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protocols::fldsgn::SheetConstraintGenerator Class Reference

#include <SheetConstraintGenerator.hh>

Inheritance diagram for protocols::fldsgn::SheetConstraintGenerator:
Inheritance graph
[legend]

Public Types

typedef core::Size Size
 
typedef core::Real Real
 
typedef core::pose::Pose Pose
 
typedef
protocols::parser::BluePrintOP 
BluePrintOP
 

Public Member Functions

 SheetConstraintGenerator ()
 
 ~SheetConstraintGenerator () override
 
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 set_secstruct (std::string const &ss)
 sets the secondary structure to be used for constraint generation More...
 
void set_strand_pairs (std::string const &spairs)
 sets the strand pair string to be used for constraint generation (e.g. "2-3.P.1" ) means strands 2 and 3 are paired in a parallel orientation with register shift of 1 More...
 
void set_use_dssp (bool const use_dssp)
 If true, and no secstruct is specified, DSSP will be used to determine the pose secondary structure. If false (and no secstruct is specified), the pose secondary structure will be directly used. More...
 
void set_flat_bottom_constraints (bool const flat_csts)
 if set, a square-well, "flat bottom" function will be used for the constraints. Otherwise, harmonic constraints will be used. More...
 
void set_weight (Real const coef)
 set the weight of the sheet constraints More...
 
void set_distance (Real const dist)
 set the maximum Ca-Ca distance between paired residues More...
 
void set_distance_tolerance (Real const dist_tol)
 sets the tolerance for the func to all atom pair constraints More...
 
void set_angle_tolerance (Real const angle_tolerance)
 set the flat-bottom tolerance for the backbone angle between strands for each pair This is N1-C1-C2 and N2-C2-C1 for parallel sheets, and N1-C1-N2/N2-C2-N1 for antiparallel. More...
 
void set_cacb_dihedral_tolerance (Real const dihedral_tolerance)
 set the flat-bottom tolerance for the Cb1-Ca1-Ca2-Cb2 dihedral angle (0 = optimal) More...
 
void set_bb_dihedral_tolerance (Real const dihedral_tolerance)
 set the flat-bottom tolerance for the backbone dihedrals (0=optimal) Dihedral 1 = O1-N1-C1-C2, Dihedral 2 = O2-N2-C2-C1 More...
 
void set_constrain_ca_ca_dist (bool const constrain_dist_only)
 sets whether we should constrain distance only, and not generate dihedral and angle constraints More...
 
void set_constrain_bb_cacb_dihedral (bool const constrain_dihedral)
 sets whether we should constrain cb_ca_ca_cb dihedrals More...
 
void set_constrain_bb_dihedral (bool const constrain_dihedral)
 sets whether we should constrain bb dihedrals More...
 
void set_constrain_bb_angle (bool const constrain_angle)
 sets whether we should constrain bb angle More...
 
void initialize_from_blueprint (std::string const &blueprint_file)
 initialize from a blueprint More...
 
void initialize_from_blueprint (protocols::parser::BluePrintCOP bp)
 
ResiduePairs compute_residue_pairs (topology::StrandPairings const &spairs) const
 computes and returns a vector of residues that are paired in the sheet More...
 
- 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)
 
static void attributes_for_sheet_constraint_generator (utility::tag::AttributeList &)
 

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...
 
std::string get_secstruct (core::pose::Pose const &pose) const
 returns secondary structure to be used in this constraint generator More...
 
utility::vector1< std::string > get_abego (core::pose::Pose const &pose) const
 returns abego to be used in this constraint generator More...
 
std::string get_strandpairings (core::pose::Pose const &pose) const
 return strand pairing string to be used in this constraint generator More...
 

Private Member Functions

core::scoring::func::FuncOP weighted_func (core::scoring::func::FuncOP func) const
 
core::scoring::func::FuncOP create_caca_atom_pair_func (core::Real const ideal_dist) const
 
core::scoring::func::FuncOP create_bb_angle_func (core::Real const ideal_angle) const
 
core::scoring::func::FuncOP create_bb_dihedral_func (core::Real const ideal_dihedral) const
 
core::scoring::func::FuncOP create_cacb_dihedral_func (core::Real const ideal_dihedral) const
 
core::scoring::constraints::ConstraintOP create_bb_dihedral_constraint (core::pose::Pose const &pose, core::Size const res1, core::Size const res2, core::scoring::func::FuncOP func1, core::scoring::func::FuncOP func2) const
 
core::scoring::constraints::ConstraintOP create_ca_ca_atom_pair_constraint (core::id::AtomID const &atom1, core::id::AtomID const &atom2, core::scoring::func::FuncOP func) const
 
core::scoring::constraints::ConstraintOP create_bb_angle_constraint (core::id::AtomID const &atom1, core::id::AtomID const &atom2, core::id::AtomID const &atom3, core::scoring::func::FuncOP func) const
 
core::scoring::constraints::ConstraintOP create_bb_cacb_dihedral_constraint (core::id::AtomID const &atom1, core::id::AtomID const &atom2, core::id::AtomID const &atom3, core::id::AtomID const &atom4, core::scoring::func::FuncOP func) const
 

Private Attributes

Real weight_
 
Real dist_
 
Real dist_tolerance_
 
Real angle_tolerance_
 
Real cacb_dihedral_tolerance_
 
Real bb_dihedral_tolerance_
 
bool constrain_ca_ca_dist_
 
bool constrain_bb_cacb_dihedral_
 
bool constrain_bb_dihedral_
 
bool constrain_bb_angle_
 
bool flat_bottom_constraints_
 
bool use_dssp_
 
std::string secstruct_
 
std::string spairs_
 
std::string sheet_name_
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::fldsgn::SheetConstraintGenerator::SheetConstraintGenerator ( )
protocols::fldsgn::SheetConstraintGenerator::~SheetConstraintGenerator ( )
overridedefault

Member Function Documentation

core::scoring::constraints::ConstraintCOPs protocols::fldsgn::SheetConstraintGenerator::apply ( core::pose::Pose const &  pose) const
overridevirtual
void protocols::fldsgn::SheetConstraintGenerator::attributes_for_sheet_constraint_generator ( utility::tag::AttributeList &  attlist)
static
std::string protocols::fldsgn::SheetConstraintGenerator::class_name ( )
static
protocols::constraint_generator::ConstraintGeneratorOP protocols::fldsgn::SheetConstraintGenerator::clone ( ) const
overridevirtual
ResiduePairs protocols::fldsgn::SheetConstraintGenerator::compute_residue_pairs ( topology::StrandPairings const &  spairs) const

computes and returns a vector of residues that are paired in the sheet

References protocols::fldsgn::TR().

Referenced by apply().

core::scoring::constraints::ConstraintOP protocols::fldsgn::SheetConstraintGenerator::create_bb_angle_constraint ( core::id::AtomID const &  atom1,
core::id::AtomID const &  atom2,
core::id::AtomID const &  atom3,
core::scoring::func::FuncOP  func 
) const
private

Referenced by apply().

core::scoring::func::FuncOP protocols::fldsgn::SheetConstraintGenerator::create_bb_angle_func ( core::Real const  ideal_angle) const
private
core::scoring::constraints::ConstraintOP protocols::fldsgn::SheetConstraintGenerator::create_bb_cacb_dihedral_constraint ( core::id::AtomID const &  atom1,
core::id::AtomID const &  atom2,
core::id::AtomID const &  atom3,
core::id::AtomID const &  atom4,
core::scoring::func::FuncOP  func 
) const
private

Referenced by apply().

core::scoring::constraints::ConstraintOP protocols::fldsgn::SheetConstraintGenerator::create_bb_dihedral_constraint ( core::pose::Pose const &  pose,
core::Size const  res1,
core::Size const  res2,
core::scoring::func::FuncOP  func1,
core::scoring::func::FuncOP  func2 
) const
private
core::scoring::func::FuncOP protocols::fldsgn::SheetConstraintGenerator::create_bb_dihedral_func ( core::Real const  ideal_dihedral) const
private
core::scoring::constraints::ConstraintOP protocols::fldsgn::SheetConstraintGenerator::create_ca_ca_atom_pair_constraint ( core::id::AtomID const &  atom1,
core::id::AtomID const &  atom2,
core::scoring::func::FuncOP  func 
) const
private

Referenced by apply().

core::scoring::func::FuncOP protocols::fldsgn::SheetConstraintGenerator::create_caca_atom_pair_func ( core::Real const  ideal_dist) const
private
core::scoring::func::FuncOP protocols::fldsgn::SheetConstraintGenerator::create_cacb_dihedral_func ( core::Real const  ideal_dihedral) const
private
utility::vector1< std::string > protocols::fldsgn::SheetConstraintGenerator::get_abego ( core::pose::Pose const &  pose) const
protected

returns abego to be used in this constraint generator

Parameters
[in]poseInput pose
Returns
ABEGO string of the pose according to the following rules:
  1. StructureData abego if use_dssp_ is false AND StructureData is present
  2. Computed abego of the input pose otherwise

References protocols::denovo_design::abego_str(), protocols::denovo_design::abego_vector(), core::sequence::get_abego(), protocols::denovo_design::components::StructureDataFactory::has_cached_data(), and use_dssp_.

Referenced by apply().

std::string protocols::fldsgn::SheetConstraintGenerator::get_secstruct ( core::pose::Pose const &  pose) const
protected

returns secondary structure to be used in this constraint generator

Parameters
[in]poseInput pose
Returns
Secondary stucture of the pose according to the following rules:
  1. secstruct_ if it is non-empty
  2. DSSP secondary structure of the input pose if use_dssp_ is true
  3. Pose secondary structure if use_dssp_ is false

References protocols::simple_filters::dssp(), core::scoring::dssp::Dssp::get_dssp_secstruct(), core::pose::Pose::secstruct(), secstruct_, and use_dssp_.

Referenced by apply().

std::string protocols::fldsgn::SheetConstraintGenerator::get_strandpairings ( core::pose::Pose const &  pose) const
protected

return strand pairing string to be used in this constraint generator

Parameters
[in]poseInput pose
Returns
Strand pairing string for desired strand pairings, according to the following rules:
  1. spairs_ if it is non-empty
  2. Gets pairing string from StructureData if it is present
  3. Throw error

References class_name(), and spairs_.

Referenced by apply().

void protocols::fldsgn::SheetConstraintGenerator::initialize_from_blueprint ( std::string const &  blueprint_file)

initialize from a blueprint

sets the blueprint file used for determining proper sheet pairing This function will create the blueprint object for you from the file and use it

References protocols::fldsgn::TR().

Referenced by parse_tag().

void protocols::fldsgn::SheetConstraintGenerator::initialize_from_blueprint ( protocols::parser::BluePrintCOP  bp)
void protocols::fldsgn::SheetConstraintGenerator::parse_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overrideprotectedvirtual
void protocols::fldsgn::SheetConstraintGenerator::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::fldsgn::SheetConstraintGenerator::set_angle_tolerance ( Real const  angle_tolerance)

set the flat-bottom tolerance for the backbone angle between strands for each pair This is N1-C1-C2 and N2-C2-C1 for parallel sheets, and N1-C1-N2/N2-C2-N1 for antiparallel.

References angle_tolerance_.

Referenced by parse_tag().

void protocols::fldsgn::SheetConstraintGenerator::set_bb_dihedral_tolerance ( Real const  dihedral_tolerance)

set the flat-bottom tolerance for the backbone dihedrals (0=optimal) Dihedral 1 = O1-N1-C1-C2, Dihedral 2 = O2-N2-C2-C1

References bb_dihedral_tolerance_.

Referenced by parse_tag().

void protocols::fldsgn::SheetConstraintGenerator::set_cacb_dihedral_tolerance ( Real const  dihedral_tolerance)

set the flat-bottom tolerance for the Cb1-Ca1-Ca2-Cb2 dihedral angle (0 = optimal)

References cacb_dihedral_tolerance_.

Referenced by parse_tag().

void protocols::fldsgn::SheetConstraintGenerator::set_constrain_bb_angle ( bool const  constrain_angle)

sets whether we should constrain bb angle

References constrain_bb_angle_.

Referenced by parse_tag().

void protocols::fldsgn::SheetConstraintGenerator::set_constrain_bb_cacb_dihedral ( bool const  constrain_dihedral)

sets whether we should constrain cb_ca_ca_cb dihedrals

References constrain_bb_cacb_dihedral_.

Referenced by parse_tag().

void protocols::fldsgn::SheetConstraintGenerator::set_constrain_bb_dihedral ( bool const  constrain_dihedral)

sets whether we should constrain bb dihedrals

References constrain_bb_dihedral_.

Referenced by parse_tag().

void protocols::fldsgn::SheetConstraintGenerator::set_constrain_ca_ca_dist ( bool const  constrain_dist_only)

sets whether we should constrain distance only, and not generate dihedral and angle constraints

References constrain_ca_ca_dist_.

Referenced by parse_tag().

void protocols::fldsgn::SheetConstraintGenerator::set_distance ( Real const  dist)

set the maximum Ca-Ca distance between paired residues

set distance of constraint

References dist_.

Referenced by parse_tag().

void protocols::fldsgn::SheetConstraintGenerator::set_distance_tolerance ( Real const  dist_tol)

sets the tolerance for the func to all atom pair constraints

References dist_tolerance_.

Referenced by parse_tag().

void protocols::fldsgn::SheetConstraintGenerator::set_flat_bottom_constraints ( bool const  flat_csts)

if set, a square-well, "flat bottom" function will be used for the constraints. Otherwise, harmonic constraints will be used.

References flat_bottom_constraints_.

Referenced by parse_tag().

void protocols::fldsgn::SheetConstraintGenerator::set_secstruct ( std::string const &  ss)

sets the secondary structure to be used for constraint generation

References secstruct_.

Referenced by initialize_from_blueprint(), and parse_tag().

void protocols::fldsgn::SheetConstraintGenerator::set_strand_pairs ( std::string const &  spairs)

sets the strand pair string to be used for constraint generation (e.g. "2-3.P.1" ) means strands 2 and 3 are paired in a parallel orientation with register shift of 1

References spairs_.

Referenced by initialize_from_blueprint(), and parse_tag().

void protocols::fldsgn::SheetConstraintGenerator::set_use_dssp ( bool const  use_dssp)

If true, and no secstruct is specified, DSSP will be used to determine the pose secondary structure. If false (and no secstruct is specified), the pose secondary structure will be directly used.

Parameters
[in]use_dsspDesired value

References use_dssp_.

Referenced by parse_tag().

void protocols::fldsgn::SheetConstraintGenerator::set_weight ( Real const  coef)

set the weight of the sheet constraints

set weight

References weight_.

Referenced by parse_tag().

core::scoring::func::FuncOP protocols::fldsgn::SheetConstraintGenerator::weighted_func ( core::scoring::func::FuncOP  func) const
private

Member Data Documentation

Real protocols::fldsgn::SheetConstraintGenerator::angle_tolerance_
private
Real protocols::fldsgn::SheetConstraintGenerator::bb_dihedral_tolerance_
private
Real protocols::fldsgn::SheetConstraintGenerator::cacb_dihedral_tolerance_
private
bool protocols::fldsgn::SheetConstraintGenerator::constrain_bb_angle_
private
bool protocols::fldsgn::SheetConstraintGenerator::constrain_bb_cacb_dihedral_
private
bool protocols::fldsgn::SheetConstraintGenerator::constrain_bb_dihedral_
private
bool protocols::fldsgn::SheetConstraintGenerator::constrain_ca_ca_dist_
private
Real protocols::fldsgn::SheetConstraintGenerator::dist_
private

Referenced by apply(), parse_tag(), and set_distance().

Real protocols::fldsgn::SheetConstraintGenerator::dist_tolerance_
private
bool protocols::fldsgn::SheetConstraintGenerator::flat_bottom_constraints_
private
std::string protocols::fldsgn::SheetConstraintGenerator::secstruct_
private
std::string protocols::fldsgn::SheetConstraintGenerator::sheet_name_
private
std::string protocols::fldsgn::SheetConstraintGenerator::spairs_
private
bool protocols::fldsgn::SheetConstraintGenerator::use_dssp_
private
Real protocols::fldsgn::SheetConstraintGenerator::weight_
private

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