Rosetta Core  2014.35
Public Member Functions | Private Member Functions | Private Attributes | List of all members
core::pack::task::ResidueLevelTask_ Class Reference

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 or_include_virtual_side_chain (bool setting)
 
virtual bool include_virtual_side_chain () const
 
virtual void sample_proton_chi (bool setting)
 sample proton chi. More...
 
virtual bool sample_proton_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 &interchangeability_group, 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 disallow_noncanonical_aas ()
 expliciitly disallow all NCAAs 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...
 
rna::RNA_ResidueLevelTask const & rna_task () const
 
rna::RNA_ResidueLevelTasknonconst_rna_task ()
 
void do_restrict_absent_canonical_aas (utility::vector1< bool > const &allowed_aas)
 

Private Attributes

bool include_current_
 
utility::vector1< std::string > behaviors_
 here we store any flagged protocol-level behaviors for this residue More...
 
bool adducts_
 include adducts at this residue More...
 
ResidueTypeCOPList allowed_residue_types_
 
chemical::ResidueTypeCOP original_residue_type_
 
chemical::ResidueTypeCOP target_residue_type_
 
bool designing_
 
bool repacking_
 
bool optimize_H_mode_
 
bool preserve_c_beta_
 
bool flip_HNQ_
 
bool fix_his_tautomer_
 
bool include_virtual_side_chain_
 
bool disabled_
 
bool design_disabled_
 
bool sample_proton_chi_
 
bool ex1_
 
bool ex2_
 
bool ex3_
 
bool ex4_
 
bool ex1aro_
 
bool ex2aro_
 
bool ex1aro_exposed_
 
bool ex2aro_exposed_
 
ExtraRotSample ex1_sample_level_
 
ExtraRotSample ex2_sample_level_
 
ExtraRotSample ex3_sample_level_
 
ExtraRotSample ex4_sample_level_
 
ExtraRotSample ex1aro_sample_level_
 
ExtraRotSample ex2aro_sample_level_
 
ExtraRotSample ex1aro_exposed_sample_level_
 
ExtraRotSample ex2aro_exposed_sample_level_
 
ExtraRotSample exdna_sample_level_
 
Size extrachi_cutoff_
 
bool operate_on_ex1_
 
bool operate_on_ex2_
 
bool operate_on_ex3_
 
bool operate_on_ex4_
 
rotamer_set::RotamerOperations rotamer_operations_
 
rotamer_set::RotSetOperationList rotsetops_
 
std::vector< std::string > mode_tokens_
 
rna::RNA_ResidueLevelTaskOP rna_task_
 

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
 

Detailed Description

Residue-level task class; contained within PackerTask.

Constructor & Destructor Documentation

core::pack::task::ResidueLevelTask_::ResidueLevelTask_ ( conformation::Residue const &  original_residue)
core::pack::task::ResidueLevelTask_::ResidueLevelTask_ ( )
core::pack::task::ResidueLevelTask_::~ResidueLevelTask_ ( )
virtual

dtor

Member Function Documentation

void core::pack::task::ResidueLevelTask_::add_behavior ( std::string const &  behavior)
virtual
bool core::pack::task::ResidueLevelTask_::adducts ( ) const
virtual
void core::pack::task::ResidueLevelTask_::allow_aa ( chemical::AA const &  aa)
virtual
void core::pack::task::ResidueLevelTask_::allow_noncanonical_aa ( std::string const &  interchangeability_group,
chemical::ResidueTypeSet const &  residue_set 
)
virtual

explicitly allow a NCAA

expand (or) the list of available aa's for non-cannonicals looking for ResidueTypes that share the input "interchangeability_group" id

Implements core::pack::task::ResidueLevelTask.

References allowed_residue_types_, design_disabled_, determine_if_designing(), determine_if_repacking(), disabled_, core::chemical::ResidueTypeSet::interchangeability_group_map(), mode_tokens_, core::chemical::num_canonical_aas, and original_residue_type_.

Referenced by allow_noncanonical_aa().

void core::pack::task::ResidueLevelTask_::allow_noncanonical_aa ( std::string const &  interchangeability_group)
virtual

explicitly allow a NCAA; assumes same ResidueTypeSet as original_residue_type_

Calls the overloaded allow_noncanonical_aas method using the same ResidueTypeSet as original_residue_type_

Implements core::pack::task::ResidueLevelTask.

References allow_noncanonical_aa(), and original_residue_type_.

void core::pack::task::ResidueLevelTask_::allow_noncanonical_aa ( chemical::AA  aa)
virtual

explicitly allow a NCAA; assumes same ResidueTypeSet as original_residue_type_

Calls the overloaded allow_noncanonical_aas method using the same ResidueTypeSet as original_residue_type_ taking as the interchangeability group what is returned by the "name_from_aa" function.

Implements core::pack::task::ResidueLevelTask.

References allow_noncanonical_aa(), core::chemical::name_from_aa(), core::chemical::num_canonical_aas, and core::pack::task::T.

ResidueLevelTask::ResidueTypeCOPList const & core::pack::task::ResidueLevelTask_::allowed_residue_types ( ) const
virtual
ResidueLevelTask::ResidueTypeCOPListConstIter core::pack::task::ResidueLevelTask_::allowed_residue_types_begin ( ) const
virtual

returns iterator to beginning of allowed residue types list (traversal only)

Implements core::pack::task::ResidueLevelTask.

References allowed_residue_types_.

Referenced by print_allowed_types().

ResidueLevelTask::ResidueTypeCOPListConstIter core::pack::task::ResidueLevelTask_::allowed_residue_types_end ( ) const
virtual

returns iterator to end of allowed residue types list (traversal only)

Implements core::pack::task::ResidueLevelTask.

References allowed_residue_types_.

Referenced by print_allowed_types().

void core::pack::task::ResidueLevelTask_::and_extrachi_cutoff ( Size  num_neighbors_to_be_called_buried)
virtual

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.

References extrachi_cutoff_.

Referenced by initialize_extra_rotamer_flags_from_command_line().

void core::pack::task::ResidueLevelTask_::append_rotamer_operation ( rotamer_set::RotamerOperationOP  rotop)
virtual
void core::pack::task::ResidueLevelTask_::append_rotamerset_operation ( rotamer_set::RotamerSetOperationOP  rotsetop)
virtual
bool core::pack::task::ResidueLevelTask_::being_designed ( ) const
virtual

is this residue up for design (variable sequence)?

Implements core::pack::task::ResidueLevelTask.

References designing_.

bool core::pack::task::ResidueLevelTask_::being_packed ( ) const
virtual

is this residue modififable at all by the packer?

Implements core::pack::task::ResidueLevelTask.

References repacking_.

Referenced by ResidueLevelTask_().

std::string core::pack::task::ResidueLevelTask_::command_string ( ) const
virtual

create a string the resfile format of all the commands applied to this residue level task

Implements core::pack::task::ResidueLevelTask.

References ex1, ex2, ex3, ex4, core::pack::task::PackerTask_::include_current(), and core::pack::task::PackerTask_::target_type().

void core::pack::task::ResidueLevelTask_::determine_if_designing ( )
private
void core::pack::task::ResidueLevelTask_::determine_if_repacking ( )
private
void core::pack::task::ResidueLevelTask_::disallow_noncanonical_aas ( )
virtual

expliciitly disallow all NCAAs

expand (or) the list of available aa's for non-cannonicals looking for ResidueTypes that share the input "interchangeability_group" id

Implements core::pack::task::ResidueLevelTask.

References allowed_residue_types_, determine_if_designing(), determine_if_repacking(), mode_tokens_, and core::chemical::num_canonical_aas.

void core::pack::task::ResidueLevelTask_::do_restrict_absent_canonical_aas ( utility::vector1< bool > const &  allowed_aas)
private
bool core::pack::task::ResidueLevelTask_::ex1 ( ) const
virtual

Implements core::pack::task::ResidueLevelTask.

References ex1_.

Referenced by or_ex1().

ExtraRotSample core::pack::task::ResidueLevelTask_::ex1_sample_level ( ) const
virtual
bool core::pack::task::ResidueLevelTask_::ex1aro ( ) const
virtual

Implements core::pack::task::ResidueLevelTask.

References ex1aro_.

Referenced by or_ex1aro().

bool core::pack::task::ResidueLevelTask_::ex1aro_exposed ( ) const
virtual
ExtraRotSample core::pack::task::ResidueLevelTask_::ex1aro_exposed_sample_level ( ) const
virtual
ExtraRotSample core::pack::task::ResidueLevelTask_::ex1aro_sample_level ( ) const
virtual
bool core::pack::task::ResidueLevelTask_::ex2 ( ) const
virtual

Implements core::pack::task::ResidueLevelTask.

References ex2_.

Referenced by or_ex2().

ExtraRotSample core::pack::task::ResidueLevelTask_::ex2_sample_level ( ) const
virtual
bool core::pack::task::ResidueLevelTask_::ex2aro ( ) const
virtual

Implements core::pack::task::ResidueLevelTask.

References ex2aro_.

Referenced by or_ex2aro().

bool core::pack::task::ResidueLevelTask_::ex2aro_exposed ( ) const
virtual
ExtraRotSample core::pack::task::ResidueLevelTask_::ex2aro_exposed_sample_level ( ) const
virtual
ExtraRotSample core::pack::task::ResidueLevelTask_::ex2aro_sample_level ( ) const
virtual
bool core::pack::task::ResidueLevelTask_::ex3 ( ) const
virtual

Implements core::pack::task::ResidueLevelTask.

References ex3_.

Referenced by or_ex3().

ExtraRotSample core::pack::task::ResidueLevelTask_::ex3_sample_level ( ) const
virtual
bool core::pack::task::ResidueLevelTask_::ex4 ( ) const
virtual

Implements core::pack::task::ResidueLevelTask.

References ex4_.

Referenced by or_ex4().

ExtraRotSample core::pack::task::ResidueLevelTask_::ex4_sample_level ( ) const
virtual
ExtraRotSample core::pack::task::ResidueLevelTask_::exdna_sample_level ( ) const
virtual
Size core::pack::task::ResidueLevelTask_::extrachi_cutoff ( ) const
virtual

get function for extrachi_cutoff

Implements core::pack::task::ResidueLevelTask.

References extrachi_cutoff_.

ExtraRotSample core::pack::task::ResidueLevelTask_::extrachi_sample_level ( bool  buried,
int  chi,
chemical::ResidueTypeCOP  concrete_residue 
) const
virtual
bool core::pack::task::ResidueLevelTask_::fix_his_tautomer ( ) const
virtual
bool core::pack::task::ResidueLevelTask_::flip_HNQ ( ) const
virtual
std::string core::pack::task::ResidueLevelTask_::get_ex_flags ( Size  chiid,
Size const  exaro_sample_level,
Size const  ex_sample_level 
) const
private

private: return the EX command for the packer task

chemical::AA const & core::pack::task::ResidueLevelTask_::get_original_residue ( ) const
virtual
chemical::ResidueTypeSet const & core::pack::task::ResidueLevelTask_::get_original_residue_set ( ) const
virtual
bool core::pack::task::ResidueLevelTask_::has_behavior ( std::string const &  behavior) const
virtual
bool core::pack::task::ResidueLevelTask_::has_behavior ( ) const
virtual
bool core::pack::task::ResidueLevelTask_::include_current ( ) const
virtual

is the pre-existing rotamer specifically allowed while packing?

Implements core::pack::task::ResidueLevelTask.

References include_current_.

Referenced by or_include_current().

bool core::pack::task::ResidueLevelTask_::include_virtual_side_chain ( ) const
virtual
void core::pack::task::ResidueLevelTask_::initialize_extra_rotamer_flags_from_command_line ( )
virtual
void core::pack::task::ResidueLevelTask_::initialize_from_command_line ( )
virtual
bool core::pack::task::ResidueLevelTask_::is_original_type ( chemical::ResidueTypeCOP  type) const
virtual
rna::RNA_ResidueLevelTask & core::pack::task::ResidueLevelTask_::nonconst_rna_task ( )
privatevirtual
bool core::pack::task::ResidueLevelTask_::operate_on_ex1 ( ) const
virtual
bool core::pack::task::ResidueLevelTask_::operate_on_ex2 ( ) const
virtual
bool core::pack::task::ResidueLevelTask_::operate_on_ex3 ( ) const
virtual
bool core::pack::task::ResidueLevelTask_::operate_on_ex4 ( ) const
virtual
bool core::pack::task::ResidueLevelTask_::optimize_h ( ) const
virtual
void core::pack::task::ResidueLevelTask_::or_adducts ( bool  setting)
virtual
void core::pack::task::ResidueLevelTask_::or_ex1 ( bool  ex1)
virtual

activate ex1 when passed true; do nothing otherwise

Implements core::pack::task::ResidueLevelTask.

References ex1(), ex1_, and refresh_ex1_sample_levels().

Referenced by initialize_extra_rotamer_flags_from_command_line().

void core::pack::task::ResidueLevelTask_::or_ex1_sample_level ( ExtraRotSample  ex1_sample_level)
virtual

increase ex1 sample level; do nothing if not an increase

Implements core::pack::task::ResidueLevelTask.

References ex1_sample_level(), ex1_sample_level_, and refresh_ex1_sample_levels().

Referenced by initialize_extra_rotamer_flags_from_command_line().

void core::pack::task::ResidueLevelTask_::or_ex1aro ( bool  ex1aro)
virtual

activate ex1 for aromatics when passed true; do nothing otherwise

Implements core::pack::task::ResidueLevelTask.

References ex1aro(), ex1aro_, and refresh_ex1_sample_levels().

Referenced by initialize_extra_rotamer_flags_from_command_line().

void core::pack::task::ResidueLevelTask_::or_ex1aro_exposed ( bool  ex1aro_exposed)
virtual

activate ex1 for exposed aromatics when passed true; do nothing otherwise

Implements core::pack::task::ResidueLevelTask.

References ex1aro_exposed(), ex1aro_exposed_, and refresh_ex1_sample_levels().

Referenced by initialize_extra_rotamer_flags_from_command_line().

void core::pack::task::ResidueLevelTask_::or_ex1aro_exposed_sample_level ( ExtraRotSample  ex1aro_exposed_sample_level)
virtual

increase ex1aro_exposed sample level; do nothing if not an increase

Implements core::pack::task::ResidueLevelTask.

References ex1aro_exposed_sample_level(), ex1aro_exposed_sample_level_, and refresh_ex1_sample_levels().

Referenced by initialize_extra_rotamer_flags_from_command_line().

void core::pack::task::ResidueLevelTask_::or_ex1aro_sample_level ( ExtraRotSample  ex1aro_sample_level)
virtual

increase ex1aro sample level; do nothing if not an increase

Implements core::pack::task::ResidueLevelTask.

References ex1aro_sample_level(), ex1aro_sample_level_, and refresh_ex1_sample_levels().

Referenced by initialize_extra_rotamer_flags_from_command_line().

void core::pack::task::ResidueLevelTask_::or_ex2 ( bool  ex2)
virtual

activate ex2 when passed true; do nothing otherwise

Implements core::pack::task::ResidueLevelTask.

References ex2(), ex2_, and refresh_ex2_sample_levels().

Referenced by initialize_extra_rotamer_flags_from_command_line().

void core::pack::task::ResidueLevelTask_::or_ex2_sample_level ( ExtraRotSample  ex2_sample_level)
virtual

increase ex2 sample level; do nothing if not an increase

Implements core::pack::task::ResidueLevelTask.

References ex2_sample_level(), ex2_sample_level_, and refresh_ex2_sample_levels().

Referenced by initialize_extra_rotamer_flags_from_command_line().

void core::pack::task::ResidueLevelTask_::or_ex2aro ( bool  ex2aro_only)
virtual

activate ex2 for aromatics when passed true; do nothing otherwise

Implements core::pack::task::ResidueLevelTask.

References ex2aro(), ex2aro_, and refresh_ex2_sample_levels().

Referenced by initialize_extra_rotamer_flags_from_command_line().

void core::pack::task::ResidueLevelTask_::or_ex2aro_exposed ( bool  ex2aro_exposed)
virtual

activate ex2 for exposed aromatics when passed true; do nothing otherwise

Implements core::pack::task::ResidueLevelTask.

References ex2aro_exposed(), ex2aro_exposed_, and refresh_ex2_sample_levels().

Referenced by initialize_extra_rotamer_flags_from_command_line().

void core::pack::task::ResidueLevelTask_::or_ex2aro_exposed_sample_level ( ExtraRotSample  ex2aro_exposed_sample_level)
virtual

increase ex2aro_exposed sample level; do nothing if not an increase

Implements core::pack::task::ResidueLevelTask.

References ex2aro_exposed_sample_level(), ex2aro_exposed_sample_level_, and refresh_ex2_sample_levels().

Referenced by initialize_extra_rotamer_flags_from_command_line().

void core::pack::task::ResidueLevelTask_::or_ex2aro_sample_level ( ExtraRotSample  ex2aro_only_sample_level)
virtual

increase ex2aro sample level; do nothing if not an increase

Implements core::pack::task::ResidueLevelTask.

References ex2aro_sample_level(), ex2aro_sample_level_, and refresh_ex2_sample_levels().

Referenced by initialize_extra_rotamer_flags_from_command_line().

void core::pack::task::ResidueLevelTask_::or_ex3 ( bool  ex3)
virtual

activate ex3 when passed true; do nothing otherwise

Implements core::pack::task::ResidueLevelTask.

References ex3(), ex3_, and refresh_ex3_sample_levels().

Referenced by initialize_extra_rotamer_flags_from_command_line().

void core::pack::task::ResidueLevelTask_::or_ex3_sample_level ( ExtraRotSample  ex3_sample_level)
virtual

increase ex3 sample level; do nothing if not an increase

Implements core::pack::task::ResidueLevelTask.

References ex3_sample_level(), ex3_sample_level_, and refresh_ex3_sample_levels().

Referenced by initialize_extra_rotamer_flags_from_command_line().

void core::pack::task::ResidueLevelTask_::or_ex4 ( bool  ex4)
virtual

activate ex4 when passed true; do nothing otherwise

Implements core::pack::task::ResidueLevelTask.

References ex4(), ex4_, and refresh_ex4_sample_levels().

Referenced by initialize_extra_rotamer_flags_from_command_line().

void core::pack::task::ResidueLevelTask_::or_ex4_sample_level ( ExtraRotSample  ex4_sample_level)
virtual

increase ex4 sample level; do nothing if not an increase

Implements core::pack::task::ResidueLevelTask.

References ex4_sample_level(), ex4_sample_level_, and refresh_ex4_sample_levels().

Referenced by initialize_extra_rotamer_flags_from_command_line().

void core::pack::task::ResidueLevelTask_::or_exdna_sample_level ( ExtraRotSample  exdna_sample_level)
virtual
void core::pack::task::ResidueLevelTask_::or_fix_his_tautomer ( bool  setting)
virtual

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.

References core::chemical::aa_his, allowed_residue_types_, fix_his_tautomer_, and original_residue_type_.

void core::pack::task::ResidueLevelTask_::or_flip_HNQ ( bool  setting)
virtual
void core::pack::task::ResidueLevelTask_::or_include_current ( bool  include_current)
virtual

include the pre-existing rotamer while packing

Implements core::pack::task::ResidueLevelTask.

References include_current(), and include_current_.

Referenced by initialize_from_command_line().

void core::pack::task::ResidueLevelTask_::or_include_virtual_side_chain ( bool  setting)
virtual

this function samples a protein conformation with a virtualized side chain.

Implements core::pack::task::ResidueLevelTask.

References include_virtual_side_chain_.

void core::pack::task::ResidueLevelTask_::or_operate_on_ex1 ( bool  operate)
virtual
void core::pack::task::ResidueLevelTask_::or_operate_on_ex2 ( bool  operate)
virtual
void core::pack::task::ResidueLevelTask_::or_operate_on_ex3 ( bool  operate)
virtual
void core::pack::task::ResidueLevelTask_::or_operate_on_ex4 ( bool  operate)
virtual
void core::pack::task::ResidueLevelTask_::or_optimize_h ( bool  setting)
virtual
void core::pack::task::ResidueLevelTask_::or_preserve_c_beta ( bool  setting)
virtual
bool core::pack::task::ResidueLevelTask_::preserve_c_beta ( ) const
virtual
void core::pack::task::ResidueLevelTask_::prevent_repacking ( )
virtual

remove all ResidueTypes from the list of allowed residue types, preventing repacking

Implements core::pack::task::ResidueLevelTask.

References allowed_residue_types_, design_disabled_, determine_if_designing(), determine_if_repacking(), disabled_, and mode_tokens_.

Referenced by initialize_from_command_line().

void core::pack::task::ResidueLevelTask_::print_allowed_types ( std::ostream &  os) const
virtual
void core::pack::task::ResidueLevelTask_::refresh_ex1_sample_levels ( )
private

private: bookkeeping for ex1

bookkeeping - increases to EX_ONE_STDDEV if boolean is on, but sample level is zero (AS IT SHOULD!)

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().

void core::pack::task::ResidueLevelTask_::refresh_ex2_sample_levels ( )
private

private: bookkeeping for ex2

bookkeeping - increases to EX_ONE_STDDEV if boolean is on, but sample level is zero

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().

void core::pack::task::ResidueLevelTask_::refresh_ex3_sample_levels ( )
private

private: bookkeeping for ex3

bookkeeping - increases to EX_ONE_STDDEV if boolean is on, but sample level is zero

References ex3_, ex3_sample_level_, and core::pack::task::EX_ONE_STDDEV.

Referenced by or_ex3(), and or_ex3_sample_level().

void core::pack::task::ResidueLevelTask_::refresh_ex4_sample_levels ( )
private

private: bookkeeping for ex4

bookkeeping - increases to EX_ONE_STDDEV if boolean is on, but sample level is zero

References ex4_, ex4_sample_level_, and core::pack::task::EX_ONE_STDDEV.

Referenced by or_ex4(), and or_ex4_sample_level().

void core::pack::task::ResidueLevelTask_::restrict_absent_canonical_aas ( utility::vector1< bool > const &  allowed_aas)
virtual

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.

References do_restrict_absent_canonical_aas(), mode_tokens_, and core::chemical::num_canonical_aas.

void core::pack::task::ResidueLevelTask_::restrict_absent_canonical_aas ( utility::vector1< bool > const &  allowed_aas,
std::string const &  mode 
)
virtual

disables designing to residues not in the passed list–and specifies the resfile command that made this list

Implements core::pack::task::ResidueLevelTask.

References do_restrict_absent_canonical_aas(), and mode_tokens_.

void core::pack::task::ResidueLevelTask_::restrict_absent_nas ( utility::vector1< chemical::AA > const &  keep_nas)
virtual

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.

References allowed_residue_types_, determine_if_designing(), determine_if_repacking(), mode_tokens_, and core::chemical::name_from_aa().

void core::pack::task::ResidueLevelTask_::restrict_nonnative_canonical_aas ( utility::vector1< bool > const &  allowed_aas)
virtual
void core::pack::task::ResidueLevelTask_::restrict_to_repacking ( )
virtual

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.

References allowed_residue_types_, design_disabled_, determine_if_designing(), determine_if_repacking(), is_original_type(), and mode_tokens_.

Referenced by or_optimize_h().

rna::RNA_ResidueLevelTask const & core::pack::task::ResidueLevelTask_::rna_task ( ) const
privatevirtual
rotamer_set::RotamerOperations const & core::pack::task::ResidueLevelTask_::rotamer_operations ( ) const
virtual
rotamer_set::RotSetOperationListIterator core::pack::task::ResidueLevelTask_::rotamer_set_operation_begin ( ) const
virtual
rotamer_set::RotSetOperationListIterator core::pack::task::ResidueLevelTask_::rotamer_set_operation_end ( ) const
virtual
void core::pack::task::ResidueLevelTask_::sample_proton_chi ( bool  setting)
virtual

sample proton chi.

Implements core::pack::task::ResidueLevelTask.

References sample_proton_chi_.

bool core::pack::task::ResidueLevelTask_::sample_proton_chi ( ) const
virtual

sample proton chi.

Implements core::pack::task::ResidueLevelTask.

References sample_proton_chi_.

void core::pack::task::ResidueLevelTask_::target_type ( chemical::ResidueTypeCOP  type)
virtual
void core::pack::task::ResidueLevelTask_::target_type ( chemical::AA  aa)
virtual
void core::pack::task::ResidueLevelTask_::target_type ( std::string  name)
virtual
chemical::ResidueTypeCOP core::pack::task::ResidueLevelTask_::target_type ( ) const
virtual
std::string core::pack::task::ResidueLevelTask_::task_mode ( ) const
private

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".

void core::pack::task::ResidueLevelTask_::update_commutative ( ResidueLevelTask const &  res_task_in)
virtual
void core::pack::task::ResidueLevelTask_::update_intersection ( ResidueLevelTask const &  res_task_in)
virtual
void core::pack::task::ResidueLevelTask_::update_union ( ResidueLevelTask const &  res_task_in)
virtual

Member Data Documentation

bool core::pack::task::ResidueLevelTask_::adducts_
private

include adducts at this residue

Referenced by adducts(), or_adducts(), update_commutative(), update_intersection(), and update_union().

ResidueTypeCOPList core::pack::task::ResidueLevelTask_::allowed_residue_types_
private
utility::vector1< std::string > core::pack::task::ResidueLevelTask_::behaviors_
private

here we store any flagged protocol-level behaviors for this residue

Referenced by add_behavior(), has_behavior(), update_commutative(), update_intersection(), and update_union().

bool core::pack::task::ResidueLevelTask_::design_disabled_
private

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

Referenced by allow_aa(), allow_noncanonical_aa(), determine_if_designing(), prevent_repacking(), restrict_to_repacking(), update_commutative(), update_intersection(), and update_union().

bool core::pack::task::ResidueLevelTask_::designing_
private

can the sequence change? true implies repacking_ is true as well

Referenced by being_designed(), determine_if_designing(), update_intersection(), and update_union().

bool core::pack::task::ResidueLevelTask_::disabled_
private

if this is true, this residue will be treated as part of the background. a disabling takes precedence over any ResidueType additions.

Referenced by allow_aa(), allow_noncanonical_aa(), determine_if_designing(), prevent_repacking(), update_commutative(), update_intersection(), and update_union().

bool core::pack::task::ResidueLevelTask_::ex1_
private
ExtraRotSample core::pack::task::ResidueLevelTask_::ex1_sample_level_
private
bool core::pack::task::ResidueLevelTask_::ex1aro_
private
bool core::pack::task::ResidueLevelTask_::ex1aro_exposed_
private
ExtraRotSample core::pack::task::ResidueLevelTask_::ex1aro_exposed_sample_level_
private
ExtraRotSample core::pack::task::ResidueLevelTask_::ex1aro_sample_level_
private
bool core::pack::task::ResidueLevelTask_::ex2_
private
ExtraRotSample core::pack::task::ResidueLevelTask_::ex2_sample_level_
private
bool core::pack::task::ResidueLevelTask_::ex2aro_
private
bool core::pack::task::ResidueLevelTask_::ex2aro_exposed_
private
ExtraRotSample core::pack::task::ResidueLevelTask_::ex2aro_exposed_sample_level_
private
ExtraRotSample core::pack::task::ResidueLevelTask_::ex2aro_sample_level_
private
bool core::pack::task::ResidueLevelTask_::ex3_
private
ExtraRotSample core::pack::task::ResidueLevelTask_::ex3_sample_level_
private
bool core::pack::task::ResidueLevelTask_::ex4_
private
ExtraRotSample core::pack::task::ResidueLevelTask_::ex4_sample_level_
private
ExtraRotSample core::pack::task::ResidueLevelTask_::exdna_sample_level_
private
Size core::pack::task::ResidueLevelTask_::extrachi_cutoff_
private
bool core::pack::task::ResidueLevelTask_::fix_his_tautomer_
private

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.

Referenced by fix_his_tautomer(), is_original_type(), or_fix_his_tautomer(), update_commutative(), update_intersection(), and update_union().

bool core::pack::task::ResidueLevelTask_::flip_HNQ_
private

are we also considering heavy atom rearrangement for the crystallographically symmetric seeming residues: histadine, asparagine and glutamine? Implies optimize_H_mode_

Referenced by flip_HNQ(), or_flip_HNQ(), update_commutative(), update_intersection(), and update_union().

bool core::pack::task::ResidueLevelTask_::include_current_
private

is the pre-existing rotamer included for the packer to choose?

Referenced by include_current(), or_include_current(), update_commutative(), update_intersection(), and update_union().

bool core::pack::task::ResidueLevelTask_::include_virtual_side_chain_
private
std::vector<std::string> core::pack::task::ResidueLevelTask_::mode_tokens_
private
bool core::pack::task::ResidueLevelTask_::operate_on_ex1_
private
bool core::pack::task::ResidueLevelTask_::operate_on_ex2_
private
bool core::pack::task::ResidueLevelTask_::operate_on_ex3_
private
bool core::pack::task::ResidueLevelTask_::operate_on_ex4_
private
bool core::pack::task::ResidueLevelTask_::optimize_H_mode_
private

are we keeping the coordinates of the heavy atoms fixed while sampling extra hydrogen placements?

Referenced by optimize_h(), or_optimize_h(), update_commutative(), update_intersection(), and update_union().

chemical::ResidueTypeCOP core::pack::task::ResidueLevelTask_::original_residue_type_
private
bool core::pack::task::ResidueLevelTask_::preserve_c_beta_
private

are c-beta positions preserved during rotamer building

Referenced by or_preserve_c_beta(), preserve_c_beta(), update_commutative(), update_intersection(), and update_union().

bool core::pack::task::ResidueLevelTask_::repacking_
private

can the residue change its conformation?

Referenced by being_packed(), determine_if_repacking(), update_intersection(), and update_union().

rna::RNA_ResidueLevelTaskOP core::pack::task::ResidueLevelTask_::rna_task_
private
rotamer_set::RotamerOperations core::pack::task::ResidueLevelTask_::rotamer_operations_
private
rotamer_set::RotSetOperationList core::pack::task::ResidueLevelTask_::rotsetops_
private
bool core::pack::task::ResidueLevelTask_::sample_proton_chi_
private
chemical::ResidueTypeCOP core::pack::task::ResidueLevelTask_::target_residue_type_
private

a member of the allowed types that can optionally respresent a target state

Referenced by target_type(), and update_commutative().


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