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Rosetta 3.5
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Rosetta 3.5
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This constraint favors the backbone landing on a "stub" backbone, which puts the sidechain in a pre-determined desirable location. More...
#include <BackboneStubConstraint.hh>
Public Member Functions | |
| virtual std::string | type () const |
| Returns a unique string identified for this constraint. Used in several places, including the ConstraintIO class. More... | |
| BackboneStubConstraint (pose::Pose const &pose, Size const seqpos, AtomID const &fixed_atom_id, conformation::Residue const &target_rsd, core::Real const &superposition_bonus, core::Real const &CB_force_constant) | |
| virtual | ~BackboneStubConstraint () |
| virtual Size | natoms () const |
| Returns the number of atoms involved in defining this constraint. If the constraint doesn't depend on particular atoms (e.g. a residue type constraint) this function can return zero. More... | |
| virtual AtomID const & | atom (Size const index) const |
| Returns the AtomID referred to by index. More... | |
| bool | operator== (Constraint const &other) const |
| possibility to compare constraint according to data and not just pointers More... | |
| virtual void | score (XYZ_Func const &xyz_func, EnergyMap const &weights, EnergyMap &emap) const |
| Calculates a score for this constraint using XYZ_Func, and puts the UNWEIGHTED score into emap. Although the current set of weights currently is provided, Constraint objects should put unweighted scores into emap because the ScoreFunction will do the weighting itself. More... | |
| virtual void | fill_f1_f2 (AtomID const &atom, XYZ_Func const &xyz, Vector &F1, Vector &F2, EnergyMap const &weights) const |
| virtual void | show (std::ostream &out) const |
| This method is intended to show the value of the Constraint function evaluated over some reasonable range of values. For example, a constraint between pairs of atoms might show the values of the Constraint function between 4 and 12 angstroms. More... | |
| core::Size | seqpos () const |
| returns the private member seqpos_ More... | |
| virtual ConstraintOP | clone () const |
| Copies the data from this Constraint into a new object and returns an OP to the new object. Intended to be implemented by derived classes and used by pose.add_constraint. More... | |
| virtual ConstraintOP | remapped_clone (pose::Pose const &src, pose::Pose const &dest, id::SequenceMappingCOP map=NULL) const |
| Copies the data from this Constraint into a new object and returns an OP atoms are mapped to atoms with the same name in dest pose ( e.g. for switch from centroid to fullatom ) if a sequence_mapping is present it is used to map residue numbers .. NULL = identity mapping to the new object. Intended to be implemented by derived classes. More... | |
 Public Member Functions inherited from core::scoring::constraints::Constraint | |
| Constraint (ScoreType const &t) | |
| Constructor for Constraint class. More... | |
| virtual | ~Constraint () |
| Virtual destructor. More... | |
| virtual ConstraintOP | clone (FuncOP) const |
| virtual utility::vector1 < core::Size > | residues () const |
| Returns the pose numbers of the residues involved in this constraint, in no particular order. More... | |
| virtual void | read_constraint (std::istream &, core::pose::Pose const &) |
| This method is totally redundant with read_def YAY. More... | |
| ScoreType const & | score_type () const |
| Returns the ScoreType that this Constraint object will use. More... | |
| virtual void | read_data (std::istream &) |
| initialize this Constraint from the given std::istream. It's amazing that there are three functions for doing this inside of Constraint.hh. SO WHAT IS THIS SUPPOSED TO DO ? not overloaded by e.g., AtomPairConstraint or CoordinateConstraint, More... | |
| virtual ConstraintOP | remap_resid (core::id::SequenceMapping const &) const |
| apply a resid remapping to this constraint, returns the remapped constraint Does this return an owning pointer to this constraint or a copy? Documentation would be nice. More... | |
| virtual core::Real | dist (core::pose::Pose const &) const |
| return the "raw" distance before handed to the FUNC object More... | |
| virtual core::Real | dist (XYZ_Func const &) const |
| virtual void | setup_for_scoring (XYZ_Func const &, ScoreFunction const &) const |
| virtual void | setup_for_derivatives (XYZ_Func const &, ScoreFunction const &) const |
| virtual Real | score (conformation::Conformation const &) const |
| Returns the score of this constraint computed over the given conformation. Not necessarily implemented in all derived classes, as it's redundant with the score( XYZ_Func, EnergyMap, EnergyMap ) method defined above. Returns 0.0 if not implemented. More... | |
| virtual void | fill_f1_f2 (AtomID const &atom, XYZ_Func const &xyz_func, Vector &F1, Vector &F2, EnergyMap const &weights) const =0 |
| Fill the f1 and f2 vectors, necessary for considering the derivative this constraint during minimization. (someone please reference Bill Wedermeyer's paper here, as I'm in an airport and can't fill it in myself!) More... | |
| virtual void | show_def (std::ostream &, pose::Pose const &) const |
| Prints the definition of a Constraint to the given std::ostream, using the given Pose, and the given FuncFactory. This method is intended to be overridden by derived classes if they'd like to use the ConstraintIO machinery. It's also not clear why this method takes a Pose, other than to be symmetric with read_def. More... | |
| virtual void | read_def (std::istream &, pose::Pose const &, FuncFactory const &) |
| virtual void | steal_def (pose::Pose const &) |
| std::string | to_string () const |
| Convenience function, returns the results of show() as a string. Not to be overriden by derived classes. More... | |
| virtual Size | show_violations (std::ostream &out, pose::Pose const &, Size, Real threshold=1) const |
| Prints the violations of this constraint to the given std::ostream. What are violations? It's not defined, and it depends on the constraint and the function! also - wtf is threshold? it was defined as a Size in CoordinateConstraint, I don't know which definition is the right one. Documentation would be nice ... More... | |
| virtual Func const & | get_func () const |
| Returns the Func object associated with this Constraint object. More... | |
| bool | operator!= (Constraint const &other) const |
| possibility to do object comparison instead of pointer comparison More... | |
| virtual core::Size | choose_effective_sequence_separation (core::kinematics::ShortestPathInFoldTree const &sp, numeric::random::RandomGenerator &) |
| virtual core::Size | effective_sequence_separation (core::kinematics::ShortestPathInFoldTree const &) const |
Static Private Attributes | |
| static utility::pointer::owning_ptr < AngleConstraint > | ang_cst_ |
| why is this static? More... | |
Additional Inherited Members | |
| Public Types inherited from core::scoring::constraints::Constraint | |
| typedef id::AtomID | AtomID |
This constraint favors the backbone landing on a "stub" backbone, which puts the sidechain in a pre-determined desirable location.
Definition at line 39 of file BackboneStubConstraint.hh.
| core::scoring::constraints::BackboneStubConstraint::BackboneStubConstraint | ( | pose::Pose const & | pose, |
| Size const | seqpos, | ||
| AtomID const & | fixed_atom_id, | ||
| conformation::Residue const & | target_rsd, | ||
| core::Real const & | superposition_bonus, | ||
| core::Real const & | CB_force_constant | ||
| ) |
Definition at line 52 of file BackboneStubConstraint.cc.
References core::conformation::Residue::aa(), core::chemical::aa_gly, ang_cst_, atom_ids_, C_atom_id_, C_N_target_, C_target_, CA_atom_id_, CA_target_, CB_atom_id_, CB_CA_target_, CB_target_, fixed_atom_id_, fixed_reference_point_, core::conformation::Residue::is_protein(), N_atom_id_, N_target_, core::pose::Pose::residue(), seqpos_, core::scoring::constraints::TR(), core::conformation::Residue::xyz(), and core::pose::Pose::xyz().
Referenced by clone(), and remapped_clone().
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Definition at line 55 of file BackboneStubConstraint.hh.
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Returns the AtomID referred to by index.
Note that this function isn't actually used by the constraint scoring machenery. If you're calling it on a generic Constraint (as opposed to specifically on a derived class) you're probably doing something wrong.
Implements core::scoring::constraints::Constraint.
Definition at line 59 of file BackboneStubConstraint.hh.
References atom_ids_.
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Copies the data from this Constraint into a new object and returns an OP to the new object. Intended to be implemented by derived classes and used by pose.add_constraint.
Implements core::scoring::constraints::Constraint.
Definition at line 359 of file BackboneStubConstraint.cc.
References BackboneStubConstraint().
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Definition at line 240 of file BackboneStubConstraint.cc.
References core::conformation::Residue::aa(), core::chemical::aa_gly, ang_cst_, C_atom_id_, C_N_target_, CA_atom_id_, CB_atom_id_, CB_CA_target_, CB_force_constant_, CB_target_, protocols::comparative_modeling::features::E, core::conformation::Residue::is_protein(), N_atom_id_, core::scoring::constraints::XYZ_Func::residue(), core::scoring::constraints::Constraint::score_type(), seqpos_, superposition_bonus_, core::scoring::constraints::TR(), and core::conformation::Residue::xyz().
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Returns the number of atoms involved in defining this constraint. If the constraint doesn't depend on particular atoms (e.g. a residue type constraint) this function can return zero.
Note that this function isn't actually used by the constraint scoring machenery. If you're calling it on a generic Constraint (as opposed to specifically on a derived class) you're probably doing something wrong.
Implements core::scoring::constraints::Constraint.
Definition at line 57 of file BackboneStubConstraint.hh.
References atom_ids_.
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possibility to compare constraint according to data and not just pointers
Reimplemented from core::scoring::constraints::Constraint.
Definition at line 121 of file BackboneStubConstraint.cc.
References C_atom_id_, C_N_target_, C_target_, CA_atom_id_, CA_target_, CB_atom_id_, CB_CA_target_, CB_force_constant_, CB_target_, fixed_atom_id_, fixed_reference_point_, N_atom_id_, N_target_, seqpos_, and superposition_bonus_.
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Copies the data from this Constraint into a new object and returns an OP atoms are mapped to atoms with the same name in dest pose ( e.g. for switch from centroid to fullatom ) if a sequence_mapping is present it is used to map residue numbers .. NULL = identity mapping to the new object. Intended to be implemented by derived classes.
Reimplemented from core::scoring::constraints::Constraint.
Definition at line 368 of file BackboneStubConstraint.cc.
References BackboneStubConstraint(), C_target_, CA_target_, CB_force_constant_, CB_target_, core::conformation::ResidueFactory::create_residue(), fixed_atom_id_, core::chemical::ChemicalManager::get_instance(), N_target_, core::chemical::ChemicalManager::residue_type_set(), core::id::AtomID::rsd(), seqpos_, and superposition_bonus_.
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Calculates a score for this constraint using XYZ_Func, and puts the UNWEIGHTED score into emap. Although the current set of weights currently is provided, Constraint objects should put unweighted scores into emap because the ScoreFunction will do the weighting itself.
Implements core::scoring::constraints::Constraint.
Definition at line 170 of file BackboneStubConstraint.cc.
References core::conformation::Residue::aa(), core::chemical::aa_gly, ang_cst_, C_N_target_, CB_CA_target_, CB_force_constant_, CB_target_, protocols::comparative_modeling::features::E, fixed_atom_id_, fixed_reference_point_, core::conformation::Residue::is_protein(), core::scoring::constraints::XYZ_Func::residue(), core::scoring::constraints::Constraint::score_type(), seqpos_, superposition_bonus_, core::scoring::constraints::TR(), and core::conformation::Residue::xyz().
| core::Size core::scoring::constraints::BackboneStubConstraint::seqpos | ( | ) | const |
returns the private member seqpos_
Definition at line 111 of file BackboneStubConstraint.cc.
References seqpos_.
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This method is intended to show the value of the Constraint function evaluated over some reasonable range of values. For example, a constraint between pairs of atoms might show the values of the Constraint function between 4 and 12 angstroms.
Reimplemented from core::scoring::constraints::Constraint.
Definition at line 114 of file BackboneStubConstraint.cc.
References CB_force_constant_, seqpos_, and superposition_bonus_.
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Returns a unique string identified for this constraint. Used in several places, including the ConstraintIO class.
Reimplemented from core::scoring::constraints::Constraint.
Definition at line 42 of file BackboneStubConstraint.hh.
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why is this static?
Definition at line 117 of file BackboneStubConstraint.hh.
Referenced by BackboneStubConstraint(), fill_f1_f2(), and score().
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Definition at line 109 of file BackboneStubConstraint.hh.
Referenced by atom(), BackboneStubConstraint(), and natoms().
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Definition at line 108 of file BackboneStubConstraint.hh.
Referenced by BackboneStubConstraint(), fill_f1_f2(), and operator==().
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Definition at line 111 of file BackboneStubConstraint.hh.
Referenced by BackboneStubConstraint(), fill_f1_f2(), operator==(), and score().
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Definition at line 111 of file BackboneStubConstraint.hh.
Referenced by BackboneStubConstraint(), operator==(), and remapped_clone().
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Definition at line 108 of file BackboneStubConstraint.hh.
Referenced by BackboneStubConstraint(), fill_f1_f2(), and operator==().
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Definition at line 111 of file BackboneStubConstraint.hh.
Referenced by BackboneStubConstraint(), operator==(), and remapped_clone().
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Definition at line 108 of file BackboneStubConstraint.hh.
Referenced by BackboneStubConstraint(), fill_f1_f2(), and operator==().
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Definition at line 111 of file BackboneStubConstraint.hh.
Referenced by BackboneStubConstraint(), fill_f1_f2(), operator==(), and score().
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Definition at line 105 of file BackboneStubConstraint.hh.
Referenced by fill_f1_f2(), operator==(), remapped_clone(), score(), and show().
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Definition at line 111 of file BackboneStubConstraint.hh.
Referenced by BackboneStubConstraint(), fill_f1_f2(), operator==(), remapped_clone(), and score().
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Definition at line 113 of file BackboneStubConstraint.hh.
Referenced by BackboneStubConstraint(), operator==(), remapped_clone(), and score().
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Definition at line 114 of file BackboneStubConstraint.hh.
Referenced by BackboneStubConstraint(), operator==(), and score().
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Definition at line 108 of file BackboneStubConstraint.hh.
Referenced by BackboneStubConstraint(), fill_f1_f2(), and operator==().
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Definition at line 111 of file BackboneStubConstraint.hh.
Referenced by BackboneStubConstraint(), operator==(), and remapped_clone().
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Definition at line 107 of file BackboneStubConstraint.hh.
Referenced by BackboneStubConstraint(), fill_f1_f2(), operator==(), remapped_clone(), score(), seqpos(), and show().
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Definition at line 104 of file BackboneStubConstraint.hh.
Referenced by fill_f1_f2(), operator==(), remapped_clone(), score(), and show().
1.8.4