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core::pack::task::ResidueLevelTask Class Referenceabstract

#include <ResidueLevelTask.hh>

Inheritance diagram for core::pack::task::ResidueLevelTask:
Inheritance graph
[legend]

Public Types

typedef std::list
< chemical::ResidueTypeCOP
ResidueTypeCOPList
 
typedef std::list
< chemical::ResidueTypeCOP >
::iterator 
ResidueTypeCOPListIter
 
typedef std::list
< chemical::ResidueTypeCOP >
::const_iterator 
ResidueTypeCOPListConstIter
 

Public Member Functions

virtual ~ResidueLevelTask ()
 
virtual ExtraRotSample extrachi_sample_level (bool buried, int chi, chemical::ResidueType const &concrete_residue) const =0
 
virtual void initialize_from_command_line ()=0
 
virtual void initialize_extra_rotamer_flags_from_command_line ()=0
 
virtual void initialize_from_options (utility::options::OptionCollection const &options)=0
 
virtual void initialize_extra_rotamer_flags_from_options (utility::options::OptionCollection const &options)=0
 
virtual void or_include_current (bool include_current)=0
 
virtual bool include_current () const =0
 
virtual void add_behavior (std::string const &behavior)=0
 
virtual bool has_behavior (std::string const &behavior) const =0
 
virtual bool has_behavior () const =0
 
virtual void target_type (chemical::ResidueTypeCOP type)=0
 
virtual void target_type (chemical::AA aa)=0
 
virtual void target_type (std::string name)=0
 
virtual void or_adducts (bool setting)=0
 
virtual bool adducts () const =0
 
virtual void or_ex1 (bool ex1)=0
 
virtual void or_ex2 (bool ex2)=0
 
virtual void or_ex3 (bool ex3)=0
 
virtual void or_ex4 (bool ex4)=0
 
virtual void or_ex1_sample_level (ExtraRotSample ex1_sample_level)=0
 
virtual void or_ex2_sample_level (ExtraRotSample ex2_sample_level)=0
 
virtual void or_ex3_sample_level (ExtraRotSample ex3_sample_level)=0
 
virtual void or_ex4_sample_level (ExtraRotSample ex4_sample_level)=0
 
virtual void or_ex1aro (bool ex1aro)=0
 
virtual void or_ex2aro (bool ex2aro)=0
 
virtual void or_ex1aro_exposed (bool ex1aro_exposed)=0
 
virtual void or_ex2aro_exposed (bool ex2aro_exposed)=0
 
virtual void or_ex1aro_sample_level (ExtraRotSample ex1aro_sample_level)=0
 
virtual void or_ex2aro_sample_level (ExtraRotSample ex2aro_only_sample_level)=0
 
virtual void or_ex1aro_exposed_sample_level (ExtraRotSample ex1aro_exposed_sample_level)=0
 
virtual void or_ex2aro_exposed_sample_level (ExtraRotSample ex2aro_exposed_sample_level)=0
 
virtual void or_exdna_sample_level (ExtraRotSample exdna_sample_level)=0
 
virtual void or_operate_on_ex1 (bool operate)=0
 
virtual void or_operate_on_ex2 (bool operate)=0
 
virtual void or_operate_on_ex3 (bool operate)=0
 
virtual void or_operate_on_ex4 (bool operate)=0
 
virtual bool ex1 () const =0
 
virtual bool ex2 () const =0
 
virtual bool ex3 () const =0
 
virtual bool ex4 () const =0
 
virtual ExtraRotSample ex1_sample_level () const =0
 
virtual ExtraRotSample ex2_sample_level () const =0
 
virtual ExtraRotSample ex3_sample_level () const =0
 
virtual ExtraRotSample ex4_sample_level () const =0
 
virtual bool ex1aro () const =0
 
virtual bool ex2aro () const =0
 
virtual bool ex1aro_exposed () const =0
 
virtual bool ex2aro_exposed () const =0
 
virtual ExtraRotSample ex1aro_sample_level () const =0
 
virtual ExtraRotSample ex2aro_sample_level () const =0
 
virtual ExtraRotSample ex1aro_exposed_sample_level () const =0
 
virtual ExtraRotSample ex2aro_exposed_sample_level () const =0
 
virtual ExtraRotSample exdna_sample_level () const =0
 
virtual bool operate_on_ex1 () const =0
 
virtual bool operate_on_ex2 () const =0
 
virtual bool operate_on_ex3 () const =0
 
virtual bool operate_on_ex4 () const =0
 
virtual void sample_proton_chi (bool setting)=0
 
virtual bool sample_proton_chi () const =0
 
virtual void or_optimize_h (bool setting)=0
 
virtual bool optimize_h () const =0
 
virtual void or_preserve_c_beta (bool setting)=0
 
virtual bool preserve_c_beta () const =0
 
virtual void or_flip_HNQ (bool setting)=0
 
virtual bool flip_HNQ () const =0
 
virtual void or_fix_his_tautomer (bool setting)=0
 
virtual bool fix_his_tautomer () const =0
 
virtual void or_include_virtual_side_chain (bool include_virtual_side_chain)=0
 
virtual bool include_virtual_side_chain () const =0
 
virtual void and_extrachi_cutoff (Size num_neighbors_to_be_called_buried)=0
 
virtual Size extrachi_cutoff () const =0
 
virtual void prevent_repacking ()=0
 
virtual void restrict_restypes (utility::vector1< std::string > const &basenames_to_keep)=0
 Restrict residue types. More...
 
virtual void disable_restypes (utility::vector1< std::string > const &basenames_to_disable)=0
 Disable residue types. More...
 
virtual void restrict_to_restypes_with_at_least_one_property (utility::vector1< core::chemical::ResidueProperty > const &properties)=0
 Given a list of residue properties, eliminate any residue type that does not have at least one of the properties in the list. More...
 
virtual void restrict_to_restypes_with_all_properties (utility::vector1< core::chemical::ResidueProperty > const &properties)=0
 Given a list of residue properties, eliminate any residue type that does not have ALL of the properties in the list. More...
 
virtual void disable_restypes_with_at_least_one_property (utility::vector1< core::chemical::ResidueProperty > const &properties)=0
 Given a list of residue properties, eliminate any residue type that has any of the properties in the list. More...
 
virtual void restrict_absent_canonical_aas (utility::vector1< bool > const &)=0
 
virtual void restrict_absent_canonical_aas (utility::vector1< bool > const &allowed_aas, std::string const &mode)=0
 
virtual void restrict_nonnative_canonical_aas (utility::vector1< bool > const &allowed_aas)=0
 
virtual void restrict_absent_nas (utility::vector1< chemical::AA > const &keep_nas)=0
 disables designing to nucleic acid residues not in the passed list More...
 
virtual void restrict_to_repacking ()=0
 
virtual bool is_original_type (chemical::ResidueTypeCOP type) const =0
 
virtual chemical::ResidueTypeSetCOP get_original_residue_set () const =0
 
virtual chemical::AA const & get_original_residue () const =0
 
virtual ResidueTypeCOPList const & allowed_residue_types () const =0
 
virtual ResidueTypeCOPListConstIter allowed_residue_types_begin () const =0
 
virtual ResidueTypeCOPListConstIter allowed_residue_types_end () const =0
 
virtual chemical::ResidueTypeCOP target_type () const =0
 
virtual void print_allowed_types (std::ostream &os) const =0
 
virtual bool being_designed () const =0
 
virtual bool being_packed () const =0
 
virtual
rotamer_set::RotamerOperations
const & 
rotamer_operations () const =0
 
virtual void append_rotamer_operation (rotamer_set::RotamerOperationOP rotop)=0
 
virtual
rotamer_set::RotSetOperationListIterator 
rotamer_set_operation_begin () const =0
 
virtual
rotamer_set::RotSetOperationListIterator 
rotamer_set_operation_end () const =0
 
virtual void append_rotamerset_operation (rotamer_set::RotamerSetOperationOP rotsetop)=0
 
virtual std::string command_string () const =0
 
virtual
rna::RNA_ResidueLevelTask
const & 
rna_task () const =0
 
virtual rna::RNA_ResidueLevelTasknonconst_rna_task ()=0
 

Static Public Member Functions

static void list_options_read (utility::options::OptionKeyList &read_options)
 

Member Typedef Documentation

Constructor & Destructor Documentation

core::pack::task::ResidueLevelTask::~ResidueLevelTask ( )
virtualdefault

Member Function Documentation

virtual void core::pack::task::ResidueLevelTask::add_behavior ( std::string const &  behavior)
pure virtual
virtual bool core::pack::task::ResidueLevelTask::adducts ( ) const
pure virtual
virtual ResidueTypeCOPList const& core::pack::task::ResidueLevelTask::allowed_residue_types ( ) const
pure virtual
virtual ResidueTypeCOPListConstIter core::pack::task::ResidueLevelTask::allowed_residue_types_begin ( ) const
pure virtual
virtual ResidueTypeCOPListConstIter core::pack::task::ResidueLevelTask::allowed_residue_types_end ( ) const
pure virtual
virtual void core::pack::task::ResidueLevelTask::and_extrachi_cutoff ( Size  num_neighbors_to_be_called_buried)
pure virtual
virtual void core::pack::task::ResidueLevelTask::append_rotamer_operation ( rotamer_set::RotamerOperationOP  rotop)
pure virtual
virtual void core::pack::task::ResidueLevelTask::append_rotamerset_operation ( rotamer_set::RotamerSetOperationOP  rotsetop)
pure virtual
virtual bool core::pack::task::ResidueLevelTask::being_designed ( ) const
pure virtual
virtual bool core::pack::task::ResidueLevelTask::being_packed ( ) const
pure virtual
virtual std::string core::pack::task::ResidueLevelTask::command_string ( ) const
pure virtual
virtual void core::pack::task::ResidueLevelTask::disable_restypes ( utility::vector1< std::string > const &  basenames_to_disable)
pure virtual

Disable residue types.

This function takes a vector of base names to prohibit. Anything in this list is turned off.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by core::pack::task::operation::ProhibitSpecifiedBaseResidueTypes::apply(), and core::pack::task::NOTAA::residue_action().

virtual void core::pack::task::ResidueLevelTask::disable_restypes_with_at_least_one_property ( utility::vector1< core::chemical::ResidueProperty > const &  properties)
pure virtual

Given a list of residue properties, eliminate any residue type that has any of the properties in the list.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by core::pack::task::operation::ProhibitResidueProperties::apply().

virtual bool core::pack::task::ResidueLevelTask::ex1 ( ) const
pure virtual
virtual ExtraRotSample core::pack::task::ResidueLevelTask::ex1_sample_level ( ) const
pure virtual
virtual bool core::pack::task::ResidueLevelTask::ex1aro ( ) const
pure virtual
virtual bool core::pack::task::ResidueLevelTask::ex1aro_exposed ( ) const
pure virtual
virtual ExtraRotSample core::pack::task::ResidueLevelTask::ex1aro_exposed_sample_level ( ) const
pure virtual
virtual ExtraRotSample core::pack::task::ResidueLevelTask::ex1aro_sample_level ( ) const
pure virtual
virtual bool core::pack::task::ResidueLevelTask::ex2 ( ) const
pure virtual
virtual ExtraRotSample core::pack::task::ResidueLevelTask::ex2_sample_level ( ) const
pure virtual
virtual bool core::pack::task::ResidueLevelTask::ex2aro ( ) const
pure virtual
virtual bool core::pack::task::ResidueLevelTask::ex2aro_exposed ( ) const
pure virtual
virtual ExtraRotSample core::pack::task::ResidueLevelTask::ex2aro_exposed_sample_level ( ) const
pure virtual
virtual ExtraRotSample core::pack::task::ResidueLevelTask::ex2aro_sample_level ( ) const
pure virtual
virtual bool core::pack::task::ResidueLevelTask::ex3 ( ) const
pure virtual
virtual ExtraRotSample core::pack::task::ResidueLevelTask::ex3_sample_level ( ) const
pure virtual
virtual bool core::pack::task::ResidueLevelTask::ex4 ( ) const
pure virtual
virtual ExtraRotSample core::pack::task::ResidueLevelTask::ex4_sample_level ( ) const
pure virtual
virtual ExtraRotSample core::pack::task::ResidueLevelTask::exdna_sample_level ( ) const
pure virtual
virtual Size core::pack::task::ResidueLevelTask::extrachi_cutoff ( ) const
pure virtual
virtual ExtraRotSample core::pack::task::ResidueLevelTask::extrachi_sample_level ( bool  buried,
int  chi,
chemical::ResidueType const &  concrete_residue 
) const
pure virtual
virtual bool core::pack::task::ResidueLevelTask::fix_his_tautomer ( ) const
pure virtual
virtual bool core::pack::task::ResidueLevelTask::flip_HNQ ( ) const
pure virtual
virtual chemical::AA const& core::pack::task::ResidueLevelTask::get_original_residue ( ) const
pure virtual
virtual chemical::ResidueTypeSetCOP core::pack::task::ResidueLevelTask::get_original_residue_set ( ) const
pure virtual
virtual bool core::pack::task::ResidueLevelTask::has_behavior ( std::string const &  behavior) const
pure virtual
virtual bool core::pack::task::ResidueLevelTask::has_behavior ( ) const
pure virtual
virtual bool core::pack::task::ResidueLevelTask::include_current ( ) const
pure virtual
virtual bool core::pack::task::ResidueLevelTask::include_virtual_side_chain ( ) const
pure virtual
virtual void core::pack::task::ResidueLevelTask::initialize_extra_rotamer_flags_from_command_line ( )
pure virtual
virtual void core::pack::task::ResidueLevelTask::initialize_extra_rotamer_flags_from_options ( utility::options::OptionCollection const &  options)
pure virtual
virtual void core::pack::task::ResidueLevelTask::initialize_from_command_line ( )
pure virtual
virtual void core::pack::task::ResidueLevelTask::initialize_from_options ( utility::options::OptionCollection const &  options)
pure virtual
virtual bool core::pack::task::ResidueLevelTask::is_original_type ( chemical::ResidueTypeCOP  type) const
pure virtual
void core::pack::task::ResidueLevelTask::list_options_read ( utility::options::OptionKeyList &  read_options)
static
virtual rna::RNA_ResidueLevelTask& core::pack::task::ResidueLevelTask::nonconst_rna_task ( )
pure virtual
virtual bool core::pack::task::ResidueLevelTask::operate_on_ex1 ( ) const
pure virtual
virtual bool core::pack::task::ResidueLevelTask::operate_on_ex2 ( ) const
pure virtual
virtual bool core::pack::task::ResidueLevelTask::operate_on_ex3 ( ) const
pure virtual
virtual bool core::pack::task::ResidueLevelTask::operate_on_ex4 ( ) const
pure virtual
virtual bool core::pack::task::ResidueLevelTask::optimize_h ( ) const
pure virtual
virtual void core::pack::task::ResidueLevelTask::or_adducts ( bool  setting)
pure virtual
virtual void core::pack::task::ResidueLevelTask::or_ex1 ( bool  ex1)
pure virtual
virtual void core::pack::task::ResidueLevelTask::or_ex1_sample_level ( ExtraRotSample  ex1_sample_level)
pure virtual
virtual void core::pack::task::ResidueLevelTask::or_ex1aro ( bool  ex1aro)
pure virtual
virtual void core::pack::task::ResidueLevelTask::or_ex1aro_exposed ( bool  ex1aro_exposed)
pure virtual
virtual void core::pack::task::ResidueLevelTask::or_ex1aro_exposed_sample_level ( ExtraRotSample  ex1aro_exposed_sample_level)
pure virtual
virtual void core::pack::task::ResidueLevelTask::or_ex1aro_sample_level ( ExtraRotSample  ex1aro_sample_level)
pure virtual
virtual void core::pack::task::ResidueLevelTask::or_ex2 ( bool  ex2)
pure virtual
virtual void core::pack::task::ResidueLevelTask::or_ex2_sample_level ( ExtraRotSample  ex2_sample_level)
pure virtual
virtual void core::pack::task::ResidueLevelTask::or_ex2aro ( bool  ex2aro)
pure virtual
virtual void core::pack::task::ResidueLevelTask::or_ex2aro_exposed ( bool  ex2aro_exposed)
pure virtual
virtual void core::pack::task::ResidueLevelTask::or_ex2aro_exposed_sample_level ( ExtraRotSample  ex2aro_exposed_sample_level)
pure virtual
virtual void core::pack::task::ResidueLevelTask::or_ex2aro_sample_level ( ExtraRotSample  ex2aro_only_sample_level)
pure virtual
virtual void core::pack::task::ResidueLevelTask::or_ex3 ( bool  ex3)
pure virtual
virtual void core::pack::task::ResidueLevelTask::or_ex3_sample_level ( ExtraRotSample  ex3_sample_level)
pure virtual
virtual void core::pack::task::ResidueLevelTask::or_ex4 ( bool  ex4)
pure virtual
virtual void core::pack::task::ResidueLevelTask::or_ex4_sample_level ( ExtraRotSample  ex4_sample_level)
pure virtual
virtual void core::pack::task::ResidueLevelTask::or_exdna_sample_level ( ExtraRotSample  exdna_sample_level)
pure virtual
virtual void core::pack::task::ResidueLevelTask::or_fix_his_tautomer ( bool  setting)
pure virtual
virtual void core::pack::task::ResidueLevelTask::or_flip_HNQ ( bool  setting)
pure virtual
virtual void core::pack::task::ResidueLevelTask::or_include_current ( bool  include_current)
pure virtual
virtual void core::pack::task::ResidueLevelTask::or_include_virtual_side_chain ( bool  include_virtual_side_chain)
pure virtual
virtual void core::pack::task::ResidueLevelTask::or_operate_on_ex1 ( bool  operate)
pure virtual
virtual void core::pack::task::ResidueLevelTask::or_operate_on_ex2 ( bool  operate)
pure virtual
virtual void core::pack::task::ResidueLevelTask::or_operate_on_ex3 ( bool  operate)
pure virtual
virtual void core::pack::task::ResidueLevelTask::or_operate_on_ex4 ( bool  operate)
pure virtual
virtual void core::pack::task::ResidueLevelTask::or_optimize_h ( bool  setting)
pure virtual
virtual void core::pack::task::ResidueLevelTask::or_preserve_c_beta ( bool  setting)
pure virtual
virtual bool core::pack::task::ResidueLevelTask::preserve_c_beta ( ) const
pure virtual
virtual void core::pack::task::ResidueLevelTask::prevent_repacking ( )
pure virtual

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by protocols::task_operations::SelectByDensityFitOperation::apply(), protocols::task_operations::SelectBySASAOperation::apply(), protocols::task_operations::SelectByDeltaScoreOperation::apply(), protocols::dna::RestrictDesignToProteinDNAInterface::apply(), protocols::hbnet::ConstrainHBondNetwork::apply(), protocols::task_operations::CrystalContactsOperation::apply(), protocols::enzdes::SetCatalyticResPackBehavior::apply(), protocols::matdes::BuildingBlockInterfaceOperation::apply(), protocols::task_operations::RestrictIdentitiesOperation::apply(), core::pack::task::operation::ReplicateTask::apply(), protocols::task_operations::RestrictToTerminiOperation::apply(), protocols::task_operations::RestrictNativeResiduesOperation::apply(), core::pack::task::operation::NoRepackDisulfides::apply(), core::pack::task::operation::ClashBasedRepackShell::apply(), core::pack::task::operation::OptH::apply(), protocols::simple_task_operations::DockingNoRepack1::apply(), protocols::enzdes::DetectProteinLigandInterface::apply(), protocols::simple_task_operations::DockingNoRepack2::apply(), core::pack::task::operation::PreventRepackingRLT::apply(), protocols::simple_task_operations::RestrictToInterface::apply(), protocols::flxbb::LayerDesignOperation::apply(), core::pack::task::operation::PreventRepacking::apply(), protocols::loop_grower::LoopGrower::refine_cycle(), core::pack::task::NATRO::residue_action(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::restrict_sequence_profile(), protocols::minimization_packing::EnergyCutRotamerTrialsMover::setup_energycut_task(), protocols::minimization_packing::EnergyCutRotamerTrialsMinMover::setup_energycut_task(), and protocols::simple_task_operations::RestrictToInterface::symmetric_task().

virtual void core::pack::task::ResidueLevelTask::print_allowed_types ( std::ostream &  os) const
pure virtual
virtual void core::pack::task::ResidueLevelTask::restrict_absent_canonical_aas ( utility::vector1< bool > const &  )
pure virtual
virtual void core::pack::task::ResidueLevelTask::restrict_absent_canonical_aas ( utility::vector1< bool > const &  allowed_aas,
std::string const &  mode 
)
pure virtual
virtual void core::pack::task::ResidueLevelTask::restrict_absent_nas ( utility::vector1< chemical::AA > const &  keep_nas)
pure virtual

disables designing to nucleic acid residues not in the passed list

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by core::pack::task::PIKNA::residue_action().

virtual void core::pack::task::ResidueLevelTask::restrict_nonnative_canonical_aas ( utility::vector1< bool > const &  allowed_aas)
pure virtual
virtual void core::pack::task::ResidueLevelTask::restrict_restypes ( utility::vector1< std::string > const &  basenames_to_keep)
pure virtual
virtual void core::pack::task::ResidueLevelTask::restrict_to_repacking ( )
pure virtual
virtual void core::pack::task::ResidueLevelTask::restrict_to_restypes_with_all_properties ( utility::vector1< core::chemical::ResidueProperty > const &  properties)
pure virtual

Given a list of residue properties, eliminate any residue type that does not have ALL of the properties in the list.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

Implemented in core::pack::task::ResidueLevelTask_.

Referenced by core::pack::task::operation::RestrictToResidueProperties::apply(), and core::pack::task::PROPERTY::residue_action().

virtual void core::pack::task::ResidueLevelTask::restrict_to_restypes_with_at_least_one_property ( utility::vector1< core::chemical::ResidueProperty > const &  properties)
pure virtual

Given a list of residue properties, eliminate any residue type that does not have at least one of the properties in the list.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

Implemented in core::pack::task::ResidueLevelTask_.

virtual rna::RNA_ResidueLevelTask const& core::pack::task::ResidueLevelTask::rna_task ( ) const
pure virtual
virtual rotamer_set::RotamerOperations const& core::pack::task::ResidueLevelTask::rotamer_operations ( ) const
pure virtual
virtual rotamer_set::RotSetOperationListIterator core::pack::task::ResidueLevelTask::rotamer_set_operation_begin ( ) const
pure virtual
virtual rotamer_set::RotSetOperationListIterator core::pack::task::ResidueLevelTask::rotamer_set_operation_end ( ) const
pure virtual
virtual void core::pack::task::ResidueLevelTask::sample_proton_chi ( bool  setting)
pure virtual
virtual bool core::pack::task::ResidueLevelTask::sample_proton_chi ( ) const
pure virtual
virtual void core::pack::task::ResidueLevelTask::target_type ( chemical::ResidueTypeCOP  type)
pure virtual
virtual void core::pack::task::ResidueLevelTask::target_type ( chemical::AA  aa)
pure virtual
virtual void core::pack::task::ResidueLevelTask::target_type ( std::string  name)
pure virtual
virtual chemical::ResidueTypeCOP core::pack::task::ResidueLevelTask::target_type ( ) const
pure virtual

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