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protocols::constraint_generator Namespace Reference

Classes

class  AddConstraints
 Adds constraints generated by ConstraintGenerators to a pose. More...
 
class  AddConstraintsCreator
 
class  AtomPairConstraintGenerator
 Generates atom pair constraints for a set of residues from the current or reference pose. More...
 
class  AtomPairConstraintGeneratorCreator
 
class  ConstraintGenerator
 pure virtual base class More...
 
class  ConstraintGeneratorCreator
 
class  ConstraintGeneratorFactory
 
class  ConstraintGeneratorRegistrator
 This templated class will register an instance of an ConstraintGeneratorCreator (class T) with the ConstraintGeneratorFactory. It will ensure that no ConstraintGenerator creator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place. More...
 
class  ConstraintsManager
 Manages lists of constraints generated by ConstraintGenerators. More...
 
class  ConstraintsMap
 Cacheable data map to cache constraint pointers in the pose. More...
 
class  CoordinateConstraintGenerator
 Generates coodinate constraints. More...
 
class  CoordinateConstraintGeneratorCreator
 
class  DihedralConstraintGenerator
 A cst generator that creates Dihedral constraints for specified residues using a residue selector. More...
 
class  DihedralConstraintGeneratorCreator
 
class  DistanceConstraintGenerator
 Generates AtomPair constraints to enforce a given distance between two residue subsets. More...
 
class  DistanceConstraintGeneratorCreator
 
class  HydrogenBondingAtom
 
class  HydrogenBondInfo
 Database to lookup atoms for hydrogen bonding. More...
 
class  HydrogenBondConstraintGenerator
 This constraint generator generates constraints for favoring formation of hydrogen bonds. More...
 
class  HydrogenBondConstraintGeneratorCreator
 
class  MembraneSpanConstraintGenerator
 Generates constraints for membrane spans to stay in the membrane. More...
 
class  MembraneSpanConstraintGeneratorCreator
 
class  MetalContactsConstraintGenerator
 This constraint generator takes residue selectors for a residue containing metal ion(s) and for residue(s) for which to set up contacts. It allows users to specify which base atoms will be used to define angles/dihedrals to constrain; ideal values for angles/dihedrals/distances; and an option to constrain to native values. More...
 
class  MetalContactsConstraintGeneratorCreator
 
class  RemoveConstraints
 Removes constraints generated by a ConstraintGenerator. More...
 
class  EXCN_RemoveCstsFailed
 
class  RemoveConstraintsCreator
 
class  ResidueTypeConstraintGenerator
 Generates atom pair constraints for a set of residues in the current pose. More...
 
class  ResidueTypeConstraintGeneratorCreator
 
class  TerminiConstraintGenerator
 Generates distance constraints between the upper and lower termini. More...
 
class  TerminiConstraintGeneratorCreator
 

Typedefs

typedef utility::pointer::shared_ptr< AddConstraints > AddConstraintsOP
 
typedef utility::pointer::shared_ptr< AddConstraints const > AddConstraintsCOP
 
typedef utility::pointer::shared_ptr< AtomPairConstraintGenerator > AtomPairConstraintGeneratorOP
 
typedef utility::pointer::shared_ptr< AtomPairConstraintGenerator const > AtomPairConstraintGeneratorCOP
 
typedef utility::pointer::shared_ptr< ConstraintGenerator > ConstraintGeneratorOP
 
typedef utility::pointer::shared_ptr< ConstraintGenerator const > ConstraintGeneratorCOP
 
typedef utility::pointer::weak_ptr< ConstraintGenerator > ConstraintGeneratorAP
 
typedef utility::pointer::weak_ptr< ConstraintGenerator const > ConstraintGeneratorCAP
 
typedef utility::vector1< ConstraintGeneratorOP > ConstraintGeneratorOPs
 
typedef utility::vector1< ConstraintGeneratorCOP > ConstraintGeneratorCOPs
 
typedef utility::pointer::shared_ptr< ConstraintGeneratorCreator > ConstraintGeneratorCreatorOP
 
typedef utility::pointer::shared_ptr< ConstraintGeneratorCreator const > ConstraintGeneratorCreatorCOP
 
typedef utility::pointer::shared_ptr< ConstraintsMap > ConstraintsMapOP
 
typedef utility::pointer::shared_ptr< ConstraintsMap const > ConstraintsMapCOP
 
typedef utility::pointer::shared_ptr< ConstraintsManager > ConstraintsManagerOP
 
typedef utility::pointer::shared_ptr< ConstraintsManager const > ConstraintsManagerCOP
 
typedef utility::pointer::shared_ptr< CoordinateConstraintGenerator > CoordinateConstraintGeneratorOP
 
typedef utility::pointer::shared_ptr< CoordinateConstraintGenerator const > CoordinateConstraintGeneratorCOP
 
typedef utility::pointer::shared_ptr< DihedralConstraintGenerator > DihedralConstraintGeneratorOP
 
typedef utility::pointer::shared_ptr< DihedralConstraintGenerator const > DihedralConstraintGeneratorCOP
 
typedef utility::pointer::shared_ptr< DistanceConstraintGenerator > DistanceConstraintGeneratorOP
 
typedef utility::pointer::shared_ptr< DistanceConstraintGenerator const > DistanceConstraintGeneratorCOP
 
typedef utility::pointer::shared_ptr< HydrogenBondConstraintGenerator > HydrogenBondConstraintGeneratorOP
 
typedef utility::pointer::shared_ptr< HydrogenBondConstraintGenerator const > HydrogenBondConstraintGeneratorCOP
 
typedef utility::vector1< HydrogenBondConstraintGeneratorOP > HydrogenBondConstraintGeneratorOPs
 
typedef utility::vector1< HydrogenBondConstraintGeneratorCOP > HydrogenBondConstraintGeneratorCOPs
 
typedef utility::pointer::shared_ptr< HBondData > HBondDataOP
 
typedef utility::pointer::shared_ptr< HBondData const > HBondDataCOP
 
typedef utility::vector1< HBondDataOP > HBondDataOPs
 
typedef utility::vector1< HBondDataCOP > HBondDataCOPs
 
typedef std::list< HydrogenBondingAtom > HydrogenBondingAtoms
 
typedef utility::pointer::shared_ptr< MembraneSpanConstraintGenerator > MembraneSpanConstraintGeneratorOP
 
typedef utility::pointer::shared_ptr< MembraneSpanConstraintGenerator const > MembraneSpanConstraintGeneratorCOP
 
typedef utility::pointer::shared_ptr< MetalContactsConstraintGenerator > MetalContactsConstraintGeneratorOP
 
typedef utility::pointer::shared_ptr< MetalContactsConstraintGenerator const > MetalContactsConstraintGeneratorCOP
 
typedef utility::pointer::shared_ptr< RemoveConstraints > RemoveConstraintsOP
 
typedef utility::pointer::shared_ptr< RemoveConstraints const > RemoveConstraintsCOP
 
typedef utility::pointer::shared_ptr< ResidueTypeConstraintGenerator > ResidueTypeConstraintGeneratorOP
 
typedef utility::pointer::shared_ptr< ResidueTypeConstraintGenerator const > ResidueTypeConstraintGeneratorCOP
 
typedef utility::pointer::shared_ptr< TerminiConstraintGenerator > TerminiConstraintGeneratorOP
 
typedef utility::pointer::shared_ptr< TerminiConstraintGenerator const > TerminiConstraintGeneratorCOP
 

Functions

std::pair< std::string, std::string > compute_hnq_atoms (core::conformation::Residue const &pose_rsd, std::string const &atom_name)
 
core::Size compute_ref_atom (std::string const &atomname, core::conformation::Residue const &pose_rsd, core::conformation::Residue const &ref_rsd)
 
utility::vector1< core::id::AtomID > parse_custom_torsion (std::string const &atom_names_list, std::string const &resnums, core::pose::Pose const &pose)
 Turn two strings, comma-separated with atom names and resnums into a custom dihedral vector. More...
 
core::id::MainchainTorsionType parse_torsion_type (std::string const &dih)
 Get the MainchainTorsionType from a string (phi/psi/omega/omega2/omega3). More...
 
core::scoring::func::FuncOP parse_func (std::string const &func_str)
 
static basic::Tracer TR ("protocols.constraint_generator.HydrogenBondConstraintGenerator")
 
utility::vector1< core::Size > existing_atoms (core::conformation::Residue const &rsd, utility::vector1< std::string > const &atoms)
 
bool can_hydrogen_bond (std::string const &element_string)
 
core::scoring::constraints::ConstraintOP ambiguous_constraint_wrap (core::scoring::constraints::ConstraintOPs const &csts)
 
std::ostream & operator<< (std::ostream &os, HydrogenBondingAtom const &atom)
 
core::Size last_protein_residue (core::pose::Pose const &pose)
 
core::Size first_protein_residue (core::pose::Pose const &pose)
 
core::pose::PoseOP get_native_pose ()
 gets native pose from command line option, if one is specified More...
 
core::scoring::func::FuncOP scalar_weighted (core::scoring::func::FuncOP func, core::Real const weight)
 helper function to wrap a function with a scalar weighted function More...
 
core::scoring::func::FuncOP create_func (std::string const &func_def)
 creates a function from a text definition More...
 
core::id::SequenceMapping generate_seqmap_from_poses (core::pose::Pose const &pose1, core::pose::Pose const &pose2)
 creates a sequencemapping from pose1 to pose2 More...
 
core::Size compute_nres_in_asymmetric_unit (core::pose::Pose const &pose)
 find number of residues – if pose is symetric, returns nubmer of symmetry-independent residues More...
 
ConstraintGeneratorCOPs parse_constraint_generators (utility::tag::TagCOP tag, basic::datacache::DataMap const &data)
 parses constraint generators from a tag returns vector of ConstraintGeneratorCOPs More...
 
void attributes_for_parse_constraint_generators (utility::tag::AttributeList &attributes)
 Appends the attributes read by parse_constraint_generators. More...
 

Typedef Documentation

◆ AddConstraintsCOP

typedef utility::pointer::shared_ptr< AddConstraints const > protocols::constraint_generator::AddConstraintsCOP

◆ AddConstraintsOP

typedef utility::pointer::shared_ptr< AddConstraints > protocols::constraint_generator::AddConstraintsOP

◆ AtomPairConstraintGeneratorCOP

typedef utility::pointer::shared_ptr< AtomPairConstraintGenerator const > protocols::constraint_generator::AtomPairConstraintGeneratorCOP

◆ AtomPairConstraintGeneratorOP

typedef utility::pointer::shared_ptr< AtomPairConstraintGenerator > protocols::constraint_generator::AtomPairConstraintGeneratorOP

◆ ConstraintGeneratorAP

typedef utility::pointer::weak_ptr< ConstraintGenerator > protocols::constraint_generator::ConstraintGeneratorAP

◆ ConstraintGeneratorCAP

typedef utility::pointer::weak_ptr< ConstraintGenerator const > protocols::constraint_generator::ConstraintGeneratorCAP

◆ ConstraintGeneratorCOP

typedef utility::pointer::shared_ptr< ConstraintGenerator const > protocols::constraint_generator::ConstraintGeneratorCOP

◆ ConstraintGeneratorCOPs

typedef utility::vector1< ConstraintGeneratorCOP > protocols::constraint_generator::ConstraintGeneratorCOPs

◆ ConstraintGeneratorCreatorCOP

typedef utility::pointer::shared_ptr< ConstraintGeneratorCreator const > protocols::constraint_generator::ConstraintGeneratorCreatorCOP

◆ ConstraintGeneratorCreatorOP

typedef utility::pointer::shared_ptr< ConstraintGeneratorCreator > protocols::constraint_generator::ConstraintGeneratorCreatorOP

◆ ConstraintGeneratorOP

typedef utility::pointer::shared_ptr< ConstraintGenerator > protocols::constraint_generator::ConstraintGeneratorOP

◆ ConstraintGeneratorOPs

typedef utility::vector1< ConstraintGeneratorOP > protocols::constraint_generator::ConstraintGeneratorOPs

◆ ConstraintsManagerCOP

typedef utility::pointer::shared_ptr< ConstraintsManager const > protocols::constraint_generator::ConstraintsManagerCOP

◆ ConstraintsManagerOP

typedef utility::pointer::shared_ptr< ConstraintsManager > protocols::constraint_generator::ConstraintsManagerOP

◆ ConstraintsMapCOP

typedef utility::pointer::shared_ptr< ConstraintsMap const > protocols::constraint_generator::ConstraintsMapCOP

◆ ConstraintsMapOP

typedef utility::pointer::shared_ptr< ConstraintsMap > protocols::constraint_generator::ConstraintsMapOP

◆ CoordinateConstraintGeneratorCOP

typedef utility::pointer::shared_ptr< CoordinateConstraintGenerator const > protocols::constraint_generator::CoordinateConstraintGeneratorCOP

◆ CoordinateConstraintGeneratorOP

typedef utility::pointer::shared_ptr< CoordinateConstraintGenerator > protocols::constraint_generator::CoordinateConstraintGeneratorOP

◆ DihedralConstraintGeneratorCOP

typedef utility::pointer::shared_ptr< DihedralConstraintGenerator const > protocols::constraint_generator::DihedralConstraintGeneratorCOP

◆ DihedralConstraintGeneratorOP

typedef utility::pointer::shared_ptr< DihedralConstraintGenerator > protocols::constraint_generator::DihedralConstraintGeneratorOP

◆ DistanceConstraintGeneratorCOP

typedef utility::pointer::shared_ptr< DistanceConstraintGenerator const > protocols::constraint_generator::DistanceConstraintGeneratorCOP

◆ DistanceConstraintGeneratorOP

typedef utility::pointer::shared_ptr< DistanceConstraintGenerator > protocols::constraint_generator::DistanceConstraintGeneratorOP

◆ HBondDataCOP

typedef utility::pointer::shared_ptr< HBondData const > protocols::constraint_generator::HBondDataCOP

◆ HBondDataCOPs

typedef utility::vector1< HBondDataCOP > protocols::constraint_generator::HBondDataCOPs

◆ HBondDataOP

typedef utility::pointer::shared_ptr< HBondData > protocols::constraint_generator::HBondDataOP

◆ HBondDataOPs

typedef utility::vector1< HBondDataOP > protocols::constraint_generator::HBondDataOPs

◆ HydrogenBondConstraintGeneratorCOP

typedef utility::pointer::shared_ptr< HydrogenBondConstraintGenerator const > protocols::constraint_generator::HydrogenBondConstraintGeneratorCOP

◆ HydrogenBondConstraintGeneratorCOPs

typedef utility::vector1< HydrogenBondConstraintGeneratorCOP > protocols::constraint_generator::HydrogenBondConstraintGeneratorCOPs

◆ HydrogenBondConstraintGeneratorOP

typedef utility::pointer::shared_ptr< HydrogenBondConstraintGenerator > protocols::constraint_generator::HydrogenBondConstraintGeneratorOP

◆ HydrogenBondConstraintGeneratorOPs

typedef utility::vector1< HydrogenBondConstraintGeneratorOP > protocols::constraint_generator::HydrogenBondConstraintGeneratorOPs

◆ HydrogenBondingAtoms

typedef std::list< HydrogenBondingAtom > protocols::constraint_generator::HydrogenBondingAtoms

◆ MembraneSpanConstraintGeneratorCOP

typedef utility::pointer::shared_ptr< MembraneSpanConstraintGenerator const > protocols::constraint_generator::MembraneSpanConstraintGeneratorCOP

◆ MembraneSpanConstraintGeneratorOP

typedef utility::pointer::shared_ptr< MembraneSpanConstraintGenerator > protocols::constraint_generator::MembraneSpanConstraintGeneratorOP

◆ MetalContactsConstraintGeneratorCOP

typedef utility::pointer::shared_ptr< MetalContactsConstraintGenerator const > protocols::constraint_generator::MetalContactsConstraintGeneratorCOP

◆ MetalContactsConstraintGeneratorOP

typedef utility::pointer::shared_ptr< MetalContactsConstraintGenerator > protocols::constraint_generator::MetalContactsConstraintGeneratorOP

◆ RemoveConstraintsCOP

typedef utility::pointer::shared_ptr< RemoveConstraints const > protocols::constraint_generator::RemoveConstraintsCOP

◆ RemoveConstraintsOP

typedef utility::pointer::shared_ptr< RemoveConstraints > protocols::constraint_generator::RemoveConstraintsOP

◆ ResidueTypeConstraintGeneratorCOP

typedef utility::pointer::shared_ptr< ResidueTypeConstraintGenerator const > protocols::constraint_generator::ResidueTypeConstraintGeneratorCOP

◆ ResidueTypeConstraintGeneratorOP

typedef utility::pointer::shared_ptr< ResidueTypeConstraintGenerator > protocols::constraint_generator::ResidueTypeConstraintGeneratorOP

◆ TerminiConstraintGeneratorCOP

typedef utility::pointer::shared_ptr< TerminiConstraintGenerator const > protocols::constraint_generator::TerminiConstraintGeneratorCOP

◆ TerminiConstraintGeneratorOP

typedef utility::pointer::shared_ptr< TerminiConstraintGenerator > protocols::constraint_generator::TerminiConstraintGeneratorOP

Function Documentation

◆ ambiguous_constraint_wrap()

core::scoring::constraints::ConstraintOP protocols::constraint_generator::ambiguous_constraint_wrap ( core::scoring::constraints::ConstraintOPs const &  csts)

Referenced by protocols::constraint_generator::HydrogenBondConstraintGenerator::create_residue_constraint().

◆ attributes_for_parse_constraint_generators()

void protocols::constraint_generator::attributes_for_parse_constraint_generators ( utility::tag::AttributeList &  attributes)

Appends the attributes read by parse_constraint_generators.

Referenced by protocols::constraint_filters::ConstraintScoreFilter::provide_xml_schema().

◆ can_hydrogen_bond()

bool protocols::constraint_generator::can_hydrogen_bond ( std::string const &  element_string)

References core::scoring::element_string().

Referenced by protocols::constraint_generator::HydrogenBondConstraintGenerator::compute_valid_atoms().

◆ compute_hnq_atoms()

std::pair< std::string, std::string > protocols::constraint_generator::compute_hnq_atoms ( core::conformation::Residue const &  pose_rsd,
std::string const &  atom_name 
)

References core::conformation::Residue::aa(), core::chemical::aa_asn, core::chemical::aa_gln, and core::chemical::aa_his.

Referenced by protocols::constraint_generator::CoordinateConstraintGenerator::create_residue_constraints().

◆ compute_nres_in_asymmetric_unit()

core::Size protocols::constraint_generator::compute_nres_in_asymmetric_unit ( core::pose::Pose const &  pose)

find number of residues – if pose is symetric, returns nubmer of symmetry-independent residues

References core::pose::Pose::conformation(), core::pose::symmetry::is_symmetric(), and core::pose::Pose::size().

Referenced by protocols::constraint_generator::AtomPairConstraintGenerator::generate_atom_pair_constraints(), protocols::constraint_movers::AddConstraintsToCurrentConformationMover::generate_atom_pair_constraints(), and protocols::constraint_generator::ResidueTypeConstraintGenerator::generate_residue_type_constraints().

◆ compute_ref_atom()

core::Size protocols::constraint_generator::compute_ref_atom ( std::string const &  atomname,
core::conformation::Residue const &  pose_rsd,
core::conformation::Residue const &  ref_rsd 
)

References core::conformation::Residue::atom_index(), core::conformation::Residue::has(), core::conformation::Residue::name(), core::conformation::Residue::seqpos(), and TR().

Referenced by protocols::constraint_generator::CoordinateConstraintGenerator::create_residue_constraints().

◆ create_func()

core::scoring::func::FuncOP protocols::constraint_generator::create_func ( std::string const &  func_def)

creates a function from a text definition

Referenced by protocols::constraint_generator::HydrogenBondConstraintGenerator::set_angle1_func(), protocols::constraint_generator::HydrogenBondConstraintGenerator::set_angle2_func(), and protocols::constraint_generator::HydrogenBondConstraintGenerator::set_atom_pair_func().

◆ existing_atoms()

utility::vector1< core::Size > protocols::constraint_generator::existing_atoms ( core::conformation::Residue const &  rsd,
utility::vector1< std::string > const &  atoms 
)

References core::chemical::ResidueType::atom_index(), core::conformation::Residue::has(), and core::conformation::Residue::type().

◆ first_protein_residue()

core::Size protocols::constraint_generator::first_protein_residue ( core::pose::Pose const &  pose)

References core::conformation::Residue::is_protein(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by protocols::surface_docking::SurfaceDockingProtocol::apply(), protocols::constraint_generator::TerminiConstraintGenerator::apply(), protocols::surface_docking::SurfaceDockingProtocol::create_surface_packer_task(), protocols::surface_docking::SurfaceDockingProtocol::initialize_surface_energies(), protocols::surface_docking::FullatomRelaxMover::setup_movers(), and protocols::surface_docking::SurfaceDockingProtocol::setup_movers().

◆ generate_seqmap_from_poses()

core::id::SequenceMapping protocols::constraint_generator::generate_seqmap_from_poses ( core::pose::Pose const &  pose1,
core::pose::Pose const &  pose2 
)

creates a sequencemapping from pose1 to pose2

References core::id::SequenceMapping::identity(), core::pose::Pose::sequence(), core::pose::sequence_map_from_pdbinfo(), core::pose::Pose::size(), and TR().

Referenced by protocols::constraint_generator::ResidueTypeConstraintGenerator::apply(), protocols::relax::AtomCoordinateCstMover::generate_constraints(), and protocols::constraint_generator::CoordinateConstraintGenerator::generate_seqmap().

◆ get_native_pose()

core::pose::PoseOP protocols::constraint_generator::get_native_pose ( )

gets native pose from command line option, if one is specified

References core::io::pdb::build_pose_from_pdb_as_is().

Referenced by protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::apply(), protocols::symmetric_docking::SymDockProtocol::calc_rms(), protocols::constraint_generator::AtomPairConstraintGenerator::parse_tag(), protocols::constraint_generator::CoordinateConstraintGenerator::parse_tag(), protocols::constraint_generator::ResidueTypeConstraintGenerator::parse_tag(), and protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::parse_tag().

◆ last_protein_residue()

core::Size protocols::constraint_generator::last_protein_residue ( core::pose::Pose const &  pose)

References core::conformation::Residue::is_protein(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by protocols::hybridization::HybridizeProtocol::align_by_domain(), and protocols::constraint_generator::TerminiConstraintGenerator::apply().

◆ operator<<()

std::ostream& protocols::constraint_generator::operator<< ( std::ostream &  os,
HydrogenBondingAtom const &  atom 
)

◆ parse_constraint_generators()

ConstraintGeneratorCOPs protocols::constraint_generator::parse_constraint_generators ( utility::tag::TagCOP  tag,
basic::datacache::DataMap const &  data 
)

parses constraint generators from a tag returns vector of ConstraintGeneratorCOPs

Referenced by protocols::constraint_filters::ConstraintScoreFilter::parse_my_tag(), and protocols::constraint_generator::RemoveConstraints::parse_my_tag().

◆ parse_custom_torsion()

utility::vector1< core::id::AtomID > protocols::constraint_generator::parse_custom_torsion ( std::string const &  atom_names_list,
std::string const &  resnums,
core::pose::Pose const &  pose 
)

Turn two strings, comma-separated with atom names and resnums into a custom dihedral vector.

References core::conformation::Residue::atom_index(), core::pose::get_resnum_list_ordered(), core::pose::Pose::residue(), core::id::to_string(), and TR().

Referenced by protocols::constraint_generator::DihedralConstraintGenerator::apply().

◆ parse_func()

core::scoring::func::FuncOP protocols::constraint_generator::parse_func ( std::string const &  func_str)

References core::scoring::func::FuncFactory::new_func().

Referenced by protocols::constraint_generator::DistanceConstraintGenerator::set_function().

◆ parse_torsion_type()

core::id::MainchainTorsionType protocols::constraint_generator::parse_torsion_type ( std::string const &  dih)

Get the MainchainTorsionType from a string (phi/psi/omega/omega2/omega3).

References core::id::omega2_dihedral, core::id::omega3_dihedral, core::id::omega_dihedral, core::id::phi_dihedral, and core::id::psi_dihedral.

Referenced by protocols::constraint_generator::DihedralConstraintGenerator::parse_tag().

◆ scalar_weighted()

core::scoring::func::FuncOP protocols::constraint_generator::scalar_weighted ( core::scoring::func::FuncOP  func,
core::Real const  weight 
)

helper function to wrap a function with a scalar weighted function

Referenced by protocols::constraint_generator::AtomPairConstraintGenerator::add_constraints(), protocols::constraint_generator::TerminiConstraintGenerator::apply(), protocols::fldsgn::SheetConstraintGenerator::weighted_func(), and protocols::fold_from_loops::constraint_generator::AutomaticSheetConstraintGenerator::weighted_func().

◆ TR()

static basic::Tracer protocols::constraint_generator::TR ( "protocols.constraint_generator.HydrogenBondConstraintGenerator"  )
static

Referenced by protocols::constraint_generator::HydrogenBondConstraintGenerator::add_atom_definitions(), protocols::constraint_generator::AtomPairConstraintGenerator::add_constraints(), protocols::constraint_generator::AddConstraints::apply(), protocols::constraint_generator::RemoveConstraints::apply(), protocols::constraint_generator::CoordinateConstraintGenerator::apply(), protocols::constraint_generator::DihedralConstraintGenerator::apply(), protocols::constraint_generator::DistanceConstraintGenerator::apply(), protocols::constraint_generator::HydrogenBondConstraintGenerator::apply(), protocols::constraint_generator::MetalContactsConstraintGenerator::apply(), protocols::constraint_generator::ResidueTypeConstraintGenerator::apply(), protocols::constraint_generator::TerminiConstraintGenerator::apply(), protocols::constraint_generator::HydrogenBondConstraintGenerator::choose_atoms(), compute_ref_atom(), protocols::constraint_generator::DistanceConstraintGenerator::create_constraint(), protocols::constraint_generator::HydrogenBondConstraintGenerator::create_residue_constraint(), protocols::constraint_generator::CoordinateConstraintGenerator::create_residue_constraints(), protocols::constraint_generator::AtomPairConstraintGenerator::create_sequence_mapping(), protocols::constraint_generator::AtomPairConstraintGenerator::generate_atom_pair_constraints(), protocols::constraint_generator::ResidueTypeConstraintGenerator::generate_residue_type_constraints(), generate_seqmap_from_poses(), protocols::constraint_generator::MetalContactsConstraintGenerator::get_contact_resnums(), parse_custom_torsion(), protocols::constraint_generator::AddConstraints::parse_my_tag(), protocols::constraint_generator::CoordinateConstraintGenerator::prepare_constraint_target_pose(), protocols::constraint_generator::ConstraintGeneratorFactory::provide_xml_schema(), protocols::constraint_generator::DistanceConstraintGenerator::set_function(), and protocols::constraint_generator::ConstraintsManager::store_constraints().

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