![]() |
Rosetta
2020.50
|
#include <SetSecStructEnergies.hh>
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... | |
![]() | |
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 Strings & | info () |
non-const accessor More... | |
virtual Strings const & | info () const |
const accessor More... | |
virtual void | provide_citation_info (basic::citation_manager::CitationCollectionList &) const |
Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More... | |
Static Public Member Functions | |
static std::string | mover_name () |
static void | provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd) |
![]() | |
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 | |
SetSecStructEnergies & | operator= (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 | |
![]() | |
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... | |
typedef protocols::parser::BluePrintOP protocols::fldsgn::potentials::SetSecStructEnergies::BluePrintOP |
typedef basic::datacache::DataMap protocols::fldsgn::potentials::SetSecStructEnergies::DataMap |
typedef protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential protocols::fldsgn::potentials::SetSecStructEnergies::NatbiasHelicesSheetPotential |
typedef protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotentialOP protocols::fldsgn::potentials::SetSecStructEnergies::NatbiasHelicesSheetPotentialOP |
typedef protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential protocols::fldsgn::potentials::SetSecStructEnergies::NatbiasHelixPairPotential |
typedef protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotentialOP protocols::fldsgn::potentials::SetSecStructEnergies::NatbiasHelixPairPotentialOP |
typedef core::scoring::ScoreFunction protocols::fldsgn::potentials::SetSecStructEnergies::ScoreFunction |
typedef core::scoring::ScoreFunctionCOP protocols::fldsgn::potentials::SetSecStructEnergies::ScoreFunctionCOP |
typedef core::scoring::ScoreFunctionOP protocols::fldsgn::potentials::SetSecStructEnergies::ScoreFunctionOP |
typedef std::string protocols::fldsgn::potentials::SetSecStructEnergies::String |
typedef core::conformation::symmetry::SymmetryInfoCOP protocols::fldsgn::potentials::SetSecStructEnergies::SymmetryInfoCOP |
typedef core::conformation::symmetry::SymmetryInfoOP protocols::fldsgn::potentials::SetSecStructEnergies::SymmetryInfoOP |
typedef utility::tag::TagCOP protocols::fldsgn::potentials::SetSecStructEnergies::TagCOP |
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().
|
overridedefault |
default destructor
|
overridevirtual |
apply defined moves to given Pose
Implements protocols::moves::Mover.
References get_secstruct(), hh_pair_, hh_weight_, hpairpot_, core::scoring::hs_pair, hs_pair_weight_, hs_weight_, hspot_, hss_triplet_, core::scoring::natbias_hh, core::scoring::natbias_hs, core::scoring::natbias_ss, core::scoring::natbias_stwist, core::scoring::rsigma, rsigma_weight_, sfx_, sfx_orig_, core::scoring::ss_pair, ss_pair_, ss_pair_weight_, ss_weight_, stwist_weight_, and protocols::fldsgn::potentials::TR().
|
overridevirtual |
clone this object
Reimplemented from protocols::moves::Mover.
|
overridevirtual |
create this type of object
Reimplemented from protocols::moves::Mover.
|
private |
|
overridevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
References mover_name().
|
private |
chooses and return the secondary structure to be used in computation
[in] | pose | Input 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().
|
private |
initializes pairings and secondary structure from blueprint file
[in] | bp | BluePrint object |
[in] | ss_from_blueprint | If 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().
|
static |
|
private |
copy assignment
|
overridevirtual |
parse xml file
parse xml
Reimplemented from protocols::moves::Mover.
References add_symmetry_, hh_pair_, hh_weight_, hpairpot_, hs_pair_weight_, hs_weight_, hspot_, hss_triplet_, init_from_blueprint(), rsigma_weight_, secstruct_, set_scorefunction_ptr(), ss_pair_, ss_pair_weight_, ss_weight_, stwist_weight_, protocols::fldsgn::potentials::TR(), and use_dssp_.
|
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
[in] | secstruct | Secondary 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_.
|
private |
make symmetric secstruct
Referenced by get_secstruct().
|
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().
|
private |
HHPAIR definition to be used.
Referenced by apply(), init_from_blueprint(), and parse_my_tag().
|
private |
weight for helix and helix pairing potential
Referenced by apply(), and parse_my_tag().
|
private |
Referenced by apply(), and parse_my_tag().
|
private |
weight for hs_pair
Referenced by apply(), and parse_my_tag().
|
private |
weight for heilx and strand pairing potential
Referenced by apply(), and parse_my_tag().
|
private |
Referenced by apply(), and parse_my_tag().
|
private |
helix-strand-strand triplet definition to be used
Referenced by apply(), init_from_blueprint(), and parse_my_tag().
|
private |
weight for strand and strand pairing potential
Referenced by apply(), and parse_my_tag().
|
private |
Secondary structure to be used.
Referenced by get_secstruct(), init_from_blueprint(), parse_my_tag(), and set_secstruct().
|
private |
the centroid scorefunction to use, default "remodel_cen"
Referenced by apply(), scorefunction_ptr(), and set_scorefunction_ptr().
|
private |
Original copy of the centroid scorefunction to use.
Referenced by apply(), and set_scorefunction_ptr().
|
private |
strand pairing definition to be used
Referenced by apply(), init_from_blueprint(), and parse_my_tag().
|
private |
weight for ss_pair
Referenced by apply(), and parse_my_tag().
|
private |
weight for strand and strand pairing potential
Referenced by apply(), and parse_my_tag().
|
private |
weight for sheet twist potential
Referenced by apply(), and parse_my_tag().
|
private |
If true, and secstruct is not set, DSSP will be used to determine secondary structure.
Referenced by get_secstruct(), and parse_my_tag().