Rosetta Protocols  2014.35
Public Types | Public Member Functions | Private Types | Private Member Functions | Private Attributes | List of all members
protocols::fldsgn::potentials::SetSecStructEnergies Class Reference

#include <SetSecStructEnergies.hh>

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 protocols::moves::MoverOP MoverOP
 
typedef
protocols::jd2::parser::BluePrint 
BluePrint
 
typedef
protocols::jd2::parser::BluePrintOP 
BluePrintOP
 
typedef
core::conformation::symmetry::SymmetryInfoOP 
SymmetryInfoOP
 
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
protocols::filters::Filters_map 
Filters_map
 
typedef basic::datacache::DataMap DataMap
 
typedef
protocols::moves::Movers_map 
Movers_map
 
- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP TagCOP
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef
protocols::filters::Filters_map 
Filters_map
 
typedef std::list< std::stringStrings
 

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 (SetSecStructEnergies const &rval)
 copy constructor More...
 
virtual ~SetSecStructEnergies ()
 default destructor More...
 
virtual MoverOP clone () const
 clone this object More...
 
virtual MoverOP fresh_instance () const
 create this type of object More...
 
void ss_from_blueprint (bool const flag)
 define secondary structrue by blueprint More...
 
void scorefunction (ScoreFunction const &sfx)
 set the centroid level score function More...
 
void scorefunction (ScoreFunctionOP sfx)
 set the centroid level score function More...
 
void set_blueprint (String const &filename)
 set blueprint file by filename More...
 
void set_blueprint (BluePrintOP const blp)
 set blueprint file More...
 
virtual void apply (Pose &pose)
 apply defined moves to given Pose More...
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data, Filters_map const &, Movers_map const &, Pose const &)
 parse xml file More...
 
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
 
virtual ~Mover ()
 
virtual MoverSP create ()
 
virtual void apply (core::io::serialization::PipeMap &pmap)
 
virtual void parse_state (SerializableState const &state)
 
virtual void parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)
 
virtual void save_state (SerializableState &state)
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
 Mover (Mover const &other)
 
Moveroperator= (Mover const &other)
 assignment operator More...
 
virtual core::Real last_proposal_density_ratio ()
 
std::string const & type () const
 
void set_type (std::string const &setting)
 
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...
 
void set_current_tag (std::string const &new_tag)
 
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
 
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...
 
void type (const std::string &type_in)
 
std::string get_type () const
 
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...
 
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 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...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...
 

Private Types

typedef protocols::moves::Mover Super
 

Private Member Functions

SetSecStructEnergiesoperator= (SetSecStructEnergies const &rval)
 copy assignment More...
 
String symmetric_secstruct (SymmetryInfoOP const syminfo, String const &ss)
 make symmetric secstruct More...
 

Private Attributes

bool loaded_
 
BluePrintOP blueprint_
 bluerprint file for setting build instruction More...
 
bool ss_from_blueprint_
 
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...
 
NatbiasHelixPairPotentialOP hpairpot_
 
NatbiasHelicesSheetPotentialOP hspot_
 

Additional Inherited Members

- 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 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

Referenced by clone(), and fresh_instance().

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

value constructor

References set_blueprint().

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

value constructor

protocols::fldsgn::potentials::SetSecStructEnergies::SetSecStructEnergies ( SetSecStructEnergies const &  rval)

copy constructor

copy constructor

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

default destructor

Member Function Documentation

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

clone this object

Reimplemented from protocols::moves::Mover.

References SetSecStructEnergies().

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

create this type of object

Reimplemented from protocols::moves::Mover.

References SetSecStructEnergies().

std::string protocols::fldsgn::potentials::SetSecStructEnergies::get_name ( ) const
virtual

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

Implements protocols::moves::Mover.

References protocols::fldsgn::potentials::SetSecStructEnergiesCreator::mover_name().

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,
Filters_map const &  ,
Movers_map const &  ,
Pose const &   
)
virtual
void protocols::fldsgn::potentials::SetSecStructEnergies::scorefunction ( ScoreFunction const &  sfx)

set the centroid level score function

References core::scoring::ScoreFunction::clone(), and sfx_.

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

set the centroid level score function

References core::scoring::ScoreFunction::clone(), and sfx_.

void protocols::fldsgn::potentials::SetSecStructEnergies::set_blueprint ( String const &  filename)

set blueprint file by filename

use blueprint

References blueprint_.

Referenced by parse_my_tag(), and SetSecStructEnergies().

void protocols::fldsgn::potentials::SetSecStructEnergies::set_blueprint ( BluePrintOP const  blp)

set blueprint file

use blueprint

References blueprint_.

void protocols::fldsgn::potentials::SetSecStructEnergies::ss_from_blueprint ( bool const  flag)
inline

define secondary structrue by blueprint

References ss_from_blueprint_.

Referenced by parse_my_tag().

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

make symmetric secstruct

References runtime_assert, and secstruct.

Referenced by apply().

Member Data Documentation

BluePrintOP protocols::fldsgn::potentials::SetSecStructEnergies::blueprint_
private

bluerprint file for setting build instruction

Referenced by apply(), and set_blueprint().

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().

bool protocols::fldsgn::potentials::SetSecStructEnergies::loaded_
private

Referenced by apply().

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

weight for strand and strand pairing potential

Referenced by apply(), and parse_my_tag().

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

the centroid scorefunction to use, default "remodel_cen"

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

bool protocols::fldsgn::potentials::SetSecStructEnergies::ss_from_blueprint_
private
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().


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