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protocols::denovo_design::DisulfidizeMover Class Reference

#include <DisulfidizeMover.hh>

Inheritance diagram for protocols::denovo_design::DisulfidizeMover:
Inheritance graph
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Public Types

typedef utility::vector1
< std::pair< core::Size,
core::Size > > 
DisulfideList
 
typedef std::list
< core::pose::PoseOP
PoseList
 
- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP TagCOP
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef std::list< std::string > Strings
 

Public Member Functions

 DisulfidizeMover ()
 Default constructor. More...
 
 DisulfidizeMover (DisulfidizeMover const &src)
 Copy constructor. More...
 
 ~DisulfidizeMover () override
 virtual constructor to allow derivation More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 Parses the DisulfidizerMoverTags. More...
 
protocols::moves::MoverOP clone () const override
 Return the name of this mover. More...
 
DisulfideList find_current_disulfides (core::pose::Pose const &pose, core::select::residue_selector::ResidueSubset const &subset1, core::select::residue_selector::ResidueSubset const &subset2) const
 finds disulfides within a pose subset More...
 
void mutate_disulfides_to_ala (core::pose::Pose &pose, DisulfideList const &current_ds) const
 mutates the given disulfides to ALA More...
 
utility::vector1< DisulfideListrecursive_multiple_disulfide_former (DisulfideList const &disulfides_formed, DisulfideList const &disulfides_possible) const
 Function for recursively creating multiple disulfides. More...
 
void tag_disulfide (core::pose::Pose &pose, core::Size const res1, core::Size const res2) const
 creates a residue tags on disulfides to inform users that this disulfide was created by disulfidize More...
 
void tag_disulfides (core::pose::Pose &pose, DisulfidizeMover::DisulfideList const &disulf) const
 creates a residue tags on disulfides to inform users that this disulfide was created by disulfidize More...
 
void make_disulfide (core::pose::Pose &pose, core::Size const res1, core::Size const res2, bool const relax_bb, core::scoring::ScoreFunctionOP sfxn) const
 forms a disulfide between res1 and res2, optionally allowing backbone movement More...
 
void make_disulfides (core::pose::Pose &pose, DisulfideList const &disulf, bool const relax_bb, core::scoring::ScoreFunctionOP sfxn) const
 creates disulfides given the list of pairs given More...
 
core::Real build_and_score_disulfide (core::pose::Pose &blank_pose, core::scoring::ScoreFunctionOP sfxn_disulfonly, core::scoring::ScoreFunctionOP sfxn_full, const bool relax_bb, core::Size const res1, core::Size const res2) const
 temporarily tries building a disulfide between the given positions, scores, and restores the pose More...
 
DisulfideList find_possible_disulfides (core::pose::Pose const &pose, core::select::residue_selector::ResidueSubset const &residueset1, core::select::residue_selector::ResidueSubset const &residueset2, core::scoring::ScoreFunctionOP sfxn) const
 find disulfides in the given neighborhood More...
 
DisulfideList find_possible_disulfides (core::pose::Pose const &pose, std::set< core::Size > const &set1, std::set< core::Size > const &set2, core::scoring::ScoreFunctionOP sfxn) const
 find disulfides in the given neighborhood between residues in set 1 and residues in set 2 More...
 
bool check_residue_type (core::pose::Pose const &pose, core::Size const res) const
 checks seqpos to ensure that min_loop is satisfied More...
 
bool check_disulfide_seqpos (core::Size const res1, core::Size const res2) const
 checks seqpos to ensure that min_loop is satisfied More...
 
bool check_disulfide_cb_distance (core::pose::Pose const &pose, core::Size const res1, core::Size const res2) const
 checks disulfide CB-CB distance More...
 
bool check_disulfide_score (core::pose::Pose &pose, core::Size const res1, core::Size const res2, core::scoring::ScoreFunctionOP sfxn_disulfonly, core::scoring::ScoreFunctionOP sfxn_full) const
 checks disulfide rosetta score More...
 
bool check_disulfide_match_rt (core::pose::Pose const &pose, core::Size const res1, core::Size const res2, core::scoring::disulfides::DisulfideMatchingPotential const &disulfPot, bool const mirror) const
 checks disulfide match rt More...
 
bool mixed_disulfide (core::pose::Pose const &pose, core::Size const res1, core::Size const res2) const
 Returns true if this is a mixed D/L disulfide, false otherwise. More...
 
bool noncanonical_disulfide (core::pose::Pose const &pose, core::Size const res1, core::Size const res2) const
 Returns true if at least one of the partners in this disulfide is NOT D-cysteine or L-cysteine. Returns false otherwise. More...
 
void set_set1_selector (core::select::residue_selector::ResidueSelectorCOP selector)
 sets the selector for set 1 – disulfides will connect residues in set 1 to residues in set 2 More...
 
void set_set2_selector (core::select::residue_selector::ResidueSelectorCOP selector)
 sets the selector for set 2 – disulfides will connect residues in set 1 to residues in set 2 More...
 
void set_min_loop (core::Size const minloopval)
 sets the min_loop value (number of residues between disulfide-joined residues) (default=8) More...
 
void set_max_disulf_score (core::Real const maxscoreval)
 sets the maximum allowed per-disulfide dslf_fa13 score (default=0.0) More...
 
void set_match_rt_limit (core::Real const matchrtval)
 sets the maximum allowed "match-rt-limit" (default=1.0) More...
 
void set_cys_types (bool const lcys, bool const dcys, bool const beta_cys)
 Set the types of cysteines that we design with: More...
 
void set_scorefxn (core::scoring::ScoreFunctionCOP sfxn_in)
 Set the scorefunction to use for scoring disulfides, minimizing, and repacking. More...
 
void set_mutate_gly (bool const mutate_gly)
 If true, GLY –> CYS mutations will be allowed. Default=false. More...
 
void set_mutate_pro (bool const mutate_pro)
 If true, PRO –> CYS mutations will be allowed. Default=false. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
- Public Member Functions inherited from protocols::rosetta_scripts::MultiplePoseMover
 MultiplePoseMover ()
 No-argument constructor. More...
 
 ~MultiplePoseMover () override=default
 Virtual destructor. More...
 
protocols::moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
 
protocols::moves::MoverOP fresh_instance () const override
 Generates a new Mover object freshly created with the default ctor. More...
 
void apply (core::pose::Pose &pose) override
 Process input pose. More...
 
core::pose::PoseOP get_additional_output () override
 Mechanism by which a mover may return multiple output poses from a single input pose. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
 Parse settings in tag. More...
 
void set_previous_mover (protocols::moves::MoverOP const m)
 Used by RosettaScripts to set the previous mover to pull poses from. More...
 
void set_rosetta_scripts_tag (utility::tag::TagCOP tag)
 sets rosettascripts tag More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
 
virtual MoverOP create ()
 
MoverCOP get_self_ptr () const
 
MoverOP get_self_ptr ()
 
MoverCAP get_self_weak_ptr () const
 
MoverAP get_self_weak_ptr ()
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
virtual void test_move (Pose &pose)
 : Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...
 
virtual bool reinitialize_for_each_job () const
 Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...
 
virtual bool reinitialize_for_new_input () const
 Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...
 
MoverStatus get_last_move_status () const
 end parser interface, start Job Distributor interface///////////// More...
 
void reset_status ()
 resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...
 
void set_type (std::string const &setting)
 Set the 'type' string. More...
 
std::string get_type () const
 
void type (const std::string &type_in)
 Set the 'type' string. More...
 
std::string const & type () const
 Get the set 'type' string. More...
 
virtual void set_input_pose (PoseCOP pose)
 setter for poses contained for rms More...
 
virtual void set_native_pose (PoseCOP pose)
 setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...
 
PoseCOP get_input_pose () const
 
PoseCOP get_native_pose () const
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 
virtual void set_current_tag (std::string const &new_tag)
 
std::string get_current_tag () const
 A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...
 
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...
 
virtual core::Real last_proposal_density_ratio ()
 
virtual void clear_info ()
 Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...
 
virtual Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 
virtual bool mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Static Public Member Functions

static std::string mover_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
- Static Public Member Functions inherited from protocols::rosetta_scripts::MultiplePoseMover
static std::string mover_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
- Static Public Member Functions inherited from protocols::moves::Mover
static std::string name ()
 
static void register_options ()
 Overload this static method if you access options within the mover. More...
 

Protected Member Functions

bool process_pose (core::pose::Pose &pose, utility::vector1< core::pose::PoseOP > &additional_poses) override
 Identifies disulfides for a given input pose. More...
 
void prune_symmetric_disulfides (core::pose::Pose const &pose, DisulfideList &disulf_list) const
 Given a list of disulfides and a symmetric pose, prune the list to remove symmetry duplicates. More...
 
- Protected Member Functions inherited from protocols::moves::Mover
void set_last_move_status (MoverStatus status)
 nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...
 

Private Attributes

core::Real match_rt_limit_
 
core::Real max_disulf_score_
 
core::Real max_dist_sq_
 
core::Size min_loop_
 
core::Size min_disulfides_
 
core::Size max_disulfides_
 
bool include_current_ds_
 
bool keep_current_ds_
 
bool score_or_matchrt_
 
bool allow_l_cys_
 Can disulfides involve L-cystine? More...
 
bool allow_d_cys_
 Can disulfides involve D-cystine? More...
 
bool allow_beta_cys_
 Can disulfides involve beta-3-cysteine? More...
 
bool mutate_gly_
 Can GLY be mutated? More...
 
bool mutate_pro_
 Can PRO be mutated? More...
 
core::select::residue_selector::ResidueSelectorCOP set1_selector_
 disulfides connect residues from set1 to residues from set2 More...
 
core::select::residue_selector::ResidueSelectorCOP set2_selector_
 
core::scoring::ScoreFunctionOP sfxn_
 The scorefunction that we will use for: – scoring disulfides – repacking/minimizing disulfides. More...
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::denovo_design::DisulfidizeMover::DisulfidizeMover ( )
protocols::denovo_design::DisulfidizeMover::DisulfidizeMover ( DisulfidizeMover const &  src)

Copy constructor.

References sfxn_.

protocols::denovo_design::DisulfidizeMover::~DisulfidizeMover ( )
overridedefault

virtual constructor to allow derivation

destructor - this class has no dynamic allocation, so

Member Function Documentation

core::Real protocols::denovo_design::DisulfidizeMover::build_and_score_disulfide ( core::pose::Pose blank_pose,
core::scoring::ScoreFunctionOP  sfxn_disulfonly,
core::scoring::ScoreFunctionOP  sfxn_full,
const bool  relax_bb,
core::Size const  res1,
core::Size const  res2 
) const

temporarily tries building a disulfide between the given positions, scores, and restores the pose

References make_disulfide(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), protocols::hybridization::score, core::pose::Pose::size(), and protocols::TR().

Referenced by check_disulfide_score().

bool protocols::denovo_design::DisulfidizeMover::check_disulfide_cb_distance ( core::pose::Pose const &  pose,
core::Size const  res1,
core::Size const  res2 
) const
bool protocols::denovo_design::DisulfidizeMover::check_disulfide_match_rt ( core::pose::Pose const &  pose,
core::Size const  res1,
core::Size const  res2,
core::scoring::disulfides::DisulfideMatchingPotential const &  disulfPot,
bool const  mirror 
) const
bool protocols::denovo_design::DisulfidizeMover::check_disulfide_score ( core::pose::Pose pose,
core::Size const  res1,
core::Size const  res2,
core::scoring::ScoreFunctionOP  sfxn_disulfonly,
core::scoring::ScoreFunctionOP  sfxn_full 
) const

checks disulfide rosetta score

References build_and_score_disulfide(), max_disulf_score_, and protocols::TR().

Referenced by find_possible_disulfides().

bool protocols::denovo_design::DisulfidizeMover::check_disulfide_seqpos ( core::Size const  res1,
core::Size const  res2 
) const

checks seqpos to ensure that min_loop is satisfied

References min_loop_, and protocols::TR().

Referenced by find_possible_disulfides().

bool protocols::denovo_design::DisulfidizeMover::check_residue_type ( core::pose::Pose const &  pose,
core::Size const  res 
) const
protocols::moves::MoverOP protocols::denovo_design::DisulfidizeMover::clone ( ) const
overridevirtual

Return the name of this mover.

Return a copy of ourselves.

return a fresh instance of this class in an owning pointer

Reimplemented from protocols::moves::Mover.

DisulfidizeMover::DisulfideList protocols::denovo_design::DisulfidizeMover::find_current_disulfides ( core::pose::Pose const &  pose,
core::select::residue_selector::ResidueSubset const &  subset1,
core::select::residue_selector::ResidueSubset const &  subset2 
) const
DisulfidizeMover::DisulfideList protocols::denovo_design::DisulfidizeMover::find_possible_disulfides ( core::pose::Pose const &  pose,
core::select::residue_selector::ResidueSubset const &  residueset1,
core::select::residue_selector::ResidueSubset const &  residueset2,
core::scoring::ScoreFunctionOP  sfxn 
) const

find disulfides in the given neighborhood

find disulfides in the given neighborhood between residues in set 1 and residues in set 2

References protocols::TR().

Referenced by process_pose().

DisulfidizeMover::DisulfideList protocols::denovo_design::DisulfidizeMover::find_possible_disulfides ( core::pose::Pose const &  pose,
std::set< core::Size > const &  set1,
std::set< core::Size > const &  set2,
core::scoring::ScoreFunctionOP  sfxn 
) const
std::string protocols::denovo_design::DisulfidizeMover::get_name ( ) const
overridevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

References mover_name().

void protocols::denovo_design::DisulfidizeMover::make_disulfide ( core::pose::Pose pose,
core::Size const  res1,
core::Size const  res2,
bool const  relax_bb,
core::scoring::ScoreFunctionOP  sfxn 
) const

forms a disulfide between res1 and res2, optionally allowing backbone movement

References allow_d_cys_, allow_l_cys_, core::pose::Pose::conformation(), core::conformation::form_disulfide(), core::util::rebuild_disulfide(), and protocols::TR().

Referenced by build_and_score_disulfide(), and make_disulfides().

void protocols::denovo_design::DisulfidizeMover::make_disulfides ( core::pose::Pose pose,
DisulfidizeMover::DisulfideList const &  disulf,
bool const  relax_bb,
core::scoring::ScoreFunctionOP  sfxn 
) const

creates disulfides given the list of pairs given

References make_disulfide().

Referenced by process_pose().

bool protocols::denovo_design::DisulfidizeMover::mixed_disulfide ( core::pose::Pose const &  pose,
core::Size const  res1,
core::Size const  res2 
) const

Returns true if this is a mixed D/L disulfide, false otherwise.

References allow_d_cys_, allow_l_cys_, core::chemical::ResidueTypeBase::is_d_aa(), core::pose::Pose::residue(), and core::conformation::Residue::type().

Referenced by find_possible_disulfides().

std::string protocols::denovo_design::DisulfidizeMover::mover_name ( )
static
void protocols::denovo_design::DisulfidizeMover::mutate_disulfides_to_ala ( core::pose::Pose pose,
DisulfideList const &  current_ds 
) const
bool protocols::denovo_design::DisulfidizeMover::noncanonical_disulfide ( core::pose::Pose const &  pose,
core::Size const  res1,
core::Size const  res2 
) const

Returns true if at least one of the partners in this disulfide is NOT D-cysteine or L-cysteine. Returns false otherwise.

References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_cys, core::chemical::aa_dcs, and core::pose::Pose::residue_type().

Referenced by find_possible_disulfides().

void protocols::denovo_design::DisulfidizeMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
bool protocols::denovo_design::DisulfidizeMover::process_pose ( core::pose::Pose pose,
utility::vector1< core::pose::PoseOP > &  additional_poses 
)
overrideprotectedvirtual
void protocols::denovo_design::DisulfidizeMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::denovo_design::DisulfidizeMover::prune_symmetric_disulfides ( core::pose::Pose const &  pose,
DisulfideList disulf_list 
) const
protected

Given a list of disulfides and a symmetric pose, prune the list to remove symmetry duplicates.

Does nothing if the pose is not symmetric.

Author
Vikram K. Mulligan, Baker laboratory (vmull.nosp@m.ig@u.nosp@m.w.edu).

References core::pose::Pose::conformation_ptr().

Referenced by process_pose().

utility::vector1< DisulfidizeMover::DisulfideList > protocols::denovo_design::DisulfidizeMover::recursive_multiple_disulfide_former ( DisulfideList const &  disulfides_formed,
DisulfideList const &  disulfides_possible 
) const

Function for recursively creating multiple disulfides.

References core::sequence::end, and max_disulfides_.

Referenced by process_pose().

void protocols::denovo_design::DisulfidizeMover::set_cys_types ( bool const  lcys,
bool const  dcys,
bool const  beta_cys 
)

Set the types of cysteines that we design with:

By default, we use only L-cysteine (not D-cysteine or beta-3-cysteine).

By default, we use only L-cysteine (not D-cysteine).

References allow_beta_cys_, allow_d_cys_, and allow_l_cys_.

Referenced by parse_my_tag().

void protocols::denovo_design::DisulfidizeMover::set_match_rt_limit ( core::Real const  matchrtval)

sets the maximum allowed "match-rt-limit" (default=1.0)

sets the maximum allowed "match-rt-limit" (default=2.0)

Changed from default=2.0 by VKM on 19 Aug 2015 after fixing major bug in DisulfideMatchPotential.

References match_rt_limit_.

Referenced by parse_my_tag().

void protocols::denovo_design::DisulfidizeMover::set_max_disulf_score ( core::Real const  maxscoreval)

sets the maximum allowed per-disulfide dslf_fa13 score (default=0.0)

References max_disulf_score_.

Referenced by parse_my_tag().

void protocols::denovo_design::DisulfidizeMover::set_min_loop ( core::Size const  minloopval)

sets the min_loop value (number of residues between disulfide-joined residues) (default=8)

References min_loop_.

Referenced by parse_my_tag().

void protocols::denovo_design::DisulfidizeMover::set_mutate_gly ( bool const  mutate_gly)

If true, GLY –> CYS mutations will be allowed. Default=false.

References mutate_gly_.

Referenced by parse_my_tag().

void protocols::denovo_design::DisulfidizeMover::set_mutate_pro ( bool const  mutate_pro)

If true, PRO –> CYS mutations will be allowed. Default=false.

References mutate_pro_.

Referenced by parse_my_tag().

void protocols::denovo_design::DisulfidizeMover::set_scorefxn ( core::scoring::ScoreFunctionCOP  sfxn_in)

Set the scorefunction to use for scoring disulfides, minimizing, and repacking.

Clones the input scorefunction; does not copy it.

References sfxn_.

Referenced by parse_my_tag().

void protocols::denovo_design::DisulfidizeMover::set_set1_selector ( core::select::residue_selector::ResidueSelectorCOP  selector)

sets the selector for set 1 – disulfides will connect residues in set 1 to residues in set 2

References set1_selector_.

Referenced by parse_my_tag().

void protocols::denovo_design::DisulfidizeMover::set_set2_selector ( core::select::residue_selector::ResidueSelectorCOP  selector)

sets the selector for set 2 – disulfides will connect residues in set 1 to residues in set 2

References set2_selector_.

Referenced by parse_my_tag().

void protocols::denovo_design::DisulfidizeMover::tag_disulfide ( core::pose::Pose pose,
core::Size const  res1,
core::Size const  res2 
) const

creates a residue tags on disulfides to inform users that this disulfide was created by disulfidize

References core::pose::Pose::pdb_info().

Referenced by tag_disulfides().

void protocols::denovo_design::DisulfidizeMover::tag_disulfides ( core::pose::Pose pose,
DisulfidizeMover::DisulfideList const &  disulf 
) const

creates a residue tags on disulfides to inform users that this disulfide was created by disulfidize

References core::pose::add_comment(), and tag_disulfide().

Referenced by process_pose().

Member Data Documentation

bool protocols::denovo_design::DisulfidizeMover::allow_beta_cys_
private

Can disulfides involve beta-3-cysteine?

Default false. If true, beta-3-cysteine is considered only at beta-amino acid positions.

Referenced by parse_my_tag(), and set_cys_types().

bool protocols::denovo_design::DisulfidizeMover::allow_d_cys_
private

Can disulfides involve D-cystine?

Default false

Referenced by find_possible_disulfides(), make_disulfide(), mixed_disulfide(), parse_my_tag(), and set_cys_types().

bool protocols::denovo_design::DisulfidizeMover::allow_l_cys_
private

Can disulfides involve L-cystine?

Default true

Referenced by find_possible_disulfides(), make_disulfide(), mixed_disulfide(), parse_my_tag(), and set_cys_types().

bool protocols::denovo_design::DisulfidizeMover::include_current_ds_
private

Referenced by parse_my_tag(), and process_pose().

bool protocols::denovo_design::DisulfidizeMover::keep_current_ds_
private
core::Real protocols::denovo_design::DisulfidizeMover::match_rt_limit_
private
core::Real protocols::denovo_design::DisulfidizeMover::max_dist_sq_
private
core::Real protocols::denovo_design::DisulfidizeMover::max_disulf_score_
private
core::Size protocols::denovo_design::DisulfidizeMover::max_disulfides_
private
core::Size protocols::denovo_design::DisulfidizeMover::min_disulfides_
private

Referenced by parse_my_tag(), and process_pose().

core::Size protocols::denovo_design::DisulfidizeMover::min_loop_
private
bool protocols::denovo_design::DisulfidizeMover::mutate_gly_
private

Can GLY be mutated?

Referenced by check_residue_type(), parse_my_tag(), and set_mutate_gly().

bool protocols::denovo_design::DisulfidizeMover::mutate_pro_
private

Can PRO be mutated?

Referenced by check_residue_type(), parse_my_tag(), and set_mutate_pro().

bool protocols::denovo_design::DisulfidizeMover::score_or_matchrt_
private
core::select::residue_selector::ResidueSelectorCOP protocols::denovo_design::DisulfidizeMover::set1_selector_
private

disulfides connect residues from set1 to residues from set2

Referenced by process_pose(), and set_set1_selector().

core::select::residue_selector::ResidueSelectorCOP protocols::denovo_design::DisulfidizeMover::set2_selector_
private

Referenced by process_pose(), and set_set2_selector().

core::scoring::ScoreFunctionOP protocols::denovo_design::DisulfidizeMover::sfxn_
private

The scorefunction that we will use for: – scoring disulfides – repacking/minimizing disulfides.

Set by user, or obtained from globals if null.

Referenced by DisulfidizeMover(), process_pose(), and set_scorefxn().


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