Rosetta  2020.37
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Member Functions | Private Member Functions | Static Private Member Functions | Private Attributes | List of all members
core::pack::task::ResidueLevelTask_ Class Reference

Residue-level task class. More...

#include <ResidueLevelTask_.hh>

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

Public Member Functions

 ResidueLevelTask_ (conformation::Residue const &original_residue, core::pose::Pose const &pose, core::pack::palette::PackerPaletteCOP packer_palette_in=MakeDefaultPackerPaletteCOP())
 constructor; requires a Residue object and a PackerPalette object. More...
 
 ResidueLevelTask_ ()
 
 ~ResidueLevelTask_ () override
 dtor More...
 
ExtraRotSample extrachi_sample_level (bool buried, int chi, chemical::ResidueType const &concrete_residue) const override
 returns the extra chi sampling level More...
 
void initialize_from_command_line () override
 initialize options from command line flags More...
 
void initialize_extra_rotamer_flags_from_command_line () override
 Initialize only the extra rotamer building flags from the command line; invoked by intialize_from_command_line();. More...
 
void initialize_from_options (utility::options::OptionCollection const &options) override
 
void initialize_extra_rotamer_flags_from_options (utility::options::OptionCollection const &options) override
 
void or_include_current (bool include_current) override
 include the pre-existing rotamer while packing More...
 
bool include_current () const override
 is the pre-existing rotamer specifically allowed while packing? More...
 
void add_behavior (std::string const &behavior) override
 
bool has_behavior (std::string const &behavior) const override
 
bool has_behavior () const override
 
void target_type (chemical::ResidueTypeCOP type) override
 
void target_type (chemical::AA aa) override
 
void target_type (std::string name) override
 
void or_adducts (bool setting) override
 include adducts at this residue More...
 
bool adducts () const override
 
void or_ex1 (bool ex1) override
 activate ex1 when passed true; do nothing otherwise More...
 
void or_ex2 (bool ex2) override
 activate ex2 when passed true; do nothing otherwise More...
 
void or_ex3 (bool ex3) override
 activate ex3 when passed true; do nothing otherwise More...
 
void or_ex4 (bool ex4) override
 activate ex4 when passed true; do nothing otherwise More...
 
void or_ex1_sample_level (ExtraRotSample ex1_sample_level) override
 increase ex1 sample level; do nothing if not an increase More...
 
void or_ex2_sample_level (ExtraRotSample ex2_sample_level) override
 increase ex2 sample level; do nothing if not an increase More...
 
void or_ex3_sample_level (ExtraRotSample ex3_sample_level) override
 increase ex3 sample level; do nothing if not an increase More...
 
void or_ex4_sample_level (ExtraRotSample ex4_sample_level) override
 increase ex4 sample level; do nothing if not an increase More...
 
void or_ex1aro (bool ex1aro) override
 activate ex1 for aromatics when passed true; do nothing otherwise More...
 
void or_ex2aro (bool ex2aro_only) override
 activate ex2 for aromatics when passed true; do nothing otherwise More...
 
void or_ex1aro_exposed (bool ex1aro_exposed) override
 activate ex1 for exposed aromatics when passed true; do nothing otherwise More...
 
void or_ex2aro_exposed (bool ex2aro_exposed) override
 activate ex2 for exposed aromatics when passed true; do nothing otherwise More...
 
void or_ex1aro_sample_level (ExtraRotSample ex1aro_sample_level) override
 increase ex1aro sample level; do nothing if not an increase More...
 
void or_ex2aro_sample_level (ExtraRotSample ex2aro_only_sample_level) override
 increase ex2aro sample level; do nothing if not an increase More...
 
void or_ex1aro_exposed_sample_level (ExtraRotSample ex1aro_exposed_sample_level) override
 increase ex1aro_exposed sample level; do nothing if not an increase More...
 
void or_ex2aro_exposed_sample_level (ExtraRotSample ex2aro_exposed_sample_level) override
 increase ex2aro_exposed sample level; do nothing if not an increase More...
 
void or_operate_on_ex1 (bool operate) override
 
void or_operate_on_ex2 (bool operate) override
 
void or_operate_on_ex3 (bool operate) override
 
void or_operate_on_ex4 (bool operate) override
 
void or_exdna_sample_level (ExtraRotSample exdna_sample_level) override
 
void or_optimize_h (bool setting) override
 
bool optimize_h () const override
 
void or_preserve_c_beta (bool setting) override
 
bool preserve_c_beta () const override
 
void or_flip_HNQ (bool setting) override
 
bool flip_HNQ () const override
 
void or_fix_his_tautomer (bool setting) override
 
bool fix_his_tautomer () const override
 
void or_include_virtual_side_chain (bool setting) override
 
bool include_virtual_side_chain () const override
 
void sample_proton_chi (bool setting) override
 sample proton chi. More...
 
bool sample_proton_chi () const override
 sample proton chi. More...
 
bool ex1 () const override
 
bool ex2 () const override
 
bool ex3 () const override
 
bool ex4 () const override
 
ExtraRotSample ex1_sample_level () const override
 
ExtraRotSample ex2_sample_level () const override
 
ExtraRotSample ex3_sample_level () const override
 
ExtraRotSample ex4_sample_level () const override
 
bool ex1aro () const override
 
bool ex2aro () const override
 
bool ex1aro_exposed () const override
 
bool ex2aro_exposed () const override
 
ExtraRotSample ex1aro_sample_level () const override
 
ExtraRotSample ex2aro_sample_level () const override
 
ExtraRotSample ex1aro_exposed_sample_level () const override
 
ExtraRotSample ex2aro_exposed_sample_level () const override
 
ExtraRotSample exdna_sample_level () const override
 
bool operate_on_ex1 () const override
 
bool operate_on_ex2 () const override
 
bool operate_on_ex3 () const override
 
bool operate_on_ex4 () const override
 
void and_extrachi_cutoff (Size num_neighbors_to_be_called_buried) override
 lower extrachi_cutoff to given value; do nothing if not a decrease More...
 
Size extrachi_cutoff () const override
 get function for extrachi_cutoff More...
 
void prevent_repacking () override
 remove all ResidueTypes from the list of allowed residue types, preventing repacking More...
 
void restrict_restypes (utility::vector1< std::string > const &basenames_to_keep) override
 Restrict residue types. More...
 
void disable_restypes (utility::vector1< std::string > const &basenames_to_disable) override
 Disable residue types. More...
 
void restrict_to_restypes_with_at_least_one_property (utility::vector1< core::chemical::ResidueProperty > const &properties) override
 Given a list of residue properties, eliminate any residue type that does not have at least one of the properties in the list. More...
 
void restrict_to_restypes_with_all_properties (utility::vector1< core::chemical::ResidueProperty > const &properties) override
 Given a list of residue properties, eliminate any residue type that does not have ALL of the properties in the list. More...
 
void disable_restypes_with_at_least_one_property (utility::vector1< core::chemical::ResidueProperty > const &properties) override
 Given a list of residue properties, eliminate any residue type that has any of the properties in the list. More...
 
void restrict_absent_canonical_aas (utility::vector1< bool > const &) override
 disables designing to residues not in the passed list More...
 
void restrict_absent_canonical_aas (utility::vector1< bool > const &allowed_aas, std::string const &mode) override
 disables designing to residues not in the passed list–and specifies the resfile command that made this list More...
 
void restrict_nonnative_canonical_aas (utility::vector1< bool > const &allowed_aas) override
 
void restrict_absent_nas (utility::vector1< chemical::AA > const &keep_nas) override
 disables designing to nucleic acid residues not in the passed list More...
 
void restrict_to_repacking () override
 only let this residue repack – prevent redesign More...
 
bool is_original_type (chemical::ResidueTypeCOP type) const override
 
chemical::ResidueTypeSetCOP get_original_residue_set () const override
 
chemical::AA const & get_original_residue () const override
 
ResidueTypeCOPList const & allowed_residue_types () const override
 
ResidueTypeCOPListConstIter allowed_residue_types_begin () const override
 returns iterator to beginning of allowed residue types list (traversal only) More...
 
ResidueTypeCOPListConstIter allowed_residue_types_end () const override
 returns iterator to end of allowed residue types list (traversal only) More...
 
chemical::ResidueTypeCOP target_type () const override
 
void print_allowed_types (std::ostream &os) const override
 
bool being_designed () const override
 is this residue up for design (variable sequence)? More...
 
bool being_packed () const override
 is this residue modififable at all by the packer? More...
 
rotamer_set::RotamerOperations
const & 
rotamer_operations () const override
 
void append_rotamer_operation (rotamer_set::RotamerOperationOP rotop) override
 
rotamer_set::RotSetOperationListIterator rotamer_set_operation_begin () const override
 
rotamer_set::RotSetOperationListIterator rotamer_set_operation_end () const override
 
void append_rotamerset_operation (rotamer_set::RotamerSetOperationOP rotsetop) override
 
std::string command_string () const override
 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 override
 
rna::RNA_ResidueLevelTasknonconst_rna_task () override
 
void do_restrict_absent_canonical_aas (utility::vector1< bool > const &allowed_aas)
 

Static Private Member Functions

static
core::pack::palette::PackerPaletteCOP 
MakeDefaultPackerPaletteCOP ()
 Workaround for https://developercommunity.visualstudio.com/content/problem/1170468/ice-when-using-make-shared-via-a-using-declaration.html. More...
 

Private Attributes

bool include_current_ = false
 
utility::vector1< std::string > behaviors_
 here we store any flagged protocol-level behaviors for this residue More...
 
bool adducts_ = true
 include adducts at this residue More...
 
chemical::ResidueTypeSetCOP original_residue_type_set_
 What ResidueTypeSet does this set of allowed residues come from? More...
 
ResidueTypeCOPList allowed_residue_types_
 
chemical::ResidueTypeCOP original_residue_type_
 
chemical::ResidueTypeCOP target_residue_type_ = nullptr
 
bool designing_
 
bool repacking_ = true
 
bool optimize_H_mode_ = false
 
bool preserve_c_beta_ = false
 
bool flip_HNQ_ = false
 
bool fix_his_tautomer_ = false
 
bool include_virtual_side_chain_ = false
 
bool disabled_ = false
 
bool design_disabled_ = false
 
bool sample_proton_chi_ = true
 
bool ex1_ = false
 
bool ex2_ = false
 
bool ex3_ = false
 
bool ex4_ = false
 
bool ex1aro_ = false
 
bool ex2aro_ = false
 
bool ex1aro_exposed_ = false
 
bool ex2aro_exposed_ = false
 
ExtraRotSample ex1_sample_level_ = NO_EXTRA_CHI_SAMPLES
 
ExtraRotSample ex2_sample_level_ = NO_EXTRA_CHI_SAMPLES
 
ExtraRotSample ex3_sample_level_ = NO_EXTRA_CHI_SAMPLES
 
ExtraRotSample ex4_sample_level_ = NO_EXTRA_CHI_SAMPLES
 
ExtraRotSample ex1aro_sample_level_ = NO_EXTRA_CHI_SAMPLES
 
ExtraRotSample ex2aro_sample_level_ = NO_EXTRA_CHI_SAMPLES
 
ExtraRotSample ex1aro_exposed_sample_level_ = NO_EXTRA_CHI_SAMPLES
 
ExtraRotSample ex2aro_exposed_sample_level_ = NO_EXTRA_CHI_SAMPLES
 
ExtraRotSample exdna_sample_level_ = NO_EXTRA_CHI_SAMPLES
 
Size extrachi_cutoff_ = EXTRACHI_CUTOFF_LIMIT
 
bool operate_on_ex1_ = false
 
bool operate_on_ex2_ = false
 
bool operate_on_ex3_ = false
 
bool operate_on_ex4_ = false
 
rotamer_set::RotamerOperations rotamer_operations_
 
rotamer_set::RotSetOperationList rotsetops_
 
std::vector< std::string > mode_tokens_
 
rna::RNA_ResidueLevelTaskOP rna_task_ = nullptr
 
core::pack::palette::PackerPaletteCOP packer_palette_
 The PackerPalette, which is responsible for initializing the allowed_residue_types_ vector. More...
 

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
 
- Static Public Member Functions inherited from core::pack::task::ResidueLevelTask
static void list_options_read (utility::options::OptionKeyList &read_options)
 

Detailed Description

Residue-level task class.

Constructor & Destructor Documentation

core::pack::task::ResidueLevelTask_::ResidueLevelTask_ ( conformation::Residue const &  original_residue,
core::pose::Pose const &  pose,
core::pack::palette::PackerPaletteCOP  packer_palette_in = MakeDefaultPackerPaletteCOP() 
)

constructor; requires a Residue object and a PackerPalette 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. Constructs a DefaultPackerPalette if not provided with an alternative.

References allowed_residue_types_, being_packed(), determine_if_designing(), determine_if_repacking(), core::conformation::Residue::is_RNA(), original_residue_type_set_, packer_palette_, and rna_task_.

core::pack::task::ResidueLevelTask_::ResidueLevelTask_ ( )
default
core::pack::task::ResidueLevelTask_::~ResidueLevelTask_ ( )
overridedefault

dtor

Member Function Documentation

void core::pack::task::ResidueLevelTask_::add_behavior ( std::string const &  behavior)
overridevirtual
bool core::pack::task::ResidueLevelTask_::adducts ( ) const
overridevirtual
ResidueLevelTask::ResidueTypeCOPList const & core::pack::task::ResidueLevelTask_::allowed_residue_types ( ) const
overridevirtual
ResidueLevelTask::ResidueTypeCOPListConstIter core::pack::task::ResidueLevelTask_::allowed_residue_types_begin ( ) const
overridevirtual

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
overridevirtual

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)
overridevirtual

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_options().

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

is this residue up for design (variable sequence)?

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

References designing_.

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

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
overridevirtual

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

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

References 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_::disable_restypes ( utility::vector1< std::string > const &  basenames_to_disable)
overridevirtual

Disable residue types.

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

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

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

References allowed_residue_types_.

void core::pack::task::ResidueLevelTask_::disable_restypes_with_at_least_one_property ( utility::vector1< core::chemical::ResidueProperty > const &  properties)
overridevirtual

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

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

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

References allowed_residue_types_.

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

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

References ex1_.

Referenced by or_ex1().

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

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

References ex1aro_.

Referenced by or_ex1aro().

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

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

References ex2_.

Referenced by or_ex2().

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

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

References ex2aro_.

Referenced by or_ex2aro().

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

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

References ex3_.

Referenced by or_ex3().

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

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

References ex4_.

Referenced by or_ex4().

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

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::ResidueType const &  concrete_residue 
) const
overridevirtual
bool core::pack::task::ResidueLevelTask_::fix_his_tautomer ( ) const
overridevirtual
bool core::pack::task::ResidueLevelTask_::flip_HNQ ( ) const
overridevirtual
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
overridevirtual
chemical::ResidueTypeSetCOP core::pack::task::ResidueLevelTask_::get_original_residue_set ( ) const
overridevirtual
bool core::pack::task::ResidueLevelTask_::has_behavior ( std::string const &  behavior) const
overridevirtual
bool core::pack::task::ResidueLevelTask_::has_behavior ( ) const
overridevirtual
bool core::pack::task::ResidueLevelTask_::include_current ( ) const
overridevirtual

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
overridevirtual
void core::pack::task::ResidueLevelTask_::initialize_extra_rotamer_flags_from_command_line ( )
overridevirtual

Initialize only the extra rotamer building flags from the command line; invoked by intialize_from_command_line();.

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

References initialize_extra_rotamer_flags_from_options().

void core::pack::task::ResidueLevelTask_::initialize_extra_rotamer_flags_from_options ( utility::options::OptionCollection const &  options)
overridevirtual
void core::pack::task::ResidueLevelTask_::initialize_from_command_line ( )
overridevirtual

initialize options from command line flags

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

References initialize_from_options().

void core::pack::task::ResidueLevelTask_::initialize_from_options ( utility::options::OptionCollection const &  options)
overridevirtual
bool core::pack::task::ResidueLevelTask_::is_original_type ( chemical::ResidueTypeCOP  type) const
overridevirtual
core::pack::palette::PackerPaletteCOP core::pack::task::ResidueLevelTask_::MakeDefaultPackerPaletteCOP ( )
staticprivate
rna::RNA_ResidueLevelTask & core::pack::task::ResidueLevelTask_::nonconst_rna_task ( )
overrideprivatevirtual
bool core::pack::task::ResidueLevelTask_::operate_on_ex1 ( ) const
overridevirtual
bool core::pack::task::ResidueLevelTask_::operate_on_ex2 ( ) const
overridevirtual
bool core::pack::task::ResidueLevelTask_::operate_on_ex3 ( ) const
overridevirtual
bool core::pack::task::ResidueLevelTask_::operate_on_ex4 ( ) const
overridevirtual
bool core::pack::task::ResidueLevelTask_::optimize_h ( ) const
overridevirtual
void core::pack::task::ResidueLevelTask_::or_adducts ( bool  setting)
overridevirtual
void core::pack::task::ResidueLevelTask_::or_ex1 ( bool  ex1)
overridevirtual

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_options().

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

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_options().

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

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_options().

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

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_options().

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

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_options().

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

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_options().

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

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_options().

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

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_options().

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

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_options().

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

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_options().

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

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_options().

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

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_options().

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

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_options().

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

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_options().

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

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_options().

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

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_options().

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

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)
overridevirtual
void core::pack::task::ResidueLevelTask_::or_include_current ( bool  include_current)
overridevirtual

include the pre-existing rotamer while packing

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

References include_current(), and include_current_.

Referenced by initialize_from_options().

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

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

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_options().

void core::pack::task::ResidueLevelTask_::print_allowed_types ( std::ostream &  os) const
overridevirtual
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)
overridevirtual

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 
)
overridevirtual

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)
overridevirtual

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)
overridevirtual
void core::pack::task::ResidueLevelTask_::restrict_restypes ( utility::vector1< std::string > const &  basenames_to_keep)
overridevirtual

Restrict residue types.

This function takes a vector of base names to allow. Anything not in this list is turned off.

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

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

References allowed_residue_types_.

void core::pack::task::ResidueLevelTask_::restrict_to_repacking ( )
overridevirtual

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 protocols::relax::LocalRelax::apply(), and or_optimize_h().

void core::pack::task::ResidueLevelTask_::restrict_to_restypes_with_all_properties ( utility::vector1< core::chemical::ResidueProperty > const &  properties)
overridevirtual

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

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

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

References allowed_residue_types_.

void core::pack::task::ResidueLevelTask_::restrict_to_restypes_with_at_least_one_property ( utility::vector1< core::chemical::ResidueProperty > const &  properties)
overridevirtual

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

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

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

References allowed_residue_types_.

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

sample proton chi.

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

References sample_proton_chi_.

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

sample proton chi.

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

References sample_proton_chi_.

void core::pack::task::ResidueLevelTask_::target_type ( chemical::ResidueTypeCOP  type)
overridevirtual
void core::pack::task::ResidueLevelTask_::target_type ( chemical::AA  aa)
overridevirtual
void core::pack::task::ResidueLevelTask_::target_type ( std::string  name)
overridevirtual
chemical::ResidueTypeCOP core::pack::task::ResidueLevelTask_::target_type ( ) const
overridevirtual
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_ = true
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_ = false
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 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_ = false
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 determine_if_designing(), prevent_repacking(), update_commutative(), update_intersection(), and update_union().

bool core::pack::task::ResidueLevelTask_::ex1_ = false
private
ExtraRotSample core::pack::task::ResidueLevelTask_::ex1_sample_level_ = NO_EXTRA_CHI_SAMPLES
private
bool core::pack::task::ResidueLevelTask_::ex1aro_ = false
private
bool core::pack::task::ResidueLevelTask_::ex1aro_exposed_ = false
private
ExtraRotSample core::pack::task::ResidueLevelTask_::ex1aro_exposed_sample_level_ = NO_EXTRA_CHI_SAMPLES
private
ExtraRotSample core::pack::task::ResidueLevelTask_::ex1aro_sample_level_ = NO_EXTRA_CHI_SAMPLES
private
bool core::pack::task::ResidueLevelTask_::ex2_ = false
private
ExtraRotSample core::pack::task::ResidueLevelTask_::ex2_sample_level_ = NO_EXTRA_CHI_SAMPLES
private
bool core::pack::task::ResidueLevelTask_::ex2aro_ = false
private
bool core::pack::task::ResidueLevelTask_::ex2aro_exposed_ = false
private
ExtraRotSample core::pack::task::ResidueLevelTask_::ex2aro_exposed_sample_level_ = NO_EXTRA_CHI_SAMPLES
private
ExtraRotSample core::pack::task::ResidueLevelTask_::ex2aro_sample_level_ = NO_EXTRA_CHI_SAMPLES
private
bool core::pack::task::ResidueLevelTask_::ex3_ = false
private
ExtraRotSample core::pack::task::ResidueLevelTask_::ex3_sample_level_ = NO_EXTRA_CHI_SAMPLES
private
bool core::pack::task::ResidueLevelTask_::ex4_ = false
private
ExtraRotSample core::pack::task::ResidueLevelTask_::ex4_sample_level_ = NO_EXTRA_CHI_SAMPLES
private
ExtraRotSample core::pack::task::ResidueLevelTask_::exdna_sample_level_ = NO_EXTRA_CHI_SAMPLES
private
Size core::pack::task::ResidueLevelTask_::extrachi_cutoff_ = EXTRACHI_CUTOFF_LIMIT
private
bool core::pack::task::ResidueLevelTask_::fix_his_tautomer_ = false
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_ = false
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_ = false
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_ = false
private
std::vector<std::string> core::pack::task::ResidueLevelTask_::mode_tokens_
private
bool core::pack::task::ResidueLevelTask_::operate_on_ex1_ = false
private
bool core::pack::task::ResidueLevelTask_::operate_on_ex2_ = false
private
bool core::pack::task::ResidueLevelTask_::operate_on_ex3_ = false
private
bool core::pack::task::ResidueLevelTask_::operate_on_ex4_ = false
private
bool core::pack::task::ResidueLevelTask_::optimize_H_mode_ = false
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
chemical::ResidueTypeSetCOP core::pack::task::ResidueLevelTask_::original_residue_type_set_
private

What ResidueTypeSet does this set of allowed residues come from?

Referenced by get_original_residue_set(), ResidueLevelTask_(), and target_type().

core::pack::palette::PackerPaletteCOP core::pack::task::ResidueLevelTask_::packer_palette_
private

The PackerPalette, which is responsible for initializing the allowed_residue_types_ vector.

Author
Vikram K. Mulligan.

Referenced by ResidueLevelTask_().

bool core::pack::task::ResidueLevelTask_::preserve_c_beta_ = false
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_ = true
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_ = nullptr
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_ = true
private
chemical::ResidueTypeCOP core::pack::task::ResidueLevelTask_::target_residue_type_ = nullptr
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: