Rosetta Protocols  2014.35
Classes | Typedefs | Functions | Variables
protocols::matdes Namespace Reference

Classes

class  BuildingBlockInterfaceOperation
 
class  BuildingBlockInterfaceOperationCreator
 
class  ClashCheckFilter
 
class  ClashCheckFilterCreator
 
class  ExtractSubposeMover
 
class  ExtractSubposeMoverCreator
 
class  GetRBDOFValues
 
class  GetRBDOFValuesCreator
 
class  InterfacePackingFilter
 
class  InterfacePackingFilterCreator
 
class  MatDesGreedyOptMutationMover
 
class  MatDesGreedyOptMutationMoverCreator
 
class  MatDesPointMutationCalculator
 
class  OligomericAverageDegreeFilter
 
class  OligomericAverageDegreeFilterCreator
 
class  SymDofMover
 
class  SymDofMoverCreator
 
class  SymDofMoverSampler
 
class  SymUnsatHbondFilter
 filters based on an upper bound # of buried unsatisfied polar residues More...
 
class  SymUnsatHbondFilterCreator
 

Typedefs

typedef
utility::pointer::owning_ptr
< BuildingBlockInterfaceOperation
BuildingBlockInterfaceOperationOP
 
typedef
utility::pointer::owning_ptr
< BuildingBlockInterfaceOperation
const > 
BuildingBlockInterfaceOperationCOP
 
typedef
utility::pointer::owning_ptr
< ClashCheckFilter
ClashCheckFilterOP
 
typedef
utility::pointer::owning_ptr
< ClashCheckFilter const > 
ClashCheckFilterCOP
 
typedef
utility::pointer::owning_ptr
< ExtractSubposeMover
ExtractSubposeMoverOP
 
typedef
utility::pointer::owning_ptr
< ExtractSubposeMover const > 
ExtractSubposeMoverCOP
 
typedef
utility::pointer::owning_ptr
< GetRBDOFValues
GetRBDOFValuesOP
 
typedef
utility::pointer::owning_ptr
< GetRBDOFValues const > 
GetRBDOFValuesCOP
 
typedef
utility::pointer::owning_ptr
< InterfacePackingFilter
InterfacePackingFilterOP
 
typedef
utility::pointer::owning_ptr
< InterfacePackingFilter const > 
InterfacePackingFilterCOP
 
typedef
utility::pointer::owning_ptr
< MatDesGreedyOptMutationMover
MatDesGreedyOptMutationMoverOP
 
typedef
utility::pointer::owning_ptr
< MatDesGreedyOptMutationMover
const > 
MatDesGreedyOptMutationMoverCOP
 
typedef
utility::pointer::owning_ptr
< MatDesPointMutationCalculator
MatDesPointMutationCalculatorOP
 
typedef
utility::pointer::owning_ptr
< MatDesPointMutationCalculator
const > 
MatDesPointMutationCalculatorCOP
 
typedef
utility::pointer::owning_ptr
< OligomericAverageDegreeFilter
OligomericAverageDegreeFilterOP
 
typedef
utility::pointer::owning_ptr
< OligomericAverageDegreeFilter
const > 
OligomericAverageDegreeFilterCOP
 
typedef numeric::xyzVector< RealVec
 
typedef numeric::xyzMatrix< RealMat
 
typedef
utility::pointer::owning_ptr
< SymDofMover
SymDofMoverOP
 
typedef
utility::pointer::owning_ptr
< SymDofMover const > 
SymDofMoverCOP
 
typedef
utility::pointer::owning_ptr
< SymUnsatHbondFilter
SymUnsatHbondFilterOP
 
typedef
utility::pointer::owning_ptr
< SymUnsatHbondFilter const > 
SymUnsatHbondFilterCOP
 

Functions

bool cmp_pair_by_second (pair< Size, Real > const pair1, pair< 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< Size, vector1< pair< AA, vector1< Real > > > > const pair1, pair< 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)
 
void insert_point_mut_filter_vals (Size const seqpos, chemical::AA const aa, vector1< Real > const vals, vector1< pair< Size, vector1< pair< AA, vector1< Real > > > > > &seqpos_aa_vals_vec)
 
static void trans_pose (Pose &pose, Vec const &trans, Size start, Size end)
 
static void rot_pose (Pose &pose, Mat const &rot, Size start, Size end)
 
static void rot_pose (Pose &pose, Mat const &rot, Vec const &cen, Size start, Size end)
 
static void rot_pose (Pose &pose, Vec const &axis, double const &ang, Size start, Size end)
 
static void rot_pose (Pose &pose, Vec const &axis, double const &ang, Vec const &cen, Size start, Size end)
 
static void alignaxis (core::pose::Pose &pose, Vec newaxis, Vec oldaxis, Vec cen, Size start, Size end)
 
numeric::Real get_intra_contacts (Pose const &pose)
 
void maximize_sub1_contact (Pose &pose, Size const &nf1, Size const &nf2, Vec const &ax1, Vec const &ax2)
 

Variables

static basic::Tracer TR ("protocols.matdes.InterfacePackingFilter")
 
static basic::Tracer TR ("protocols.matdes.MatDesGreedyOptMutationMover")
 
static
numeric::random::RandomGenerator 
RG (21378)
 
static basic::Tracer TR ("protocols.matdes.MatDesPointMutationCalculator")
 
static
numeric::random::RandomGenerator 
RG (51423)
 
static basic::Tracer TR ("protocols.matdes.SymUnsatHbondFilter")
 

Typedef Documentation

Function Documentation

static void protocols::matdes::alignaxis ( core::pose::Pose pose,
Vec  newaxis,
Vec  oldaxis,
Vec  cen,
Size  start,
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< Size, Real > const  pair1,
pair< Size, Real > const  pair2 
)
bool protocols::matdes::cmp_pair_vec_by_first_vec_val ( pair< Size, vector1< pair< AA, vector1< Real > > > > const  pair1,
pair< Size, vector1< pair< AA, vector1< Real > > > > const  pair2 
)
numeric::Real protocols::matdes::get_intra_contacts ( Pose const &  pose)
void protocols::matdes::insert_point_mut_filter_vals ( Size const  seqpos,
chemical::AA const  aa,
vector1< Real > const  vals,
vector1< pair< Size, vector1< pair< AA, vector1< Real > > > > > &  seqpos_aa_vals_vec 
)

References pair.

void protocols::matdes::maximize_sub1_contact ( Pose pose,
Size const &  nf1,
Size const &  nf2,
Vec const &  ax1,
Vec const &  ax2 
)
static void protocols::matdes::rot_pose ( Pose pose,
Mat const &  rot,
Size  start,
Size  end 
)
static
static void protocols::matdes::rot_pose ( Pose pose,
Mat const &  rot,
Vec const &  cen,
Size  start,
Size  end 
)
static

References rot_pose(), and trans_pose().

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

Variable Documentation

numeric::random::RandomGenerator protocols::matdes::RG(21378)
static
numeric::random::RandomGenerator protocols::matdes::RG(51423)
static
basic::Tracer protocols::matdes::TR("protocols.matdes.InterfacePackingFilter")
static
basic::Tracer protocols::matdes::TR("protocols.matdes.MatDesGreedyOptMutationMover")
static
basic::Tracer protocols::matdes::TR("protocols.matdes.SymUnsatHbondFilter")
static
basic::Tracer protocols::matdes::TR("protocols.matdes.MatDesPointMutationCalculator")
static