core::pack::rotamer_set Namespace Reference

Namespaces
	symmetry

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

Typedefs
typedef utility::pointer::owning_ptr < ContinuousRotamerSet >	ContinuousRotamerSetOP
typedef utility::pointer::owning_ptr < ContinuousRotamerSet const >	ContinuousRotamerSetCOP
typedef utility::pointer::owning_ptr < ContinuousRotamerSets >	ContinuousRotamerSetsOP
typedef utility::pointer::owning_ptr < ContinuousRotamerSets const >	ContinuousRotamerSetsCOP
typedef utility::pointer::owning_ptr < FixbbRotamerSets >	FixbbRotamerSetsOP
typedef utility::pointer::owning_ptr < FixbbRotamerSets const >	FixbbRotamerSetsCOP
typedef utility::vector1< 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 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...
static numeric::random::RandomGenerator	RG (32241)
static basic::Tracer	tt ("core.pack.rotamer_set.rotamer_building_functions", basic::t_info)
void	read_DNA_rotlib (utility::io::izstream &lib_stream, utility::vector1< DihedralSet * > &library)
void	build_lib_dna_rotamers (utility::vector1< DihedralSet * > const &library, Size const resid, pose::Pose const &pose, chemical::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	fill_chi_rotamers_with_center_and_stddev (conformation::ResidueOP const &rot, utility::vector1< conformation::ResidueOP > &rotamers, utility::vector1< Real > const &chi_steps, Real const &center, Real const &width)
void	add_rna_chi_rotamers (conformation::ResidueOP const &rot, utility::vector1< conformation::ResidueOP > &rotamers, pack::task::ExtraRotSample const &level, scoring::rna::Gaussian_parameter_set const &gaussian_parameter_set)
void	build_rna_chi_rotamers (Size const resid, pose::Pose const &pose, chemical::ResidueTypeCOP concrete_residue, pack::task::ExtraRotSample const &level, bool const sample_rna_chi, bool const &include_current, utility::vector1< conformation::ResidueOP > &rotamers)
void	build_rna_rotamers (Size const resid, pose::Pose const &pose, chemical::ResidueTypeCOP concrete_residue, pack::task::PackerTask const &task, utility::vector1< conformation::ResidueOP > &new_rotamers, Size &id_for_current_rotamer)
void	debug_dump_rotamers (utility::vector1< conformation::ResidueOP > &rotamers)
conformation::ResidueOP	create_oriented_water_rotamer (chemical::ResidueType const &h2o_type, Vector const &xyz_atom1, Vector const &xyz_O, Vector const &xyz_atom2, std::string const &name1, std::string const &name2, conformation::Residue const &tp5)
void	build_fixed_O_water_rotamers_independent (Size const seqpos, chemical::ResidueType const &h2o_type, pose::Pose const &pose, graph::GraphCOP packer_neighbor_graph, utility::vector1< conformation::ResidueOP > &new_rotamers)
Vector	build_optimal_water_O_on_donor (Vector const &hxyz, Vector const &dxyz)
void	build_optimal_water_Os_on_acceptor (Vector const &a_xyz, Vector b1_xyz, Vector const &b2_xyz, chemical::Hybridization const &hybrid, utility::vector1< Vector > &O_list)
void	build_donor_donor_waters (conformation::Residue const &rsd1, Size const hatm1, conformation::Residue const &rsd2, Size const hatm2, chemical::ResidueType const &h2o_type, conformation::Residue const &tp5, Size const nstep, utility::vector1< conformation::ResidueOP > &new_waters)
void	build_donor_acceptor_waters (conformation::Residue const &rsd1, Size const hatm1, conformation::Residue const &rsd2, Size const aatm2, chemical::ResidueType const &h2o_type, conformation::Residue const &tp5, Size const nstep, utility::vector1< conformation::ResidueOP > &new_waters)
void	build_acceptor_acceptor_waters (conformation::Residue const &rsd1, Size const aatm1, conformation::Residue const &rsd2, Size const aatm2, chemical::ResidueType const &h2o_type, conformation::Residue const &tp5, Size const nstep, utility::vector1< conformation::ResidueOP > &new_waters)
void	build_moving_O_bridge_waters (conformation::Residue const &rsd1, Size const anchor_atom, conformation::Residue const &rsd2, chemical::ResidueType const &h2o_type, conformation::Residue const &tp5, Size const nstep, utility::vector1< conformation::ResidueOP > &new_rotamers)
void	build_moving_O_water_rotamers_dependent (RotamerSets const &rotsets, WaterAnchorInfo const &water_info, chemical::ResidueType const &h2o_type, pack::task::PackerTask const &task, pose::Pose const &pose, graph::GraphCOP packer_neighbor_graph, utility::vector1< conformation::ResidueOP > &new_rotamers)
void	build_moving_O_water_rotamers_independent (WaterAnchorInfo const &water_info, chemical::ResidueType const &h2o_type, pack::task::PackerTask const &task, pose::Pose const &pose, graph::GraphCOP packer_neighbor_graph, utility::vector1< conformation::ResidueOP > &new_rotamers)
void	build_independent_water_rotamers (Size const seqpos_water, chemical::ResidueType const &h2o_type, pack::task::PackerTask const &task, pose::Pose const &pose, graph::GraphCOP packer_neighbor_graph, utility::vector1< conformation::ResidueOP > &new_rotamers)
void	build_dependent_water_rotamers (RotamerSets const &rotsets, Size const seqpos_water, chemical::ResidueType const &h2o_type, pack::task::PackerTask const &task, pose::Pose const &pose, graph::GraphCOP packer_neighbor_graph, utility::vector1< conformation::ResidueOP > &new_rotamers)
static basic::Tracer	tt ("core.pack.rotamer_set.RotamerSet_", basic::t_info)
static basic::Tracer	tt ("core.pack.rotamer_set.RotamerSubset", basic::t_info)
static basic::Tracer	TR ("core.pack.rotamer_set.UnboundRotamersOperation")
conformation::ResidueOP	dup_residue (conformation::Residue const &existing, conformation::Residue const &conformer)
	Helper function, combines existing's metadata with conformer's conformation. More...

Typedef Documentation

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

Definition at line 29 of file ContinuousRotamerSet.fwd.hh.

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

Definition at line 26 of file ContinuousRotamerSet.fwd.hh.

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

Definition at line 32 of file ContinuousRotamerSet.fwd.hh.

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

Definition at line 31 of file ContinuousRotamerSet.fwd.hh.

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

Definition at line 47 of file rotamer_building_functions.hh.

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

Definition at line 28 of file FixbbRotamerSets.fwd.hh.

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

Definition at line 25 of file FixbbRotamerSets.fwd.hh.

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

Definition at line 34 of file RotamerCouplings.fwd.hh.

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

Definition at line 30 of file RotamerCouplings.fwd.hh.

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

Definition at line 30 of file RotamerLinks.fwd.hh.

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

Definition at line 26 of file RotamerLinks.fwd.hh.

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

Definition at line 32 of file RotamerSetOperation.fwd.hh.

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

Definition at line 29 of file RotamerSetOperation.fwd.hh.

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

Definition at line 34 of file RotamerSetOperation.fwd.hh.

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

Definition at line 28 of file RotamerSet.fwd.hh.

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

Definition at line 32 of file RotamerSet.fwd.hh.

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

Definition at line 24 of file RotamerSetFactory.fwd.hh.

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

Definition at line 31 of file RotamerSet.fwd.hh.

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

Definition at line 37 of file RotamerSetOperation.fwd.hh.

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

Definition at line 36 of file RotamerSetOperation.fwd.hh.

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

Definition at line 28 of file RotamerSetsBase.fwd.hh.

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

Definition at line 25 of file RotamerSetsBase.fwd.hh.

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

Definition at line 28 of file RotamerSets.fwd.hh.

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

Definition at line 25 of file RotamerSets.fwd.hh.

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

Definition at line 28 of file RotamerSubsets.fwd.hh.

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

Definition at line 25 of file RotamerSubsets.fwd.hh.

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

Definition at line 39 of file RotamerSetOperation.fwd.hh.

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

Definition at line 40 of file RotamerSetOperation.fwd.hh.

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

Definition at line 28 of file UnboundRotamersOperation.fwd.hh.

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

Definition at line 26 of file UnboundRotamersOperation.fwd.hh.

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

Definition at line 24 of file WaterAnchorInfo.fwd.hh.

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

Definition at line 24 of file WaterPackingInfo.fwd.hh.

Enumeration Type Documentation

enum core::pack::rotamer_set::BumpSelectorDecision

Enumerator
KEEP_ROTAMER
DELETE_ROTAMER
DELETE_PREVIOUS_ROTAMER

Definition at line 23 of file BumpSelector.hh.

Function Documentation

void core::pack::rotamer_set::add_rna_chi_rotamers	(	conformation::ResidueOP const &	rot,
		utility::vector1< conformation::ResidueOP > &	rotamers,
		pack::task::ExtraRotSample const &	level,
		scoring::rna::Gaussian_parameter_set const &	gaussian_parameter_set
	)

Definition at line 654 of file rotamer_building_functions.cc.

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, and core::pack::task::NO_EXTRA_CHI_SAMPLES.

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

Definition at line 38 of file bb_independent_rotamers.cc.

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

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

void core::pack::rotamer_set::build_acceptor_acceptor_waters	(	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
	)

Definition at line 1321 of file rotamer_building_functions.cc.

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(), rot(), 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
	)

Definition at line 1669 of file rotamer_building_functions.cc.

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().

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
	)

Definition at line 566 of file rotamer_building_functions.cc.

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().

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
	)

Definition at line 1221 of file rotamer_building_functions.cc.

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(), rot(), 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
	)

Definition at line 1150 of file rotamer_building_functions.cc.

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, rot(), 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_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
	)

Definition at line 945 of file rotamer_building_functions.cc.

References create_oriented_water_rotamer(), core::conformation::ResidueFactory::create_residue(), core::chemical::ResidueType::natoms(), core::pose::Pose::residue(), core::chemical::ResidueType::residue_type_set(), tt(), and protocols::kinmatch::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
	)

Definition at line 1631 of file rotamer_building_functions.cc.

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

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

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
	)

Definition at line 152 of file rotamer_building_functions.cc.

References core::scoring::angle_constraint, core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), core::scoring::atom_pair_constraint, core::id::BB, core::id::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::pose::Pose::residue(), rot(), 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().

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
	)

Definition at line 1411 of file rotamer_building_functions.cc.

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(), 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
	)

Definition at line 1485 of file rotamer_building_functions.cc.

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(), 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
	)

Definition at line 1576 of file rotamer_building_functions.cc.

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(), 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
	)

Definition at line 1077 of file rotamer_building_functions.cc.

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
	)

Definition at line 1090 of file rotamer_building_functions.cc.

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(), and build_donor_acceptor_waters().

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
	)

Definition at line 343 of file rotamer_building_functions.cc.

References core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), core::id::BB, core::id::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, protocols::antibody2::l1, protocols::antibody2::l2, core::pack::task::NO_EXTRA_CHI_SAMPLES, core::pose::Pose::residue(), RG(), rot(), core::pose::Pose::set_torsion(), core::pose::Pose::torsion(), and core::conformation::Residue::xyz().

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
	)

Definition at line 748 of file rotamer_building_functions.cc.

References add_rna_chi_rotamers(), core::pose::Pose::conformation(), core::conformation::ResidueFactory::create_residue(), core::scoring::rna::DELTA, core::scoring::rna::RNA_FittedTorsionInfo::delta_cutoff(), core::pose::Pose::residue(), and rot().

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
	)

Definition at line 812 of file rotamer_building_functions.cc.

References build_rna_chi_rotamers(), core::io::serialization::clone(), core::pack::dunbrack::expand_proton_chi(), core::pack::task::ResidueLevelTask::extrachi_sample_level(), core::pack::task::PackerTask::include_current(), core::pose::Pose::residue(), core::pack::task::PackerTask::residue_task(), rot(), core::pack::task::ResidueLevelTask::sample_proton_chi(), and core::pack::task::ResidueLevelTask::sample_rna_chi().

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

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
	)

Definition at line 915 of file rotamer_building_functions.cc.

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_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)

Definition at line 894 of file rotamer_building_functions.cc.

References rot(), tt(), 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.

Definition at line 98 of file UnboundRotamersOperation.cc.

References core::conformation::Residue::chain(), core::conformation::Residue::clone(), 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
	)

Definition at line 639 of file rotamer_building_functions.cc.

Referenced by add_rna_chi_rotamers().

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

Definition at line 111 of file rotamer_building_functions.cc.

Referenced by build_dna_rotamers().

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

static

Referenced by build_random_dna_rotamers().

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

static

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

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

static

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

static

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(), and debug_dump_rotamers().