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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  EXCN_RemoveCstsFailed
 
class  HydrogenBondConstraintGenerator
 This constraint generator generates constraints for favoring formation of hydrogen bonds. More...
 
class  HydrogenBondConstraintGeneratorCreator
 
class  HydrogenBondInfo
 Database to lookup atoms for hydrogen bonding. More...
 
class  HydrogenBondingAtom
 
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  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::Sizeexisting_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

typedef utility::pointer::shared_ptr< AddConstraints const > protocols::constraint_generator::AddConstraintsCOP
typedef utility::pointer::shared_ptr< AddConstraints > protocols::constraint_generator::AddConstraintsOP
typedef utility::pointer::shared_ptr< ConstraintsManager const > protocols::constraint_generator::ConstraintsManagerCOP
typedef utility::pointer::shared_ptr< ConstraintsMap const > protocols::constraint_generator::ConstraintsMapCOP
typedef utility::pointer::shared_ptr< ConstraintsMap > protocols::constraint_generator::ConstraintsMapOP
typedef utility::pointer::shared_ptr< HBondData const > protocols::constraint_generator::HBondDataCOP
typedef utility::pointer::shared_ptr< HBondData > protocols::constraint_generator::HBondDataOP
typedef utility::pointer::shared_ptr< RemoveConstraints const > protocols::constraint_generator::RemoveConstraintsCOP

Function Documentation

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

bool protocols::constraint_generator::can_hydrogen_bond ( std::string const &  element_string)
std::pair< std::string, std::string > protocols::constraint_generator::compute_hnq_atoms ( core::conformation::Residue const &  pose_rsd,
std::string const &  atom_name 
)
core::Size protocols::constraint_generator::compute_nres_in_asymmetric_unit ( core::pose::Pose const &  pose)
core::Size protocols::constraint_generator::compute_ref_atom ( std::string const &  atomname,
core::conformation::Residue const &  pose_rsd,
core::conformation::Residue const &  ref_rsd 
)
core::scoring::func::FuncOP protocols::constraint_generator::create_func ( std::string const &  func_def)
utility::vector1< core::Size > protocols::constraint_generator::existing_atoms ( core::conformation::Residue const &  rsd,
utility::vector1< std::string > const &  atoms 
)
core::Size protocols::constraint_generator::first_protein_residue ( core::pose::Pose const &  pose)
core::id::SequenceMapping protocols::constraint_generator::generate_seqmap_from_poses ( core::pose::Pose const &  pose1,
core::pose::Pose const &  pose2 
)
core::pose::PoseOP protocols::constraint_generator::get_native_pose ( )
core::Size protocols::constraint_generator::last_protein_residue ( core::pose::Pose const &  pose)
std::ostream& protocols::constraint_generator::operator<< ( std::ostream &  os,
HydrogenBondingAtom const &  atom 
)
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_generator::RemoveConstraints::parse_my_tag(), and protocols::constraint_filters::ConstraintScoreFilter::parse_my_tag().

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().

core::scoring::func::FuncOP protocols::constraint_generator::parse_func ( std::string const &  func_str)
core::id::MainchainTorsionType protocols::constraint_generator::parse_torsion_type ( std::string const &  dih)
core::scoring::func::FuncOP protocols::constraint_generator::scalar_weighted ( core::scoring::func::FuncOP  func,
core::Real const  weight 
)
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::MetalContactsConstraintGenerator::apply(), protocols::constraint_generator::TerminiConstraintGenerator::apply(), protocols::constraint_generator::DistanceConstraintGenerator::apply(), protocols::constraint_generator::RemoveConstraints::apply(), protocols::constraint_generator::CoordinateConstraintGenerator::apply(), protocols::constraint_generator::ResidueTypeConstraintGenerator::apply(), protocols::constraint_generator::DihedralConstraintGenerator::apply(), protocols::constraint_generator::HydrogenBondConstraintGenerator::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::DistanceConstraintGenerator::set_function(), and protocols::constraint_generator::ConstraintsManager::store_constraints().