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protocols::matdes Namespace Reference

Classes

class  BuildingBlockInterfaceOperation
 
class  BuildingBlockInterfaceOperationCreator
 
class  ClashCheckFilter
 
class  ClashCheckFilterCreator
 
class  ExtractSubposeMover
 
class  ExtractSubposeMoverCreator
 
class  GetRBDOFValues
 WARNING WARNING WARNING THIS CLASS USES THE THREAD UNSAFE SymDofMoverSampler AND MAKES ANY PROTOCOL THAT USES THIS CLASS THREAD UNSAFE. More...
 
class  GetRBDOFValuesCreator
 
class  InterfacePackingFilter
 
class  InterfacePackingFilterCreator
 
class  MatDesGreedyOptMutationMover
 
class  MatDesGreedyOptMutationMoverCreator
 
class  MatDesPointMutationCalculator
 
class  MotifHitsRotamersOperation
 
class  OligomericAverageDegreeFilter
 
class  OligomericAverageDegreeFilterCreator
 
class  SchemePlaceMotifsMover
 
class  SchemePlaceMotifsMoverCreator
 
class  SymDofMover
 
class  SymDofMoverCreator
 
class  SymDofMoverSampler
 WARNING WARNING WARNING THIS SINGLETON CLASS HOLDS NON-CONST, JOB SPECIFIC DATA AND MAKES EVERY CLASS THAT USES THIS DATA THREAD UNSAFE. THIS IS NOT HOW SINGLETONS SHOULD BE USED. More...
 
class  SymUnsatHbondFilter
 filters based on an upper bound # of buried unsatisfied polar residues More...
 
class  SymUnsatHbondFilterCreator
 

Typedefs

typedef
utility::pointer::shared_ptr
< BuildingBlockInterfaceOperation
BuildingBlockInterfaceOperationOP
 
typedef
utility::pointer::shared_ptr
< BuildingBlockInterfaceOperation
const > 
BuildingBlockInterfaceOperationCOP
 
typedef
utility::pointer::shared_ptr
< ClashCheckFilter
ClashCheckFilterOP
 
typedef
utility::pointer::shared_ptr
< ClashCheckFilter const > 
ClashCheckFilterCOP
 
typedef
utility::pointer::shared_ptr
< ExtractSubposeMover
ExtractSubposeMoverOP
 
typedef
utility::pointer::shared_ptr
< ExtractSubposeMover const > 
ExtractSubposeMoverCOP
 
typedef
utility::pointer::shared_ptr
< GetRBDOFValues
GetRBDOFValuesOP
 
typedef
utility::pointer::shared_ptr
< GetRBDOFValues const > 
GetRBDOFValuesCOP
 
typedef
utility::pointer::shared_ptr
< InterfacePackingFilter
InterfacePackingFilterOP
 
typedef
utility::pointer::shared_ptr
< InterfacePackingFilter const > 
InterfacePackingFilterCOP
 
typedef
utility::pointer::shared_ptr
< MatDesGreedyOptMutationMover
MatDesGreedyOptMutationMoverOP
 
typedef
utility::pointer::shared_ptr
< MatDesGreedyOptMutationMover
const > 
MatDesGreedyOptMutationMoverCOP
 
typedef
utility::pointer::shared_ptr
< MatDesPointMutationCalculator
MatDesPointMutationCalculatorOP
 
typedef
utility::pointer::shared_ptr
< MatDesPointMutationCalculator
const > 
MatDesPointMutationCalculatorCOP
 
typedef
utility::pointer::shared_ptr
< MotifHitsRotamersOperation
MotifHitsRotamersOperationOP
 
typedef
utility::pointer::shared_ptr
< MotifHitsRotamersOperation
const > 
MotifHitsRotamersOperationCOP
 
typedef
utility::pointer::shared_ptr
< OligomericAverageDegreeFilter
OligomericAverageDegreeFilterOP
 
typedef
utility::pointer::shared_ptr
< OligomericAverageDegreeFilter
const > 
OligomericAverageDegreeFilterCOP
 
typedef
utility::pointer::shared_ptr
< SchemePlaceMotifsMover
SchemePlaceMotifsMoverOP
 
typedef
utility::pointer::shared_ptr
< SchemePlaceMotifsMover const > 
SchemePlaceMotifsMoverCOP
 
using Vec = numeric::xyzVector< Real >
 
using Mat = numeric::xyzMatrix< Real >
 
typedef
utility::pointer::shared_ptr
< SymDofMover
SymDofMoverOP
 
typedef
utility::pointer::shared_ptr
< SymDofMover const > 
SymDofMoverCOP
 
typedef
utility::pointer::shared_ptr
< SymUnsatHbondFilter
SymUnsatHbondFilterOP
 
typedef
utility::pointer::shared_ptr
< SymUnsatHbondFilter const > 
SymUnsatHbondFilterCOP
 

Functions

utility::vector1< core::Sizeget_matching_subunits (core::pose::Pose const &pose, core::pose::Pose const &subpose)
 
static basic::Tracer TR ("protocols.matdes.InterfacePackingFilter")
 
static basic::Tracer TR ("protocols.matdes.MatDesGreedyOptMutationMover")
 
bool cmp_pair_by_second (pair< core::Size, Real > const pair1, pair< core::Size, Real > const pair2)
 
bool cmp_pair_by_first_vec_val (pair< AA, vector1< Real > > const pair1, pair< AA, vector1< Real > > const pair2)
 
bool cmp_pair_vec_by_first_vec_val (pair< core::Size, vector1< pair< AA, vector1< Real > > > > const pair1, pair< core::Size, vector1< pair< AA, vector1< Real > > > > const pair2)
 
void calc_pareto_front_nbrs (vector1< vector1< Real > > coords, vector1< bool > const &is_pfront, vector1< bool > &is_pfront_nbr, vector1< Real > const &nbr_dist)
 
void calc_pareto_front (vector1< vector1< Real > > coords, vector1< bool > &is_pfront, vector1< Real > const &coord_perts, bool const div, bool const incl_nbrs)
 
static basic::Tracer TR ("protocols.matdes.MatDesPointMutationCalculator")
 
void insert_point_mut_filter_vals (core::Size const seqpos, chemical::AA const aa, vector1< Real > const vals, vector1< pair< core::Size, vector1< pair< AA, vector1< Real > > > > > &seqpos_aa_vals_vec)
 
static basic::Tracer TR ("protocols.matdes.MotifHitsRotamersOperation")
 
core::conformation::ResidueOP dup_residue (core::conformation::Residue const &existing, core::conformation::Residue const &conformer)
 Helper function, combines existing's metadata with conformer's conformation. More...
 
static void trans_pose (Pose &pose, Vec const &trans, core::Size start, core::Size end)
 
static void rot_pose (Pose &pose, Mat const &rot, core::Size start, core::Size end)
 
static void rot_pose (Pose &pose, Mat const &rot, Vec const &cen, core::Size start, core::Size end)
 
static void rot_pose (Pose &pose, Vec const &axis, core::Real const &ang, core::Size start, core::Size end)
 
static void rot_pose (Pose &pose, Vec const &axis, core::Real const &ang, Vec const &cen, core::Size start, core::Size end)
 
static void alignaxis (core::pose::Pose &pose, Vec newaxis, Vec oldaxis, Vec cen, core::Size start, core::Size end)
 
numeric::Real get_intra_contacts (Pose const &pose)
 
void maximize_sub1_contact (Pose &pose, core::Size const &nf1, core::Size const &nf2, Vec const &ax1, Vec const &ax2)
 
static basic::Tracer TR ("protocols.matdes.SymUnsatHbondFilter")
 

Typedef Documentation

typedef utility::pointer::shared_ptr< ClashCheckFilter const > protocols::matdes::ClashCheckFilterCOP
typedef utility::pointer::shared_ptr< ClashCheckFilter > protocols::matdes::ClashCheckFilterOP
typedef utility::pointer::shared_ptr< ExtractSubposeMover const > protocols::matdes::ExtractSubposeMoverCOP
typedef utility::pointer::shared_ptr< ExtractSubposeMover > protocols::matdes::ExtractSubposeMoverOP
typedef utility::pointer::shared_ptr< GetRBDOFValues const > protocols::matdes::GetRBDOFValuesCOP
typedef utility::pointer::shared_ptr< GetRBDOFValues > protocols::matdes::GetRBDOFValuesOP
typedef utility::pointer::shared_ptr< InterfacePackingFilter const > protocols::matdes::InterfacePackingFilterCOP
using protocols::matdes::Mat = typedef numeric::xyzMatrix<Real>
typedef utility::pointer::shared_ptr< SchemePlaceMotifsMover const > protocols::matdes::SchemePlaceMotifsMoverCOP
typedef utility::pointer::shared_ptr< SymDofMover const > protocols::matdes::SymDofMoverCOP
typedef utility::pointer::shared_ptr< SymDofMover > protocols::matdes::SymDofMoverOP
typedef utility::pointer::shared_ptr< SymUnsatHbondFilter const > protocols::matdes::SymUnsatHbondFilterCOP
typedef utility::pointer::shared_ptr< SymUnsatHbondFilter > protocols::matdes::SymUnsatHbondFilterOP
using protocols::matdes::Vec = typedef numeric::xyzVector<Real>

Function Documentation

static void protocols::matdes::alignaxis ( core::pose::Pose pose,
Vec  newaxis,
Vec  oldaxis,
Vec  cen,
core::Size  start,
core::Size  end 
)
static
void protocols::matdes::calc_pareto_front ( vector1< vector1< Real > >  coords,
vector1< bool > &  is_pfront,
vector1< Real > const &  coord_perts,
bool const  div,
bool const  incl_nbrs 
)
void protocols::matdes::calc_pareto_front_nbrs ( vector1< vector1< Real > >  coords,
vector1< bool > const &  is_pfront,
vector1< bool > &  is_pfront_nbr,
vector1< Real > const &  nbr_dist 
)
bool protocols::matdes::cmp_pair_by_first_vec_val ( pair< AA, vector1< Real > > const  pair1,
pair< AA, vector1< Real > > const  pair2 
)
bool protocols::matdes::cmp_pair_by_second ( pair< core::Size, Real > const  pair1,
pair< core::Size, Real > const  pair2 
)
bool protocols::matdes::cmp_pair_vec_by_first_vec_val ( pair< core::Size, vector1< pair< AA, vector1< Real > > > > const  pair1,
pair< core::Size, vector1< pair< AA, vector1< Real > > > > const  pair2 
)
core::conformation::ResidueOP protocols::matdes::dup_residue ( core::conformation::Residue const &  existing,
core::conformation::Residue const &  conformer 
)
numeric::Real protocols::matdes::get_intra_contacts ( Pose const &  pose)
utility::vector1< core::Size > protocols::matdes::get_matching_subunits ( core::pose::Pose const &  pose,
core::pose::Pose const &  subpose 
)
void protocols::matdes::insert_point_mut_filter_vals ( core::Size const  seqpos,
chemical::AA const  aa,
vector1< Real > const  vals,
vector1< pair< core::Size, vector1< pair< AA, vector1< Real > > > > > &  seqpos_aa_vals_vec 
)
void protocols::matdes::maximize_sub1_contact ( Pose pose,
core::Size const &  nf1,
core::Size const &  nf2,
Vec const &  ax1,
Vec const &  ax2 
)
static void protocols::matdes::rot_pose ( Pose pose,
Mat const &  rot,
core::Size  start,
core::Size  end 
)
static
static void protocols::matdes::rot_pose ( Pose pose,
Mat const &  rot,
Vec const &  cen,
core::Size  start,
core::Size  end 
)
static

References rot_pose(), and trans_pose().

static void protocols::matdes::rot_pose ( Pose pose,
Vec const &  axis,
core::Real const &  ang,
core::Size  start,
core::Size  end 
)
static

References rot_pose().

static void protocols::matdes::rot_pose ( Pose pose,
Vec const &  axis,
core::Real const &  ang,
Vec const &  cen,
core::Size  start,
core::Size  end 
)
static

References rot_pose().

static basic::Tracer protocols::matdes::TR ( "protocols.matdes.MotifHitsRotamersOperation"  )
static
static basic::Tracer protocols::matdes::TR ( "protocols.matdes.InterfacePackingFilter"  )
static

Referenced by protocols::matdes::SymDofMover::add_components_to_pose_if_necessary(), protocols::matdes::MotifHitsRotamersOperation::alter_rotamer_set(), protocols::matdes::SchemePlaceMotifsMover::apply(), protocols::matdes::InterfacePackingFilter::apply(), protocols::matdes::ExtractSubposeMover::apply(), protocols::matdes::BuildingBlockInterfaceOperation::apply(), protocols::matdes::SymDofMover::apply(), protocols::matdes::MatDesGreedyOptMutationMover::apply(), protocols::matdes::SymUnsatHbondFilter::apply(), protocols::matdes::ClashCheckFilter::apply(), protocols::matdes::InterfacePackingFilter::compute(), protocols::matdes::SymUnsatHbondFilter::compute(), protocols::matdes::ClashCheckFilter::compute(), protocols::matdes::OligomericAverageDegreeFilter::compute(), protocols::matdes::GetRBDOFValues::compute(), protocols::matdes::MatDesGreedyOptMutationMover::dump_scoring_table(), protocols::matdes::MatDesPointMutationCalculator::eval_filters(), get_matching_subunits(), protocols::matdes::MatDesPointMutationCalculator::MatDesPointMutationCalculator(), protocols::matdes::SchemePlaceMotifsMover::parse_my_tag(), protocols::matdes::InterfacePackingFilter::parse_my_tag(), protocols::matdes::SymDofMover::parse_my_tag(), protocols::matdes::MatDesGreedyOptMutationMover::parse_my_tag(), protocols::matdes::SymUnsatHbondFilter::parse_my_tag(), protocols::matdes::OligomericAverageDegreeFilter::parse_my_tag(), protocols::matdes::MatDesGreedyOptMutationMover::reset_delta_filter_baselines(), protocols::matdes::SymDofMoverSampler::set_angle_ranges(), protocols::matdes::SymDofMoverSampler::set_radial_disp_ranges(), and protocols::matdes::SymDofMoverSampler::step().

static basic::Tracer protocols::matdes::TR ( "protocols.matdes.MatDesGreedyOptMutationMover"  )
static
static basic::Tracer protocols::matdes::TR ( "protocols.matdes.SymUnsatHbondFilter"  )
static
static basic::Tracer protocols::matdes::TR ( "protocols.matdes.MatDesPointMutationCalculator"  )
static
static void protocols::matdes::trans_pose ( Pose pose,
Vec const &  trans,
core::Size  start,
core::Size  end 
)
static