Rosetta 3.4
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core::pack::rotamer_set Namespace Reference

Namespaces

namespace  symmetry

Classes

class  BumpSelector
class  ContinuousRotamerSet
class  ContinuousRotamerSets
class  FixbbRotamerSets
class  RotamerCouplings
class  RotamerLinks
class  RotamerSet
class  RotamerSet_
 Container for a set of rotamers for use in packing. Rotamers are sorted into groups of the same residue type. Offsets into these rotamer groups are maintained by this class, as is information concerning the "original rotamer" -- the rotamer present on the input pose before packing began. More...
class  RotamerSetFactory
class  RotamerOperation
 RotamerSetOperations are able to modify the contents of a RotamerSet within the packer immediately after rotamer creation. More...
class  RotamerSetOperation
class  RotamerSets
class  RotamerSetsBase
class  RotamerSubset
 Container for a subset of rotamers that have been created by another rotamer set. This subset object copies pointers to the rotamers contained in another set, as opposed to cloning the rotamers. It's main purpose is to manage the bookkeeping involved in packing with a subset of rotamers (when it might be faster to use a subset and to create an interaction graph specifically for that subset than to simply pass an abreviated list of rotamers to the SimAnnealer with the "rot_to_pack" vector). More...
class  RotamerSubsets
class  UnboundRotamersOperation
 Adds in rotamers from the "unbound" or native structure(s), pulled from one or more PDBs supplied on the command line. More...
class  WaterAnchorInfo
class  WaterPackingInfo

Typedefs

typedef
utility::pointer::owning_ptr
< ContinuousRotamerSet
ContinuousRotamerSetOP
typedef
utility::pointer::owning_ptr
< ContinuousRotamerSet const > 
ContinuousRotamerSetCOP
typedef
utility::pointer::owning_ptr
< ContinuousRotamerSets
ContinuousRotamerSetsOP
typedef
utility::pointer::owning_ptr
< ContinuousRotamerSets const > 
ContinuousRotamerSetsCOP
typedef
utility::pointer::owning_ptr
< FixbbRotamerSets
FixbbRotamerSetsOP
typedef
utility::pointer::owning_ptr
< FixbbRotamerSets const > 
FixbbRotamerSetsCOP
typedef utility::vector1< RealDihedralSet
typedef
utility::pointer::owning_ptr
< RotamerCouplings
RotamerCouplingsOP
typedef
utility::pointer::owning_ptr
< RotamerCouplings const > 
RotamerCouplingsCOP
typedef
utility::pointer::owning_ptr
< RotamerLinks
RotamerLinksOP
typedef
utility::pointer::owning_ptr
< RotamerLinks const > 
RotamerLinksCOP
typedef utility::vector1
< conformation::ResidueOP
Rotamers
typedef
utility::pointer::owning_ptr
< RotamerSet
RotamerSetOP
typedef
utility::pointer::owning_ptr
< RotamerSet const > 
RotamerSetCOP
typedef
utility::pointer::owning_ptr
< RotamerSetFactory
RotamerSetFactoryOP
typedef
utility::pointer::owning_ptr
< RotamerOperation
RotamerOperationOP
typedef
utility::pointer::owning_ptr
< RotamerOperation const > 
RotamerOperationCOP
typedef std::list
< RotamerOperationOP
RotamerOperations
typedef
utility::pointer::owning_ptr
< RotamerSetOperation
RotamerSetOperationOP
typedef
utility::pointer::owning_ptr
< RotamerSetOperation const > 
RotamerSetOperationCOP
typedef std::list
< RotamerSetOperationOP
RotSetOperationList
typedef std::list
< RotamerSetOperationOP >
::const_iterator 
RotSetOperationListIterator
typedef
utility::pointer::owning_ptr
< RotamerSets
RotamerSetsOP
typedef
utility::pointer::owning_ptr
< RotamerSets const > 
RotamerSetsCOP
typedef
utility::pointer::owning_ptr
< RotamerSetsBase
RotamerSetsBaseOP
typedef
utility::pointer::owning_ptr
< RotamerSetsBase const > 
RotamerSetsBaseCOP
typedef
utility::pointer::owning_ptr
< RotamerSubsets
RotamerSubsetsOP
typedef
utility::pointer::owning_ptr
< RotamerSubsets const > 
RotamerSubsetsCOP
typedef
utility::pointer::owning_ptr
< UnboundRotamersOperation
UnboundRotamersOperationOP
typedef
utility::pointer::owning_ptr
< UnboundRotamersOperation
const > 
UnboundRotamersOperationCOP
typedef
utility::pointer::owning_ptr
< WaterAnchorInfo
WaterAnchorInfoOP
typedef
utility::pointer::owning_ptr
< WaterPackingInfo
WaterPackingInfoOP

Enumerations

enum  BumpSelectorDecision { KEEP_ROTAMER, DELETE_ROTAMER, DELETE_PREVIOUS_ROTAMER }

Functions

utility::vector1
< core::conformation::ResidueCOP
bb_independent_rotamers (core::chemical::ResidueTypeCAP rot_restype, bool ignore_cmdline=false)
 a crude function to spit out a list of rotamers given the residue type only, independent of backbone currently there is no proper way of doing this, since the Dunbrack bbind library is not implemented in rosetta. this function tries to circumvent that by constructing a one residue pose and then using the regular dunbrack library, which will use neutral phi/psi for the only residue in the pose the bool ignore_cmdline can be used if someone only wants base inverse rotamers but use the full set in packing
static
numeric::random::RandomGenerator 
RG (32241)
static basic::Tracer tt ("core.pack.rotamer_set.rotamer_building_functions", basic::t_info)
void read_DNA_rotlib (utility::io::izstream &lib_stream, utility::vector1< DihedralSet * > &library)
void build_lib_dna_rotamers (utility::vector1< DihedralSet * > const &library, Size const resid, pose::Pose const &pose, chemical::ResidueTypeCAP concrete_residue, utility::vector1< conformation::ResidueOP > &rotamers)
void build_random_dna_rotamers (Size const resid, pose::Pose const &pose, chemical::ResidueTypeCAP concrete_residue, pack::task::ExtraRotSample const &level, utility::vector1< conformation::ResidueOP > &rotamers)
void build_dna_rotamers (Size const resid, pose::Pose const &pose, chemical::ResidueTypeCAP concrete_residue, pack::task::PackerTask const &task, utility::vector1< conformation::ResidueOP > &rotamers)
void fill_chi_rotamers_with_center_and_stddev (conformation::ResidueOP const &rot, utility::vector1< conformation::ResidueOP > &rotamers, utility::vector1< Real > const &chi_steps, Real const &center, Real const &width)
void add_rna_chi_rotamers (conformation::ResidueOP const &rot, utility::vector1< conformation::ResidueOP > &rotamers, pack::task::ExtraRotSample const &level, scoring::rna::Gaussian_parameter_set const &gaussian_parameter_set)
void build_rna_chi_rotamers (Size const resid, pose::Pose const &pose, chemical::ResidueTypeCAP concrete_residue, pack::task::ExtraRotSample const &level, bool const sample_rna_chi, bool const &include_current, utility::vector1< conformation::ResidueOP > &rotamers)
void build_rna_rotamers (Size const resid, pose::Pose const &pose, chemical::ResidueTypeCAP concrete_residue, pack::task::PackerTask const &task, utility::vector1< conformation::ResidueOP > &new_rotamers, Size &id_for_current_rotamer)
void debug_dump_rotamers (utility::vector1< conformation::ResidueOP > &rotamers)
conformation::ResidueOP create_oriented_water_rotamer (chemical::ResidueType const &h2o_type, Vector const &xyz_atom1, Vector const &xyz_O, Vector const &xyz_atom2, std::string const &name1, std::string const &name2, conformation::Residue const &tp5)
void build_fixed_O_water_rotamers_independent (Size const seqpos, chemical::ResidueType const &h2o_type, pose::Pose const &pose, graph::GraphCOP packer_neighbor_graph, utility::vector1< conformation::ResidueOP > &new_rotamers)
Vector build_optimal_water_O_on_donor (Vector const &hxyz, Vector const &dxyz)
void build_optimal_water_Os_on_acceptor (Vector const &a_xyz, Vector b1_xyz, Vector const &b2_xyz, chemical::Hybridization const &hybrid, utility::vector1< Vector > &O_list)
void build_donor_donor_waters (conformation::Residue const &rsd1, Size const hatm1, conformation::Residue const &rsd2, Size const hatm2, chemical::ResidueType const &h2o_type, conformation::Residue const &tp5, Size const nstep, utility::vector1< conformation::ResidueOP > &new_waters)
void build_donor_acceptor_waters (conformation::Residue const &rsd1, Size const hatm1, conformation::Residue const &rsd2, Size const aatm2, chemical::ResidueType const &h2o_type, conformation::Residue const &tp5, Size const nstep, utility::vector1< conformation::ResidueOP > &new_waters)
void build_acceptor_acceptor_waters (conformation::Residue const &rsd1, Size const aatm1, conformation::Residue const &rsd2, Size const aatm2, chemical::ResidueType const &h2o_type, conformation::Residue const &tp5, Size const nstep, utility::vector1< conformation::ResidueOP > &new_waters)
void build_moving_O_bridge_waters (conformation::Residue const &rsd1, Size const anchor_atom, conformation::Residue const &rsd2, chemical::ResidueType const &h2o_type, conformation::Residue const &tp5, Size const nstep, utility::vector1< conformation::ResidueOP > &new_rotamers)
void build_moving_O_water_rotamers_dependent (RotamerSets const &rotsets, WaterAnchorInfo const &water_info, chemical::ResidueType const &h2o_type, pack::task::PackerTask const &task, pose::Pose const &pose, graph::GraphCOP packer_neighbor_graph, utility::vector1< conformation::ResidueOP > &new_rotamers)
void build_moving_O_water_rotamers_independent (WaterAnchorInfo const &water_info, chemical::ResidueType const &h2o_type, pack::task::PackerTask const &task, pose::Pose const &pose, graph::GraphCOP packer_neighbor_graph, utility::vector1< conformation::ResidueOP > &new_rotamers)
void build_independent_water_rotamers (Size const seqpos_water, chemical::ResidueType const &h2o_type, pack::task::PackerTask const &task, pose::Pose const &pose, graph::GraphCOP packer_neighbor_graph, utility::vector1< conformation::ResidueOP > &new_rotamers)
void build_dependent_water_rotamers (RotamerSets const &rotsets, Size const seqpos_water, chemical::ResidueType const &h2o_type, pack::task::PackerTask const &task, pose::Pose const &pose, graph::GraphCOP packer_neighbor_graph, utility::vector1< conformation::ResidueOP > &new_rotamers)
static basic::Tracer tt ("core.pack.rotamer_set.RotamerSet_", basic::t_info)
static basic::Tracer tt ("core.pack.rotamer_set.RotamerSubset", basic::t_info)
static basic::Tracer TR ("core.pack.rotamer_set.UnboundRotamersOperation")
conformation::ResidueOP dup_residue (conformation::Residue const &existing, conformation::Residue const &conformer)
 Helper function, combines existing's metadata with conformer's conformation.

Typedef Documentation


Enumeration Type Documentation

Enumerator:
KEEP_ROTAMER 
DELETE_ROTAMER 
DELETE_PREVIOUS_ROTAMER 

Function Documentation

void core::pack::rotamer_set::add_rna_chi_rotamers ( conformation::ResidueOP const &  rot,
utility::vector1< conformation::ResidueOP > &  rotamers,
pack::task::ExtraRotSample const &  level,
scoring::rna::Gaussian_parameter_set const &  gaussian_parameter_set 
)
utility::vector1< core::conformation::ResidueCOP > core::pack::rotamer_set::bb_independent_rotamers ( core::chemical::ResidueTypeCAP  rot_restype,
bool  ignore_cmdline 
)

a crude function to spit out a list of rotamers given the residue type only, independent of backbone currently there is no proper way of doing this, since the Dunbrack bbind library is not implemented in rosetta. this function tries to circumvent that by constructing a one residue pose and then using the regular dunbrack library, which will use neutral phi/psi for the only residue in the pose the bool ignore_cmdline can be used if someone only wants base inverse rotamers but use the full set in packing

References core::pose::add_lower_terminus_type_to_pose_residue(), core::pose::add_upper_terminus_type_to_pose_residue(), core::pose::Pose::append_residue_by_jump(), core::conformation::Residue::clone(), core::pack::create_packer_graph(), core::pack::task::TaskFactory::create_packer_task(), core::pack::rotamer_set::RotamerSetFactory::create_rotamer_set(), core::conformation::Residue::nchi(), core::pose::Pose::residue(), and rot().

Referenced by protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::inverse_rotamers_against_residue().

void core::pack::rotamer_set::build_acceptor_acceptor_waters ( conformation::Residue const &  rsd1,
Size const  aatm1,
conformation::Residue const &  rsd2,
Size const  aatm2,
chemical::ResidueType const &  h2o_type,
conformation::Residue const &  tp5,
Size const  nstep,
utility::vector1< conformation::ResidueOP > &  new_waters 
)
void core::pack::rotamer_set::build_dependent_water_rotamers ( RotamerSets const &  rotsets,
Size const  seqpos_water,
chemical::ResidueType const &  h2o_type,
pack::task::PackerTask const &  task,
pose::Pose const &  pose,
graph::GraphCOP  packer_neighbor_graph,
utility::vector1< conformation::ResidueOP > &  new_rotamers 
)
void core::pack::rotamer_set::build_dna_rotamers ( Size const  resid,
pose::Pose const &  pose,
chemical::ResidueTypeCAP  concrete_residue,
pack::task::PackerTask const &  task,
utility::vector1< conformation::ResidueOP > &  rotamers 
)
void core::pack::rotamer_set::build_donor_acceptor_waters ( conformation::Residue const &  rsd1,
Size const  hatm1,
conformation::Residue const &  rsd2,
Size const  aatm2,
chemical::ResidueType const &  h2o_type,
conformation::Residue const &  tp5,
Size const  nstep,
utility::vector1< conformation::ResidueOP > &  new_waters 
)
void core::pack::rotamer_set::build_donor_donor_waters ( conformation::Residue const &  rsd1,
Size const  hatm1,
conformation::Residue const &  rsd2,
Size const  hatm2,
chemical::ResidueType const &  h2o_type,
conformation::Residue const &  tp5,
Size const  nstep,
utility::vector1< conformation::ResidueOP > &  new_waters 
)
void core::pack::rotamer_set::build_fixed_O_water_rotamers_independent ( Size const  seqpos,
chemical::ResidueType const &  h2o_type,
pose::Pose const &  pose,
graph::GraphCOP  packer_neighbor_graph,
utility::vector1< conformation::ResidueOP > &  new_rotamers 
)
void core::pack::rotamer_set::build_independent_water_rotamers ( Size const  seqpos_water,
chemical::ResidueType const &  h2o_type,
pack::task::PackerTask const &  task,
pose::Pose const &  pose,
graph::GraphCOP  packer_neighbor_graph,
utility::vector1< conformation::ResidueOP > &  new_rotamers 
)
void core::pack::rotamer_set::build_lib_dna_rotamers ( utility::vector1< DihedralSet * > const &  library,
Size const  resid,
pose::Pose const &  pose,
chemical::ResidueTypeCAP  concrete_residue,
utility::vector1< conformation::ResidueOP > &  rotamers 
)
void core::pack::rotamer_set::build_moving_O_bridge_waters ( conformation::Residue const &  rsd1,
Size const  anchor_atom,
conformation::Residue const &  rsd2,
chemical::ResidueType const &  h2o_type,
conformation::Residue const &  tp5,
Size const  nstep,
utility::vector1< conformation::ResidueOP > &  new_rotamers 
)
void core::pack::rotamer_set::build_moving_O_water_rotamers_dependent ( RotamerSets const &  rotsets,
WaterAnchorInfo const &  water_info,
chemical::ResidueType const &  h2o_type,
pack::task::PackerTask const &  task,
pose::Pose const &  pose,
graph::GraphCOP  packer_neighbor_graph,
utility::vector1< conformation::ResidueOP > &  new_rotamers 
)
void core::pack::rotamer_set::build_moving_O_water_rotamers_independent ( WaterAnchorInfo const &  water_info,
chemical::ResidueType const &  h2o_type,
pack::task::PackerTask const &  task,
pose::Pose const &  pose,
graph::GraphCOP  packer_neighbor_graph,
utility::vector1< conformation::ResidueOP > &  new_rotamers 
)
Vector core::pack::rotamer_set::build_optimal_water_O_on_donor ( Vector const &  hxyz,
Vector const &  dxyz 
)
void core::pack::rotamer_set::build_optimal_water_Os_on_acceptor ( Vector const &  a_xyz,
Vector  b1_xyz,
Vector const &  b2_xyz,
chemical::Hybridization const &  hybrid,
utility::vector1< Vector > &  O_list 
)
void core::pack::rotamer_set::build_random_dna_rotamers ( Size const  resid,
pose::Pose const &  pose,
chemical::ResidueTypeCAP  concrete_residue,
pack::task::ExtraRotSample const &  level,
utility::vector1< conformation::ResidueOP > &  rotamers 
)
void core::pack::rotamer_set::build_rna_chi_rotamers ( Size const  resid,
pose::Pose const &  pose,
chemical::ResidueTypeCAP  concrete_residue,
pack::task::ExtraRotSample const &  level,
bool const  sample_rna_chi,
bool const &  include_current,
utility::vector1< conformation::ResidueOP > &  rotamers 
)
void core::pack::rotamer_set::build_rna_rotamers ( Size const  resid,
pose::Pose const &  pose,
chemical::ResidueTypeCAP  concrete_residue,
pack::task::PackerTask const &  task,
utility::vector1< conformation::ResidueOP > &  new_rotamers,
Size id_for_current_rotamer 
)
conformation::ResidueOP core::pack::rotamer_set::create_oriented_water_rotamer ( chemical::ResidueType const &  h2o_type,
Vector const &  xyz_atom1,
Vector const &  xyz_O,
Vector const &  xyz_atom2,
std::string const &  name1,
std::string const &  name2,
conformation::Residue const &  tp5 
)
void core::pack::rotamer_set::debug_dump_rotamers ( utility::vector1< conformation::ResidueOP > &  rotamers)
conformation::ResidueOP core::pack::rotamer_set::dup_residue ( conformation::Residue const &  existing,
conformation::Residue const &  conformer 
)
void core::pack::rotamer_set::fill_chi_rotamers_with_center_and_stddev ( conformation::ResidueOP const &  rot,
utility::vector1< conformation::ResidueOP > &  rotamers,
utility::vector1< Real > const &  chi_steps,
Real const &  center,
Real const &  width 
)

Referenced by add_rna_chi_rotamers().

void core::pack::rotamer_set::read_DNA_rotlib ( utility::io::izstream &  lib_stream,
utility::vector1< DihedralSet * > &  library 
)

Referenced by build_dna_rotamers().

static numeric::random::RandomGenerator core::pack::rotamer_set::RG ( 32241  ) [static]
static basic::Tracer core::pack::rotamer_set::TR ( "core.pack.rotamer_set.UnboundRotamersOperation"  ) [static]
static basic::Tracer core::pack::rotamer_set::tt ( "core.pack.rotamer_set.rotamer_building_functions"  ,
basic::t_info   
) [static]
static basic::Tracer core::pack::rotamer_set::tt ( "core.pack.rotamer_set.RotamerSet_"  ,
basic::t_info   
) [static]
static basic::Tracer core::pack::rotamer_set::tt ( "core.pack.rotamer_set.RotamerSubset"  ,
basic::t_info   
) [static]
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