Namespaces
	symmetry

Classes
class	AddResiduesRotamerSetOperation
	Adds in rotamers from a list of Residues,. More...

class	BumpSelector

class	ContinuousRotamerSet

class	ContinuousRotamerSets

class	FixbbRotamerSets

class	RotamerCouplings

class	RotamerLinks

class	RotamerOperation
	RotamerSetOperations are able to modify the contents of a RotamerSet within the packer immediately after rotamer creation. More...

class	RotamerSet

class	RotamerSet_
	Container for a set of rotamers for use in packing. Rotamers are sorted into groups of the same residue type. Offsets into these rotamer groups are maintained by this class, as is information concerning the "original rotamer" – the rotamer present on the input pose before packing began. More...

class	RotamerSetFactory

class	RotamerSetOperation

class	RotamerSets

class	RotamerSetsBase

class	RotamerSubset
	Container for a subset of rotamers that have been created by another rotamer set. This subset object copies pointers to the rotamers contained in another set, as opposed to cloning the rotamers. It's main purpose is to manage the bookkeeping involved in packing with a subset of rotamers (when it might be faster to use a subset and to create an interaction graph specifically for that subset than to simply pass an abreviated list of rotamers to the SimAnnealer with the "rot_to_pack" vector). More...

class	RotamerSubsets

class	UnboundRotamersOperation
	Adds in rotamers from the "unbound" or native structure(s), pulled from one or more PDBs supplied on the command line. More...

class	WaterAnchorInfo

class	WaterPackingInfo

Typedefs
typedef utility::pointer::owning_ptr < ContinuousRotamerSet >	ContinuousRotamerSetOP

typedef utility::pointer::owning_ptr < ContinuousRotamerSet const >	ContinuousRotamerSetCOP

typedef utility::pointer::owning_ptr < ContinuousRotamerSets >	ContinuousRotamerSetsOP

typedef utility::pointer::owning_ptr < ContinuousRotamerSets const >	ContinuousRotamerSetsCOP

typedef utility::pointer::owning_ptr < FixbbRotamerSets >	FixbbRotamerSetsOP

typedef utility::pointer::owning_ptr < FixbbRotamerSets const >	FixbbRotamerSetsCOP

typedef utility::vector1< Real >	DihedralSet

typedef utility::pointer::owning_ptr < RotamerCouplings >	RotamerCouplingsOP

typedef utility::pointer::owning_ptr < RotamerCouplings const >	RotamerCouplingsCOP

typedef utility::pointer::owning_ptr < RotamerLinks >	RotamerLinksOP

typedef utility::pointer::owning_ptr < RotamerLinks const >	RotamerLinksCOP

typedef utility::vector1 < conformation::ResidueOP >	Rotamers

typedef utility::pointer::owning_ptr < RotamerSet >	RotamerSetOP

typedef utility::pointer::owning_ptr < RotamerSet const >	RotamerSetCOP

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

typedef utility::vector1 < RotamerBin >	RotamerBins

typedef utility::pointer::owning_ptr < RotamerSetFactory >	RotamerSetFactoryOP

typedef utility::pointer::owning_ptr < RotamerOperation >	RotamerOperationOP

typedef utility::pointer::owning_ptr < RotamerOperation const >	RotamerOperationCOP

typedef std::list < RotamerOperationOP >	RotamerOperations

typedef utility::pointer::owning_ptr < RotamerSetOperation >	RotamerSetOperationOP

typedef utility::pointer::owning_ptr < RotamerSetOperation const >	RotamerSetOperationCOP

typedef std::list < RotamerSetOperationOP >	RotSetOperationList

typedef std::list < RotamerSetOperationOP > ::const_iterator	RotSetOperationListIterator

typedef utility::pointer::owning_ptr < RotamerSets >	RotamerSetsOP

typedef utility::pointer::owning_ptr < RotamerSets const >	RotamerSetsCOP

typedef utility::pointer::owning_ptr < RotamerSetsBase >	RotamerSetsBaseOP

typedef utility::pointer::owning_ptr < RotamerSetsBase const >	RotamerSetsBaseCOP

typedef utility::pointer::owning_ptr < RotamerSubsets >	RotamerSubsetsOP

typedef utility::pointer::owning_ptr < RotamerSubsets const >	RotamerSubsetsCOP

typedef utility::pointer::owning_ptr < UnboundRotamersOperation >	UnboundRotamersOperationOP

typedef utility::pointer::owning_ptr < UnboundRotamersOperation const >	UnboundRotamersOperationCOP

typedef utility::pointer::owning_ptr < WaterAnchorInfo >	WaterAnchorInfoOP

typedef utility::pointer::owning_ptr < WaterPackingInfo >	WaterPackingInfoOP

Enumerations
enum	BumpSelectorDecision { KEEP_ROTAMER, DELETE_ROTAMER, DELETE_PREVIOUS_ROTAMER }

Functions
utility::vector1 < core::conformation::ResidueCOP >	bb_independent_rotamers (core::chemical::ResidueTypeCOP rot_restype, bool ignore_cmdline=false)
	a crude function to spit out a list of rotamers given the residue type only, independent of backbone currently there is no proper way of doing this, since the Dunbrack bbind library is not implemented in rosetta. this function tries to circumvent that by constructing a one residue pose and then using the regular dunbrack library, which will use neutral phi/psi for the only residue in the pose the bool ignore_cmdline can be used if someone only wants base inverse rotamers but use the full set in packing More...

void	fill_chi_rotamers_with_center_and_stddev (conformation::ResidueOP const &rot, utility::vector1< conformation::ResidueOP > &rotamers, utility::vector1< Real > const &chi_steps, Real const &center, Real const &width)

void	add_rna_chi_rotamers (conformation::ResidueOP const &rot, utility::vector1< conformation::ResidueOP > &rotamers, pack::task::ExtraRotSample const &level, utility::vector1< chemical::rna::GaussianParameter > const &gaussian_parameter_set)

void	build_rna_chi_rotamers (Size const resid, pose::Pose const &pose, chemical::ResidueTypeCOP concrete_residue, pack::task::ExtraRotSample const &level, bool const sample_rna_chi, bool const &include_current, utility::vector1< conformation::ResidueOP > &rotamers)

void	build_proton_chi_rotamers (Size const , pose::Pose const &pose, chemical::ResidueTypeCOP concrete_residue, pack::task::ResidueLevelTask const &residue_task, utility::vector1< conformation::ResidueOP > &rotamers)

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

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

void	build_rna_rotamers (Size const resid, pose::Pose const &pose, chemical::ResidueTypeCOP concrete_residue, pack::task::PackerTask const &task, utility::vector1< conformation::ResidueOP > &new_rotamers, Size &id_for_current_rotamer)

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

void	build_lib_dna_rotamers (utility::vector1< DihedralSet * > const &library, Size const resid, pose::Pose const &pose, chemical::ResidueTypeCOP concrete_residue, utility::vector1< conformation::ResidueOP > &rotamers)

void	build_random_dna_rotamers (Size const resid, pose::Pose const &pose, chemical::ResidueTypeCOP concrete_residue, pack::task::ExtraRotSample const &level, utility::vector1< conformation::ResidueOP > &rotamers)

void	build_dna_rotamers (Size const resid, pose::Pose const &pose, chemical::ResidueTypeCOP concrete_residue, pack::task::PackerTask const &task, utility::vector1< conformation::ResidueOP > &rotamers)

void	build_rotamers_from_rotamer_bins (conformation::Residue const &residue, utility::vector1< conformation::ResidueOP > &rotamers, uint current_chi_index=1, utility::vector1< uint > *current_bin_indices=NULL)
	Make a rotamer (Residue) for every combination of torsion angle in the rotamer bins listed in the params file for the given Residue. More...

void	debug_dump_rotamers (utility::vector1< conformation::ResidueOP > &rotamers)

conformation::ResidueOP	create_oriented_water_rotamer (chemical::ResidueType const &h2o_type, Vector const &xyz_atom1, Vector const &xyz_O, Vector const &xyz_atom2, std::string const &name1, std::string const &name2, conformation::Residue const &tp5)

void	build_fixed_O_water_rotamers_independent (Size const seqpos, chemical::ResidueType const &h2o_type, pose::Pose const &pose, graph::GraphCOP packer_neighbor_graph, utility::vector1< conformation::ResidueOP > &new_rotamers)

Vector	build_optimal_water_O_on_donor (Vector const &hxyz, Vector const &dxyz)

void	build_optimal_water_Os_on_acceptor (Vector const &a_xyz, Vector b1_xyz, Vector const &b2_xyz, chemical::Hybridization const &hybrid, utility::vector1< Vector > &O_list)

void	build_donor_donor_waters (conformation::Residue const &rsd1, Size const hatm1, conformation::Residue const &rsd2, Size const hatm2, chemical::ResidueType const &h2o_type, conformation::Residue const &tp5, Size const nstep, utility::vector1< conformation::ResidueOP > &new_waters)

void	build_donor_acceptor_waters (conformation::Residue const &rsd1, Size const hatm1, conformation::Residue const &rsd2, Size const aatm2, chemical::ResidueType const &h2o_type, conformation::Residue const &tp5, Size const nstep, utility::vector1< conformation::ResidueOP > &new_waters)

void	build_acceptor_acceptor_waters (conformation::Residue const &rsd1, Size const aatm1, conformation::Residue const &rsd2, Size const aatm2, chemical::ResidueType const &h2o_type, conformation::Residue const &tp5, Size const nstep, utility::vector1< conformation::ResidueOP > &new_waters)

void	build_moving_O_bridge_waters (conformation::Residue const &rsd1, Size const anchor_atom, conformation::Residue const &rsd2, chemical::ResidueType const &h2o_type, conformation::Residue const &tp5, Size const nstep, utility::vector1< conformation::ResidueOP > &new_rotamers)

void	build_moving_O_water_rotamers_dependent (RotamerSets const &rotsets, WaterAnchorInfo const &water_info, chemical::ResidueType const &h2o_type, pack::task::PackerTask const &task, pose::Pose const &pose, graph::GraphCOP packer_neighbor_graph, utility::vector1< conformation::ResidueOP > &new_rotamers)

void	build_moving_O_water_rotamers_independent (WaterAnchorInfo const &water_info, chemical::ResidueType const &h2o_type, pack::task::PackerTask const &task, pose::Pose const &pose, graph::GraphCOP packer_neighbor_graph, utility::vector1< conformation::ResidueOP > &new_rotamers)

void	build_independent_water_rotamers (Size const seqpos_water, chemical::ResidueType const &h2o_type, pack::task::PackerTask const &task, pose::Pose const &pose, graph::GraphCOP packer_neighbor_graph, utility::vector1< conformation::ResidueOP > &new_rotamers)

void	build_dependent_water_rotamers (RotamerSets const &rotsets, Size const seqpos_water, chemical::ResidueType const &h2o_type, pack::task::PackerTask const &task, pose::Pose const &pose, graph::GraphCOP packer_neighbor_graph, utility::vector1< conformation::ResidueOP > &new_rotamers)

conformation::ResidueOP	dup_residue (conformation::Residue const &existing, conformation::Residue const &conformer)
	Helper function, combines existing's metadata with conformer's conformation. More...

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

static numeric::random::RandomGenerator	RG (32241)

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

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

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

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

Typedef Documentation

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

typedef utility::pointer::owning_ptr< RotamerSetsBase const > core::pack::rotamer_set::RotamerSetsBaseCOP

typedef utility::pointer::owning_ptr< RotamerSetsBase > core::pack::rotamer_set::RotamerSetsBaseOP

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

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

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

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

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

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

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

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

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

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

Enumeration Type Documentation

enum core::pack::rotamer_set::BumpSelectorDecision

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
	)

Referenced by build_rna_chi_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 core::pose::Pose::residue().

void core::pack::rotamer_set::build_acceptor_acceptor_waters	(	conformation::Residue const &	rsd1,
		Size const	aatm1,
		conformation::Residue const &	rsd2,
		Size const	aatm2,
		chemical::ResidueType const &	h2o_type,
		conformation::Residue const &	tp5,
		Size const	nstep,
		utility::vector1< conformation::ResidueOP > &	new_waters
	)

References core::conformation::Residue::abase2(), core::conformation::Residue::atom_base(), core::conformation::Residue::atom_type(), build_optimal_water_Os_on_acceptor(), chemical, create_oriented_water_rotamer(), numeric::xyzVector< class >::distance_squared(), core::chemical::element::F, core::scoring::hbonds::get_hb_acc_chem_type(), core::scoring::hbonds::hb_energy_deriv(), core::scoring::hbonds::hbdon_H2O, core::chemical::AtomType::hybridization(), core::scoring::hbonds::seq_sep_other, tt, and core::conformation::Residue::xyz().

Referenced by build_moving_O_bridge_waters().

void core::pack::rotamer_set::build_dependent_water_rotamers	(	RotamerSets const &	rotsets,
		Size const	seqpos_water,
		chemical::ResidueType const &	h2o_type,
		pack::task::PackerTask const &	task,
		pose::Pose const &	pose,
		graph::GraphCOP	packer_neighbor_graph,
		utility::vector1< conformation::ResidueOP > &	new_rotamers
	)

References build_moving_O_water_rotamers_dependent(), core::pose::Pose::data(), basic::datacache::BasicDataCache::get(), basic::datacache::BasicDataCache::has(), and core::pose::datacache::CacheableDataType::WATER_PACKING_INFO.

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

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(), utility::io::izstream::close(), core::pack::task::EX_SIX_QUARTER_STEP_STDDEVS, core::pack::task::ResidueLevelTask::extrachi_sample_level(), level, basic::database::open(), core::pack::task::PackerTask::pack_residue(), read_DNA_rotlib(), core::pose::Pose::residue(), core::pack::task::PackerTask::residue_task(), 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().

void core::pack::rotamer_set::build_donor_acceptor_waters	(	conformation::Residue const &	rsd1,
		Size const	hatm1,
		conformation::Residue const &	rsd2,
		Size const	aatm2,
		chemical::ResidueType const &	h2o_type,
		conformation::Residue const &	tp5,
		Size const	nstep,
		utility::vector1< conformation::ResidueOP > &	new_waters
	)

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(), chemical, create_oriented_water_rotamer(), numeric::xyzVector< class >::distance_squared(), core::chemical::element::F, 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(), core::scoring::hbonds::seq_sep_other, tt, and core::conformation::Residue::xyz().

Referenced by build_moving_O_bridge_waters().

void core::pack::rotamer_set::build_donor_donor_waters	(	conformation::Residue const &	rsd1,
		Size const	hatm1,
		conformation::Residue const &	rsd2,
		Size const	hatm2,
		chemical::ResidueType const &	h2o_type,
		conformation::Residue const &	tp5,
		Size const	nstep,
		utility::vector1< conformation::ResidueOP > &	new_waters
	)

References core::conformation::Residue::atom_base(), build_optimal_water_O_on_donor(), create_oriented_water_rotamer(), numeric::xyzVector< class >::distance_squared(), core::chemical::element::F, core::scoring::hbonds::get_hb_don_chem_type(), core::scoring::hbonds::hb_energy_deriv(), core::scoring::hbonds::hbacc_H2O, core::scoring::hbonds::seq_sep_other, tt, and core::conformation::Residue::xyz().

Referenced by build_moving_O_bridge_waters().

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

References core::chemical::rna::get_full_torsions(), core::pose::remove_variant_type_from_residue(), runtime_assert, and core::conformation::Residue::set_chi().

Referenced by build_rna_rotamers().

void core::pack::rotamer_set::build_fixed_O_water_rotamers_independent	(	Size const	seqpos,
		chemical::ResidueType const &	h2o_type,
		pose::Pose const &	pose,
		graph::GraphCOP	packer_neighbor_graph,
		utility::vector1< conformation::ResidueOP > &	new_rotamers
	)

References angle_of(), create_oriented_water_rotamer(), core::conformation::ResidueFactory::create_residue(), numeric::conversions::degrees(), degrees(), core::chemical::ResidueType::natoms(), core::pose::Pose::residue(), core::chemical::ResidueType::residue_type_set(), tt, and xyz.

Referenced by 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,
		graph::GraphCOP	packer_neighbor_graph,
		utility::vector1< conformation::ResidueOP > &	new_rotamers
	)

References build_fixed_O_water_rotamers_independent(), build_moving_O_water_rotamers_independent(), core::pose::Pose::data(), basic::datacache::BasicDataCache::get(), basic::datacache::BasicDataCache::has(), tt, and core::pose::datacache::CacheableDataType::WATER_PACKING_INFO.

Referenced by core::pack::rotamer_set::RotamerSet_::build_tp3_water_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, angle_of(), core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), core::scoring::atom_pair_constraint, core::id::BB, core::chemical::rna::CHI, core::conformation::Residue::clone(), core::pose::Pose::conformation(), core::pose::Pose::constraint_set(), constraints, core::conformation::ResidueFactory::create_residue(), distance_cutoff, core::conformation::Residue::is_NA(), numeric::xyzVector< class >::length(), min_tolerance, optimization, options, pi, numeric::constants::d::pi, rad2deg, core::pose::Pose::residue(), scoring, core::conformation::Residue::seqpos(), core::kinematics::MoveMap::set(), core::conformation::Residue::set_chi(), core::pose::Pose::set_torsion(), sf, core::pose::Pose::torsion(), tt, and core::conformation::Residue::xyz().

Referenced by build_dna_rotamers().

void core::pack::rotamer_set::build_moving_O_bridge_waters	(	conformation::Residue const &	rsd1,
		Size const	anchor_atom,
		conformation::Residue const &	rsd2,
		chemical::ResidueType const &	h2o_type,
		conformation::Residue const &	tp5,
		Size const	nstep,
		utility::vector1< conformation::ResidueOP > &	new_rotamers
	)

References core::conformation::Residue::accpt_pos(), core::conformation::Residue::atom_name(), core::conformation::Residue::atom_type(), build_acceptor_acceptor_waters(), build_donor_acceptor_waters(), build_donor_donor_waters(), numeric::xyzVector< class >::distance_squared(), core::conformation::Residue::Hpos_polar(), core::chemical::AtomType::is_polar_hydrogen(), core::conformation::Residue::name(), core::conformation::Residue::seqpos(), tt, and core::conformation::Residue::xyz().

Referenced by build_moving_O_water_rotamers_dependent(), and build_moving_O_water_rotamers_independent().

void core::pack::rotamer_set::build_moving_O_water_rotamers_dependent	(	RotamerSets const &	rotsets,
		WaterAnchorInfo const &	water_info,
		chemical::ResidueType const &	h2o_type,
		pack::task::PackerTask const &	task,
		pose::Pose const &	pose,
		graph::GraphCOP	packer_neighbor_graph,
		utility::vector1< conformation::ResidueOP > &	new_rotamers
	)

References core::pack::rotamer_set::WaterAnchorInfo::anchor_atom(), core::pack::rotamer_set::WaterAnchorInfo::anchor_residue(), core::pack::rotamer_set::WaterAnchorInfo::attaches_to_residue_type(), build_moving_O_bridge_waters(), core::conformation::ResidueFactory::create_residue(), numeric::conversions::degrees(), core::conformation::Residue::name(), core::chemical::ResidueTypeSet::name_map(), core::chemical::ResidueType::natoms(), core::pack::rotamer_set::WaterAnchorInfo::nstep(), core::pack::task::PackerTask::pack_residue(), core::pose::Pose::residue(), core::chemical::ResidueType::residue_type_set(), core::pack::rotamer_set::RotamerSets::rotamer_set_for_residue(), tt, and core::conformation::Residue::type().

Referenced by build_dependent_water_rotamers().

void core::pack::rotamer_set::build_moving_O_water_rotamers_independent	(	WaterAnchorInfo const &	water_info,
		chemical::ResidueType const &	h2o_type,
		pack::task::PackerTask const &	task,
		pose::Pose const &	pose,
		graph::GraphCOP	packer_neighbor_graph,
		utility::vector1< conformation::ResidueOP > &	new_rotamers
	)

References core::pack::rotamer_set::WaterAnchorInfo::anchor_atom(), core::pack::rotamer_set::WaterAnchorInfo::anchor_residue(), core::pack::rotamer_set::WaterAnchorInfo::attaches_to_residue_type(), build_moving_O_bridge_waters(), core::conformation::ResidueFactory::create_residue(), numeric::conversions::degrees(), core::conformation::Residue::name(), core::chemical::ResidueTypeSet::name_map(), core::chemical::ResidueType::natoms(), core::pack::rotamer_set::WaterAnchorInfo::nstep(), core::pack::task::PackerTask::pack_residue(), core::pose::Pose::residue(), core::chemical::ResidueType::residue_type_set(), and tt.

Referenced by build_independent_water_rotamers().

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().

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 chemical, numeric::xyzVector< class >::clear(), core::kinematics::distance(), numeric::conversions::radians(), radians(), core::chemical::RING_HYBRID, core::chemical::SP2_HYBRID, core::chemical::SP3_HYBRID, core::kinematics::Stub::spherical(), tt, and utility_exit.

Referenced by build_acceptor_acceptor_waters(), and build_donor_acceptor_waters().

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::pack::dunbrack::expand_proton_chi(), core::pack::task::ResidueLevelTask::extrachi_sample_level(), core::pack::task::ResidueLevelTask::include_virtual_side_chain(), core::scoring::rna_torsion, rna_torsion_potential, and runtime_assert.

Referenced by build_rna_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
	)

Referenced by build_dna_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::conformation::Residue::clone(), core::pose::Pose::conformation(), core::conformation::ResidueFactory::create_residue(), core::chemical::rna::DELTA, numeric::principal_angle_degrees(), principal_angle_degrees(), and core::pose::Pose::residue().

Referenced by 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 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(), level, core::pose::Pose::residue(), core::pack::task::PackerTask::residue_task(), core::pack::task::ResidueLevelTask::rna_task(), core::pack::task::ResidueLevelTask::sample_proton_chi(), core::pack::task::rna::RNA_ResidueLevelTask::sample_rna_chi(), TR, and type.

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

void core::pack::rotamer_set::build_rotamers_from_rotamer_bins	(	conformation::Residue const &	residue,
		utility::vector1< conformation::ResidueOP > &	rotamers,
		uint	current_chi_index,
		utility::vector1< uint > *	current_bin_indices
	)

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

Parameters

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

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

Author: Labonte

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

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

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

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

References core::chemical::rna::DELTA, core::chemical::rna::get_epsilon_torsions(), core::chemical::rna::get_full_torsions(), core::pose::remove_variant_type_from_residue(), runtime_assert, and core::conformation::Residue::set_chi().

Referenced by build_rna_rotamers().

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(), core::conformation::Residue::natoms(), core::conformation::Residue::set_xyz(), and core::conformation::Residue::xyz().

Referenced by build_acceptor_acceptor_waters(), build_donor_acceptor_waters(), build_donor_donor_waters(), and build_fixed_O_water_rotamers_independent().

void core::pack::rotamer_set::debug_dump_rotamers ( utility::vector1< conformation::ResidueOP > & rotamers )

References core::conformation::Residue::atom(), core::conformation::Residue::atom_name(), core::chemical::ResidueType::name(), core::conformation::Residue::natoms(), core::conformation::Residue::seqpos(), tt, core::conformation::Residue::type(), and core::conformation::Atom::xyz().

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(), core::conformation::Residue::copy_residue_connections_from(), and core::conformation::Residue::seqpos().

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

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::Residue::clone(), and core::conformation::Residue::set_chi().

Referenced by add_rna_chi_rotamers().

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

References utility::io::izstream::eof(), and getline().

Referenced by build_dna_rotamers().

Variable Documentation

numeric::random::RandomGenerator core::pack::rotamer_set::RG(32241)

static

Referenced by build_random_dna_rotamers().

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

static

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

static

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

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

static

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

static

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

static

Referenced by build_acceptor_acceptor_waters(), build_donor_acceptor_waters(), build_donor_donor_waters(), build_fixed_O_water_rotamers_independent(), build_independent_water_rotamers(), build_lib_dna_rotamers(), build_moving_O_bridge_waters(), build_moving_O_water_rotamers_dependent(), build_moving_O_water_rotamers_independent(), 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().

Namespaces

Classes

Typedefs

Enumerations

Functions

Variables

Typedef Documentation

Enumeration Type Documentation

Function Documentation

Variable Documentation