Rosetta
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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...
#include <MetalContactsConstraintGenerator.hh>
Static Public Member Functions | |
static std::string | class_name () |
static void | provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd) |
Protected Member Functions | |
void | parse_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override |
called by parse_my_tag – should not be used directly More... | |
Private Member Functions | |
core::Size | get_ligand_resnum (core::pose::Pose const &pose) const |
Uses private data to compute ligand resnums based on selector/resnum string and pose. More... | |
void | get_contact_resnums (core::pose::Pose const &pose, std::set< core::Size > &output) const |
Uses private data to compute contact residue numbers based on selector/resnum string and pose; inserts them into the provided set. More... | |
Private Attributes | |
core::Real | dist_cutoff_multiplier_ =1.0 |
bool | use_ligand_selector_ =false |
std::string | ligand_atom_name_ ="" |
core::select::residue_selector::ResidueSelectorCOP | ligand_selector_ |
std::string | ligand_resnum_string_ ="" |
bool | use_contact_selector_ =false |
core::select::residue_selector::ResidueSelectorCOP | contact_selector_ |
std::string | contact_resnum_string_ ="" |
std::string | base_atom_name_ ="" |
std::string | base_base_atom_name_ ="" |
core::Real | ideal_distance_ =-1.0 |
utility::vector1< core::Real > | ideal_angle_about_contact_ |
utility::vector1< core::Real > | ideal_dihedral_about_contact_ |
utility::vector1< core::Real > | ideal_angle_about_metal_ |
utility::vector1< core::Real > | ideal_dihedral_about_metal_ |
utility::vector1< core::Real > | ideal_dihedral_3_ |
bool | score_against_internal_contacts_ =false |
bool | constrain_to_closest_ =true |
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.
protocols::constraint_generator::MetalContactsConstraintGenerator::MetalContactsConstraintGenerator | ( | ) |
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generates constraints and adds them to the pose
Implements protocols::constraint_generator::ConstraintGenerator.
References protocols::mean_field::arg_min(), core::conformation::Residue::atom(), core::conformation::Residue::atom_base(), core::conformation::Residue::atom_index(), core::id::AtomID::atomno(), base_atom_name_, base_base_atom_name_, core::conformation::Residue::bonded_neighbor(), constrain_to_closest_, dist_cutoff_multiplier_, core::kinematics::distance(), core::util::find_metalbinding_atoms_helper(), get_contact_resnums(), get_ligand_resnum(), ideal_angle_about_contact_, ideal_angle_about_metal_, ideal_dihedral_3_, ideal_dihedral_about_contact_, ideal_dihedral_about_metal_, ideal_distance_, core::pose::Pose::is_fullatom(), ligand_atom_name_, core::scoring::metalbinding_constraint, core::pose::Pose::residue(), core::id::AtomID::rsd(), score_against_internal_contacts_, protocols::constraint_generator::TR(), core::conformation::Atom::type(), and core::conformation::Atom::xyz().
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std::string protocols::constraint_generator::MetalContactsConstraintGenerator::get_base_atom_name | ( | ) | const |
References base_atom_name_.
std::string protocols::constraint_generator::MetalContactsConstraintGenerator::get_base_base_atom_name | ( | ) | const |
References base_base_atom_name_.
bool protocols::constraint_generator::MetalContactsConstraintGenerator::get_constrain_to_closest | ( | ) | const |
References constrain_to_closest_.
std::string protocols::constraint_generator::MetalContactsConstraintGenerator::get_contact_resnum_string | ( | ) | const |
References contact_resnum_string_.
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Uses private data to compute contact residue numbers based on selector/resnum string and pose; inserts them into the provided set.
References contact_resnum_string_, contact_selector_, core::pose::get_resnum_list(), core::pose::Pose::total_residue(), protocols::constraint_generator::TR(), and use_contact_selector_.
Referenced by apply().
core::select::residue_selector::ResidueSelectorCOP protocols::constraint_generator::MetalContactsConstraintGenerator::get_contact_selector | ( | ) | const |
References contact_selector_.
core::Real protocols::constraint_generator::MetalContactsConstraintGenerator::get_dist_cutoff_multiplier | ( | ) | const |
References dist_cutoff_multiplier_.
utility::vector1< core::Real > protocols::constraint_generator::MetalContactsConstraintGenerator::get_ideal_angle_about_contact | ( | ) | const |
References ideal_angle_about_contact_.
utility::vector1< core::Real > protocols::constraint_generator::MetalContactsConstraintGenerator::get_ideal_angle_about_metal | ( | ) | const |
References ideal_angle_about_metal_.
utility::vector1< core::Real > protocols::constraint_generator::MetalContactsConstraintGenerator::get_ideal_dihedral_3 | ( | ) | const |
References ideal_dihedral_3_.
utility::vector1< core::Real > protocols::constraint_generator::MetalContactsConstraintGenerator::get_ideal_dihedral_about_contact | ( | ) | const |
References ideal_dihedral_about_contact_.
utility::vector1< core::Real > protocols::constraint_generator::MetalContactsConstraintGenerator::get_ideal_dihedral_about_metal | ( | ) | const |
References ideal_dihedral_about_metal_.
core::Real protocols::constraint_generator::MetalContactsConstraintGenerator::get_ideal_distance | ( | ) | const |
References ideal_distance_.
std::string protocols::constraint_generator::MetalContactsConstraintGenerator::get_ligand_atom_name | ( | ) | const |
References ligand_atom_name_.
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Uses private data to compute ligand resnums based on selector/resnum string and pose.
References ligand_resnum_string_, ligand_selector_, core::pose::parse_resnum(), core::pose::Pose::total_residue(), and use_ligand_selector_.
Referenced by apply().
std::string protocols::constraint_generator::MetalContactsConstraintGenerator::get_ligand_resnum_string | ( | ) | const |
References ligand_resnum_string_.
core::select::residue_selector::ResidueSelectorCOP protocols::constraint_generator::MetalContactsConstraintGenerator::get_ligand_selector | ( | ) | const |
References ligand_selector_.
bool protocols::constraint_generator::MetalContactsConstraintGenerator::get_score_against_internal_contacts | ( | ) | const |
References score_against_internal_contacts_.
bool protocols::constraint_generator::MetalContactsConstraintGenerator::get_use_contact_selector | ( | ) | const |
References use_contact_selector_.
bool protocols::constraint_generator::MetalContactsConstraintGenerator::get_use_ligand_selector | ( | ) | const |
References use_ligand_selector_.
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overrideprotectedvirtual |
called by parse_my_tag – should not be used directly
Implements protocols::constraint_generator::ConstraintGenerator.
References base_atom_name_, base_base_atom_name_, constrain_to_closest_, contact_resnum_string_, contact_selector_, dist_cutoff_multiplier_, core::select::residue_selector::get_residue_selector(), ideal_angle_about_contact_, ideal_angle_about_metal_, ideal_dihedral_3_, ideal_dihedral_about_contact_, ideal_dihedral_about_metal_, ideal_distance_, ligand_atom_name_, ligand_resnum_string_, ligand_selector_, score_against_internal_contacts_, use_contact_selector_, use_ligand_selector_, and protocols::hybridization::val.
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Provide citations to the passed CitationCollectionList. This allows the constraint generator to provide citations for itself and for any modules that it invokes.
Cites Sharon Guffy.
Reimplemented from protocols::constraint_generator::ConstraintGenerator.
References class_name().
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References core::select::residue_selector::attributes_for_parse_residue_selector(), class_name(), and protocols::constraint_generator::ConstraintGeneratorFactory::xsd_constraint_generator_type_definition_w_attributes().
Referenced by protocols::constraint_generator::MetalContactsConstraintGeneratorCreator::provide_xml_schema().
void protocols::constraint_generator::MetalContactsConstraintGenerator::set_base_atom_name | ( | std::string | setting | ) |
References base_atom_name_.
void protocols::constraint_generator::MetalContactsConstraintGenerator::set_base_base_atom_name | ( | std::string | setting | ) |
References base_base_atom_name_.
void protocols::constraint_generator::MetalContactsConstraintGenerator::set_constrain_to_closest | ( | bool | setting | ) |
References constrain_to_closest_.
void protocols::constraint_generator::MetalContactsConstraintGenerator::set_contact_resnum_string | ( | std::string | setting | ) |
References contact_resnum_string_.
void protocols::constraint_generator::MetalContactsConstraintGenerator::set_contact_selector | ( | core::select::residue_selector::ResidueSelectorCOP | setting | ) |
References contact_selector_.
void protocols::constraint_generator::MetalContactsConstraintGenerator::set_dist_cutoff_multiplier | ( | core::Real | setting | ) |
References dist_cutoff_multiplier_.
void protocols::constraint_generator::MetalContactsConstraintGenerator::set_ideal_angle_about_contact | ( | utility::vector1< core::Real > | setting | ) |
References ideal_angle_about_contact_.
void protocols::constraint_generator::MetalContactsConstraintGenerator::set_ideal_angle_about_metal | ( | utility::vector1< core::Real > | setting | ) |
References ideal_angle_about_metal_.
void protocols::constraint_generator::MetalContactsConstraintGenerator::set_ideal_dihedral_3 | ( | utility::vector1< core::Real > | setting | ) |
References ideal_dihedral_3_.
void protocols::constraint_generator::MetalContactsConstraintGenerator::set_ideal_dihedral_about_contact | ( | utility::vector1< core::Real > | setting | ) |
References ideal_dihedral_about_contact_.
void protocols::constraint_generator::MetalContactsConstraintGenerator::set_ideal_dihedral_about_metal | ( | utility::vector1< core::Real > | setting | ) |
References ideal_dihedral_about_metal_.
void protocols::constraint_generator::MetalContactsConstraintGenerator::set_ideal_distance | ( | core::Real | setting | ) |
References ideal_distance_.
void protocols::constraint_generator::MetalContactsConstraintGenerator::set_ligand_atom_name | ( | std::string | setting | ) |
References ligand_atom_name_.
void protocols::constraint_generator::MetalContactsConstraintGenerator::set_ligand_resnum_string | ( | std::string | setting | ) |
References ligand_resnum_string_.
void protocols::constraint_generator::MetalContactsConstraintGenerator::set_ligand_selector | ( | core::select::residue_selector::ResidueSelectorCOP | setting | ) |
References ligand_selector_.
void protocols::constraint_generator::MetalContactsConstraintGenerator::set_score_against_internal_contacts | ( | bool | setting | ) |
References score_against_internal_contacts_.
void protocols::constraint_generator::MetalContactsConstraintGenerator::set_use_contact_selector | ( | bool | setting | ) |
References use_contact_selector_.
void protocols::constraint_generator::MetalContactsConstraintGenerator::set_use_ligand_selector | ( | bool | setting | ) |
References use_ligand_selector_.
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Referenced by apply(), get_base_atom_name(), parse_tag(), and set_base_atom_name().
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Referenced by apply(), get_base_base_atom_name(), parse_tag(), and set_base_base_atom_name().
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Referenced by apply(), get_constrain_to_closest(), parse_tag(), and set_constrain_to_closest().
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Referenced by get_contact_resnum_string(), get_contact_resnums(), parse_tag(), and set_contact_resnum_string().
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Referenced by get_contact_resnums(), get_contact_selector(), parse_tag(), and set_contact_selector().
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Referenced by apply(), get_dist_cutoff_multiplier(), parse_tag(), and set_dist_cutoff_multiplier().
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Referenced by apply(), get_ideal_angle_about_contact(), parse_tag(), and set_ideal_angle_about_contact().
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Referenced by apply(), get_ideal_angle_about_metal(), parse_tag(), and set_ideal_angle_about_metal().
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Referenced by apply(), get_ideal_dihedral_3(), parse_tag(), and set_ideal_dihedral_3().
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Referenced by apply(), get_ideal_dihedral_about_contact(), parse_tag(), and set_ideal_dihedral_about_contact().
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Referenced by apply(), get_ideal_dihedral_about_metal(), parse_tag(), and set_ideal_dihedral_about_metal().
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Referenced by apply(), get_ideal_distance(), parse_tag(), and set_ideal_distance().
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Referenced by apply(), get_ligand_atom_name(), parse_tag(), and set_ligand_atom_name().
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Referenced by get_ligand_resnum(), get_ligand_resnum_string(), parse_tag(), and set_ligand_resnum_string().
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Referenced by get_ligand_resnum(), get_ligand_selector(), parse_tag(), and set_ligand_selector().
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Referenced by apply(), get_score_against_internal_contacts(), parse_tag(), and set_score_against_internal_contacts().
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Referenced by get_contact_resnums(), get_use_contact_selector(), parse_tag(), and set_use_contact_selector().
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Referenced by get_ligand_resnum(), get_use_ligand_selector(), parse_tag(), and set_use_ligand_selector().