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	PyRotamerEliminator
class	PyRotamerEliminatorTaskOperation
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	RotamerSetsOperation
	RotamerSetsOperations are able to modify the RotamerSets object such that changes can be correlated accros multiple rotamer sets. More...
class	RotamerSets
class	RotamerSetsFactory
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
using	PyRotamerEliminatorOP = utility::pointer::shared_ptr< PyRotamerEliminator >
using	PyRotamerEliminatorCOP = utility::pointer::shared_ptr< PyRotamerEliminator const >
using	PyRotamerEliminatorTaskOperationOP = utility::pointer::shared_ptr< PyRotamerEliminatorTaskOperation >
using	PyRotamerEliminatorTaskOperationCOP = utility::pointer::shared_ptr< PyRotamerEliminatorTaskOperation const >
typedef utility::vector1< Real >	DihedralSet
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

ContinuousRotamerSetCOP

typedef utility::pointer::shared_ptr< ContinuousRotamerSet const > core::pack::rotamer_set::ContinuousRotamerSetCOP

ContinuousRotamerSetOP

typedef utility::pointer::shared_ptr< ContinuousRotamerSet > core::pack::rotamer_set::ContinuousRotamerSetOP

ContinuousRotamerSetsCOP

typedef utility::pointer::shared_ptr< ContinuousRotamerSets const > core::pack::rotamer_set::ContinuousRotamerSetsCOP

ContinuousRotamerSetsOP

typedef utility::pointer::shared_ptr< ContinuousRotamerSets > core::pack::rotamer_set::ContinuousRotamerSetsOP

DeleteAllRotamerSetOperationCOP

typedef utility::pointer::shared_ptr< DeleteAllRotamerSetOperation const > core::pack::rotamer_set::DeleteAllRotamerSetOperationCOP

DeleteAllRotamerSetOperationOP

typedef utility::pointer::shared_ptr< DeleteAllRotamerSetOperation > core::pack::rotamer_set::DeleteAllRotamerSetOperationOP

DihedralSet

typedef utility::vector1< Real > core::pack::rotamer_set::DihedralSet

FixbbRotamerSetsCOP

typedef utility::pointer::shared_ptr< FixbbRotamerSets const > core::pack::rotamer_set::FixbbRotamerSetsCOP

FixbbRotamerSetsOP

typedef utility::pointer::shared_ptr< FixbbRotamerSets > core::pack::rotamer_set::FixbbRotamerSetsOP

PyRotamerEliminatorCOP

using core::pack::rotamer_set::PyRotamerEliminatorCOP = typedef utility::pointer::shared_ptr< PyRotamerEliminator const >

PyRotamerEliminatorOP

using core::pack::rotamer_set::PyRotamerEliminatorOP = typedef utility::pointer::shared_ptr< PyRotamerEliminator >

PyRotamerEliminatorTaskOperationCOP

using core::pack::rotamer_set::PyRotamerEliminatorTaskOperationCOP = typedef utility::pointer::shared_ptr< PyRotamerEliminatorTaskOperation const >

PyRotamerEliminatorTaskOperationOP

using core::pack::rotamer_set::PyRotamerEliminatorTaskOperationOP = typedef utility::pointer::shared_ptr< PyRotamerEliminatorTaskOperation >

RotamerBin

typedef std::pair<core::Angle, core::Angle> core::pack::rotamer_set::RotamerBin

RotamerBins

typedef utility::vector1<RotamerBin> core::pack::rotamer_set::RotamerBins

RotamerCouplingsCOP

typedef utility::pointer::shared_ptr< RotamerCouplings const > core::pack::rotamer_set::RotamerCouplingsCOP

RotamerCouplingsOP

typedef utility::pointer::shared_ptr< RotamerCouplings > core::pack::rotamer_set::RotamerCouplingsOP

RotamerLinksCOP

typedef utility::pointer::shared_ptr< RotamerLinks const > core::pack::rotamer_set::RotamerLinksCOP

RotamerLinksOP

typedef utility::pointer::shared_ptr< RotamerLinks > core::pack::rotamer_set::RotamerLinksOP

RotamerOperationCOP

typedef utility::pointer::shared_ptr< RotamerOperation const > core::pack::rotamer_set::RotamerOperationCOP

RotamerOperationOP

typedef utility::pointer::shared_ptr< RotamerOperation > core::pack::rotamer_set::RotamerOperationOP

RotamerOperations

typedef std::list< RotamerOperationOP > core::pack::rotamer_set::RotamerOperations

Rotamers

typedef utility::vector1< conformation::ResidueOP > core::pack::rotamer_set::Rotamers

RotamerSetCOP

typedef utility::pointer::shared_ptr< RotamerSet const > core::pack::rotamer_set::RotamerSetCOP

RotamerSetFactoryOP

typedef utility::pointer::shared_ptr< RotamerSetFactory > core::pack::rotamer_set::RotamerSetFactoryOP

RotamerSetOP

typedef utility::pointer::shared_ptr< RotamerSet > core::pack::rotamer_set::RotamerSetOP

RotamerSetOperationCOP

typedef utility::pointer::shared_ptr< RotamerSetOperation const > core::pack::rotamer_set::RotamerSetOperationCOP

RotamerSetOperationOP

typedef utility::pointer::shared_ptr< RotamerSetOperation > core::pack::rotamer_set::RotamerSetOperationOP

RotamerSetsCOP

typedef utility::pointer::shared_ptr< RotamerSets const > core::pack::rotamer_set::RotamerSetsCOP

RotamerSetsFactoryOP

typedef utility::pointer::shared_ptr< RotamerSetsFactory > core::pack::rotamer_set::RotamerSetsFactoryOP

RotamerSetsOP

typedef utility::pointer::shared_ptr< RotamerSets > core::pack::rotamer_set::RotamerSetsOP

RotamerSetsOperationCOP

typedef utility::pointer::shared_ptr< RotamerSetsOperation const > core::pack::rotamer_set::RotamerSetsOperationCOP

RotamerSetsOperationOP

typedef utility::pointer::shared_ptr< RotamerSetsOperation > core::pack::rotamer_set::RotamerSetsOperationOP

RotamerSubsetsCOP

typedef utility::pointer::shared_ptr< RotamerSubsets const > core::pack::rotamer_set::RotamerSubsetsCOP

RotamerSubsetsOP

typedef utility::pointer::shared_ptr< RotamerSubsets > core::pack::rotamer_set::RotamerSubsetsOP

RotSetOperationList

typedef std::list< RotamerSetOperationOP > core::pack::rotamer_set::RotSetOperationList

RotSetOperationListIterator

typedef std::list< RotamerSetOperationOP >::const_iterator core::pack::rotamer_set::RotSetOperationListIterator

RotSetsOperationList

typedef std::list< RotamerSetsOperationOP > core::pack::rotamer_set::RotSetsOperationList

RotSetsOperationListIterator

typedef std::list< RotamerSetsOperationOP >::const_iterator core::pack::rotamer_set::RotSetsOperationListIterator

UnboundRotamersOperationCOP

typedef utility::pointer::shared_ptr< UnboundRotamersOperation const > core::pack::rotamer_set::UnboundRotamersOperationCOP

UnboundRotamersOperationOP

typedef utility::pointer::shared_ptr< UnboundRotamersOperation > core::pack::rotamer_set::UnboundRotamersOperationOP

WaterAnchorInfoOP

typedef utility::pointer::shared_ptr< WaterAnchorInfo > core::pack::rotamer_set::WaterAnchorInfoOP

WaterPackingInfoOP

typedef utility::pointer::shared_ptr< WaterPackingInfo > core::pack::rotamer_set::WaterPackingInfoOP

Enumeration Type Documentation

BumpSelectorDecision

enum core::pack::rotamer_set::BumpSelectorDecision

Enumerator
KEEP_ROTAMER
DELETE_ROTAMER
DELETE_PREVIOUS_ROTAMER

Function Documentation

add_rna_chi_rotamers()

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
	)

References core::pack::task::EX_FOUR_HALF_STEP_STDDEVS, core::pack::task::EX_ONE_HALF_STEP_STDDEV, core::pack::task::EX_ONE_STDDEV, core::pack::task::EX_SIX_QUARTER_STEP_STDDEVS, core::pack::task::EX_THREE_THIRD_STEP_STDDEVS, core::pack::task::EX_TWO_FULL_STEP_STDDEVS, core::pack::task::EX_TWO_HALF_STEP_STDDEVS, core::pack::task::ExtraRotSampleCardinality, fill_chi_rotamers_with_center_and_stddev(), core::chemical::na_rad, core::chemical::na_rgu, core::pack::task::NO_EXTRA_CHI_SAMPLES, and rot().

Referenced by build_rna_chi_rotamers().

bb_independent_rotamers()

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().

build_acceptor_acceptor_waters()

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
	)

References core::conformation::Residue::abase2(), core::conformation::Residue::atom_base(), core::conformation::Residue::atom_type(), build_optimal_water_Os_on_acceptor(), create_oriented_water_rotamer(), core::scoring::hbonds::get_hb_acc_chem_type(), core::scoring::hbonds::hb_energy_deriv(), core::scoring::hbonds::hbdon_H2O, core::chemical::AtomType::hybridization(), pre_bump_check(), rot(), core::scoring::hbonds::seq_sep_other, and core::conformation::Residue::xyz().

Referenced by build_moving_O_bridge_waters().

build_anchorless_water_rotamers()

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
	)

builds water molecule rotamers on top of cubic lattice in hydrate/SPaDES protocol

References create_oriented_water_rotamer(), core::conformation::ResidueFactory::create_residue(), core::chemical::ResidueTypeBase::mode(), core::chemical::ResidueType::natoms(), core::conformation::Residue::nbr_atom_xyz(), PI, pre_bump_check(), core::pose::Pose::residue(), core::pose::Pose::residue_type_set_for_pose(), protocols::jumping::rot1, and protocols::jumping::rot2.

Referenced by build_independent_water_rotamers().

build_dependent_water_rotamers()

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
	)

References build_moving_O_water_rotamers_dependent(), core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::WATER_PACKING_INFO.

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

build_dna_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
	)

References build_lib_dna_rotamers(), build_random_dna_rotamers(), core::pack::task::EX_SIX_QUARTER_STEP_STDDEVS, core::pack::task::ResidueLevelTask::extrachi_sample_level(), core::pack::task::PackerTask::pack_residue(), read_DNA_rotlib(), core::pose::Pose::residue(), core::pack::task::PackerTask::residue_task(), rot(), core::pack::task::PackerTask::rotamer_couplings(), and core::pack::task::PackerTask::rotamer_couplings_exist().

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

build_donor_acceptor_waters()

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
	)

References core::conformation::Residue::abase2(), core::conformation::Residue::atom_base(), core::conformation::Residue::atom_type(), build_optimal_water_O_on_donor(), build_optimal_water_Os_on_acceptor(), create_oriented_water_rotamer(), core::scoring::hbonds::get_hb_acc_chem_type(), core::scoring::hbonds::get_hb_don_chem_type(), core::scoring::hbonds::hb_energy_deriv(), core::scoring::hbonds::hbacc_H2O, core::scoring::hbonds::hbdon_H2O, core::chemical::AtomType::hybridization(), pre_bump_check(), rot(), protocols::jumping::rot2, core::scoring::hbonds::seq_sep_other, and core::conformation::Residue::xyz().

Referenced by build_moving_O_bridge_waters().

build_donor_donor_waters()

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
	)

References core::conformation::Residue::atom_base(), build_optimal_water_O_on_donor(), create_oriented_water_rotamer(), core::scoring::hbonds::get_hb_don_chem_type(), core::scoring::hbonds::hb_energy_deriv(), core::scoring::hbonds::hbacc_H2O, pre_bump_check(), rot(), core::scoring::hbonds::seq_sep_other, and core::conformation::Residue::xyz().

Referenced by build_moving_O_bridge_waters().

build_five_prime_phosphate_rotamers()

void core::pack::rotamer_set::build_five_prime_phosphate_rotamers	(	utility::vector1< conformation::ResidueOP > &	rotamers,
		pose::Pose const &	pose,
		bool const	allow_phosphate_virtualization
	)

References core::chemical::FIVE_PRIME_PACKABLE_PHOSPHATE, core::chemical::rna::get_full_torsions(), and core::pose::remove_variant_type_from_residue().

Referenced by build_rna_rotamers().

build_fixed_O_water_rotamers_independent()

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
	)

References core::conformation::Residue::accpt_pos(), core::conformation::Residue::atom_base(), core::conformation::Residue::chain(), create_oriented_water_rotamer(), core::conformation::ResidueFactory::create_residue(), core::conformation::Residue::Hpos_polar(), core::chemical::ResidueTypeBase::mode(), core::chemical::ResidueType::natoms(), core::conformation::Residue::nbr_atom_xyz(), core::pose::Pose::residue(), core::pose::Pose::residue_type_set_for_pose(), tt(), protocols::kinmatch::xyz(), and core::conformation::Residue::xyz().

Referenced by build_independent_water_rotamers().

build_independent_water_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
	)

References build_anchorless_water_rotamers(), build_fixed_O_water_rotamers_independent(), build_moving_O_water_rotamers_independent(), build_single_anchor_water_rotamers_independet(), core::pose::Pose::data(), tt(), and core::pose::datacache::CacheableDataType::WATER_PACKING_INFO.

Referenced by core::pack::rotamer_set::RotamerSet_::build_filtered_tp3_water_rotamers(), and core::pack::rotamer_set::RotamerSet_::build_tp3_water_rotamers().

build_lib_dna_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
	)

References core::scoring::angle_constraint, core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), core::conformation::Residue::atom_index(), core::scoring::atom_pair_constraint, core::id::BB, core::conformation::Residue::chain(), core::chemical::rna::CHI, core::conformation::Residue::chi(), core::conformation::Residue::clone(), core::pose::Pose::conformation(), core::pose::Pose::constraint_set(), core::conformation::ResidueFactory::create_residue(), core::conformation::Residue::is_NA(), core::conformation::Residue::is_terminus(), core::pose::Pose::residue(), rot(), core::conformation::Residue::seqpos(), core::kinematics::MoveMap::set(), core::pose::Pose::set_torsion(), core::scoring::ScoreFunction::set_weight(), core::pose::Pose::torsion(), tt(), and core::conformation::Residue::xyz().

Referenced by build_dna_rotamers().

build_moving_O_bridge_waters()

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
	)

References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_his, core::conformation::Residue::accpt_pos(), core::conformation::Residue::atom_is_backbone(), core::conformation::Residue::atom_type(), build_acceptor_acceptor_waters(), build_donor_acceptor_waters(), build_donor_donor_waters(), core::conformation::Residue::Hpos_polar(), core::chemical::AtomType::is_polar_hydrogen(), core::conformation::Residue::name(), core::conformation::Residue::seqpos(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

Referenced by build_moving_O_water_rotamers_dependent(), and build_moving_O_water_rotamers_independent().

build_moving_O_water_rotamers_dependent()

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
	)

References core::pack::rotamer_set::WaterAnchorInfo::anchor_atom(), core::pack::rotamer_set::WaterAnchorInfo::anchor_residue(), core::conformation::Residue::atom_is_backbone(), core::conformation::Residue::atom_is_polar_hydrogen(), build_moving_O_bridge_waters(), core::conformation::ResidueFactory::create_residue(), core::pack::rotamer_set::WaterAnchorInfo::design_anchor_index(), core::conformation::Residue::get_self_ptr(), core::conformation::Residue::heavyatom_is_an_acceptor(), core::chemical::ResidueTypeBase::mode(), core::conformation::Residue::name(), core::conformation::Residue::natoms(), core::chemical::ResidueType::natoms(), core::pack::rotamer_set::WaterAnchorInfo::nstep(), core::pack::task::PackerTask::pack_residue(), core::pose::Pose::residue(), core::pose::Pose::residue_type_set_for_pose(), core::pack::rotamer_set::RotamerSets::rotamer_set_for_residue(), and core::conformation::Residue::type().

Referenced by build_dependent_water_rotamers().

build_moving_O_water_rotamers_independent()

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
	)

References core::pack::rotamer_set::WaterAnchorInfo::anchor_atom(), core::pack::rotamer_set::WaterAnchorInfo::anchor_residue(), core::conformation::Residue::atom_is_polar_hydrogen(), build_moving_O_bridge_waters(), core::conformation::ResidueFactory::create_residue(), core::pack::rotamer_set::WaterAnchorInfo::design_anchor_index(), core::conformation::Residue::heavyatom_is_an_acceptor(), core::chemical::ResidueTypeBase::mode(), core::conformation::Residue::name(), core::conformation::Residue::natoms(), core::chemical::ResidueType::natoms(), core::pack::rotamer_set::WaterAnchorInfo::nstep(), core::pack::task::PackerTask::pack_residue(), core::pose::Pose::residue(), core::pose::Pose::residue_type_set_for_pose(), and core::conformation::Residue::type().

Referenced by build_independent_water_rotamers().

build_optimal_hyp_H_for_acceptor()

Vector core::pack::rotamer_set::build_optimal_hyp_H_for_acceptor	(	Vector const &	o2,
		Vector const &	aatm2_xyz,
		Vector const &	reference,
		Real	angle
	)

Referenced by build_sew_waters_to_acceptor().

build_optimal_hyp_H_for_donor()

Vector core::pack::rotamer_set::build_optimal_hyp_H_for_donor	(	Vector const &	o1,
		Vector const &	hatm1_xyz,
		Vector const &	reference,
		Real	angle
	)

Referenced by build_sew_waters_to_donor().

build_optimal_water_O_on_donor()

Vector core::pack::rotamer_set::build_optimal_water_O_on_donor	(	Vector const &	hxyz,
		Vector const &	dxyz
	)

References core::kinematics::distance().

Referenced by build_donor_acceptor_waters(), and build_donor_donor_waters().

build_optimal_water_Os_on_acceptor()

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
	)

References core::kinematics::distance(), core::chemical::RING_HYBRID, core::chemical::SP2_HYBRID, core::chemical::SP3_HYBRID, core::kinematics::Stub::spherical(), and tt().

Referenced by build_acceptor_acceptor_waters(), build_donor_acceptor_waters(), and build_sew_waters_to_acceptor().

build_proton_chi_rotamers()

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
	)

References core::pose::add_variant_type_to_residue(), core::scoring::rna::RNA_TorsionPotential::eval_intrares_energy(), core::pack::task::ResidueLevelTask::include_virtual_side_chain(), core::scoring::rna_torsion, rot(), and core::chemical::VIRTUAL_O2PRIME_HYDROGEN.

Referenced by build_rna_rotamers().

build_random_dna_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
	)

References core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), core::id::BB, core::chemical::rna::CHI, core::conformation::Residue::chi(), core::conformation::Residue::clone(), core::pose::Pose::conformation(), core::conformation::ResidueFactory::create_residue(), core::pack::task::EX_FOUR_HALF_STEP_STDDEVS, core::pack::task::EX_ONE_HALF_STEP_STDDEV, core::pack::task::EX_ONE_STDDEV, core::pack::task::EX_SIX_QUARTER_STEP_STDDEVS, core::pack::task::EX_THREE_THIRD_STEP_STDDEVS, core::pack::task::EX_TWO_FULL_STEP_STDDEVS, core::pack::task::EX_TWO_HALF_STEP_STDDEVS, core::pack::task::ExtraRotSampleCardinality, core::conformation::Residue::is_NA(), core::conformation::Residue::is_terminus(), protocols::antibody::l1, protocols::antibody::l2, core::pack::task::NO_EXTRA_CHI_SAMPLES, core::pose::Pose::residue(), core::scoring::rg, rot(), core::pose::Pose::set_torsion(), core::pose::Pose::torsion(), and core::conformation::Residue::xyz().

Referenced by build_dna_rotamers().

build_rna_chi_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
	)

References add_rna_chi_rotamers(), core::pose::Pose::conformation(), core::conformation::ResidueFactory::create_residue(), core::chemical::rna::DELTA, core::chemical::rna::RNA_FittedTorsionInfo::delta_cutoff(), core::chemical::rna::RNA_FittedTorsionInfo::gaussian_parameter_set_chi_north(), core::chemical::rna::RNA_FittedTorsionInfo::gaussian_parameter_set_chi_south(), core::conformation::Residue::is_RNA(), core::conformation::Residue::mainchain_torsion(), core::pose::Pose::residue(), and rot().

Referenced by build_rna_rotamers().

build_rna_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
	)

References core::conformation::Residue::aa(), core::pack::task::rna::RNA_ResidueLevelTask::allow_phosphate_virtualization(), build_five_prime_phosphate_rotamers(), build_proton_chi_rotamers(), build_rna_chi_rotamers(), build_three_prime_phosphate_rotamers(), core::pack::task::ResidueLevelTask::extrachi_sample_level(), core::pack::task::PackerTask::include_current(), core::pose::remove_variant_type_from_residue(), core::pose::Pose::residue(), core::pack::task::PackerTask::residue_task(), core::pack::task::ResidueLevelTask::rna_task(), rot(), core::pack::task::rna::RNA_ResidueLevelTask::sample_five_prime_phosphate(), core::pack::task::ResidueLevelTask::sample_proton_chi(), core::pack::task::rna::RNA_ResidueLevelTask::sample_rna_chi(), core::pack::task::rna::RNA_ResidueLevelTask::sample_three_prime_phosphate(), TR(), and core::chemical::VIRTUAL_O2PRIME_HYDROGEN.

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

build_rotamers_from_rotamer_bins() [1/2]

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().

build_rotamers_from_rotamer_bins() [2/2]

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
	)

Internal, recursive function to implement the external interface of build_rotamers_from_rotamer_bins(), below.

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

Referenced by core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete(), and build_rotamers_from_rotamer_bins().

build_rotated_water_rotamers()

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
	)

References bump_check(), core::conformation::ResidueFactory::create_residue(), core::chemical::FA_STANDARD, protocols::antibody::H1, protocols::antibody::H2, core::chemical::ResidueTypeBase::is_protein(), core::pack::task::PackerTask::max_rotbump_energy(), core::chemical::element::O, core::pose::Pose::residue(), core::pose::Pose::residue_type(), and core::conformation::Residue::xyz().

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

build_sew_waters_to_acceptor()

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
	)

References core::conformation::Residue::abase2(), core::conformation::Residue::atom_base(), core::conformation::Residue::atom_type(), build_optimal_hyp_H_for_acceptor(), build_optimal_water_Os_on_acceptor(), create_oriented_water_rotamer(), core::scoring::hbonds::get_hb_acc_chem_type(), core::scoring::hbonds::hb_energy_deriv(), core::scoring::hbonds::hbdon_H2O, core::chemical::AtomType::hybridization(), PI, pre_bump_check(), rot(), core::scoring::hbonds::seq_sep_other, and core::conformation::Residue::xyz().

Referenced by build_single_edge_waters().

build_sew_waters_to_donor()

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
	)

References core::conformation::Residue::atom_base(), build_optimal_hyp_H_for_donor(), build_water_O_on_donor(), create_oriented_water_rotamer(), core::scoring::hbonds::get_hb_don_chem_type(), core::scoring::hbonds::hb_energy_deriv(), core::scoring::hbonds::hbacc_H2O, PI, pre_bump_check(), rot(), core::scoring::hbonds::seq_sep_other, and core::conformation::Residue::xyz().

Referenced by build_single_edge_waters().

build_single_anchor_water_rotamers_independet()

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
	)

References core::pack::rotamer_set::WaterAnchorInfo::anchor_atom(), core::pack::rotamer_set::WaterAnchorInfo::anchor_residue(), core::conformation::Residue::atom_is_polar_hydrogen(), build_single_edge_waters(), core::conformation::ResidueFactory::create_residue(), core::pack::rotamer_set::WaterAnchorInfo::design_anchor_index(), core::conformation::Residue::heavyatom_is_an_acceptor(), core::chemical::ResidueTypeBase::mode(), core::conformation::Residue::natoms(), core::chemical::ResidueType::natoms(), core::pose::Pose::residue(), core::pose::Pose::residue_type_set_for_pose(), and core::conformation::Residue::type().

Referenced by build_independent_water_rotamers().

build_single_edge_waters()

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
	)

References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_his, core::conformation::Residue::atom_type(), build_sew_waters_to_acceptor(), build_sew_waters_to_donor(), core::chemical::AtomType::is_polar_hydrogen(), core::conformation::Residue::name(), and core::conformation::Residue::type().

Referenced by build_single_anchor_water_rotamers_independet().

build_three_prime_phosphate_rotamers()

void core::pack::rotamer_set::build_three_prime_phosphate_rotamers	(	utility::vector1< conformation::ResidueOP > &	rotamers,
		pose::Pose const &	pose,
		bool const	allow_phosphate_virtualization
	)

References core::chemical::rna::DELTA, core::chemical::rna::get_epsilon_torsions(), core::chemical::rna::get_full_torsions(), core::pose::remove_variant_type_from_residue(), and core::chemical::THREE_PRIME_PACKABLE_PHOSPHATE.

Referenced by build_rna_rotamers().

build_water_O_on_donor()

Vector core::pack::rotamer_set::build_water_O_on_donor	(	Vector const &	hxyz,
		Vector const &	dxyz,
		Real	phi,
		Real	theta
	)

Referenced by build_sew_waters_to_donor().

bump_check()

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
	)

duplicate code – consolidate?

Bump check does not include long range energies, though, maybe this should change.

References core::scoring::ScoreFunction::bump_check_backbone(), core::scoring::ScoreFunction::bump_check_full(), core::scoring::EMapVector::dot(), core::pack::task::PackerTask::pack_residue(), core::pose::Pose::residue(), and core::scoring::ScoreFunction::weights().

Referenced by protocols::motifs::build_rotamers_lite(), build_rotated_water_rotamers(), protocols::motifs::MotifSearch::override_option_input(), protocols::minimization_packing::BoltzmannRotamerMover::set_bump_check(), protocols::simple_moves::CoupledMover::set_bump_check(), and protocols::coupled_moves::CoupledMovesProtocol::setup_coupled_mover().

create_oriented_water_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
	)

References core::conformation::ResidueFactory::create_residue(), core::kinematics::Stub::global2local(), core::kinematics::Stub::local2global(), rot(), and core::conformation::Residue::xyz().

Referenced by build_acceptor_acceptor_waters(), build_anchorless_water_rotamers(), build_donor_acceptor_waters(), build_donor_donor_waters(), build_fixed_O_water_rotamers_independent(), build_sew_waters_to_acceptor(), and build_sew_waters_to_donor().

debug_dump_rotamers()

void core::pack::rotamer_set::debug_dump_rotamers

(

utility::vector1< conformation::ResidueOP > &

rotamers

)

References rot(), tt(), and core::conformation::Atom::xyz().

different_resgroup()

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().

different_restype()

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

should two residue types be considered the same residue type?

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

dup_residue()

conformation::ResidueOP core::pack::rotamer_set::dup_residue	(	conformation::Residue const &	existing,
		conformation::Residue const &	conformer
	)

Helper function, combines existing's metadata with conformer's conformation.

References core::conformation::Residue::chain(), core::conformation::Residue::clone(), and core::conformation::Residue::seqpos().

Referenced by core::pack::rotamer_set::UnboundRotamersOperation::alter_rotamer_set().

fill_chi_rotamers_with_center_and_stddev()

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
	)

References core::conformation::membrane::center, and rot().

Referenced by add_rna_chi_rotamers().

operator<<()

std::ostream& core::pack::rotamer_set::operator<< ( std::ostream &  out, RotamerSet const &  rs  )

inline

References core::conformation::membrane::out, and core::pack::rotamer_set::RotamerSet::show().

pre_bump_check()

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
	)

References core::scoring::ScoreFunction::clone(), core::scoring::fa_rep, core::pack::task::PackerTask::pack_residue(), core::pose::Pose::residue(), and rot().

Referenced by build_acceptor_acceptor_waters(), build_anchorless_water_rotamers(), build_donor_acceptor_waters(), build_donor_donor_waters(), build_sew_waters_to_acceptor(), build_sew_waters_to_donor(), and core::pack::rotamer_set::RotamerSet_::filter_water_rotamers().

read_DNA_rotlib()

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

Referenced by build_dna_rotamers().

sort_new_rotamers_into_rotset_vector()

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
	)

References different_resgroup(), core::pack::rotamer_set::RotamerSet_::id_for_current_rotamer(), rot(), and core::pack::rotamer_set::RotamerSet_::rotamer().

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

TR() [1/3]

static basic::Tracer core::pack::rotamer_set::TR ( "core.pack.rotamer_set.rna_rotamer_building_functions"  , basic::t_info    )

static

Referenced by core::pack::rotamer_set::UnboundRotamersOperation::alter_rotamer_set(), build_rna_rotamers(), core::pack::rotamer_set::ContinuousRotamerSet::build_rotamers(), and core::pack::rotamer_set::UnboundRotamersOperation::initialize_from_command_line().

TR() [2/3]

static basic::Tracer core::pack::rotamer_set::TR ( "core.pack.rotamer_set.UnboundRotamersOperation"  )

static

TR() [3/3]

static basic::Tracer core::pack::rotamer_set::TR ( "core.pack.rotamer_set.water_rotamer_building_functions"  )

static

tt() [1/3]

static basic::Tracer core::pack::rotamer_set::tt ( "core.pack.rotamer_set.rotamer_building_functions"  , basic::t_info    )

static

Referenced by core::pack::rotamer_set::RotamerSet_::build_dependent_rotamers(), core::pack::rotamer_set::RotamerSet_::build_filtered_tp3_water_rotamers(), build_fixed_O_water_rotamers_independent(), build_independent_water_rotamers(), build_lib_dna_rotamers(), build_optimal_water_Os_on_acceptor(), core::pack::rotamer_set::RotamerSet_::build_rotamers(), core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete(), build_rotamers_from_rotamer_bins(), and debug_dump_rotamers().

tt() [2/3]

static basic::Tracer core::pack::rotamer_set::tt ( "core.pack.rotamer_set.RotamerSet_"  )

static

tt() [3/3]

static basic::Tracer core::pack::rotamer_set::tt ( "core.pack.rotamer_set.RotamerSubset"  , basic::t_info    )

static