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Rosetta 3.5
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All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
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Rosetta 3.5
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Residue-level task class; contained within PackerTask. More...
#include <PackerTask_.hh>
Public Member Functions | |
| ResidueLevelTask_ (conformation::Residue const &original_residue) | |
| constructor; requires a Residue object More... | |
| ResidueLevelTask_ () | |
| virtual | ~ResidueLevelTask_ () |
| dtor More... | |
| virtual ExtraRotSample | extrachi_sample_level (bool buried, int chi, chemical::ResidueTypeCOP concrete_residue) const |
| returns the extra chi sampling level More... | |
| virtual void | initialize_from_command_line () |
| initialize options from command line flags More... | |
| virtual void | initialize_extra_rotamer_flags_from_command_line () |
| Initialize only the extra rotamer building flags from the command line; invoked by intialize_from_command_line();. More... | |
| virtual void | or_include_current (bool include_current) |
| include the pre-existing rotamer while packing More... | |
| virtual bool | include_current () const |
| is the pre-existing rotamer specifically allowed while packing? More... | |
| virtual void | add_behavior (std::string const &behavior) |
| virtual bool | has_behavior (std::string const &behavior) const |
| virtual bool | has_behavior () const |
| virtual void | target_type (chemical::ResidueTypeCOP type) |
| virtual void | target_type (chemical::AA aa) |
| virtual void | target_type (std::string name) |
| virtual void | or_adducts (bool setting) |
| include adducts at this residue More... | |
| virtual bool | adducts () const |
| virtual void | or_ex1 (bool ex1) |
| activate ex1 when passed true; do nothing otherwise More... | |
| virtual void | or_ex2 (bool ex2) |
| activate ex2 when passed true; do nothing otherwise More... | |
| virtual void | or_ex3 (bool ex3) |
| activate ex3 when passed true; do nothing otherwise More... | |
| virtual void | or_ex4 (bool ex4) |
| activate ex4 when passed true; do nothing otherwise More... | |
| virtual void | or_ex1_sample_level (ExtraRotSample ex1_sample_level) |
| increase ex1 sample level; do nothing if not an increase More... | |
| virtual void | or_ex2_sample_level (ExtraRotSample ex2_sample_level) |
| increase ex2 sample level; do nothing if not an increase More... | |
| virtual void | or_ex3_sample_level (ExtraRotSample ex3_sample_level) |
| increase ex3 sample level; do nothing if not an increase More... | |
| virtual void | or_ex4_sample_level (ExtraRotSample ex4_sample_level) |
| increase ex4 sample level; do nothing if not an increase More... | |
| virtual void | or_ex1aro (bool ex1aro) |
| activate ex1 for aromatics when passed true; do nothing otherwise More... | |
| virtual void | or_ex2aro (bool ex2aro_only) |
| activate ex2 for aromatics when passed true; do nothing otherwise More... | |
| virtual void | or_ex1aro_exposed (bool ex1aro_exposed) |
| activate ex1 for exposed aromatics when passed true; do nothing otherwise More... | |
| virtual void | or_ex2aro_exposed (bool ex2aro_exposed) |
| activate ex2 for exposed aromatics when passed true; do nothing otherwise More... | |
| virtual void | or_ex1aro_sample_level (ExtraRotSample ex1aro_sample_level) |
| increase ex1aro sample level; do nothing if not an increase More... | |
| virtual void | or_ex2aro_sample_level (ExtraRotSample ex2aro_only_sample_level) |
| increase ex2aro sample level; do nothing if not an increase More... | |
| virtual void | or_ex1aro_exposed_sample_level (ExtraRotSample ex1aro_exposed_sample_level) |
| increase ex1aro_exposed sample level; do nothing if not an increase More... | |
| virtual void | or_ex2aro_exposed_sample_level (ExtraRotSample ex2aro_exposed_sample_level) |
| increase ex2aro_exposed sample level; do nothing if not an increase More... | |
| virtual void | or_operate_on_ex1 (bool operate) |
| virtual void | or_operate_on_ex2 (bool operate) |
| virtual void | or_operate_on_ex3 (bool operate) |
| virtual void | or_operate_on_ex4 (bool operate) |
| virtual void | or_exdna_sample_level (ExtraRotSample exdna_sample_level) |
| virtual void | or_optimize_h (bool setting) |
| virtual bool | optimize_h () const |
| virtual void | or_preserve_c_beta (bool setting) |
| virtual bool | preserve_c_beta () const |
| virtual void | or_flip_HNQ (bool setting) |
| virtual bool | flip_HNQ () const |
| virtual void | or_fix_his_tautomer (bool setting) |
| virtual bool | fix_his_tautomer () const |
| virtual void | sample_proton_chi (bool setting) |
| sample proton chi. More... | |
| virtual bool | sample_proton_chi () const |
| sample proton chi. More... | |
| virtual void | sample_rna_chi (bool setting) |
| sample proton chi. More... | |
| virtual bool | sample_rna_chi () const |
| sample proton chi. More... | |
| virtual bool | ex1 () const |
| virtual bool | ex2 () const |
| virtual bool | ex3 () const |
| virtual bool | ex4 () const |
| virtual ExtraRotSample | ex1_sample_level () const |
| virtual ExtraRotSample | ex2_sample_level () const |
| virtual ExtraRotSample | ex3_sample_level () const |
| virtual ExtraRotSample | ex4_sample_level () const |
| virtual bool | ex1aro () const |
| virtual bool | ex2aro () const |
| virtual bool | ex1aro_exposed () const |
| virtual bool | ex2aro_exposed () const |
| virtual ExtraRotSample | ex1aro_sample_level () const |
| virtual ExtraRotSample | ex2aro_sample_level () const |
| virtual ExtraRotSample | ex1aro_exposed_sample_level () const |
| virtual ExtraRotSample | ex2aro_exposed_sample_level () const |
| virtual ExtraRotSample | exdna_sample_level () const |
| virtual bool | operate_on_ex1 () const |
| virtual bool | operate_on_ex2 () const |
| virtual bool | operate_on_ex3 () const |
| virtual bool | operate_on_ex4 () const |
| virtual void | and_extrachi_cutoff (Size num_neighbors_to_be_called_buried) |
| lower extrachi_cutoff to given value; do nothing if not a decrease More... | |
| virtual Size | extrachi_cutoff () const |
| get function for extrachi_cutoff More... | |
| virtual void | prevent_repacking () |
| remove all ResidueTypes from the list of allowed residue types, preventing repacking More... | |
| virtual void | restrict_absent_canonical_aas (utility::vector1< bool > const &) |
| disables designing to residues not in the passed list More... | |
| virtual void | restrict_absent_canonical_aas (utility::vector1< bool > const &allowed_aas, std::string const &mode) |
| disables designing to residues not in the passed list–and specifies the resfile command that made this list More... | |
| virtual void | restrict_nonnative_canonical_aas (utility::vector1< bool > const &allowed_aas) |
| virtual void | restrict_absent_nas (utility::vector1< chemical::AA > const &keep_nas) |
| disables designing to nucleic acid residues not in the passed list More... | |
| virtual void | restrict_to_repacking () |
| only let this residue repack – prevent redesign More... | |
| virtual bool | is_original_type (chemical::ResidueTypeCOP type) const |
| virtual chemical::ResidueTypeSet const & | get_original_residue_set () const |
| virtual chemical::AA const & | get_original_residue () const |
| virtual void | allow_noncanonical_aa (std::string const &aaname, chemical::ResidueTypeSet const &residue_set) |
| explicitly allow a NCAA More... | |
| virtual void | allow_noncanonical_aa (std::string const &aaname) |
| explicitly allow a NCAA; assumes same ResidueTypeSet as original_residue_type_ More... | |
| virtual void | allow_noncanonical_aa (chemical::AA aa) |
| explicitly allow a NCAA; assumes same ResidueTypeSet as original_residue_type_ More... | |
| virtual void | allow_aa (chemical::AA const &aa) |
| explicitly allow a canonical AA More... | |
| virtual ResidueTypeCOPList const & | allowed_residue_types () const |
| virtual ResidueTypeCOPListConstIter | allowed_residue_types_begin () const |
| returns iterator to beginning of allowed residue types list (traversal only) More... | |
| virtual ResidueTypeCOPListConstIter | allowed_residue_types_end () const |
| returns iterator to end of allowed residue types list (traversal only) More... | |
| virtual chemical::ResidueTypeCOP | target_type () const |
| virtual void | print_allowed_types (std::ostream &os) const |
| virtual bool | being_designed () const |
| is this residue up for design (variable sequence)? More... | |
| virtual bool | being_packed () const |
| is this residue modififable at all by the packer? More... | |
| virtual rotamer_set::RotamerOperations const & | rotamer_operations () const |
| virtual void | append_rotamer_operation (rotamer_set::RotamerOperationOP rotop) |
| virtual rotamer_set::RotSetOperationListIterator | rotamer_set_operation_begin () const |
| virtual rotamer_set::RotSetOperationListIterator | rotamer_set_operation_end () const |
| virtual void | append_rotamerset_operation (rotamer_set::RotamerSetOperationOP rotsetop) |
| virtual std::string | command_string () const |
| create a string the resfile format of all the commands applied to this residue level task More... | |
| virtual void | update_union (ResidueLevelTask const &res_task_in) |
| virtual void | update_intersection (ResidueLevelTask const &res_task_in) |
| virtual void | update_commutative (ResidueLevelTask const &res_task_in) |
 Public Member Functions inherited from core::pack::task::ResidueLevelTask | |
| virtual | ~ResidueLevelTask () |
Private Member Functions | |
| void | refresh_ex1_sample_levels () |
| private: bookkeeping for ex1 More... | |
| void | refresh_ex2_sample_levels () |
| private: bookkeeping for ex2 More... | |
| void | refresh_ex3_sample_levels () |
| private: bookkeeping for ex3 More... | |
| void | refresh_ex4_sample_levels () |
| private: bookkeeping for ex4 More... | |
| void | determine_if_designing () |
| private: bookkeeping for whether sequence can change More... | |
| void | determine_if_repacking () |
| private: bookkeeping for whether rotamer can change More... | |
| std::string | get_ex_flags (Size chiid, Size const exaro_sample_level, Size const ex_sample_level) const |
| private: return the EX command for the packer task More... | |
| std::string | task_mode () const |
| private: return the task mode that can be used to recreate the task. If the residue level task was made with POLAR it should return the string "POLAR". More... | |
| void | do_restrict_absent_canonical_aas (utility::vector1< bool > const &allowed_aas) |
Additional Inherited Members | |
| Public Types inherited from core::pack::task::ResidueLevelTask | |
| typedef std::list < chemical::ResidueTypeCOP > | ResidueTypeCOPList |
| typedef std::list < chemical::ResidueTypeCOP > ::iterator | ResidueTypeCOPListIter |
| typedef std::list < chemical::ResidueTypeCOP > ::const_iterator | ResidueTypeCOPListConstIter |
Residue-level task class; contained within PackerTask.
Definition at line 55 of file PackerTask_.hh.
| core::pack::task::ResidueLevelTask_::ResidueLevelTask_ | ( | conformation::Residue const & | original_residue) |
constructor; requires a Residue object
ResidueLevelTask constructor has following defaults: all ex set to false with zero sample level position is packable and designable to any of the canonical aa's, with variant matching (for termini, etc) current rotamer is not included for packer. bump check is deactivated by default.
Definition at line 71 of file PackerTask_.cc.
References core::conformation::Residue::aa(), core::chemical::aa_unk, allowed_residue_types_, being_packed(), determine_if_designing(), determine_if_repacking(), core::sequence::end, core::conformation::Residue::is_DNA(), core::conformation::Residue::is_protein(), core::chemical::ResidueType::nonadduct_variants_match(), core::chemical::num_canonical_aas, core::conformation::Residue::residue_type_set(), core::conformation::Residue::type(), and core::chemical::ResidueType::variants_match().
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Definition at line 63 of file PackerTask_.hh.
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dtor
Definition at line 155 of file PackerTask_.cc.
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Implements core::pack::task::ResidueLevelTask.
Definition at line 299 of file PackerTask_.cc.
References behaviors_.
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Implements core::pack::task::ResidueLevelTask.
Definition at line 346 of file PackerTask_.cc.
References adducts_.
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explicitly allow a canonical AA
Implements core::pack::task::ResidueLevelTask.
Definition at line 901 of file PackerTask_.cc.
References allowed_residue_types_, design_disabled_, determine_if_designing(), determine_if_repacking(), disabled_, and original_residue_type_.
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explicitly allow a NCAA
Implements core::pack::task::ResidueLevelTask.
Definition at line 862 of file PackerTask_.cc.
References allowed_residue_types_, design_disabled_, determine_if_designing(), determine_if_repacking(), disabled_, mode_tokens_, original_residue_type_, and core::chemical::ResidueTypeSet::residue_types().
Referenced by allow_noncanonical_aa().
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explicitly allow a NCAA; assumes same ResidueTypeSet as original_residue_type_
assumes same ResidueTypeSet as original_residue_type_ and calls other overloaded allow_noncanonical_aas
Implements core::pack::task::ResidueLevelTask.
Definition at line 889 of file PackerTask_.cc.
References allow_noncanonical_aa(), and original_residue_type_.
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explicitly allow a NCAA; assumes same ResidueTypeSet as original_residue_type_
assumes same ResidueTypeSet as original_residue_type_ and calls overloaded allow_noncanonical_aas
Implements core::pack::task::ResidueLevelTask.
Definition at line 895 of file PackerTask_.cc.
References allow_noncanonical_aa(), and core::chemical::name_from_aa().
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Implements core::pack::task::ResidueLevelTask.
Definition at line 926 of file PackerTask_.cc.
References allowed_residue_types_.
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returns iterator to beginning of allowed residue types list (traversal only)
Implements core::pack::task::ResidueLevelTask.
Definition at line 932 of file PackerTask_.cc.
References allowed_residue_types_.
Referenced by print_allowed_types().
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returns iterator to end of allowed residue types list (traversal only)
Implements core::pack::task::ResidueLevelTask.
Definition at line 938 of file PackerTask_.cc.
References allowed_residue_types_.
Referenced by print_allowed_types().
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lower extrachi_cutoff to given value; do nothing if not a decrease
and operation – min – move only toward a lower cutoff for #neighbors w/i 10A that qualify a residue to be considered buried.
Implements core::pack::task::ResidueLevelTask.
Definition at line 669 of file PackerTask_.cc.
References extrachi_cutoff_.
Referenced by initialize_extra_rotamer_flags_from_command_line().
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Implements core::pack::task::ResidueLevelTask.
Definition at line 1054 of file PackerTask_.cc.
References rotamer_operations_.
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Implements core::pack::task::ResidueLevelTask.
Definition at line 1074 of file PackerTask_.cc.
References rotsetops_.
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is this residue up for design (variable sequence)?
Implements core::pack::task::ResidueLevelTask.
Definition at line 961 of file PackerTask_.cc.
References designing_.
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is this residue modififable at all by the packer?
Implements core::pack::task::ResidueLevelTask.
Definition at line 962 of file PackerTask_.cc.
References repacking_.
Referenced by ResidueLevelTask_().
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create a string the resfile format of all the commands applied to this residue level task
Implements core::pack::task::ResidueLevelTask.
Definition at line 2135 of file PackerTask_.cc.
References core::pack::task::PackerTask_::include_current(), and core::pack::task::PackerTask_::target_type().
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private: bookkeeping for whether sequence can change
Definition at line 1018 of file PackerTask_.cc.
References allowed_residue_types_, design_disabled_, designing_, disabled_, and original_residue_type_.
Referenced by allow_aa(), allow_noncanonical_aa(), do_restrict_absent_canonical_aas(), or_adducts(), prevent_repacking(), ResidueLevelTask_(), restrict_absent_nas(), restrict_nonnative_canonical_aas(), restrict_to_repacking(), update_commutative(), update_intersection(), and update_union().
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private: bookkeeping for whether rotamer can change
Definition at line 1038 of file PackerTask_.cc.
References allowed_residue_types_, and repacking_.
Referenced by allow_aa(), allow_noncanonical_aa(), do_restrict_absent_canonical_aas(), or_adducts(), prevent_repacking(), ResidueLevelTask_(), restrict_absent_nas(), restrict_nonnative_canonical_aas(), restrict_to_repacking(), update_commutative(), update_intersection(), and update_union().
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Definition at line 734 of file PackerTask_.cc.
References allowed_residue_types_, determine_if_designing(), determine_if_repacking(), and core::chemical::num_canonical_aas.
Referenced by restrict_absent_canonical_aas().
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Implements core::pack::task::ResidueLevelTask.
Definition at line 501 of file PackerTask_.cc.
References ex1_.
Referenced by or_ex1().
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Implements core::pack::task::ResidueLevelTask.
Definition at line 518 of file PackerTask_.cc.
References ex1_sample_level_.
Referenced by or_ex1_sample_level().
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Implements core::pack::task::ResidueLevelTask.
Definition at line 535 of file PackerTask_.cc.
References ex1aro_.
Referenced by or_ex1aro().
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Implements core::pack::task::ResidueLevelTask.
Definition at line 543 of file PackerTask_.cc.
References ex1aro_exposed_.
Referenced by or_ex1aro_exposed().
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Implements core::pack::task::ResidueLevelTask.
Definition at line 560 of file PackerTask_.cc.
References ex1aro_exposed_sample_level_.
Referenced by or_ex1aro_exposed_sample_level().
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Implements core::pack::task::ResidueLevelTask.
Definition at line 552 of file PackerTask_.cc.
References ex1aro_sample_level_.
Referenced by or_ex1aro_sample_level().
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Implements core::pack::task::ResidueLevelTask.
Definition at line 505 of file PackerTask_.cc.
References ex2_.
Referenced by or_ex2().
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Implements core::pack::task::ResidueLevelTask.
Definition at line 522 of file PackerTask_.cc.
References ex2_sample_level_.
Referenced by or_ex2_sample_level().
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Implements core::pack::task::ResidueLevelTask.
Definition at line 539 of file PackerTask_.cc.
References ex2aro_.
Referenced by or_ex2aro().
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Implements core::pack::task::ResidueLevelTask.
Definition at line 547 of file PackerTask_.cc.
References ex2aro_exposed_.
Referenced by or_ex2aro_exposed().
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Implements core::pack::task::ResidueLevelTask.
Definition at line 564 of file PackerTask_.cc.
References ex2aro_exposed_sample_level_.
Referenced by or_ex2aro_exposed_sample_level().
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Implements core::pack::task::ResidueLevelTask.
Definition at line 556 of file PackerTask_.cc.
References ex2aro_sample_level_.
Referenced by or_ex2aro_sample_level().
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Implements core::pack::task::ResidueLevelTask.
Definition at line 509 of file PackerTask_.cc.
References ex3_.
Referenced by or_ex3().
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Implements core::pack::task::ResidueLevelTask.
Definition at line 526 of file PackerTask_.cc.
References ex3_sample_level_.
Referenced by or_ex3_sample_level().
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Implements core::pack::task::ResidueLevelTask.
Definition at line 513 of file PackerTask_.cc.
References ex4_.
Referenced by or_ex4().
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Implements core::pack::task::ResidueLevelTask.
Definition at line 530 of file PackerTask_.cc.
References ex4_sample_level_.
Referenced by or_ex4_sample_level().
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Implements core::pack::task::ResidueLevelTask.
Definition at line 569 of file PackerTask_.cc.
References exdna_sample_level_.
Referenced by or_exdna_sample_level().
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get function for extrachi_cutoff
Implements core::pack::task::ResidueLevelTask.
Definition at line 676 of file PackerTask_.cc.
References extrachi_cutoff_.
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returns the extra chi sampling level
Implements core::pack::task::ResidueLevelTask.
Definition at line 159 of file PackerTask_.cc.
References ex1_sample_level_, ex1aro_exposed_sample_level_, ex1aro_sample_level_, ex2_sample_level_, ex2aro_exposed_sample_level_, ex2aro_sample_level_, ex3_sample_level_, ex4_sample_level_, exdna_sample_level_, and core::pack::task::NO_EXTRA_CHI_SAMPLES.
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Implements core::pack::task::ResidueLevelTask.
Definition at line 662 of file PackerTask_.cc.
References fix_his_tautomer_.
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Implements core::pack::task::ResidueLevelTask.
Definition at line 622 of file PackerTask_.cc.
References flip_HNQ_.
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private: return the EX command for the packer task
Definition at line 2114 of file PackerTask_.cc.
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Implements core::pack::task::ResidueLevelTask.
Definition at line 857 of file PackerTask_.cc.
References original_residue_type_.
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Implements core::pack::task::ResidueLevelTask.
Definition at line 853 of file PackerTask_.cc.
References original_residue_type_.
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Implements core::pack::task::ResidueLevelTask.
Definition at line 304 of file PackerTask_.cc.
References behaviors_.
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Implements core::pack::task::ResidueLevelTask.
Definition at line 308 of file PackerTask_.cc.
References behaviors_.
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is the pre-existing rotamer specifically allowed while packing?
Implements core::pack::task::ResidueLevelTask.
Definition at line 294 of file PackerTask_.cc.
References include_current_.
Referenced by or_include_current().
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Initialize only the extra rotamer building flags from the command line; invoked by intialize_from_command_line();.
Implements core::pack::task::ResidueLevelTask.
Definition at line 215 of file PackerTask_.cc.
References and_extrachi_cutoff(), core::pack::task::EX_ONE_STDDEV, or_ex1(), or_ex1_sample_level(), or_ex1aro(), or_ex1aro_exposed(), or_ex1aro_exposed_sample_level(), or_ex1aro_sample_level(), or_ex2(), or_ex2_sample_level(), or_ex2aro(), or_ex2aro_exposed(), or_ex2aro_exposed_sample_level(), or_ex2aro_sample_level(), or_ex3(), or_ex3_sample_level(), or_ex4(), or_ex4_sample_level(), or_exdna_sample_level(), or_operate_on_ex1(), or_operate_on_ex2(), or_operate_on_ex3(), and or_operate_on_ex4().
Referenced by initialize_from_command_line().
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initialize options from command line flags
Implements core::pack::task::ResidueLevelTask.
Definition at line 201 of file PackerTask_.cc.
References initialize_extra_rotamer_flags_from_command_line(), or_include_current(), or_preserve_c_beta(), and prevent_repacking().
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Implements core::pack::task::ResidueLevelTask.
Definition at line 839 of file PackerTask_.cc.
References core::chemical::aa_his, core::chemical::aa_unk, fix_his_tautomer_, and original_residue_type_.
Referenced by restrict_nonnative_canonical_aas(), and restrict_to_repacking().
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Implements core::pack::task::ResidueLevelTask.
Definition at line 574 of file PackerTask_.cc.
References operate_on_ex1_.
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Implements core::pack::task::ResidueLevelTask.
Definition at line 578 of file PackerTask_.cc.
References operate_on_ex2_.
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Implements core::pack::task::ResidueLevelTask.
Definition at line 582 of file PackerTask_.cc.
References operate_on_ex3_.
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Implements core::pack::task::ResidueLevelTask.
Definition at line 586 of file PackerTask_.cc.
References operate_on_ex4_.
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Implements core::pack::task::ResidueLevelTask.
Definition at line 601 of file PackerTask_.cc.
References optimize_H_mode_.
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include adducts at this residue
Implements core::pack::task::ResidueLevelTask.
Definition at line 330 of file PackerTask_.cc.
References core::chemical::ADDUCT, adducts_, allowed_residue_types_, determine_if_designing(), and determine_if_repacking().
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activate ex1 when passed true; do nothing otherwise
Implements core::pack::task::ResidueLevelTask.
Definition at line 348 of file PackerTask_.cc.
References ex1(), ex1_, and refresh_ex1_sample_levels().
Referenced by initialize_extra_rotamer_flags_from_command_line().
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increase ex1 sample level; do nothing if not an increase
Implements core::pack::task::ResidueLevelTask.
Definition at line 372 of file PackerTask_.cc.
References ex1_sample_level(), ex1_sample_level_, and refresh_ex1_sample_levels().
Referenced by initialize_extra_rotamer_flags_from_command_line().
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activate ex1 for aromatics when passed true; do nothing otherwise
Implements core::pack::task::ResidueLevelTask.
Definition at line 410 of file PackerTask_.cc.
References ex1aro(), ex1aro_, and refresh_ex1_sample_levels().
Referenced by initialize_extra_rotamer_flags_from_command_line().
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activate ex1 for exposed aromatics when passed true; do nothing otherwise
Implements core::pack::task::ResidueLevelTask.
Definition at line 422 of file PackerTask_.cc.
References ex1aro_exposed(), ex1aro_exposed_, and refresh_ex1_sample_levels().
Referenced by initialize_extra_rotamer_flags_from_command_line().
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increase ex1aro_exposed sample level; do nothing if not an increase
Implements core::pack::task::ResidueLevelTask.
Definition at line 450 of file PackerTask_.cc.
References ex1aro_exposed_sample_level(), ex1aro_exposed_sample_level_, and refresh_ex1_sample_levels().
Referenced by initialize_extra_rotamer_flags_from_command_line().
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increase ex1aro sample level; do nothing if not an increase
Implements core::pack::task::ResidueLevelTask.
Definition at line 434 of file PackerTask_.cc.
References ex1aro_sample_level(), ex1aro_sample_level_, and refresh_ex1_sample_levels().
Referenced by initialize_extra_rotamer_flags_from_command_line().
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activate ex2 when passed true; do nothing otherwise
Implements core::pack::task::ResidueLevelTask.
Definition at line 354 of file PackerTask_.cc.
References ex2(), ex2_, and refresh_ex2_sample_levels().
Referenced by initialize_extra_rotamer_flags_from_command_line().
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increase ex2 sample level; do nothing if not an increase
Implements core::pack::task::ResidueLevelTask.
Definition at line 388 of file PackerTask_.cc.
References ex2_sample_level(), ex2_sample_level_, and refresh_ex2_sample_levels().
Referenced by initialize_extra_rotamer_flags_from_command_line().
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activate ex2 for aromatics when passed true; do nothing otherwise
Implements core::pack::task::ResidueLevelTask.
Definition at line 416 of file PackerTask_.cc.
References ex2aro(), ex2aro_, and refresh_ex2_sample_levels().
Referenced by initialize_extra_rotamer_flags_from_command_line().
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activate ex2 for exposed aromatics when passed true; do nothing otherwise
Implements core::pack::task::ResidueLevelTask.
Definition at line 428 of file PackerTask_.cc.
References ex2aro_exposed(), ex2aro_exposed_, and refresh_ex2_sample_levels().
Referenced by initialize_extra_rotamer_flags_from_command_line().
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increase ex2aro_exposed sample level; do nothing if not an increase
Implements core::pack::task::ResidueLevelTask.
Definition at line 460 of file PackerTask_.cc.
References ex2aro_exposed_sample_level(), ex2aro_exposed_sample_level_, and refresh_ex2_sample_levels().
Referenced by initialize_extra_rotamer_flags_from_command_line().
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increase ex2aro sample level; do nothing if not an increase
Implements core::pack::task::ResidueLevelTask.
Definition at line 442 of file PackerTask_.cc.
References ex2aro_sample_level(), ex2aro_sample_level_, and refresh_ex2_sample_levels().
Referenced by initialize_extra_rotamer_flags_from_command_line().
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activate ex3 when passed true; do nothing otherwise
Implements core::pack::task::ResidueLevelTask.
Definition at line 360 of file PackerTask_.cc.
References ex3(), ex3_, and refresh_ex3_sample_levels().
Referenced by initialize_extra_rotamer_flags_from_command_line().
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increase ex3 sample level; do nothing if not an increase
Implements core::pack::task::ResidueLevelTask.
Definition at line 395 of file PackerTask_.cc.
References ex3_sample_level(), ex3_sample_level_, and refresh_ex3_sample_levels().
Referenced by initialize_extra_rotamer_flags_from_command_line().
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activate ex4 when passed true; do nothing otherwise
Implements core::pack::task::ResidueLevelTask.
Definition at line 366 of file PackerTask_.cc.
References ex4(), ex4_, and refresh_ex4_sample_levels().
Referenced by initialize_extra_rotamer_flags_from_command_line().
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increase ex4 sample level; do nothing if not an increase
Implements core::pack::task::ResidueLevelTask.
Definition at line 402 of file PackerTask_.cc.
References ex4_sample_level(), ex4_sample_level_, and refresh_ex4_sample_levels().
Referenced by initialize_extra_rotamer_flags_from_command_line().
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Implements core::pack::task::ResidueLevelTask.
Definition at line 380 of file PackerTask_.cc.
References exdna_sample_level(), exdna_sample_level_, and refresh_ex1_sample_levels().
Referenced by initialize_extra_rotamer_flags_from_command_line().
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this function forces a fixed histidine tautomer by removing the alternate tautomer from the ResidueTypesCAPList. The fix_his_tautomer_ boolean is maintained for reference that this has been done, but the boolean is not the source of the effect.
Implements core::pack::task::ResidueLevelTask.
Definition at line 628 of file PackerTask_.cc.
References core::chemical::aa_his, allowed_residue_types_, fix_his_tautomer_, and original_residue_type_.
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Implements core::pack::task::ResidueLevelTask.
Definition at line 616 of file PackerTask_.cc.
References flip_HNQ_, and or_optimize_h().
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include the pre-existing rotamer while packing
Implements core::pack::task::ResidueLevelTask.
Definition at line 289 of file PackerTask_.cc.
References include_current(), and include_current_.
Referenced by initialize_from_command_line().
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Implements core::pack::task::ResidueLevelTask.
Definition at line 470 of file PackerTask_.cc.
References operate_on_ex1_.
Referenced by initialize_extra_rotamer_flags_from_command_line().
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Implements core::pack::task::ResidueLevelTask.
Definition at line 472 of file PackerTask_.cc.
References operate_on_ex2_.
Referenced by initialize_extra_rotamer_flags_from_command_line().
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Implements core::pack::task::ResidueLevelTask.
Definition at line 474 of file PackerTask_.cc.
References operate_on_ex3_.
Referenced by initialize_extra_rotamer_flags_from_command_line().
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Implements core::pack::task::ResidueLevelTask.
Definition at line 476 of file PackerTask_.cc.
References operate_on_ex4_.
Referenced by initialize_extra_rotamer_flags_from_command_line().
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Implements core::pack::task::ResidueLevelTask.
Definition at line 591 of file PackerTask_.cc.
References optimize_H_mode_, and restrict_to_repacking().
Referenced by or_flip_HNQ().
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Implements core::pack::task::ResidueLevelTask.
Definition at line 606 of file PackerTask_.cc.
References preserve_c_beta_.
Referenced by initialize_from_command_line().
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Implements core::pack::task::ResidueLevelTask.
Definition at line 611 of file PackerTask_.cc.
References preserve_c_beta_.
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remove all ResidueTypes from the list of allowed residue types, preventing repacking
Implements core::pack::task::ResidueLevelTask.
Definition at line 682 of file PackerTask_.cc.
References allowed_residue_types_, design_disabled_, determine_if_designing(), determine_if_repacking(), disabled_, and mode_tokens_.
Referenced by initialize_from_command_line().
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Implements core::pack::task::ResidueLevelTask.
Definition at line 953 of file PackerTask_.cc.
References allowed_residue_types_begin(), and allowed_residue_types_end().
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private: bookkeeping for ex1
bookkeeping - increases to EX_ONE_STDDEV if boolean is on, but sample level is zero (AS IT SHOULD!)
Definition at line 965 of file PackerTask_.cc.
References ex1_, ex1_sample_level_, ex1aro_, ex1aro_exposed_, ex1aro_exposed_sample_level_, ex1aro_sample_level_, and core::pack::task::EX_ONE_STDDEV.
Referenced by or_ex1(), or_ex1_sample_level(), or_ex1aro(), or_ex1aro_exposed(), or_ex1aro_exposed_sample_level(), or_ex1aro_sample_level(), and or_exdna_sample_level().
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private: bookkeeping for ex2
bookkeeping - increases to EX_ONE_STDDEV if boolean is on, but sample level is zero
Definition at line 984 of file PackerTask_.cc.
References ex2_, ex2_sample_level_, ex2aro_, ex2aro_exposed_, ex2aro_exposed_sample_level_, ex2aro_sample_level_, and core::pack::task::EX_ONE_STDDEV.
Referenced by or_ex2(), or_ex2_sample_level(), or_ex2aro(), or_ex2aro_exposed(), or_ex2aro_exposed_sample_level(), and or_ex2aro_sample_level().
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private: bookkeeping for ex3
bookkeeping - increases to EX_ONE_STDDEV if boolean is on, but sample level is zero
Definition at line 1001 of file PackerTask_.cc.
References ex3_, ex3_sample_level_, and core::pack::task::EX_ONE_STDDEV.
Referenced by or_ex3(), and or_ex3_sample_level().
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private: bookkeeping for ex4
bookkeeping - increases to EX_ONE_STDDEV if boolean is on, but sample level is zero
Definition at line 1009 of file PackerTask_.cc.
References ex4_, ex4_sample_level_, and core::pack::task::EX_ONE_STDDEV.
Referenced by or_ex4(), and or_ex4_sample_level().
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disables designing to residues not in the passed list
contract (and) the list of available aas for canonical aa's if an amino acid is not present (false) in the boolean vector, then do not allow it at this position boolean vector is based on the aa enum; see another example with PIKAA. The boolean vector is a 20-length vector in alphabetical order by one-letter code.
Implements core::pack::task::ResidueLevelTask.
Definition at line 698 of file PackerTask_.cc.
References do_restrict_absent_canonical_aas(), mode_tokens_, and core::chemical::num_canonical_aas.
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disables designing to residues not in the passed list–and specifies the resfile command that made this list
Implements core::pack::task::ResidueLevelTask.
Definition at line 726 of file PackerTask_.cc.
References do_restrict_absent_canonical_aas(), and mode_tokens_.
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disables designing to nucleic acid residues not in the passed list
contract (and) the list of available nas for canonical na's if a nucleic acid is not present in the vector, then do not allow it at this position
Implements core::pack::task::ResidueLevelTask.
Definition at line 783 of file PackerTask_.cc.
References allowed_residue_types_, determine_if_designing(), determine_if_repacking(), mode_tokens_, and core::chemical::name_from_aa().
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Implements core::pack::task::ResidueLevelTask.
Definition at line 757 of file PackerTask_.cc.
References allowed_residue_types_, determine_if_designing(), determine_if_repacking(), is_original_type(), and core::chemical::num_canonical_aas.
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only let this residue repack – prevent redesign
removes all residues from the allowed residue types list, except the one that matches the original residue; this means only rotameric and not sequence changes are allowed if the original residue type has been disabled elsewhere, this function will prevent repacking at that residue.
Implements core::pack::task::ResidueLevelTask.
Definition at line 821 of file PackerTask_.cc.
References allowed_residue_types_, design_disabled_, determine_if_designing(), determine_if_repacking(), is_original_type(), and mode_tokens_.
Referenced by or_optimize_h().
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Implements core::pack::task::ResidueLevelTask.
Definition at line 1048 of file PackerTask_.cc.
References rotamer_operations_.
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Implements core::pack::task::ResidueLevelTask.
Definition at line 1062 of file PackerTask_.cc.
References rotsetops_.
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Implements core::pack::task::ResidueLevelTask.
Definition at line 1068 of file PackerTask_.cc.
References rotsetops_.
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sample proton chi.
Implements core::pack::task::ResidueLevelTask.
Definition at line 480 of file PackerTask_.cc.
References sample_proton_chi_.
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sample proton chi.
Implements core::pack::task::ResidueLevelTask.
Definition at line 485 of file PackerTask_.cc.
References sample_proton_chi_.
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sample proton chi.
Implements core::pack::task::ResidueLevelTask.
Definition at line 490 of file PackerTask_.cc.
References sample_rna_chi_.
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sample proton chi.
Implements core::pack::task::ResidueLevelTask.
Definition at line 495 of file PackerTask_.cc.
References sample_rna_chi_.
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Implements core::pack::task::ResidueLevelTask.
Definition at line 313 of file PackerTask_.cc.
References allowed_residue_types_, core::pack::task::T(), and target_residue_type_.
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Implements core::pack::task::ResidueLevelTask.
Definition at line 323 of file PackerTask_.cc.
References original_residue_type_, and target_type().
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Implements core::pack::task::ResidueLevelTask.
Definition at line 326 of file PackerTask_.cc.
References original_residue_type_, and target_type().
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Implements core::pack::task::ResidueLevelTask.
Definition at line 944 of file PackerTask_.cc.
References allowed_residue_types_, and target_residue_type_.
Referenced by target_type().
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private: return the task mode that can be used to recreate the task. If the residue level task was made with POLAR it should return the string "POLAR".
Definition at line 2106 of file PackerTask_.cc.
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Definition at line 1256 of file PackerTask_.cc.
References adducts_, allowed_residue_types_, behaviors_, design_disabled_, determine_if_designing(), determine_if_repacking(), disabled_, ex1_, ex1_sample_level_, ex1aro_, ex1aro_exposed_, ex1aro_exposed_sample_level_, ex1aro_sample_level_, ex2_, ex2_sample_level_, ex2aro_, ex2aro_exposed_, ex2aro_exposed_sample_level_, ex2aro_sample_level_, ex3_, ex3_sample_level_, ex4_, ex4_sample_level_, exdna_sample_level_, extrachi_cutoff_, fix_his_tautomer_, flip_HNQ_, include_current_, mode_tokens_, operate_on_ex1_, operate_on_ex2_, operate_on_ex3_, operate_on_ex4_, optimize_H_mode_, preserve_c_beta_, rotamer_operations_, rotsetops_, sample_proton_chi_, sample_rna_chi_, and target_residue_type_.
Referenced by core::pack::task::PackerTask_::update_commutative().
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Definition at line 1165 of file PackerTask_.cc.
References adducts_, allowed_residue_types_, behaviors_, design_disabled_, designing_, determine_if_designing(), determine_if_repacking(), disabled_, ex1_, ex1_sample_level_, ex1aro_, ex1aro_exposed_, ex1aro_exposed_sample_level_, ex1aro_sample_level_, ex2_, ex2_sample_level_, ex2aro_, ex2aro_exposed_, ex2aro_exposed_sample_level_, ex2aro_sample_level_, ex3_, ex3_sample_level_, ex4_, ex4_sample_level_, exdna_sample_level_, extrachi_cutoff_, fix_his_tautomer_, flip_HNQ_, include_current_, mode_tokens_, operate_on_ex1_, operate_on_ex2_, operate_on_ex3_, operate_on_ex4_, optimize_H_mode_, preserve_c_beta_, repacking_, rotamer_operations_, rotsetops_, sample_proton_chi_, and sample_rna_chi_.
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Definition at line 1087 of file PackerTask_.cc.
References adducts_, allowed_residue_types_, behaviors_, design_disabled_, designing_, determine_if_designing(), determine_if_repacking(), disabled_, ex1_, ex1_sample_level_, ex1aro_, ex1aro_exposed_, ex1aro_exposed_sample_level_, ex1aro_sample_level_, ex2_, ex2_sample_level_, ex2aro_, ex2aro_exposed_, ex2aro_exposed_sample_level_, ex2aro_sample_level_, ex3_, ex3_sample_level_, ex4_, ex4_sample_level_, exdna_sample_level_, extrachi_cutoff_, fix_his_tautomer_, flip_HNQ_, include_current_, mode_tokens_, operate_on_ex1_, operate_on_ex2_, operate_on_ex3_, operate_on_ex4_, optimize_H_mode_, preserve_c_beta_, repacking_, rotamer_operations_, rotsetops_, sample_proton_chi_, and sample_rna_chi_.
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include adducts at this residue
Definition at line 484 of file PackerTask_.hh.
Referenced by adducts(), or_adducts(), update_commutative(), update_intersection(), and update_union().
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std::list of ResidueTypeCOP objects - these are only residue types allowed at position
Definition at line 486 of file PackerTask_.hh.
Referenced by allow_aa(), allow_noncanonical_aa(), allowed_residue_types(), allowed_residue_types_begin(), allowed_residue_types_end(), determine_if_designing(), determine_if_repacking(), do_restrict_absent_canonical_aas(), or_adducts(), or_fix_his_tautomer(), prevent_repacking(), ResidueLevelTask_(), restrict_absent_nas(), restrict_nonnative_canonical_aas(), restrict_to_repacking(), target_type(), update_commutative(), update_intersection(), and update_union().
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here we store any flagged protocol-level behaviors for this residue
Definition at line 482 of file PackerTask_.hh.
Referenced by add_behavior(), has_behavior(), update_commutative(), update_intersection(), and update_union().
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if this is true, this residue will only be allowed to repack; ResidueTypes that do not match the original_residue_type cannot be added. Design disabling takes precedence over SOMETHING, ANDREW TELL ME WHAT IT IS
Definition at line 516 of file PackerTask_.hh.
Referenced by allow_aa(), allow_noncanonical_aa(), determine_if_designing(), prevent_repacking(), restrict_to_repacking(), update_commutative(), update_intersection(), and update_union().
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can the sequence change? true implies repacking_ is true as well
Definition at line 492 of file PackerTask_.hh.
Referenced by being_designed(), determine_if_designing(), update_intersection(), and update_union().
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if this is true, this residue will be treated as part of the background. a disabling takes precedence over any ResidueType additions.
Definition at line 512 of file PackerTask_.hh.
Referenced by allow_aa(), allow_noncanonical_aa(), determine_if_designing(), prevent_repacking(), update_commutative(), update_intersection(), and update_union().
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Definition at line 522 of file PackerTask_.hh.
Referenced by ex1(), or_ex1(), refresh_ex1_sample_levels(), update_commutative(), update_intersection(), and update_union().
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Definition at line 530 of file PackerTask_.hh.
Referenced by ex1_sample_level(), extrachi_sample_level(), or_ex1_sample_level(), refresh_ex1_sample_levels(), update_commutative(), update_intersection(), and update_union().
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Definition at line 526 of file PackerTask_.hh.
Referenced by ex1aro(), or_ex1aro(), refresh_ex1_sample_levels(), update_commutative(), update_intersection(), and update_union().
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Definition at line 528 of file PackerTask_.hh.
Referenced by ex1aro_exposed(), or_ex1aro_exposed(), refresh_ex1_sample_levels(), update_commutative(), update_intersection(), and update_union().
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Definition at line 536 of file PackerTask_.hh.
Referenced by ex1aro_exposed_sample_level(), extrachi_sample_level(), or_ex1aro_exposed_sample_level(), refresh_ex1_sample_levels(), update_commutative(), update_intersection(), and update_union().
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Definition at line 534 of file PackerTask_.hh.
Referenced by ex1aro_sample_level(), extrachi_sample_level(), or_ex1aro_sample_level(), refresh_ex1_sample_levels(), update_commutative(), update_intersection(), and update_union().
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Definition at line 523 of file PackerTask_.hh.
Referenced by ex2(), or_ex2(), refresh_ex2_sample_levels(), update_commutative(), update_intersection(), and update_union().
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Definition at line 531 of file PackerTask_.hh.
Referenced by ex2_sample_level(), extrachi_sample_level(), or_ex2_sample_level(), refresh_ex2_sample_levels(), update_commutative(), update_intersection(), and update_union().
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Definition at line 527 of file PackerTask_.hh.
Referenced by ex2aro(), or_ex2aro(), refresh_ex2_sample_levels(), update_commutative(), update_intersection(), and update_union().
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Definition at line 529 of file PackerTask_.hh.
Referenced by ex2aro_exposed(), or_ex2aro_exposed(), refresh_ex2_sample_levels(), update_commutative(), update_intersection(), and update_union().
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Definition at line 537 of file PackerTask_.hh.
Referenced by ex2aro_exposed_sample_level(), extrachi_sample_level(), or_ex2aro_exposed_sample_level(), refresh_ex2_sample_levels(), update_commutative(), update_intersection(), and update_union().
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Definition at line 535 of file PackerTask_.hh.
Referenced by ex2aro_sample_level(), extrachi_sample_level(), or_ex2aro_sample_level(), refresh_ex2_sample_levels(), update_commutative(), update_intersection(), and update_union().
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Definition at line 524 of file PackerTask_.hh.
Referenced by ex3(), or_ex3(), refresh_ex3_sample_levels(), update_commutative(), update_intersection(), and update_union().
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Definition at line 532 of file PackerTask_.hh.
Referenced by ex3_sample_level(), extrachi_sample_level(), or_ex3_sample_level(), refresh_ex3_sample_levels(), update_commutative(), update_intersection(), and update_union().
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Definition at line 525 of file PackerTask_.hh.
Referenced by ex4(), or_ex4(), refresh_ex4_sample_levels(), update_commutative(), update_intersection(), and update_union().
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Definition at line 533 of file PackerTask_.hh.
Referenced by ex4_sample_level(), extrachi_sample_level(), or_ex4_sample_level(), refresh_ex4_sample_levels(), update_commutative(), update_intersection(), and update_union().
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Definition at line 538 of file PackerTask_.hh.
Referenced by exdna_sample_level(), extrachi_sample_level(), or_exdna_sample_level(), update_commutative(), update_intersection(), and update_union().
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Definition at line 539 of file PackerTask_.hh.
Referenced by and_extrachi_cutoff(), extrachi_cutoff(), update_commutative(), update_intersection(), and update_union().
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has this histidine tautomer been fixed? This value is kept for bookkeeping; the tautomer's fixation is effected by removing the other tautomer from the ResidueTypeCOPList.
Definition at line 508 of file PackerTask_.hh.
Referenced by fix_his_tautomer(), is_original_type(), or_fix_his_tautomer(), update_commutative(), update_intersection(), and update_union().
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are we also considering heavy atom rearrangement for the crystallographically symmetric seeming residues: histadine, asparagine and glutamine? Implies optimize_H_mode_
Definition at line 505 of file PackerTask_.hh.
Referenced by flip_HNQ(), or_flip_HNQ(), update_commutative(), update_intersection(), and update_union().
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is the pre-existing rotamer included for the packer to choose?
Definition at line 480 of file PackerTask_.hh.
Referenced by include_current(), or_include_current(), update_commutative(), update_intersection(), and update_union().
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Definition at line 550 of file PackerTask_.hh.
Referenced by allow_noncanonical_aa(), prevent_repacking(), restrict_absent_canonical_aas(), restrict_absent_nas(), restrict_to_repacking(), update_commutative(), update_intersection(), and update_union().
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Definition at line 541 of file PackerTask_.hh.
Referenced by operate_on_ex1(), or_operate_on_ex1(), update_commutative(), update_intersection(), and update_union().
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Definition at line 542 of file PackerTask_.hh.
Referenced by operate_on_ex2(), or_operate_on_ex2(), update_commutative(), update_intersection(), and update_union().
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Definition at line 543 of file PackerTask_.hh.
Referenced by operate_on_ex3(), or_operate_on_ex3(), update_commutative(), update_intersection(), and update_union().
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Definition at line 544 of file PackerTask_.hh.
Referenced by operate_on_ex4(), or_operate_on_ex4(), update_commutative(), update_intersection(), and update_union().
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are we keeping the coordinates of the heavy atoms fixed while sampling extra hydrogen placements?
Definition at line 498 of file PackerTask_.hh.
Referenced by optimize_h(), or_optimize_h(), update_commutative(), update_intersection(), and update_union().
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Definition at line 487 of file PackerTask_.hh.
Referenced by allow_aa(), allow_noncanonical_aa(), determine_if_designing(), get_original_residue(), get_original_residue_set(), is_original_type(), or_fix_his_tautomer(), and target_type().
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are c-beta positions preserved during rotamer building
Definition at line 501 of file PackerTask_.hh.
Referenced by or_preserve_c_beta(), preserve_c_beta(), update_commutative(), update_intersection(), and update_union().
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can the residue change its conformation?
Definition at line 494 of file PackerTask_.hh.
Referenced by being_packed(), determine_if_repacking(), update_intersection(), and update_union().
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Definition at line 546 of file PackerTask_.hh.
Referenced by append_rotamer_operation(), rotamer_operations(), update_commutative(), update_intersection(), and update_union().
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Definition at line 547 of file PackerTask_.hh.
Referenced by append_rotamerset_operation(), rotamer_set_operation_begin(), rotamer_set_operation_end(), update_commutative(), update_intersection(), and update_union().
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Definition at line 518 of file PackerTask_.hh.
Referenced by sample_proton_chi(), update_commutative(), update_intersection(), and update_union().
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Definition at line 520 of file PackerTask_.hh.
Referenced by sample_rna_chi(), update_commutative(), update_intersection(), and update_union().
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a member of the allowed types that can optionally respresent a target state
Definition at line 489 of file PackerTask_.hh.
Referenced by target_type(), and update_commutative().
1.8.4