Rosetta 3.4
Public Member Functions | Protected Member Functions
protocols::constraints_additional::MaxSeqSepConstraintSet Class Reference

#include <MaxSeqSepConstraintSet.hh>

Inheritance diagram for protocols::constraints_additional::MaxSeqSepConstraintSet:
Inheritance graph
[legend]
Collaboration diagram for protocols::constraints_additional::MaxSeqSepConstraintSet:
Collaboration graph
[legend]

List of all members.

Public Member Functions

 MaxSeqSepConstraintSet (ConstraintSet const &other, core::kinematics::FoldTree const &f)
 MaxSeqSepConstraintSet (MaxSeqSepConstraintSet const &other)
 constructor. Does nothing.
 ~MaxSeqSepConstraintSet ()
 a ConstraintsSet whose constraints can be switched off, according to sequence separation in residues between residue pair constraints.
ConstraintSetOP clone () const
virtual ConstraintSetOP remapped_clone (core::pose::Pose const &src, core::pose::Pose const &dest, core::id::SequenceMappingCOP smap=NULL) const
 Copies the data from this ConstraintSet into a new object and returns its 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. This will really clone all constraints since they have to change their atom-numbers and residue-numbers.
Size max_seq_sep () const
void set_max_seq_sep (Size setting)
void residue_pair_energy (Residue const &rsd1, Residue const &rsd2, Pose const &pose, core::scoring::ScoreFunction const &scorefxn, core::scoring::EnergyMap &emap) const
bool too_far (int const pos1, int const pos2) const
Size largest_possible_sequence_sep (core::pose::Pose const &pose) const
bool residue_pair_constraint_exists (int const pos1, int const pos2) const
 uses the dof constraints
virtual void setup_for_minimizing_for_residue_pair (core::conformation::Residue const &rsd1, core::conformation::Residue const &rsd2, core::pose::Pose const &pose, core::scoring::ScoreFunction const &sfxn, core::kinematics::MinimizerMapBase const &minmap, core::scoring::ResSingleMinimizationData const &res1_data_cache, core::scoring::ResSingleMinimizationData const &res2_data_cache, core::scoring::ResPairMinimizationData &respair_data_cache) const
 If a pair of residues are not too far, then let the parent class implementation add the constraints for this respair to the respair_data_cache. This is the only opportunity the MaxSeqSepConstraint set has to influence how constraints are evaluated during minimization.
Size show_violations (std::ostream &out, core::pose::Pose &, Size verbose_level, core::Real threshold=1)
core::kinematics::ShortestPathInFoldTree
const & 
shortest_path () const
virtual void eval_non_residue_pair_energy (core::pose::Pose const &pose, core::scoring::ScoreFunction const &sfxn, core::scoring::EnergyMap &emap) const

Protected Member Functions

 MaxSeqSepConstraintSet (ConstraintSet const &other, core::kinematics::ShortestPathInFoldTreeOP sp)

Constructor & Destructor Documentation

protocols::constraints_additional::MaxSeqSepConstraintSet::MaxSeqSepConstraintSet ( ConstraintSet const &  other,
core::kinematics::FoldTree const &  f 
)

Referenced by clone(), and remapped_clone().

protocols::constraints_additional::MaxSeqSepConstraintSet::MaxSeqSepConstraintSet ( MaxSeqSepConstraintSet const &  other)

constructor. Does nothing.

protocols::constraints_additional::MaxSeqSepConstraintSet::~MaxSeqSepConstraintSet ( )

a ConstraintsSet whose constraints can be switched off, according to sequence separation in residues between residue pair constraints.

protocols::constraints_additional::MaxSeqSepConstraintSet::MaxSeqSepConstraintSet ( ConstraintSet const &  other,
core::kinematics::ShortestPathInFoldTreeOP  sp 
) [protected]

Member Function Documentation

ConstraintSetOP protocols::constraints_additional::MaxSeqSepConstraintSet::clone ( ) const [inline, virtual]
void protocols::constraints_additional::MaxSeqSepConstraintSet::eval_non_residue_pair_energy ( core::pose::Pose const &  pose,
core::scoring::ScoreFunction const &  sfxn,
core::scoring::EnergyMap emap 
) const [virtual]
Size protocols::constraints_additional::MaxSeqSepConstraintSet::largest_possible_sequence_sep ( core::pose::Pose const &  pose) const
Size protocols::constraints_additional::MaxSeqSepConstraintSet::max_seq_sep ( ) const [inline]
ConstraintSetOP protocols::constraints_additional::MaxSeqSepConstraintSet::remapped_clone ( core::pose::Pose const &  src,
core::pose::Pose const &  dest,
core::id::SequenceMappingCOP  smap = NULL 
) const [virtual]

Copies the data from this ConstraintSet into a new object and returns its 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. This will really clone all constraints since they have to change their atom-numbers and residue-numbers.

Copies the data from this ConstraintSet 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. This will really clone all constraints since they have to change their atom-numbers and residue-numbers.

Reimplemented from core::scoring::constraints::ConstraintSet.

References max_seq_sep(), MaxSeqSepConstraintSet(), and core::scoring::constraints::ConstraintSet::remapped_clone().

bool protocols::constraints_additional::MaxSeqSepConstraintSet::residue_pair_constraint_exists ( int const  pos1,
int const  pos2 
) const [inline, virtual]
void protocols::constraints_additional::MaxSeqSepConstraintSet::residue_pair_energy ( Residue const &  rsd1,
Residue const &  rsd2,
Pose const &  pose,
core::scoring::ScoreFunction const &  scorefxn,
core::scoring::EnergyMap emap 
) const [virtual]
void protocols::constraints_additional::MaxSeqSepConstraintSet::set_max_seq_sep ( Size  setting) [inline]
void protocols::constraints_additional::MaxSeqSepConstraintSet::setup_for_minimizing_for_residue_pair ( core::conformation::Residue const &  rsd1,
core::conformation::Residue const &  rsd2,
core::pose::Pose const &  pose,
core::scoring::ScoreFunction const &  sfxn,
core::kinematics::MinimizerMapBase const &  minmap,
core::scoring::ResSingleMinimizationData const &  res1_data_cache,
core::scoring::ResSingleMinimizationData const &  res2_data_cache,
core::scoring::ResPairMinimizationData respair_data_cache 
) const [virtual]

If a pair of residues are not too far, then let the parent class implementation add the constraints for this respair to the respair_data_cache. This is the only opportunity the MaxSeqSepConstraint set has to influence how constraints are evaluated during minimization.

Reimplemented from core::scoring::constraints::ConstraintSet.

References core::conformation::Residue::seqpos(), core::scoring::constraints::ConstraintSet::setup_for_minimizing_for_residue_pair(), and too_far().

core::kinematics::ShortestPathInFoldTree const& protocols::constraints_additional::MaxSeqSepConstraintSet::shortest_path ( ) const [inline]
Size protocols::constraints_additional::MaxSeqSepConstraintSet::show_violations ( std::ostream &  out,
core::pose::Pose pose,
Size  verbose_level,
core::Real  threshold = 1 
)
bool protocols::constraints_additional::MaxSeqSepConstraintSet::too_far ( int const  pos1,
int const  pos2 
) const

The documentation for this class was generated from the following files:
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Defines