protocols::forge::components::VarLengthBuild::clear_setup_movers | ( | ) |
References setup_movers_.
Referenced by protocols::fldsgn::BluePrintBDR::setup_invrot_tree_in_vlb().
◆ clear_user_provided_movers()
| void protocols::forge::components::VarLengthBuild::clear_user_provided_movers | ( | ) |
References user_provided_movers_.
Referenced by protocols::fldsgn::BluePrintBDR::setup_invrot_tree_in_vlb().
◆ clone()
|
overridevirtual |
clone this object
Reimplemented from protocols::moves::Mover.
◆ fresh_instance()
|
overridevirtual |
create a new instance of this type of object
Reimplemented from protocols::moves::Mover.
◆ get_name()
|
overridevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
◆ ignore_cmdline_enzdes_cstfile()
|
inline |
References ignore_cmdline_enzdes_cstfile_.
◆ loop_mover_fold_tree_constant()
|
inline |
References loop_mover_fold_tree_constant_.
Referenced by protocols::fldsgn::BluePrintBDR::setup_invrot_tree_in_vlb().
◆ loop_mover_instance()
|
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().
◆ loop_mover_str() [1/2]
|
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_.
◆ loop_mover_str() [2/2]
|
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().
◆ manager() [1/2]
|
inline |
◆ manager() [2/2]
| void protocols::forge::components::VarLengthBuild::manager | ( | BuildManager const & | manager | ) |
set build manager; also clears any cached fragments
References clear_fragments(), manager(), and manager_.
◆ max_linear_chainbreak() [1/2]
|
inline |
return the highest linear chainbreak score a chainbreak can have and still be considered closed
- Remarks
- default 0.07
References max_linear_chainbreak_.
◆ max_linear_chainbreak() [2/2]
|
inline |
set the highest linear chainbreak score a chainbreak can have and still be considered closed
References max_linear_chainbreak_.
◆ new_secondary_structure_override() [1/2]
|
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_.
◆ new_secondary_structure_override() [2/2]
|
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().
◆ new_sequence_override() [1/2]
|
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_.
◆ new_sequence_override() [2/2]
|
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().
◆ num_fragpick() [1/2]
|
inline |
the number of fragments to pick at each position (default 200)
References num_fragpick_.
◆ num_fragpick() [2/2]
|
inline |
the number of fragments to pick at each position (default 200)
References num_fragpick_.
◆ operator=()
|
private |
disallow copy assignment
- Remarks
- Mover base class prevents this from working...
◆ original_sequence() [1/2]
|
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_.
◆ original_sequence() [2/2]
|
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_.
◆ pick_all_fragments()
|
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().
◆ pick_fragments()
|
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().
◆ recover_original_on_failure() [1/2]
|
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_.
◆ recover_original_on_failure() [2/2]
|
inline |
at the end of apply(), reset the Pose to the original Pose if mover was not successful?
References recover_original_on_failure_.
◆ remove_remodel_constraints()
|
protected |
telling all rcgs to remove their constraints from the pose
References rcgs_.
Referenced by centroid_build().
◆ restart_mode() [1/2]
|
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_.
◆ restart_mode() [2/2]
|
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_.
◆ scorefunction() [1/2]
| 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().
◆ scorefunction() [2/2]
| void protocols::forge::components::VarLengthBuild::scorefunction | ( | ScoreFunctionOP const & | sfx | ) |
set ScoreFunction used during build
References sfx_.
◆ set_abego()
|
inline |
set abego definition for fragments
References core::scoring::abego, and abego_.
◆ set_starting_non_canonical()
|
protected |
◆ setup_remodel_constraints()
|
protected |
telling all rcgs to setup and insert constraints into the pose
References manager(), rcgs_, and protocols::forge::components::TR().
Referenced by centroid_build().
◆ use_fullmer() [1/2]
|
inline |
also use fragments spanning the entire length of a loop? (default false)
References use_fullmer_.
◆ use_fullmer() [2/2]
|
inline |
also use fragments spanning the entire length of a loop?
References use_fullmer_.
◆ vall_memory_usage() [1/2]
|
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_.
◆ vall_memory_usage() [2/2]
|
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
◆ abego_
|
private |
abego for picking fragments
Referenced by apply(), centroid_build(), and set_abego().
◆ 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().
◆ frag1_
|
private |
1-mers to use during fragment insertion
Referenced by centroid_build(), clear_fragments(), loop_mover_instance(), pick_all_fragments(), and VarLengthBuild().
◆ frag3_
|
private |
3-mers to use during fragment insertion
Referenced by centroid_build(), clear_fragments(), loop_mover_instance(), pick_all_fragments(), and VarLengthBuild().
◆ frag9_
|
private |
9-mers to use during fragment insertion
Referenced by centroid_build(), clear_fragments(), loop_mover_instance(), pick_all_fragments(), and VarLengthBuild().
◆ fragfull_
|
private |
full-mer to use during fragment insertion
Referenced by centroid_build(), clear_fragments(), loop_mover_instance(), pick_all_fragments(), and VarLengthBuild().
◆ fragments_picked_
|
private |
internal flag indicating if fragments for all intervals have been picked
Referenced by centroid_build(), clear_fragments(), and 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().
◆ 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().
◆ 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().
◆ manager_
|
private |
manages desired build instructions
Referenced by apply(), centroid_build(), and manager().
◆ 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().
◆ 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().
◆ 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().
◆ num_fragpick_
|
private |
the number of fragments to pick at each position (default 200)
Referenced by centroid_build(), and num_fragpick().
◆ 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().
◆ rcgs_
|
private |
collection of RCGs to manage remodel constraints
Referenced by add_rcg(), clear_rcgs(), remove_remodel_constraints(), and setup_remodel_constraints().
◆ 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().
◆ remodel_data_
|
private |
@remodelData, used when constraints are defined through Remodel
Referenced by apply(), centroid_build(), and loop_mover_instance().
◆ repeat_tail_length_
|
private |
Referenced by apply(), and loop_mover_instance().
◆ 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().
◆ 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().
◆ sfx_
|
private |
the ScoreFunction used during build
Referenced by centroid_build(), loop_mover_instance(), and scorefunction().
◆ 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().
◆ 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().
◆ 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().
◆ 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
