core::chemical::gasteiger Namespace Reference

Classes
class	GasteigerAtomTypeData
class	GasteigerAtomTypeSet
	A set of Bcl Atom types. More...
class	PossibleAtomTypesForAtom
	A helper class by which AtomTypes can return all possible atom types for a given atom in a structure that is easily accessed by orbital type. More...

Typedefs
typedef utility::pointer::shared_ptr < GasteigerAtomTypeData >	GasteigerAtomTypeDataOP
typedef utility::pointer::shared_ptr < GasteigerAtomTypeData const >	GasteigerAtomTypeDataCOP
typedef utility::pointer::weak_ptr < GasteigerAtomTypeSet >	GasteigerAtomTypeSetAP
typedef utility::pointer::weak_ptr < GasteigerAtomTypeSet const >	GasteigerAtomTypeSetCAP
typedef utility::pointer::shared_ptr < GasteigerAtomTypeSet >	GasteigerAtomTypeSetOP
typedef utility::pointer::shared_ptr < GasteigerAtomTypeSet const >	GasteigerAtomTypeSetCOP

Functions
std::ostream &	operator<< (std::ostream &out, GasteigerAtomTypeData const &obj)
static basic::Tracer	TR ("core.chemical.gasteiger.GasteigerAtomTyper")
void	assign_gasteiger_atom_types (core::chemical::MutableResidueType &restype, bool keep_existing=true, bool allow_unknown=false)
	Version which gets typeset from ResidueType, or just uses default More...
void	assign_gasteiger_atom_types (core::chemical::MutableResidueType &restype, GasteigerAtomTypeSetCOP gasteiger_atom_type_set, bool keep_existing, bool allow_unknown)
	Assign gasteiger atom types to the atoms in restype. If "keep_existing" is true keep any already-assigned types Otherwise assign all new types. More...
PossibleAtomTypesForAtom	GetPossibleTypesForAtom (const core::chemical::RealResidueGraph &graph, VD const &atomVD, GasteigerAtomTypeSetCOP gasteiger_atom_type_set, core::Size connections)
	get all atom types matching a given atom considering its bonds More...
PossibleAtomTypesForAtom	GetPossibleTypesForAtom (core::chemical::RealResidueGraph const &graph, RealResidueVD const &atomVD, GasteigerAtomTypeSetCOP gasteiger_atom_type_set, core::Size connections)
static basic::Tracer	tr ("core.chemical.gasteiger.GasteigerAtomTypeSet")
void	safe_write (std::ostream &out, core::Size const &val, bool sep=true)
void	safe_write (std::ostream &out, core::Real const &val, bool sep=true)
void	safe_read (std::istream &in, core::Size &val)
void	safe_read (std::istream &in, core::Real &val)
template<typename T >
std::set< T >	parse_enum_set (std::string in)
template<typename T >
std::string	compact_enum_set (std::set< T > in, std::string prefix="xx")

Typedef Documentation

typedef utility::pointer::shared_ptr< GasteigerAtomTypeData const > core::chemical::gasteiger::GasteigerAtomTypeDataCOP

typedef utility::pointer::shared_ptr< GasteigerAtomTypeData > core::chemical::gasteiger::GasteigerAtomTypeDataOP

typedef utility::pointer::weak_ptr< GasteigerAtomTypeSet > core::chemical::gasteiger::GasteigerAtomTypeSetAP

typedef utility::pointer::weak_ptr< GasteigerAtomTypeSet const > core::chemical::gasteiger::GasteigerAtomTypeSetCAP

typedef utility::pointer::shared_ptr< GasteigerAtomTypeSet const > core::chemical::gasteiger::GasteigerAtomTypeSetCOP

typedef utility::pointer::shared_ptr< GasteigerAtomTypeSet > core::chemical::gasteiger::GasteigerAtomTypeSetOP

Function Documentation

void core::chemical::gasteiger::assign_gasteiger_atom_types	(	core::chemical::MutableResidueType &	restype,
		bool	keep_existing,
		bool	allow_unknown
	)

Version which gets typeset from ResidueType, or just uses default

References core::chemical::ResidueTypeBase::gasteiger_atom_typeset(), and core::chemical::ResidueTypeBase::set_gasteiger_atom_typeset().

Referenced by core::chemical::ResidueTypeSet::prep_restype().

void core::chemical::gasteiger::assign_gasteiger_atom_types	(	core::chemical::MutableResidueType &	restype,
		GasteigerAtomTypeSetCOP	gasteiger_atom_type_set,
		bool	keep_existing,
		bool	allow_unknown
	)

Assign gasteiger atom types to the atoms in restype. If "keep_existing" is true keep any already-assigned types Otherwise assign all new types.

Remaining issues:

• Input with explicitly mentioned aromatic bonds is not necessarily handled correctly. ** (I haven't extensively tested these yet.)
• Oxygen typing in aromatic rings is still an issue. ** While most work, N-O-N bridges like in PDB ligands G98 and 3C3 are missed. ** Conversely, methylated/oxidized dibenzofurans like in KRC and FCM are mistyped as trigonal when they're not.
• Rosetta needs to have formal charges notated. (Cannot calculate them from the number of hydrogens present.

Differences from gasteiger types which aren't necessarily errors:

• Phosphooxime oxygens like SEH & CGT are typed trig versus gasteiger tet.
• Carbamoyl oxime oxygens like GHR and VPU are typed trig versus gasteiger tet.
• 5 member ring oxygens where there's an exocyclic double bond like PHX and FUR are typed trig versus gasteiger tet.
• 5 member carbamoyl oxygens like CLW and A91 are typed trig versus gasteiger tet.
• The nitroperoxide oxygens of 16X are typed tet versus gasteiger trig
• The bridge nitrogens of fused ring structures like PO5, C7M and AZQ are typed trig versus gasteiger tet.

References core::chemical::MutableResidueType::atom(), core::chemical::MutableResidueType::atom_iterators(), core::chemical::MutableResidueType::atom_name(), core::chemical::Atom::gasteiger_atom_type(), core::chemical::gasteiger::PossibleAtomTypesForAtom::GetMostStableType(), GetPossibleTypesForAtom(), core::chemical::MutableResidueType::graph(), core::chemical::Atom::is_fake(), core::chemical::ResidueTypeBase::is_polymer(), core::chemical::MutableResidueType::lower_connect(), core::chemical::MutableResidueType::lower_connect_id(), core::chemical::MutableResidueType::n_residue_connections_for_atom(), core::chemical::MutableResidueType::null_vertex, core::chemical::sdf::output_residue(), core::chemical::regenerate_graph_vertex_index(), TR(), and core::chemical::MutableResidueConnection::vertex().

template<typename T >

std::string core::chemical::gasteiger::compact_enum_set	(	std::set< T >	in,
		std::string	prefix = "xx"
	)

References core::sequence::end, core::conformation::membrane::out, and protocols::hybridization::val.

Referenced by core::chemical::gasteiger::GasteigerAtomTypeData::write().

PossibleAtomTypesForAtom core::chemical::gasteiger::GetPossibleTypesForAtom	(	core::chemical::RealResidueGraph const &	graph,
		RealResidueVD const &	atomVD,
		GasteigerAtomTypeSetCOP	gasteiger_atom_type_set,
		core::Size	connections
	)

PossibleAtomTypesForAtom core::chemical::gasteiger::GetPossibleTypesForAtom	(	const core::chemical::RealResidueGraph &	graph,
		VD const &	atomVD,
		GasteigerAtomTypeSetCOP	gasteiger_atom_type_set,
		core::Size	connections
	)

get all atom types matching a given atom considering its bonds

Parameters

ATOM	atom of interest

Returns

PossibleAtomTypesForAtom

References core::chemical::gasteiger::PossibleAtomTypesForAtom::FindPossibleAtomTypesForAtom(), core::chemical::IsAromaticBond, protocols::mean_field::max(), protocols::mean_field::min(), and TR().

Referenced by assign_gasteiger_atom_types().

std::ostream& core::chemical::gasteiger::operator<< ( std::ostream &  out, GasteigerAtomTypeData const &  obj  )

inline

References core::chemical::gasteiger::GasteigerAtomTypeData::write().

template<typename T >

std::set< T > core::chemical::gasteiger::parse_enum_set

(

std::string

in

)

References core::pack::dunbrack::c, core::conformation::membrane::out, and protocols::hybridization::val.

void core::chemical::gasteiger::safe_read ( std::istream &  in, core::Size &  val  )

inline

References protocols::hybridization::val.

Referenced by core::chemical::Element::read(), core::chemical::ElectronConfiguration::read(), and core::chemical::gasteiger::GasteigerAtomTypeData::read().

void core::chemical::gasteiger::safe_read ( std::istream &  in, core::Real &  val  )

inline

References protocols::hybridization::val.

void core::chemical::gasteiger::safe_write ( std::ostream &  out, core::Size const &  val, bool  sep = true  )

inline

References protocols::hybridization::val.

Referenced by core::chemical::Element::write(), core::chemical::ElectronConfiguration::write(), and core::chemical::gasteiger::GasteigerAtomTypeData::write().

void core::chemical::gasteiger::safe_write ( std::ostream &  out, core::Real const &  val, bool  sep = true  )

inline

References protocols::hybridization::val.

static basic::Tracer core::chemical::gasteiger::tr ( "core.chemical.gasteiger.GasteigerAtomTypeSet"  )

static

Referenced by core::chemical::gasteiger::GasteigerAtomTypeSet::read_file().

static basic::Tracer core::chemical::gasteiger::TR ( "core.chemical.gasteiger.GasteigerAtomTyper"  )

static

Referenced by assign_gasteiger_atom_types(), core::chemical::gasteiger::PossibleAtomTypesForAtom::CreateAtomicEnvironmentToTypesMap(), core::chemical::gasteiger::PossibleAtomTypesForAtom::Finalize(), core::chemical::gasteiger::PossibleAtomTypesForAtom::FindPossibleAtomTypesForAtom(), GetPossibleTypesForAtom(), core::chemical::gasteiger::PossibleAtomTypesForAtom::hybridization_rank(), and core::chemical::gasteiger::PossibleAtomTypesForAtom::SetToType().