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protocols::constraint_generator::MetalContactsConstraintGenerator Class Reference

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>

Inheritance diagram for protocols::constraint_generator::MetalContactsConstraintGenerator:
Inheritance graph
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Public Member Functions

 MetalContactsConstraintGenerator ()
 
protocols::constraint_generator::ConstraintGeneratorOP clone () const override
 
core::scoring::constraints::ConstraintCOPs apply (core::pose::Pose const &pose) const override
 generates constraints and adds them to the pose More...
 
std::string get_ligand_atom_name () const
 
bool get_use_ligand_selector () const
 
core::select::residue_selector::ResidueSelectorCOP get_ligand_selector () const
 
std::string get_ligand_resnum_string () const
 
bool get_use_contact_selector () const
 
core::select::residue_selector::ResidueSelectorCOP get_contact_selector () const
 
std::string get_contact_resnum_string () const
 
std::string get_base_atom_name () const
 
std::string get_base_base_atom_name () const
 
core::Real get_ideal_distance () const
 
utility::vector1< core::Realget_ideal_angle_about_contact () const
 
utility::vector1< core::Realget_ideal_dihedral_about_contact () const
 
utility::vector1< core::Realget_ideal_angle_about_metal () const
 
utility::vector1< core::Realget_ideal_dihedral_about_metal () const
 
utility::vector1< core::Realget_ideal_dihedral_3 () const
 
bool get_score_against_internal_contacts () const
 
core::Real get_dist_cutoff_multiplier () const
 
bool get_constrain_to_closest () const
 
void set_ligand_atom_name (std::string)
 
void set_use_ligand_selector (bool)
 
void set_ligand_selector (core::select::residue_selector::ResidueSelectorCOP)
 
void set_ligand_resnum_string (std::string)
 
void set_use_contact_selector (bool)
 
void set_contact_selector (core::select::residue_selector::ResidueSelectorCOP)
 
void set_contact_resnum_string (std::string)
 
void set_base_atom_name (std::string)
 
void set_base_base_atom_name (std::string)
 
void set_ideal_distance (core::Real)
 
void set_ideal_angle_about_contact (utility::vector1< core::Real >)
 
void set_ideal_dihedral_about_contact (utility::vector1< core::Real >)
 
void set_ideal_angle_about_metal (utility::vector1< core::Real >)
 
void set_ideal_dihedral_about_metal (utility::vector1< core::Real >)
 
void set_ideal_dihedral_3 (utility::vector1< core::Real >)
 
void set_score_against_internal_contacts (bool)
 
void set_dist_cutoff_multiplier (core::Real)
 
void set_constrain_to_closest (bool)
 
- Public Member Functions inherited from protocols::constraint_generator::ConstraintGenerator
 ConstraintGenerator (std::string const &class_name)
 
 ~ConstraintGenerator () override
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data)
 parses XML tag – calls protected parse_tag() function More...
 
std::string const & id () const
 
void set_id (std::string const &id)
 
std::string const & class_name () const
 

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::Realideal_angle_about_contact_
 
utility::vector1< core::Realideal_dihedral_about_contact_
 
utility::vector1< core::Realideal_angle_about_metal_
 
utility::vector1< core::Realideal_dihedral_about_metal_
 
utility::vector1< core::Realideal_dihedral_3_
 
bool score_against_internal_contacts_ =false
 
bool constrain_to_closest_ =true
 

Detailed Description

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.

Constructor & Destructor Documentation

protocols::constraint_generator::MetalContactsConstraintGenerator::MetalContactsConstraintGenerator ( )

Member Function Documentation

core::scoring::constraints::ConstraintCOPs protocols::constraint_generator::MetalContactsConstraintGenerator::apply ( core::pose::Pose const &  pose) const
overridevirtual
std::string protocols::constraint_generator::MetalContactsConstraintGenerator::class_name ( )
static
protocols::constraint_generator::ConstraintGeneratorOP protocols::constraint_generator::MetalContactsConstraintGenerator::clone ( ) const
overridevirtual
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
void protocols::constraint_generator::MetalContactsConstraintGenerator::get_contact_resnums ( core::pose::Pose const &  pose,
std::set< core::Size > &  output 
) const
private

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
utility::vector1< core::Real > protocols::constraint_generator::MetalContactsConstraintGenerator::get_ideal_angle_about_contact ( ) const
utility::vector1< core::Real > protocols::constraint_generator::MetalContactsConstraintGenerator::get_ideal_angle_about_metal ( ) const
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
utility::vector1< core::Real > protocols::constraint_generator::MetalContactsConstraintGenerator::get_ideal_dihedral_about_metal ( ) const
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_.

core::Size protocols::constraint_generator::MetalContactsConstraintGenerator::get_ligand_resnum ( core::pose::Pose const &  pose) const
private

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
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_.

void protocols::constraint_generator::MetalContactsConstraintGenerator::parse_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overrideprotectedvirtual
void protocols::constraint_generator::MetalContactsConstraintGenerator::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
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)
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)
void protocols::constraint_generator::MetalContactsConstraintGenerator::set_ideal_angle_about_contact ( utility::vector1< core::Real setting)
void protocols::constraint_generator::MetalContactsConstraintGenerator::set_ideal_angle_about_metal ( utility::vector1< core::Real setting)
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)
void protocols::constraint_generator::MetalContactsConstraintGenerator::set_ideal_dihedral_about_metal ( utility::vector1< core::Real setting)
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)
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_.

Member Data Documentation

std::string protocols::constraint_generator::MetalContactsConstraintGenerator::base_atom_name_ =""
private
std::string protocols::constraint_generator::MetalContactsConstraintGenerator::base_base_atom_name_ =""
private
bool protocols::constraint_generator::MetalContactsConstraintGenerator::constrain_to_closest_ =true
private
std::string protocols::constraint_generator::MetalContactsConstraintGenerator::contact_resnum_string_ =""
private
core::select::residue_selector::ResidueSelectorCOP protocols::constraint_generator::MetalContactsConstraintGenerator::contact_selector_
private
core::Real protocols::constraint_generator::MetalContactsConstraintGenerator::dist_cutoff_multiplier_ =1.0
private
utility::vector1< core::Real > protocols::constraint_generator::MetalContactsConstraintGenerator::ideal_angle_about_contact_
private
utility::vector1< core::Real > protocols::constraint_generator::MetalContactsConstraintGenerator::ideal_angle_about_metal_
private
utility::vector1< core::Real > protocols::constraint_generator::MetalContactsConstraintGenerator::ideal_dihedral_3_
private
utility::vector1< core::Real > protocols::constraint_generator::MetalContactsConstraintGenerator::ideal_dihedral_about_contact_
private
utility::vector1< core::Real > protocols::constraint_generator::MetalContactsConstraintGenerator::ideal_dihedral_about_metal_
private
core::Real protocols::constraint_generator::MetalContactsConstraintGenerator::ideal_distance_ =-1.0
private
std::string protocols::constraint_generator::MetalContactsConstraintGenerator::ligand_atom_name_ =""
private
std::string protocols::constraint_generator::MetalContactsConstraintGenerator::ligand_resnum_string_ =""
private
core::select::residue_selector::ResidueSelectorCOP protocols::constraint_generator::MetalContactsConstraintGenerator::ligand_selector_
private
bool protocols::constraint_generator::MetalContactsConstraintGenerator::score_against_internal_contacts_ =false
private
bool protocols::constraint_generator::MetalContactsConstraintGenerator::use_contact_selector_ =false
private
bool protocols::constraint_generator::MetalContactsConstraintGenerator::use_ligand_selector_ =false
private

The documentation for this class was generated from the following files: