Rosetta 3.4
Public Member Functions
core::pack::task::ResidueLevelTask_ Class Reference

Residue-level task class; contained within PackerTask. More...

#include <PackerTask_.hh>

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List of all members.

Public Member Functions

 ResidueLevelTask_ (conformation::Residue const &original_residue)
 constructor; requires a Residue object
virtual ~ResidueLevelTask_ ()
 dtor
virtual ExtraRotSample extrachi_sample_level (bool buried, int chi, chemical::ResidueTypeCAP concrete_residue) const
 returns the extra chi sampling level
virtual void initialize_from_command_line ()
 initialize options from command line flags
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();.
virtual void or_include_current (bool include_current)
 include the pre-existing rotamer while packing
virtual bool include_current () const
 is the pre-existing rotamer specifically allowed while packing?
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::ResidueTypeCAP 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
virtual bool adducts () const
virtual void or_ex1 (bool ex1)
 activate ex1 when passed true; do nothing otherwise
virtual void or_ex2 (bool ex2)
 activate ex2 when passed true; do nothing otherwise
virtual void or_ex3 (bool ex3)
 activate ex3 when passed true; do nothing otherwise
virtual void or_ex4 (bool ex4)
 activate ex4 when passed true; do nothing otherwise
virtual void or_ex1_sample_level (ExtraRotSample ex1_sample_level)
 increase ex1 sample level; do nothing if not an increase
virtual void or_ex2_sample_level (ExtraRotSample ex2_sample_level)
 increase ex2 sample level; do nothing if not an increase
virtual void or_ex3_sample_level (ExtraRotSample ex3_sample_level)
 increase ex3 sample level; do nothing if not an increase
virtual void or_ex4_sample_level (ExtraRotSample ex4_sample_level)
 increase ex4 sample level; do nothing if not an increase
virtual void or_ex1aro (bool ex1aro)
 activate ex1 for aromatics when passed true; do nothing otherwise
virtual void or_ex2aro (bool ex2aro_only)
 activate ex2 for aromatics when passed true; do nothing otherwise
virtual void or_ex1aro_exposed (bool ex1aro_exposed)
 activate ex1 for exposed aromatics when passed true; do nothing otherwise
virtual void or_ex2aro_exposed (bool ex2aro_exposed)
 activate ex2 for exposed aromatics when passed true; do nothing otherwise
virtual void or_ex1aro_sample_level (ExtraRotSample ex1aro_sample_level)
 increase ex1aro sample level; do nothing if not an increase
virtual void or_ex2aro_sample_level (ExtraRotSample ex2aro_only_sample_level)
 increase ex2aro sample level; do nothing if not an increase
virtual void or_ex1aro_exposed_sample_level (ExtraRotSample ex1aro_exposed_sample_level)
 increase ex1aro_exposed sample level; do nothing if not an increase
virtual void or_ex2aro_exposed_sample_level (ExtraRotSample ex2aro_exposed_sample_level)
 increase ex2aro_exposed sample level; do nothing if not an increase
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 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 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.
virtual bool sample_proton_chi () const
 sample proton chi.
virtual void sample_rna_chi (bool setting)
 sample proton chi.
virtual bool sample_rna_chi () const
 sample proton chi.
virtual bool ex1 () const
 return ex1.
virtual void and_extrachi_cutoff (Size num_neighbors_to_be_called_buried)
 lower extrachi_cutoff to given value; do nothing if not a decrease
virtual Size extrachi_cutoff () const
 get function for extrachi_cutoff
virtual void prevent_repacking ()
 remove all ResidueTypes from the list of allowed residue types, preventing repacking
virtual void restrict_absent_canonical_aas (utility::vector1< bool > const &)
 disables designing to residues not in the passed list
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
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
virtual void restrict_to_repacking ()
 only let this residue repack -- prevent redesign
virtual bool is_original_type (chemical::ResidueTypeCAP type) const
virtual
chemical::ResidueTypeSet const & 
get_original_residue_set () const
virtual void allow_noncanonical_aa (std::string const &aaname, chemical::ResidueTypeSet const &residue_set)
 explicitly allow a NCAA
virtual void allow_noncanonical_aa (std::string const &aaname)
 explicitly allow a NCAA; assumes same ResidueTypeSet as original_residue_type_
virtual void allow_noncanonical_aa (chemical::AA aa)
 explicitly allow a NCAA; assumes same ResidueTypeSet as original_residue_type_
virtual void allow_aa (chemical::AA const &aa)
 explicitly allow a canonical AA
virtual ResidueTypeCAPList const & allowed_residue_types () const
virtual ResidueTypeCAPListConstIter allowed_residue_types_begin () const
 returns iterator to beginning of allowed residue types list (traversal only)
virtual ResidueTypeCAPListConstIter allowed_residue_types_end () const
 returns iterator to end of allowed residue types list (traversal only)
virtual chemical::ResidueTypeCAP 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)?
virtual bool being_packed () const
 is this residue modififable at all by the packer?
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

Detailed Description

Residue-level task class; contained within PackerTask.


Constructor & Destructor Documentation

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.

References core::conformation::Residue::aa(), core::chemical::aa_unk, being_packed(), 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().

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]

explicitly allow a canonical AA

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

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

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.

References allow_noncanonical_aa(), and core::chemical::name_from_aa().

void core::pack::task::ResidueLevelTask_::allow_noncanonical_aa ( std::string const &  aaname,
chemical::ResidueTypeSet const &  residue_set 
) [virtual]
void core::pack::task::ResidueLevelTask_::allow_noncanonical_aa ( std::string const &  aaname) [virtual]

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.

References allow_noncanonical_aa().

ResidueLevelTask::ResidueTypeCAPList const & core::pack::task::ResidueLevelTask_::allowed_residue_types ( ) const [virtual]
ResidueLevelTask::ResidueTypeCAPListConstIter 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.

Referenced by print_allowed_types().

ResidueLevelTask::ResidueTypeCAPListConstIter 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.

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.

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.

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

is this residue modififable at all by the packer?

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

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 core::pack::task::PackerTask_::include_current(), and core::pack::task::PackerTask_::target_type().

bool core::pack::task::ResidueLevelTask_::ex1 ( ) const [virtual]

return ex1.

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

Referenced by or_ex1().

Size core::pack::task::ResidueLevelTask_::extrachi_cutoff ( ) const [virtual]

get function for extrachi_cutoff

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

ExtraRotSample core::pack::task::ResidueLevelTask_::extrachi_sample_level ( bool  buried,
int  chi,
chemical::ResidueTypeCAP  concrete_residue 
) const [virtual]

returns the extra chi sampling level

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

References core::pack::task::NO_EXTRA_CHI_SAMPLES.

bool core::pack::task::ResidueLevelTask_::fix_his_tautomer ( ) const [virtual]
bool core::pack::task::ResidueLevelTask_::flip_HNQ ( ) const [virtual]
chemical::ResidueTypeSet const & core::pack::task::ResidueLevelTask_::get_original_residue_set ( ) const [virtual]
bool core::pack::task::ResidueLevelTask_::has_behavior ( ) const [virtual]
bool core::pack::task::ResidueLevelTask_::has_behavior ( std::string const &  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.

Referenced by or_include_current().

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::ResidueTypeCAP  type) const [virtual]
virtual bool core::pack::task::ResidueLevelTask_::operate_on_ex1 ( ) const [inline, virtual]
virtual bool core::pack::task::ResidueLevelTask_::operate_on_ex2 ( ) const [inline, virtual]
virtual bool core::pack::task::ResidueLevelTask_::operate_on_ex3 ( ) const [inline, virtual]
virtual bool core::pack::task::ResidueLevelTask_::operate_on_ex4 ( ) const [inline, virtual]
bool core::pack::task::ResidueLevelTask_::optimize_h ( ) const [virtual]
void core::pack::task::ResidueLevelTask_::or_adducts ( bool  setting) [virtual]

include adducts at this residue

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

References core::chemical::ADDUCT.

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().

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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().

Referenced by initialize_from_command_line().

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.

Referenced by initialize_from_command_line().

void core::pack::task::ResidueLevelTask_::print_allowed_types ( std::ostream &  os) const [virtual]
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 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

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

References 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.

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 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 is_original_type().

Referenced by or_optimize_h().

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.

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

sample proton chi.

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

void core::pack::task::ResidueLevelTask_::sample_rna_chi ( bool  setting) [virtual]

sample proton chi.

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

bool core::pack::task::ResidueLevelTask_::sample_rna_chi ( ) const [virtual]

sample proton chi.

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

void core::pack::task::ResidueLevelTask_::target_type ( std::string  name) [virtual]
chemical::ResidueTypeCAP core::pack::task::ResidueLevelTask_::target_type ( ) const [virtual]
void core::pack::task::ResidueLevelTask_::target_type ( chemical::AA  aa) [virtual]
void core::pack::task::ResidueLevelTask_::target_type ( chemical::ResidueTypeCAP  type) [virtual]

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