Rosetta 3.4
Public Types | Public Member Functions
core::pack::task::ResidueLevelTask Class Reference

#include <PackerTask.hh>

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

List of all members.

Public Types

typedef std::list
< chemical::ResidueTypeCAP
ResidueTypeCAPList
typedef std::list
< chemical::ResidueTypeCAP >
::iterator 
ResidueTypeCAPListIter
typedef std::list
< chemical::ResidueTypeCAP >
::const_iterator 
ResidueTypeCAPListConstIter

Public Member Functions

virtual ~ResidueLevelTask ()
virtual ExtraRotSample extrachi_sample_level (bool buried, int chi, chemical::ResidueTypeCAP concrete_residue) const =0
virtual void initialize_from_command_line ()=0
virtual void initialize_extra_rotamer_flags_from_command_line ()=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::ResidueTypeCAP 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_only)=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 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 sample_rna_chi (bool setting)=0
virtual bool sample_rna_chi () const =0
virtual bool ex1 () 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 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_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
virtual void restrict_to_repacking ()=0
virtual bool is_original_type (chemical::ResidueTypeCAP type) const =0
virtual
chemical::ResidueTypeSet const & 
get_original_residue_set () const =0
virtual void allow_noncanonical_aa (std::string const &aaname, chemical::ResidueTypeSet const &residue_set)=0
virtual void allow_noncanonical_aa (std::string const &aaname)=0
virtual void allow_noncanonical_aa (chemical::AA aa)=0
 explicitly allow a NCAA; assumes same ResidueTypeSet as original_residue_type_
virtual void allow_aa (chemical::AA const &aa)=0
virtual ResidueTypeCAPList const & allowed_residue_types () const =0
virtual ResidueTypeCAPListConstIter allowed_residue_types_begin () const =0
virtual ResidueTypeCAPListConstIter allowed_residue_types_end () const =0
virtual chemical::ResidueTypeCAP 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

Member Typedef Documentation


Constructor & Destructor Documentation

core::pack::task::ResidueLevelTask::~ResidueLevelTask ( ) [virtual]

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 void core::pack::task::ResidueLevelTask::allow_aa ( chemical::AA const &  aa) [pure virtual]
virtual void core::pack::task::ResidueLevelTask::allow_noncanonical_aa ( chemical::AA  aa) [pure virtual]

explicitly allow a NCAA; assumes same ResidueTypeSet as original_residue_type_

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

virtual void core::pack::task::ResidueLevelTask::allow_noncanonical_aa ( std::string const &  aaname,
chemical::ResidueTypeSet const &  residue_set 
) [pure virtual]
virtual void core::pack::task::ResidueLevelTask::allow_noncanonical_aa ( std::string const &  aaname) [pure virtual]
virtual ResidueTypeCAPList const& core::pack::task::ResidueLevelTask::allowed_residue_types ( ) const [pure virtual]
virtual ResidueTypeCAPListConstIter core::pack::task::ResidueLevelTask::allowed_residue_types_begin ( ) const [pure virtual]
virtual ResidueTypeCAPListConstIter 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 bool core::pack::task::ResidueLevelTask::ex1 ( ) 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::ResidueTypeCAP  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::ResidueTypeSet const& core::pack::task::ResidueLevelTask::get_original_residue_set ( ) const [pure virtual]
virtual bool core::pack::task::ResidueLevelTask::has_behavior ( ) const [pure virtual]
virtual bool core::pack::task::ResidueLevelTask::has_behavior ( std::string const &  behavior) const [pure virtual]
virtual bool core::pack::task::ResidueLevelTask::include_current ( ) 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_from_command_line ( ) [pure virtual]
virtual bool core::pack::task::ResidueLevelTask::is_original_type ( chemical::ResidueTypeCAP  type) const [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_only) [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_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]
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 &  allowed_aas,
std::string const &  mode 
) [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_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_to_repacking ( ) [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::sample_rna_chi ( bool  setting) [pure virtual]
virtual bool core::pack::task::ResidueLevelTask::sample_rna_chi ( ) const [pure virtual]
virtual chemical::ResidueTypeCAP core::pack::task::ResidueLevelTask::target_type ( ) const [pure virtual]
virtual void core::pack::task::ResidueLevelTask::target_type ( std::string  name) [pure virtual]
virtual void core::pack::task::ResidueLevelTask::target_type ( chemical::ResidueTypeCAP  type) [pure virtual]
virtual void core::pack::task::ResidueLevelTask::target_type ( chemical::AA  aa) [pure virtual]

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