Rosetta Core  2014.35
Namespaces | Classes | Typedefs | Enumerations | Functions | Variables
core::pack::rotamer_set Namespace Reference

Namespaces

 symmetry
 

Classes

class  AddResiduesRotamerSetOperation
 Adds in rotamers from a list of Residues,. More...
 
class  BumpSelector
 
class  ContinuousRotamerSet
 
class  ContinuousRotamerSets
 
class  FixbbRotamerSets
 
class  RotamerCouplings
 
class  RotamerLinks
 
class  RotamerOperation
 RotamerSetOperations are able to modify the contents of a RotamerSet within the packer immediately after rotamer creation. More...
 
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  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 std::pair< core::Angle,
core::Angle
RotamerBin
 
typedef utility::vector1
< RotamerBin
RotamerBins
 
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::ResidueTypeCOP 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 More...
 
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, utility::vector1< chemical::rna::GaussianParameter > const &gaussian_parameter_set)
 
void build_rna_chi_rotamers (Size const resid, pose::Pose const &pose, chemical::ResidueTypeCOP concrete_residue, pack::task::ExtraRotSample const &level, bool const sample_rna_chi, bool const &include_current, utility::vector1< conformation::ResidueOP > &rotamers)
 
void build_proton_chi_rotamers (Size const , pose::Pose const &pose, chemical::ResidueTypeCOP concrete_residue, pack::task::ResidueLevelTask const &residue_task, utility::vector1< conformation::ResidueOP > &rotamers)
 
void build_five_prime_phosphate_rotamers (utility::vector1< conformation::ResidueOP > &rotamers, pose::Pose const &pose, bool const allow_phosphate_virtualization)
 
void build_three_prime_phosphate_rotamers (utility::vector1< conformation::ResidueOP > &rotamers, pose::Pose const &pose, bool const allow_phosphate_virtualization)
 
void build_rna_rotamers (Size const resid, pose::Pose const &pose, chemical::ResidueTypeCOP concrete_residue, pack::task::PackerTask const &task, utility::vector1< conformation::ResidueOP > &new_rotamers, Size &id_for_current_rotamer)
 
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::ResidueTypeCOP concrete_residue, utility::vector1< conformation::ResidueOP > &rotamers)
 
void build_random_dna_rotamers (Size const resid, pose::Pose const &pose, chemical::ResidueTypeCOP concrete_residue, pack::task::ExtraRotSample const &level, utility::vector1< conformation::ResidueOP > &rotamers)
 
void build_dna_rotamers (Size const resid, pose::Pose const &pose, chemical::ResidueTypeCOP concrete_residue, pack::task::PackerTask const &task, utility::vector1< conformation::ResidueOP > &rotamers)
 
void build_rotamers_from_rotamer_bins (conformation::Residue const &residue, utility::vector1< conformation::ResidueOP > &rotamers, uint current_chi_index=1, utility::vector1< uint > *current_bin_indices=NULL)
 Make a rotamer (Residue) for every combination of torsion angle in the rotamer bins listed in the params file for the given Residue. More...
 
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)
 
conformation::ResidueOP dup_residue (conformation::Residue const &existing, conformation::Residue const &conformer)
 Helper function, combines existing's metadata with conformer's conformation. More...
 

Variables

static basic::Tracer TR ("core.pack.rotamer_set.rna_rotamer_building_functions", basic::t_info)
 
static
numeric::random::RandomGenerator 
RG (32241)
 
static basic::Tracer tt ("core.pack.rotamer_set.rotamer_building_functions", basic::t_info)
 
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")
 

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,
utility::vector1< chemical::rna::GaussianParameter > const &  gaussian_parameter_set 
)
utility::vector1< core::conformation::ResidueCOP > core::pack::rotamer_set::bb_independent_rotamers ( core::chemical::ResidueTypeCOP  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(), and core::pose::Pose::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::ResidueTypeCOP  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_five_prime_phosphate_rotamers ( utility::vector1< conformation::ResidueOP > &  rotamers,
pose::Pose const &  pose,
bool const  allow_phosphate_virtualization 
)
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::ResidueTypeCOP  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_proton_chi_rotamers ( Size  const,
pose::Pose const &  pose,
chemical::ResidueTypeCOP  concrete_residue,
pack::task::ResidueLevelTask const &  residue_task,
utility::vector1< conformation::ResidueOP > &  rotamers 
)
void core::pack::rotamer_set::build_random_dna_rotamers ( Size const  resid,
pose::Pose const &  pose,
chemical::ResidueTypeCOP  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::ResidueTypeCOP  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::ResidueTypeCOP  concrete_residue,
pack::task::PackerTask const &  task,
utility::vector1< conformation::ResidueOP > &  new_rotamers,
Size id_for_current_rotamer 
)
void core::pack::rotamer_set::build_rotamers_from_rotamer_bins ( conformation::Residue const &  residue,
utility::vector1< conformation::ResidueOP > &  rotamers,
uint  current_chi_index,
utility::vector1< uint > *  current_bin_indices 
)

Make a rotamer (Residue) for every combination of torsion angle in the rotamer bins listed in the params file for the given Residue.

Parameters
<residue>the Residue for which rotamers are to be made
<rotamers>a list of rotamers (Residues) to which this method will add new rotamers
<current_chi_index>internally used by this recursive method; DO NOT PASS A VALUE!
<current_bin_indices>internally used by this recursive method; DO NOT PASS A VALUE!

Uses recursion to make a nested loop n levels deep, where n is the number of side-chain torsions ("chis").

Author
Labonte
Note
This currently assumes that all torsions are independent. For now, this is the default method of handling carbohydrate rotamers. Ideally, we will find an alternative method for handling carbohydrate rotamer libraries....

References bin, core::conformation::Residue::chi_rotamers(), core::conformation::Residue::create_rotamer(), core::chemical::ResidueType::nchi(), torsion(), tt, and core::conformation::Residue::type().

Referenced by core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete().

void core::pack::rotamer_set::build_three_prime_phosphate_rotamers ( utility::vector1< conformation::ResidueOP > &  rotamers,
pose::Pose const &  pose,
bool const  allow_phosphate_virtualization 
)
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 
)
void core::pack::rotamer_set::read_DNA_rotlib ( utility::io::izstream lib_stream,
utility::vector1< DihedralSet * > &  library 
)

Variable Documentation

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