Rosetta Protocols  2014.35
Public Member Functions | Static Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::toolbox::match_enzdes_util::EnzConstraintParameters Class Reference

class that holds all the parameters for one specific constraint More...

#include <EnzConstraintParameters.hh>

Public Member Functions

void set_mcfi (toolbox::match_enzdes_util::MatchConstraintFileInfoCOP mcfi)
 
 EnzConstraintParameters ()
 
 EnzConstraintParameters (core::Size cst_block, core::chemical::ResidueTypeSetCAP src_restype_set, EnzConstraintIOCAP src_enz_io)
 
 EnzConstraintParameters (EnzConstraintParameters const &other)
 copy constructor More...
 
virtual ~EnzConstraintParameters ()
 
void show_definitions () const
 
void generate_pose_specific_data (core::pose::Pose &pose, core::scoring::ScoreFunctionCOP scofx) const
 
bool is_empty () const
 
bool is_covalent () const
 
bool missing_in_pose (core::pose::Pose const &pose) const
 
core::Size cst_block () const
 function that takes all rotamers for the ResidueType(s) of the residue that's missing in the pose and places them according to the geometry specified in the mcfi More...
 
void set_cst_block (core::Size cst_block)
 
bool update_pdb_remarks (core::pose::Pose &pose) const
 updates the pdb remarks according to what is in the EnzCstTemplateRes member data. returns false in case any error occured More...
 
EnzConstraintIOCAP enz_io () const
 
EnzCstTemplateResOP nonconst_resA ()
 
EnzCstTemplateResOP nonconst_resB ()
 
EnzCstTemplateResCOP resA () const
 
EnzCstTemplateResCOP resB () const
 
EnzCstTemplateResCOP get_missing_template_res (core::pose::Pose const &pose) const
 
EnzCstTemplateResCOP get_missing_template_other_res (core::pose::Pose const &pose) const
 
std::set< std::string > allowed_res_name3_at_position (core::pose::Pose const &pose, core::Size seqpos) const
 all residue names specified in the cstfile returns an empty set if the constraints don't apply to the specifed position More...
 
void set_external_position_for_resA (core::Size pos)
 
void set_external_position_for_resB (core::Size pos)
 
void remove_covalent_connections_from_pose (core::pose::Pose &pose) const
 
void remap_resid (core::id::SequenceMapping const &smap)
 

Static Public Member Functions

static core::scoring::func::FuncOP convert_GeomSampleInfo_to_FuncOP (toolbox::match_enzdes_util::GeomSampleInfoCOP gsi, core::Real &ideal_val)
 

Private Member Functions

void generate_active_pose_constraints (core::pose::Pose &pose, core::scoring::ScoreFunctionCOP scofx) const
 process the information in template residues and the func op pointers to add More...
 
void make_constraint_covalent (core::pose::Pose &pose, Size resA_pos, Size resB_pos, Size resA_At, Size resB_At) const
 
void make_constraint_covalent_helper (core::pose::Pose &pose, EnzCstTemplateResOP template_res, core::Size res_pos, core::Size Atpos, core::Real itorsion, core::Real iangle, core::Real idis, std::string &res_varname) const
 helper function so stuff doesn't need to be written twice More...
 
core::Size determine_best_constraint (core::pose::Pose const &pose, core::scoring::ScoreFunctionCOP scofx, utility::vector1< core::scoring::constraints::ConstraintCOP > candidate_csts) const
 function to determine the lowest scoring constraint in a vector of input constraints More...
 

Private Attributes

EnzCstTemplateResOP resA_
 
EnzCstTemplateResOP resB_
 
toolbox::match_enzdes_util::MatchConstraintFileInfoCOP mcfi_
 
core::scoring::func::FuncOP disAB_
 
core::scoring::func::FuncOP angleA_
 
core::scoring::func::FuncOP angleB_
 
core::scoring::func::FuncOP torsionA_
 
core::scoring::func::FuncOP torsionB_
 
core::scoring::func::FuncOP torsionAB_
 
core::Real ndisAB_
 
core::Real nangleA_
 
core::Real nangleB_
 
core::Real ntorsionA_
 
core::Real ntorsionB_
 
core::Real ntorsionAB_
 
bool is_covalent_
 
bool empty_
 
core::chemical::ResidueTypeSetCAP restype_set_
 
EnzConstraintIOCAP enz_io_
 
core::Size cst_block_
 

Detailed Description

class that holds all the parameters for one specific constraint

Constructor & Destructor Documentation

protocols::toolbox::match_enzdes_util::EnzConstraintParameters::EnzConstraintParameters ( )
protocols::toolbox::match_enzdes_util::EnzConstraintParameters::EnzConstraintParameters ( core::Size  cst_block,
core::chemical::ResidueTypeSetCAP  src_restype_set,
EnzConstraintIOCAP  src_enz_io 
)

References angleA_, angleB_, disAB_, empty_, is_covalent_, resA_, resB_, torsionA_, torsionAB_, and torsionB_.

protocols::toolbox::match_enzdes_util::EnzConstraintParameters::EnzConstraintParameters ( EnzConstraintParameters const &  other)

copy constructor

WARNING: currently this probably doesn't copy the functions or active pose constraints

References enz_io_, resA_, and resB_.

protocols::toolbox::match_enzdes_util::EnzConstraintParameters::~EnzConstraintParameters ( )
virtual

Member Function Documentation

std::set< std::string > protocols::toolbox::match_enzdes_util::EnzConstraintParameters::allowed_res_name3_at_position ( core::pose::Pose const &  pose,
core::Size  seqpos 
) const

all residue names specified in the cstfile returns an empty set if the constraints don't apply to the specifed position

References cst_block_, protocols::toolbox::match_enzdes_util::get_enzdes_observer(), resA_, and resB_.

core::scoring::func::FuncOP protocols::toolbox::match_enzdes_util::EnzConstraintParameters::convert_GeomSampleInfo_to_FuncOP ( toolbox::match_enzdes_util::GeomSampleInfoCOP  gsi,
core::Real &  ideal_val 
)
static

References numeric::constants::f::degrees_to_radians, utility::exit(), numeric::constants::f::pi_2, and protocols::toolbox::match_enzdes_util::tr.

Referenced by set_mcfi().

core::Size protocols::toolbox::match_enzdes_util::EnzConstraintParameters::cst_block ( ) const
inline

function that takes all rotamers for the ResidueType(s) of the residue that's missing in the pose and places them according to the geometry specified in the mcfi

References cst_block_.

Referenced by set_cst_block(), and update_pdb_remarks().

core::Size protocols::toolbox::match_enzdes_util::EnzConstraintParameters::determine_best_constraint ( core::pose::Pose const &  pose,
core::scoring::ScoreFunctionCOP  scofx,
utility::vector1< core::scoring::constraints::ConstraintCOP >  candidate_csts 
) const
private

function to determine the lowest scoring constraint in a vector of input constraints

there might be a slightly faster and slightly more complicated way to implement this, but since this function will only be called once per input pose (if it is called at all), it probably doesn't matter.

References core::scoring::constraints::ConstraintSet::add_constraint(), core::scoring::angle_constraint, core::scoring::atom_pair_constraint, core::pose::Pose::constraint_set(), core::scoring::coordinate_constraint, core::scoring::dihedral_constraint, core::pose::Pose::energies(), utility::exit(), and core::scoring::Energies::total_energies().

Referenced by generate_active_pose_constraints().

EnzConstraintIOCAP protocols::toolbox::match_enzdes_util::EnzConstraintParameters::enz_io ( ) const
inline

References enz_io_.

void protocols::toolbox::match_enzdes_util::EnzConstraintParameters::generate_active_pose_constraints ( core::pose::Pose &  pose,
core::scoring::ScoreFunctionCOP  scofx 
) const
private

process the information in template residues and the func op pointers to add

to the constraint set in the right format

References angleA_, angleB_, core::conformation::Residue::atom_name(), cst_block_, determine_best_constraint(), disAB_, empty_, basic::options::OptionKeys::enzdes::enz_debug, protocols::toolbox::match_enzdes_util::get_enzdes_observer(), is_covalent_, make_constraint_covalent(), basic::options::option, remove_covalent_connections_from_pose(), core::pose::Pose::residue(), runtime_assert, torsionA_, torsionAB_, torsionB_, and protocols::toolbox::match_enzdes_util::tr.

Referenced by generate_pose_specific_data().

void protocols::toolbox::match_enzdes_util::EnzConstraintParameters::generate_pose_specific_data ( core::pose::Pose &  pose,
core::scoring::ScoreFunctionCOP  scofx 
) const

References generate_active_pose_constraints(), resA_, and resB_.

EnzCstTemplateResCOP protocols::toolbox::match_enzdes_util::EnzConstraintParameters::get_missing_template_other_res ( core::pose::Pose const &  pose) const

References cst_block_, protocols::toolbox::match_enzdes_util::get_enzdes_observer(), resA_, resB_, and utility_exit_with_message.

EnzCstTemplateResCOP protocols::toolbox::match_enzdes_util::EnzConstraintParameters::get_missing_template_res ( core::pose::Pose const &  pose) const

References cst_block_, protocols::toolbox::match_enzdes_util::get_enzdes_observer(), resA_, resB_, and utility_exit_with_message.

bool protocols::toolbox::match_enzdes_util::EnzConstraintParameters::is_covalent ( ) const
inline

References is_covalent_.

bool protocols::toolbox::match_enzdes_util::EnzConstraintParameters::is_empty ( ) const
inline

References empty_.

void protocols::toolbox::match_enzdes_util::EnzConstraintParameters::make_constraint_covalent ( core::pose::Pose &  pose,
Size  resA_pos,
Size  resB_pos,
Size  resA_At,
Size  resB_At 
) const
private

References core::conformation::Residue::atom_name(), core::pose::Pose::conformation(), cst_block_, core::conformation::Conformation::declare_chemical_bond(), disAB_, core::pose::Pose::dump_pdb(), basic::options::OptionKeys::enzdes::enz_debug, protocols::toolbox::match_enzdes_util::get_enzdes_observer(), make_constraint_covalent_helper(), core::conformation::Residue::name(), nangleA_, nangleB_, ntorsionA_, ntorsionB_, basic::options::option, resA_, resB_, core::pose::Pose::residue(), core::pose::Pose::residue_type(), residue_type_base_name(), restype_set_, and protocols::toolbox::match_enzdes_util::tr.

Referenced by generate_active_pose_constraints().

void protocols::toolbox::match_enzdes_util::EnzConstraintParameters::make_constraint_covalent_helper ( core::pose::Pose &  pose,
EnzCstTemplateResOP  template_res,
core::Size  res_pos,
core::Size  Atpos,
core::Real  itorsion,
core::Real  iangle,
core::Real  idis,
std::string &  res_varname 
) const
private

helper function so stuff doesn't need to be written twice

References core::chemical::ResidueType::add_residue_connection(), core::chemical::ResidueTypeSet::add_residue_type(), core::chemical::ResidueType::add_variant_type(), core::conformation::Residue::atom_name(), protocols::vip::base_name(), core::chemical::ResidueType::base_restype_name(), core::conformation::Residue::chi(), core::chemical::ResidueType::clone(), utility::exit(), core::chemical::ResidueType::finalize(), core::chemical::ResidueType::has_variant_type(), core::chemical::ResidueType::is_ligand(), core::chemical::ResidueType::name(), core::chemical::ResidueType::name3(), core::chemical::ResidueTypeSet::name3_map(), core::conformation::Residue::natoms(), core::chemical::ResidueType::nondefault(), protocols::toolbox::match_enzdes_util::replace_residue_keeping_all_atom_positions(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), residue_type_all_patches_name(), residue_type_base_name(), restype_set_, core::chemical::ResidueType::set_icoor(), core::conformation::Residue::set_xyz(), utility::to_string(), and utility_exit_with_message.

Referenced by make_constraint_covalent().

bool protocols::toolbox::match_enzdes_util::EnzConstraintParameters::missing_in_pose ( core::pose::Pose const &  pose) const

References cst_block_, and protocols::toolbox::match_enzdes_util::get_enzdes_observer().

EnzCstTemplateResOP protocols::toolbox::match_enzdes_util::EnzConstraintParameters::nonconst_resA ( )

References resA_.

EnzCstTemplateResOP protocols::toolbox::match_enzdes_util::EnzConstraintParameters::nonconst_resB ( )

References resB_.

void protocols::toolbox::match_enzdes_util::EnzConstraintParameters::remap_resid ( core::id::SequenceMapping const &  smap)

References resA_, and resB_.

void protocols::toolbox::match_enzdes_util::EnzConstraintParameters::remove_covalent_connections_from_pose ( core::pose::Pose &  pose) const

References cst_block_, and protocols::toolbox::match_enzdes_util::get_enzdes_observer().

Referenced by generate_active_pose_constraints().

EnzCstTemplateResCOP protocols::toolbox::match_enzdes_util::EnzConstraintParameters::resA ( ) const

References resA_.

Referenced by update_pdb_remarks().

EnzCstTemplateResCOP protocols::toolbox::match_enzdes_util::EnzConstraintParameters::resB ( ) const

References resB_.

Referenced by update_pdb_remarks().

void protocols::toolbox::match_enzdes_util::EnzConstraintParameters::set_cst_block ( core::Size  cst_block)
inline

References cst_block(), and cst_block_.

void protocols::toolbox::match_enzdes_util::EnzConstraintParameters::set_external_position_for_resA ( core::Size  pos)

References resA_.

void protocols::toolbox::match_enzdes_util::EnzConstraintParameters::set_external_position_for_resB ( core::Size  pos)

References resB_.

void protocols::toolbox::match_enzdes_util::EnzConstraintParameters::set_mcfi ( toolbox::match_enzdes_util::MatchConstraintFileInfoCOP  mcfi)

References angleA_, angleB_, convert_GeomSampleInfo_to_FuncOP(), disAB_, is_covalent_, mcfi_, nangleA_, nangleB_, ndisAB_, ntorsionA_, ntorsionAB_, ntorsionB_, resA_, resB_, torsionA_, torsionAB_, and torsionB_.

void protocols::toolbox::match_enzdes_util::EnzConstraintParameters::show_definitions ( ) const

References resA_, resB_, and protocols::toolbox::match_enzdes_util::tr.

bool protocols::toolbox::match_enzdes_util::EnzConstraintParameters::update_pdb_remarks ( core::pose::Pose &  pose) const

updates the pdb remarks according to what is in the EnzCstTemplateRes member data. returns false in case any error occured

References protocols::toolbox::match_enzdes_util::assemble_remark_line(), core::pose::PDBInfo::chain(), cst_block(), cst_block_, protocols::toolbox::match_enzdes_util::get_enzdes_observer(), core::conformation::Residue::is_ligand(), core::conformation::Residue::name3(), core::pose::PDBInfo::number(), core::pose::Pose::pdb_info(), resA(), resB(), core::pose::Pose::residue(), protocols::toolbox::match_enzdes_util::split_up_remark_line(), and protocols::toolbox::match_enzdes_util::tr.

Member Data Documentation

core::scoring::func::FuncOP protocols::toolbox::match_enzdes_util::EnzConstraintParameters::angleA_
private

Referenced by EnzConstraintParameters(), generate_active_pose_constraints(), and set_mcfi().

core::scoring::func::FuncOP protocols::toolbox::match_enzdes_util::EnzConstraintParameters::angleB_
private

Referenced by EnzConstraintParameters(), generate_active_pose_constraints(), and set_mcfi().

core::Size protocols::toolbox::match_enzdes_util::EnzConstraintParameters::cst_block_
private

Referenced by allowed_res_name3_at_position(), cst_block(), generate_active_pose_constraints(), get_missing_template_other_res(), get_missing_template_res(), make_constraint_covalent(), missing_in_pose(), remove_covalent_connections_from_pose(), set_cst_block(), and update_pdb_remarks().

core::scoring::func::FuncOP protocols::toolbox::match_enzdes_util::EnzConstraintParameters::disAB_
private

Referenced by EnzConstraintParameters(), generate_active_pose_constraints(), make_constraint_covalent(), and set_mcfi().

bool protocols::toolbox::match_enzdes_util::EnzConstraintParameters::empty_
mutableprivate

Referenced by EnzConstraintParameters(), generate_active_pose_constraints(), and is_empty().

EnzConstraintIOCAP protocols::toolbox::match_enzdes_util::EnzConstraintParameters::enz_io_
private

Referenced by enz_io(), and EnzConstraintParameters().

bool protocols::toolbox::match_enzdes_util::EnzConstraintParameters::is_covalent_
private

Referenced by EnzConstraintParameters(), generate_active_pose_constraints(), is_covalent(), and set_mcfi().

toolbox::match_enzdes_util::MatchConstraintFileInfoCOP protocols::toolbox::match_enzdes_util::EnzConstraintParameters::mcfi_
private

Referenced by set_mcfi().

core::Real protocols::toolbox::match_enzdes_util::EnzConstraintParameters::nangleA_
private

Referenced by make_constraint_covalent(), and set_mcfi().

core::Real protocols::toolbox::match_enzdes_util::EnzConstraintParameters::nangleB_
private

Referenced by make_constraint_covalent(), and set_mcfi().

core::Real protocols::toolbox::match_enzdes_util::EnzConstraintParameters::ndisAB_
private

Referenced by set_mcfi().

core::Real protocols::toolbox::match_enzdes_util::EnzConstraintParameters::ntorsionA_
private

Referenced by make_constraint_covalent(), and set_mcfi().

core::Real protocols::toolbox::match_enzdes_util::EnzConstraintParameters::ntorsionAB_
private

Referenced by set_mcfi().

core::Real protocols::toolbox::match_enzdes_util::EnzConstraintParameters::ntorsionB_
private

Referenced by make_constraint_covalent(), and set_mcfi().

EnzCstTemplateResOP protocols::toolbox::match_enzdes_util::EnzConstraintParameters::resA_
private

Referenced by allowed_res_name3_at_position(), EnzConstraintParameters(), generate_pose_specific_data(), get_missing_template_other_res(), get_missing_template_res(), make_constraint_covalent(), nonconst_resA(), remap_resid(), resA(), set_external_position_for_resA(), set_mcfi(), and show_definitions().

EnzCstTemplateResOP protocols::toolbox::match_enzdes_util::EnzConstraintParameters::resB_
private

Referenced by allowed_res_name3_at_position(), EnzConstraintParameters(), generate_pose_specific_data(), get_missing_template_other_res(), get_missing_template_res(), make_constraint_covalent(), nonconst_resB(), remap_resid(), resB(), set_external_position_for_resB(), set_mcfi(), and show_definitions().

core::chemical::ResidueTypeSetCAP protocols::toolbox::match_enzdes_util::EnzConstraintParameters::restype_set_
private

Referenced by make_constraint_covalent(), and make_constraint_covalent_helper().

core::scoring::func::FuncOP protocols::toolbox::match_enzdes_util::EnzConstraintParameters::torsionA_
private

Referenced by EnzConstraintParameters(), generate_active_pose_constraints(), and set_mcfi().

core::scoring::func::FuncOP protocols::toolbox::match_enzdes_util::EnzConstraintParameters::torsionAB_
private

Referenced by EnzConstraintParameters(), generate_active_pose_constraints(), and set_mcfi().

core::scoring::func::FuncOP protocols::toolbox::match_enzdes_util::EnzConstraintParameters::torsionB_
private

Referenced by EnzConstraintParameters(), generate_active_pose_constraints(), and set_mcfi().

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