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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  DeleteAllRotamerSetOperation
 Adds in rotamers from a list of Residues,. More...
 
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  RotamerSetsFactory
 
class  RotamerSetsOperation
 RotamerSetsOperations are able to modify the RotamerSets object such that changes can be correlated accros multiple rotamer sets. More...
 
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::shared_ptr
< ContinuousRotamerSet
ContinuousRotamerSetOP
 
typedef
utility::pointer::shared_ptr
< ContinuousRotamerSet const > 
ContinuousRotamerSetCOP
 
typedef
utility::pointer::shared_ptr
< ContinuousRotamerSets
ContinuousRotamerSetsOP
 
typedef
utility::pointer::shared_ptr
< ContinuousRotamerSets const > 
ContinuousRotamerSetsCOP
 
typedef
utility::pointer::shared_ptr
< DeleteAllRotamerSetOperation
DeleteAllRotamerSetOperationOP
 
typedef
utility::pointer::shared_ptr
< DeleteAllRotamerSetOperation
const > 
DeleteAllRotamerSetOperationCOP
 
typedef
utility::pointer::shared_ptr
< FixbbRotamerSets
FixbbRotamerSetsOP
 
typedef
utility::pointer::shared_ptr
< FixbbRotamerSets const > 
FixbbRotamerSetsCOP
 
typedef utility::vector1< RealDihedralSet
 
typedef
utility::pointer::shared_ptr
< RotamerCouplings
RotamerCouplingsOP
 
typedef
utility::pointer::shared_ptr
< RotamerCouplings const > 
RotamerCouplingsCOP
 
typedef
utility::pointer::shared_ptr
< RotamerLinks
RotamerLinksOP
 
typedef
utility::pointer::shared_ptr
< RotamerLinks const > 
RotamerLinksCOP
 
typedef utility::vector1
< conformation::ResidueOP
Rotamers
 
typedef
utility::pointer::shared_ptr
< RotamerSet
RotamerSetOP
 
typedef
utility::pointer::shared_ptr
< RotamerSet const > 
RotamerSetCOP
 
typedef std::pair< core::Angle,
core::Angle
RotamerBin
 
typedef utility::vector1
< RotamerBin
RotamerBins
 
typedef
utility::pointer::shared_ptr
< RotamerSetFactory
RotamerSetFactoryOP
 
typedef
utility::pointer::shared_ptr
< RotamerOperation
RotamerOperationOP
 
typedef
utility::pointer::shared_ptr
< RotamerOperation const > 
RotamerOperationCOP
 
typedef std::list
< RotamerOperationOP
RotamerOperations
 
typedef
utility::pointer::shared_ptr
< RotamerSetOperation
RotamerSetOperationOP
 
typedef
utility::pointer::shared_ptr
< RotamerSetOperation const > 
RotamerSetOperationCOP
 
typedef std::list
< RotamerSetOperationOP
RotSetOperationList
 
typedef std::list
< RotamerSetOperationOP >
::const_iterator 
RotSetOperationListIterator
 
typedef
utility::pointer::shared_ptr
< RotamerSetsOperation
RotamerSetsOperationOP
 
typedef
utility::pointer::shared_ptr
< RotamerSetsOperation const > 
RotamerSetsOperationCOP
 
typedef std::list
< RotamerSetsOperationOP
RotSetsOperationList
 
typedef std::list
< RotamerSetsOperationOP >
::const_iterator 
RotSetsOperationListIterator
 
typedef
utility::pointer::shared_ptr
< RotamerSetsFactory
RotamerSetsFactoryOP
 
typedef
utility::pointer::shared_ptr
< RotamerSubsets
RotamerSubsetsOP
 
typedef
utility::pointer::shared_ptr
< RotamerSubsets const > 
RotamerSubsetsCOP
 
typedef
utility::pointer::shared_ptr
< UnboundRotamersOperation
UnboundRotamersOperationOP
 
typedef
utility::pointer::shared_ptr
< UnboundRotamersOperation
const > 
UnboundRotamersOperationCOP
 
typedef
utility::pointer::shared_ptr
< WaterAnchorInfo
WaterAnchorInfoOP
 
typedef
utility::pointer::shared_ptr
< WaterPackingInfo
WaterPackingInfoOP
 
typedef
utility::pointer::shared_ptr
< RotamerSets
RotamerSetsOP
 
typedef
utility::pointer::shared_ptr
< RotamerSets const > 
RotamerSetsCOP
 

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...
 
static basic::Tracer TR ("core.pack.rotamer_set.rna_rotamer_building_functions", basic::t_info)
 
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)
 
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::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, utility::vector1< uint > &current_bin_indices)
 Internal, recursive function to implement the external interface of build_rotamers_from_rotamer_bins(), below. More...
 
void build_rotamers_from_rotamer_bins (conformation::Residue const &residue, utility::vector1< conformation::ResidueOP > &rotamers)
 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, utility::graph::GraphCOP packer_neighbor_graph, utility::vector1< conformation::ResidueOP > &new_rotamers)
 
Vector build_water_O_on_donor (Vector const &hxyz, Vector const &dxyz, Real phi, Real theta)
 
Vector build_optimal_water_O_on_donor (Vector const &hxyz, Vector const &dxyz)
 
Vector build_optimal_hyp_H_for_donor (Vector const &o1, Vector const &hatm1_xyz, Vector const &reference, Real angle)
 
Vector build_optimal_hyp_H_for_acceptor (Vector const &o2, Vector const &aatm2_xyz, Vector const &reference, Real angle)
 
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)
 
core::PackerEnergy pre_bump_check (Size const &seqpos_water, conformation::ResidueOP rot, scoring::ScoreFunction const &score_fxn, pose::Pose const &pose, task::PackerTask const &task, utility::graph::GraphCOP packer_neighbor_graph)
 
void build_donor_donor_waters (Size const &seqpos_water, 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, pose::Pose const &pose, pack::task::PackerTask const &task, utility::graph::GraphCOP packer_neighbor_graph, scoring::ScoreFunction const &score_fxn)
 
void build_sew_waters_to_donor (Size const &seqpos_water, conformation::Residue const &rsd, Size const hatm, chemical::ResidueType const &h2o_type, conformation::Residue const &tp5, utility::vector1< conformation::ResidueOP > &new_waters, pose::Pose const &pose, pack::task::PackerTask const &task, utility::graph::GraphCOP packer_neighbor_graph, scoring::ScoreFunction const &score_fxn)
 
void build_sew_waters_to_acceptor (Size const &seqpos_water, conformation::Residue const &rsd, Size const aatm, chemical::ResidueType const &h2o_type, conformation::Residue const &tp5, utility::vector1< conformation::ResidueOP > &new_waters, pose::Pose const &pose, pack::task::PackerTask const &task, utility::graph::GraphCOP packer_neighbor_graph, scoring::ScoreFunction const &score_fxn)
 
void build_donor_acceptor_waters (Size const &seqpos_water, 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, pose::Pose const &pose, pack::task::PackerTask const &task, utility::graph::GraphCOP packer_neighbor_graph, scoring::ScoreFunction const &score_fxn)
 
void build_acceptor_acceptor_waters (Size const &seqpos_water, 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, pose::Pose const &pose, pack::task::PackerTask const &task, utility::graph::GraphCOP packer_neighbor_graph, scoring::ScoreFunction const &score_fxn)
 
void build_single_edge_waters (Size const &seqpos_water, conformation::Residue const &rsd, Size anchor_atom, chemical::ResidueType const &h2o_type, conformation::Residue const &tp5, utility::vector1< conformation::ResidueOP > &new_rotamers, pose::Pose const &pose, pack::task::PackerTask const &task, utility::graph::GraphCOP packer_neighbor_graph, scoring::ScoreFunction const &score_fxn)
 
void build_moving_O_bridge_waters (Size const &seqpos_water, conformation::Residue const &rsd1, Size anchor_atom, conformation::Residue const &rsd2, chemical::ResidueType const &h2o_type, conformation::Residue const &tp5, Size const nstep, utility::vector1< conformation::ResidueOP > &new_rotamers, pose::Pose const &pose, pack::task::PackerTask const &task, utility::graph::GraphCOP packer_neighbor_graph, scoring::ScoreFunction const &scorefxn, bool is_first_rsd)
 
void build_moving_O_water_rotamers_dependent (RotamerSets const &rotsets, Size const seqpos_water, WaterAnchorInfo const &water_info, chemical::ResidueType const &h2o_type, pack::task::PackerTask const &task, pose::Pose const &pose, utility::graph::GraphCOP packer_neighbor_graph, utility::vector1< conformation::ResidueOP > &new_rotamers, scoring::ScoreFunction const &scorefxn)
 
void build_anchorless_water_rotamers (Size const seqpos, chemical::ResidueType const &h2o_type, pose::Pose const &pose, utility::vector1< conformation::ResidueOP > &new_rotamers, pack::task::PackerTask const &task, utility::graph::GraphCOP packer_neighbor_graph, scoring::ScoreFunction const &score_fxn)
 builds water molecule rotamers on top of cubic lattice in hydrate/SPaDES protocol More...
 
void build_moving_O_water_rotamers_independent (Size const &seqpos_water, WaterAnchorInfo const &water_info, chemical::ResidueType const &h2o_type, pack::task::PackerTask const &task, pose::Pose const &pose, utility::graph::GraphCOP packer_neighbor_graph, utility::vector1< conformation::ResidueOP > &new_rotamers, scoring::ScoreFunction const &scorefxn)
 
void build_single_anchor_water_rotamers_independet (Size const &seqpos_water, WaterAnchorInfo const &water_info, chemical::ResidueType const &h2o_type, pose::Pose const &pose, utility::vector1< conformation::ResidueOP > &new_rotamers, pack::task::PackerTask const &task, utility::graph::GraphCOP packer_neighbor_graph, scoring::ScoreFunction const &score_fxn)
 
void build_independent_water_rotamers (Size const seqpos_water, chemical::ResidueType const &h2o_type, pack::task::PackerTask const &task, pose::Pose const &pose, utility::graph::GraphCOP packer_neighbor_graph, utility::vector1< conformation::ResidueOP > &new_rotamers, scoring::ScoreFunction const &scorefxn)
 
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, utility::graph::GraphCOP packer_neighbor_graph, utility::vector1< conformation::ResidueOP > &new_rotamers, scoring::ScoreFunction const &scorefxn)
 
std::ostream & operator<< (std::ostream &out, RotamerSet const &rs)
 
static basic::Tracer tt ("core.pack.rotamer_set.RotamerSet_")
 
bool different_restype (core::chemical::ResidueType const &rt1, core::chemical::ResidueType const &rt2)
 should two residue types be considered the same residue type? More...
 
bool different_resgroup (core::chemical::ResidueType const &rt1, core::chemical::ResidueType const &rt2)
 should two residue types be considered to belong to the same residue-type group? More...
 
void sort_new_rotamers_into_rotset_vector (utility::vector1< conformation::ResidueOP > &rotamers, std::list< conformation::ResidueOP > &rotamers_waiting_for_sort, core::Size &id_for_current_rotamer)
 
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. More...
 
static basic::Tracer TR ("core.pack.rotamer_set.water_rotamer_building_functions")
 
core::PackerEnergy bump_check (core::conformation::ResidueCOP rotamer, core::Size resid, scoring::ScoreFunction const &sf, pose::Pose const &pose, task::PackerTask const &task, utility::graph::GraphCOP packer_neighbor_graph)
 
void build_rotated_water_rotamers (Size const seqpos, pack::task::PackerTask const &task, pose::Pose const &pose, scoring::ScoreFunction const &scorefxn, utility::graph::GraphCOP packer_neighbor_graph, utility::vector1< conformation::ResidueOP > &new_rotamers, bool incl_vrt)
 

Typedef Documentation

typedef utility::pointer::shared_ptr< ContinuousRotamerSet const > core::pack::rotamer_set::ContinuousRotamerSetCOP
typedef utility::pointer::shared_ptr< ContinuousRotamerSets const > core::pack::rotamer_set::ContinuousRotamerSetsCOP
typedef utility::vector1< Real > core::pack::rotamer_set::DihedralSet
typedef utility::pointer::shared_ptr< FixbbRotamerSets const > core::pack::rotamer_set::FixbbRotamerSetsCOP
typedef utility::pointer::shared_ptr< FixbbRotamerSets > core::pack::rotamer_set::FixbbRotamerSetsOP
typedef utility::pointer::shared_ptr< RotamerCouplings const > core::pack::rotamer_set::RotamerCouplingsCOP
typedef utility::pointer::shared_ptr< RotamerCouplings > core::pack::rotamer_set::RotamerCouplingsOP
typedef utility::pointer::shared_ptr< RotamerLinks const > core::pack::rotamer_set::RotamerLinksCOP
typedef utility::pointer::shared_ptr< RotamerLinks > core::pack::rotamer_set::RotamerLinksOP
typedef utility::pointer::shared_ptr< RotamerOperation const > core::pack::rotamer_set::RotamerOperationCOP
typedef utility::pointer::shared_ptr< RotamerOperation > core::pack::rotamer_set::RotamerOperationOP
typedef utility::pointer::shared_ptr< RotamerSet const > core::pack::rotamer_set::RotamerSetCOP
typedef utility::pointer::shared_ptr< RotamerSetFactory > core::pack::rotamer_set::RotamerSetFactoryOP
typedef utility::pointer::shared_ptr< RotamerSet > core::pack::rotamer_set::RotamerSetOP
typedef utility::pointer::shared_ptr< RotamerSetOperation const > core::pack::rotamer_set::RotamerSetOperationCOP
typedef utility::pointer::shared_ptr< RotamerSets const > core::pack::rotamer_set::RotamerSetsCOP
typedef utility::pointer::shared_ptr< RotamerSetsFactory > core::pack::rotamer_set::RotamerSetsFactoryOP
typedef utility::pointer::shared_ptr< RotamerSets > core::pack::rotamer_set::RotamerSetsOP
typedef utility::pointer::shared_ptr< RotamerSetsOperation const > core::pack::rotamer_set::RotamerSetsOperationCOP
typedef utility::pointer::shared_ptr< RotamerSubsets const > core::pack::rotamer_set::RotamerSubsetsCOP
typedef utility::pointer::shared_ptr< RotamerSubsets > core::pack::rotamer_set::RotamerSubsetsOP
typedef utility::pointer::shared_ptr< WaterAnchorInfo > core::pack::rotamer_set::WaterAnchorInfoOP
typedef utility::pointer::shared_ptr< WaterPackingInfo > core::pack::rotamer_set::WaterPackingInfoOP

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 rot().

Referenced by protocols::toolbox::match_enzdes_util::TheozymeInvrotTree::generate_targets_and_inverse_rotamers(), and protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::inverse_rotamers_against_residue().

void core::pack::rotamer_set::build_acceptor_acceptor_waters ( Size const &  seqpos_water,
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,
pose::Pose const &  pose,
pack::task::PackerTask const &  task,
utility::graph::GraphCOP  packer_neighbor_graph,
scoring::ScoreFunction const &  score_fxn 
)
void core::pack::rotamer_set::build_anchorless_water_rotamers ( Size const  seqpos,
chemical::ResidueType const &  h2o_type,
pose::Pose const &  pose,
utility::vector1< conformation::ResidueOP > &  new_rotamers,
pack::task::PackerTask const &  task,
utility::graph::GraphCOP  packer_neighbor_graph,
scoring::ScoreFunction const &  score_fxn 
)
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,
utility::graph::GraphCOP  packer_neighbor_graph,
utility::vector1< conformation::ResidueOP > &  new_rotamers,
scoring::ScoreFunction const &  scorefxn 
)
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 ( Size const &  seqpos_water,
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,
pose::Pose const &  pose,
pack::task::PackerTask const &  task,
utility::graph::GraphCOP  packer_neighbor_graph,
scoring::ScoreFunction const &  score_fxn 
)
void core::pack::rotamer_set::build_donor_donor_waters ( Size const &  seqpos_water,
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,
pose::Pose const &  pose,
pack::task::PackerTask const &  task,
utility::graph::GraphCOP  packer_neighbor_graph,
scoring::ScoreFunction const &  score_fxn 
)
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,
utility::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,
utility::graph::GraphCOP  packer_neighbor_graph,
utility::vector1< conformation::ResidueOP > &  new_rotamers,
scoring::ScoreFunction const &  scorefxn 
)
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 ( Size const &  seqpos_water,
conformation::Residue const &  rsd1,
Size  anchor_atom,
conformation::Residue const &  rsd2,
chemical::ResidueType const &  h2o_type,
conformation::Residue const &  tp5,
Size const  nstep,
utility::vector1< conformation::ResidueOP > &  new_rotamers,
pose::Pose const &  pose,
pack::task::PackerTask const &  task,
utility::graph::GraphCOP  packer_neighbor_graph,
scoring::ScoreFunction const &  scorefxn,
bool  is_first_rsd 
)
void core::pack::rotamer_set::build_moving_O_water_rotamers_dependent ( RotamerSets const &  rotsets,
Size const  seqpos_water,
WaterAnchorInfo const &  water_info,
chemical::ResidueType const &  h2o_type,
pack::task::PackerTask const &  task,
pose::Pose const &  pose,
utility::graph::GraphCOP  packer_neighbor_graph,
utility::vector1< conformation::ResidueOP > &  new_rotamers,
scoring::ScoreFunction const &  scorefxn 
)
void core::pack::rotamer_set::build_moving_O_water_rotamers_independent ( Size const &  seqpos_water,
WaterAnchorInfo const &  water_info,
chemical::ResidueType const &  h2o_type,
pack::task::PackerTask const &  task,
pose::Pose const &  pose,
utility::graph::GraphCOP  packer_neighbor_graph,
utility::vector1< conformation::ResidueOP > &  new_rotamers,
scoring::ScoreFunction const &  scorefxn 
)
Vector core::pack::rotamer_set::build_optimal_hyp_H_for_acceptor ( Vector const &  o2,
Vector const &  aatm2_xyz,
Vector const &  reference,
Real  angle 
)
Vector core::pack::rotamer_set::build_optimal_hyp_H_for_donor ( Vector const &  o1,
Vector const &  hatm1_xyz,
Vector const &  reference,
Real  angle 
)
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 
)
void core::pack::rotamer_set::build_rotamers_from_rotamer_bins ( conformation::Residue const &  residue,
utility::vector1< conformation::ResidueOP > &  rotamers 
)

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

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 build_rotamers_from_rotamer_bins(), core::chemical::ResidueType::nchi(), tt(), and core::conformation::Residue::type().

void core::pack::rotamer_set::build_rotated_water_rotamers ( Size const  seqpos,
pack::task::PackerTask const &  task,
pose::Pose const &  pose,
scoring::ScoreFunction const &  scorefxn,
utility::graph::GraphCOP  packer_neighbor_graph,
utility::vector1< conformation::ResidueOP > &  new_rotamers,
bool  incl_vrt 
)
void core::pack::rotamer_set::build_sew_waters_to_acceptor ( Size const &  seqpos_water,
conformation::Residue const &  rsd,
Size const  aatm,
chemical::ResidueType const &  h2o_type,
conformation::Residue const &  tp5,
utility::vector1< conformation::ResidueOP > &  new_waters,
pose::Pose const &  pose,
pack::task::PackerTask const &  task,
utility::graph::GraphCOP  packer_neighbor_graph,
scoring::ScoreFunction const &  score_fxn 
)
void core::pack::rotamer_set::build_sew_waters_to_donor ( Size const &  seqpos_water,
conformation::Residue const &  rsd,
Size const  hatm,
chemical::ResidueType const &  h2o_type,
conformation::Residue const &  tp5,
utility::vector1< conformation::ResidueOP > &  new_waters,
pose::Pose const &  pose,
pack::task::PackerTask const &  task,
utility::graph::GraphCOP  packer_neighbor_graph,
scoring::ScoreFunction const &  score_fxn 
)
void core::pack::rotamer_set::build_single_anchor_water_rotamers_independet ( Size const &  seqpos_water,
WaterAnchorInfo const &  water_info,
chemical::ResidueType const &  h2o_type,
pose::Pose const &  pose,
utility::vector1< conformation::ResidueOP > &  new_rotamers,
pack::task::PackerTask const &  task,
utility::graph::GraphCOP  packer_neighbor_graph,
scoring::ScoreFunction const &  score_fxn 
)
void core::pack::rotamer_set::build_single_edge_waters ( Size const &  seqpos_water,
conformation::Residue const &  rsd,
Size  anchor_atom,
chemical::ResidueType const &  h2o_type,
conformation::Residue const &  tp5,
utility::vector1< conformation::ResidueOP > &  new_rotamers,
pose::Pose const &  pose,
pack::task::PackerTask const &  task,
utility::graph::GraphCOP  packer_neighbor_graph,
scoring::ScoreFunction const &  score_fxn 
)
void core::pack::rotamer_set::build_three_prime_phosphate_rotamers ( utility::vector1< conformation::ResidueOP > &  rotamers,
pose::Pose const &  pose,
bool const  allow_phosphate_virtualization 
)
Vector core::pack::rotamer_set::build_water_O_on_donor ( Vector const &  hxyz,
Vector const &  dxyz,
Real  phi,
Real  theta 
)
core::PackerEnergy core::pack::rotamer_set::bump_check ( core::conformation::ResidueCOP  rotamer,
core::Size  resid,
scoring::ScoreFunction const &  sf,
pose::Pose const &  pose,
task::PackerTask const &  task,
utility::graph::GraphCOP  packer_neighbor_graph 
)
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)
bool core::pack::rotamer_set::different_resgroup ( core::chemical::ResidueType const &  rt1,
core::chemical::ResidueType const &  rt2 
)

should two residue types be considered to belong to the same residue-type group?

The logic to determine if two residue types should be classified as part of the same group. The thinking is as follows. Two residue types are in the same group if they have the same residue type. OR, they're in the same group if their residue types differ but they have the same name3 (HIS vs HIS_D have the same name3) and they have the same neighbor radius (SER and PhosphoSER should have different groups). The goal is to organize residue types together which will be packed together (as happens in multistate design with HIS and HISD) and that have the same reach (as is needed for the AANeighborSparseMatrix).

References core::chemical::ResidueTypeBase::name3(), and core::chemical::ResidueType::nbr_radius().

Referenced by core::pack::rotamer_set::RotamerSet_::prepare_for_new_residue_type(), sort_new_rotamers_into_rotset_vector(), and core::pack::rotamer_set::RotamerSet_::update_rotamer_offsets().

bool core::pack::rotamer_set::different_restype ( core::chemical::ResidueType const &  rt1,
core::chemical::ResidueType const &  rt2 
)
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().

std::ostream& core::pack::rotamer_set::operator<< ( std::ostream &  out,
RotamerSet const &  rs 
)
inline
core::PackerEnergy core::pack::rotamer_set::pre_bump_check ( Size const &  seqpos_water,
conformation::ResidueOP  rot,
scoring::ScoreFunction const &  score_fxn,
pose::Pose const &  pose,
task::PackerTask const &  task,
utility::graph::GraphCOP  packer_neighbor_graph 
)
void core::pack::rotamer_set::read_DNA_rotlib ( utility::io::izstream &  lib_stream,
utility::vector1< DihedralSet * > &  library 
)

Referenced by build_dna_rotamers().

void core::pack::rotamer_set::sort_new_rotamers_into_rotset_vector ( utility::vector1< conformation::ResidueOP > &  rotamers,
std::list< conformation::ResidueOP > &  rotamers_waiting_for_sort,
core::Size id_for_current_rotamer 
)
static basic::Tracer core::pack::rotamer_set::TR ( "core.pack.rotamer_set.UnboundRotamersOperation"  )
static
static basic::Tracer core::pack::rotamer_set::TR ( "core.pack.rotamer_set.rna_rotamer_building_functions"  ,
basic::t_info   
)
static
static basic::Tracer core::pack::rotamer_set::TR ( "core.pack.rotamer_set.water_rotamer_building_functions"  )
static
static basic::Tracer core::pack::rotamer_set::tt ( "core.pack.rotamer_set.RotamerSubset"  ,
basic::t_info   
)
static
static basic::Tracer core::pack::rotamer_set::tt ( "core.pack.rotamer_set.RotamerSet_"  )
static
static basic::Tracer core::pack::rotamer_set::tt ( "core.pack.rotamer_set.rotamer_building_functions"  ,
basic::t_info   
)
static