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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...
 
void provide_citation_info (basic::citation_manager::CitationCollectionList &citations) const override
 Provide citations to the passed CitationCollectionList. This allows the constraint generator to provide citations for itself and for any modules that it invokes. 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_citation_info ( basic::citation_manager::CitationCollectionList &  citations) const
overridevirtual

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.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

Reimplemented from protocols::constraint_generator::ConstraintGenerator.

References class_name().

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: