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protocols::fldsgn::potentials::SetSecStructEnergies Class Reference

#include <SetSecStructEnergies.hh>

Inheritance diagram for protocols::fldsgn::potentials::SetSecStructEnergies:
Inheritance graph
[legend]

Public Types

typedef std::string String
 
typedef core::Real Real
 
typedef core::Size Size
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseOP PoseOP
 
typedef
core::scoring::ScoreFunction 
ScoreFunction
 
typedef
core::scoring::ScoreFunctionOP 
ScoreFunctionOP
 
typedef
core::scoring::ScoreFunctionCOP 
ScoreFunctionCOP
 
typedef protocols::moves::MoverOP MoverOP
 
typedef
protocols::parser::BluePrint 
BluePrint
 
typedef
protocols::parser::BluePrintOP 
BluePrintOP
 
typedef
core::conformation::symmetry::SymmetryInfoOP 
SymmetryInfoOP
 
typedef
core::conformation::symmetry::SymmetryInfoCOP 
SymmetryInfoCOP
 
typedef
protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential 
NatbiasHelixPairPotential
 
typedef
protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotentialOP 
NatbiasHelixPairPotentialOP
 
typedef
protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential 
NatbiasHelicesSheetPotential
 
typedef
protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotentialOP 
NatbiasHelicesSheetPotentialOP
 
typedef utility::tag::TagCOP TagCOP
 
typedef basic::datacache::DataMap DataMap
 
- 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

 SetSecStructEnergies ()
 default constructor More...
 
 SetSecStructEnergies (ScoreFunctionOP const sfx, String const &filename, bool const ss_from_blueprint=true)
 value constructor More...
 
 SetSecStructEnergies (ScoreFunctionOP const sfx, BluePrintOP const blueprintOP, bool const ss_from_blueprint=true)
 value constructor More...
 
 ~SetSecStructEnergies () override
 default destructor More...
 
MoverOP clone () const override
 clone this object More...
 
MoverOP fresh_instance () const override
 create this type of object More...
 
ScoreFunctionOP scorefunction_ptr () const
 access ptr to the modified score function More...
 
void set_scorefunction_ptr (ScoreFunctionOP sfx)
 set the centroid level score function to be modified More...
 
void set_secstruct (String const &secstruct)
 sets the secondary structure to be used for computation More...
 
void apply (Pose &pose) override
 apply defined moves to given Pose More...
 
void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data) override
 parse xml file 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...
 
virtual core::pose::PoseOP get_additional_output ()
 Mechanism by which a mover may return multiple output poses from a single input pose. 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::moves::Mover
static std::string name ()
 
static void register_options ()
 Overload this static method if you access options within the mover. More...
 

Private Types

typedef protocols::moves::Mover Super
 

Private Member Functions

SetSecStructEnergiesoperator= (SetSecStructEnergies const &rval)
 copy assignment More...
 
String symmetric_secstruct (SymmetryInfoCOP const syminfo, String const &ss) const
 make symmetric secstruct More...
 
std::string get_secstruct (Pose const &pose) const
 chooses and return the secondary structure to be used in computation More...
 
std::string get_helix_pairings (Pose const &pose) const
 
void init_from_blueprint (BluePrint const &bp, bool const ss_from_blueprint)
 initializes pairings and secondary structure from blueprint file More...
 

Private Attributes

std::string secstruct_
 Secondary structure to be used. More...
 
bool use_dssp_
 If true, and secstruct is not set, DSSP will be used to determine secondary structure. More...
 
std::string hh_pair_
 HHPAIR definition to be used. More...
 
std::string ss_pair_
 strand pairing definition to be used More...
 
std::string hss_triplet_
 helix-strand-strand triplet definition to be used More...
 
ScoreFunctionCOP sfx_orig_
 Original copy of the centroid scorefunction to use. More...
 
ScoreFunctionOP sfx_
 the centroid scorefunction to use, default "remodel_cen" More...
 
Real hh_weight_
 weight for helix and helix pairing potential More...
 
Real hs_weight_
 weight for heilx and strand pairing potential More...
 
Real ss_weight_
 weight for strand and strand pairing potential More...
 
Real stwist_weight_
 weight for sheet twist potential More...
 
Real hs_pair_weight_
 weight for hs_pair More...
 
Real ss_pair_weight_
 weight for ss_pair More...
 
Real rsigma_weight_
 weight for strand and strand pairing potential More...
 
bool add_symmetry_
 if this option is set, a copy of the input pose will have symmetry added to it, and this symmetry will be used to modify the secondary structure. The input pose will be unchanged. I can't think of any reason why anyone would want this to be true if the input pose is already symmetric. More...
 
NatbiasHelixPairPotentialOP hpairpot_
 
NatbiasHelicesSheetPotentialOP hspot_
 

Additional Inherited Members

- 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...
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::fldsgn::potentials::SetSecStructEnergies::SetSecStructEnergies ( )

default constructor

protocols::fldsgn::potentials::SetSecStructEnergies::SetSecStructEnergies ( ScoreFunctionOP const  sfx,
String const &  filename,
bool const  ss_from_blueprint = true 
)

value constructor

References init_from_blueprint().

protocols::fldsgn::potentials::SetSecStructEnergies::SetSecStructEnergies ( ScoreFunctionOP const  sfx,
BluePrintOP const  blueprintOP,
bool const  ss_from_blueprint = true 
)

value constructor

References init_from_blueprint().

protocols::fldsgn::potentials::SetSecStructEnergies::~SetSecStructEnergies ( )
overridedefault

default destructor

Member Function Documentation

void protocols::fldsgn::potentials::SetSecStructEnergies::apply ( Pose pose)
overridevirtual
SetSecStructEnergies::MoverOP protocols::fldsgn::potentials::SetSecStructEnergies::clone ( ) const
overridevirtual

clone this object

Reimplemented from protocols::moves::Mover.

SetSecStructEnergies::MoverOP protocols::fldsgn::potentials::SetSecStructEnergies::fresh_instance ( ) const
overridevirtual

create this type of object

Reimplemented from protocols::moves::Mover.

std::string protocols::fldsgn::potentials::SetSecStructEnergies::get_helix_pairings ( Pose const &  pose) const
private
std::string protocols::fldsgn::potentials::SetSecStructEnergies::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

std::string protocols::fldsgn::potentials::SetSecStructEnergies::get_secstruct ( Pose const &  pose) const
private

chooses and return the secondary structure to be used in computation

Parameters
[in]poseInput pose

If secstruct_ is set, returns that. If use_dssp_ is set, returns DSSP secstruct string Otherwise, returns pose secondary structure

References add_symmetry_, core::pose::Pose::conformation(), protocols::simple_filters::dssp(), core::scoring::dssp::Dssp::get_dssp_secstruct(), core::pose::symmetry::is_symmetric(), core::conformation::symmetry::is_symmetric(), core::pose::Pose::secstruct(), secstruct_, symmetric_secstruct(), and use_dssp_.

Referenced by apply().

void protocols::fldsgn::potentials::SetSecStructEnergies::init_from_blueprint ( BluePrint const &  bp,
bool const  ss_from_blueprint 
)
private

initializes pairings and secondary structure from blueprint file

Parameters
[in]bpBluePrint object
[in]ss_from_blueprintIf true, secstruct_ will be set from the blueprint. If false, secstruct_ will be unchanged, and only the pairings will be set.

References protocols::parser::BluePrint::helix_pairings(), hh_pair_, hss_triplet_, protocols::parser::BluePrint::hss_triplets(), protocols::parser::BluePrint::secstruct(), secstruct_, ss_pair_, and protocols::parser::BluePrint::strand_pairings().

Referenced by parse_my_tag(), and SetSecStructEnergies().

std::string protocols::fldsgn::potentials::SetSecStructEnergies::mover_name ( )
static
SetSecStructEnergies& protocols::fldsgn::potentials::SetSecStructEnergies::operator= ( SetSecStructEnergies const &  rval)
private

copy assignment

Remarks
Mover base class prevents this from working properly...
void protocols::fldsgn::potentials::SetSecStructEnergies::parse_my_tag ( TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
void protocols::fldsgn::potentials::SetSecStructEnergies::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
SetSecStructEnergies::ScoreFunctionOP protocols::fldsgn::potentials::SetSecStructEnergies::scorefunction_ptr ( ) const

access ptr to the modified score function

References sfx_.

void protocols::fldsgn::potentials::SetSecStructEnergies::set_scorefunction_ptr ( ScoreFunctionOP  sfx)

set the centroid level score function to be modified

set the centroid level score function

this also clones the object of ptr isn't null and stores the clone in sfx_orig_

References sfx_, and sfx_orig_.

Referenced by parse_my_tag().

void protocols::fldsgn::potentials::SetSecStructEnergies::set_secstruct ( String const &  secstruct)

sets the secondary structure to be used for computation

Parameters
[in]secstructSecondary structure to be forced on the pose

If this is non-empty, it will be used as the pose secondary structure to determine secondary structure elements in the pose

References secstruct_.

SetSecStructEnergies::String protocols::fldsgn::potentials::SetSecStructEnergies::symmetric_secstruct ( SymmetryInfoCOP const  syminfo,
String const &  ss 
) const
private

make symmetric secstruct

Referenced by get_secstruct().

Member Data Documentation

bool protocols::fldsgn::potentials::SetSecStructEnergies::add_symmetry_
private

if this option is set, a copy of the input pose will have symmetry added to it, and this symmetry will be used to modify the secondary structure. The input pose will be unchanged. I can't think of any reason why anyone would want this to be true if the input pose is already symmetric.

TL: this is added as a hack to work around behavior by SetupForSymmetryMover. SetupForSymmetry sets this command line flag to a bogus value in its parse_my_tag() function. Therefore, the presence of the option at runtime does not indicate the user's intentions. As a workaround, the option is queried set at parse time and this variable is used after than. WARNING: You should declare your SetupForSymmetry movers AFTER this one, or you will probably get crashes. Default is the value of option[ symmetry::symmetry_definition ].active() at parse-time

Referenced by get_secstruct(), and parse_my_tag().

std::string protocols::fldsgn::potentials::SetSecStructEnergies::hh_pair_
private

HHPAIR definition to be used.

Referenced by apply(), init_from_blueprint(), and parse_my_tag().

Real protocols::fldsgn::potentials::SetSecStructEnergies::hh_weight_
private

weight for helix and helix pairing potential

Referenced by apply(), and parse_my_tag().

NatbiasHelixPairPotentialOP protocols::fldsgn::potentials::SetSecStructEnergies::hpairpot_
private

Referenced by apply(), and parse_my_tag().

Real protocols::fldsgn::potentials::SetSecStructEnergies::hs_pair_weight_
private

weight for hs_pair

Referenced by apply(), and parse_my_tag().

Real protocols::fldsgn::potentials::SetSecStructEnergies::hs_weight_
private

weight for heilx and strand pairing potential

Referenced by apply(), and parse_my_tag().

NatbiasHelicesSheetPotentialOP protocols::fldsgn::potentials::SetSecStructEnergies::hspot_
private

Referenced by apply(), and parse_my_tag().

std::string protocols::fldsgn::potentials::SetSecStructEnergies::hss_triplet_
private

helix-strand-strand triplet definition to be used

Referenced by apply(), init_from_blueprint(), and parse_my_tag().

Real protocols::fldsgn::potentials::SetSecStructEnergies::rsigma_weight_
private

weight for strand and strand pairing potential

Referenced by apply(), and parse_my_tag().

std::string protocols::fldsgn::potentials::SetSecStructEnergies::secstruct_
private

Secondary structure to be used.

Referenced by get_secstruct(), init_from_blueprint(), parse_my_tag(), and set_secstruct().

ScoreFunctionOP protocols::fldsgn::potentials::SetSecStructEnergies::sfx_
private

the centroid scorefunction to use, default "remodel_cen"

Referenced by apply(), scorefunction_ptr(), and set_scorefunction_ptr().

ScoreFunctionCOP protocols::fldsgn::potentials::SetSecStructEnergies::sfx_orig_
private

Original copy of the centroid scorefunction to use.

Referenced by apply(), and set_scorefunction_ptr().

std::string protocols::fldsgn::potentials::SetSecStructEnergies::ss_pair_
private

strand pairing definition to be used

Referenced by apply(), init_from_blueprint(), and parse_my_tag().

Real protocols::fldsgn::potentials::SetSecStructEnergies::ss_pair_weight_
private

weight for ss_pair

Referenced by apply(), and parse_my_tag().

Real protocols::fldsgn::potentials::SetSecStructEnergies::ss_weight_
private

weight for strand and strand pairing potential

Referenced by apply(), and parse_my_tag().

Real protocols::fldsgn::potentials::SetSecStructEnergies::stwist_weight_
private

weight for sheet twist potential

Referenced by apply(), and parse_my_tag().

bool protocols::fldsgn::potentials::SetSecStructEnergies::use_dssp_
private

If true, and secstruct is not set, DSSP will be used to determine secondary structure.

Referenced by get_secstruct(), and parse_my_tag().


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