Namespaces
namespace	tok

Data Structures
struct	AtomGroup

struct	AtomGroupEntry

class	AtomImpl

class	AtomProp

class	ChainImpl

class	ConnectorImpl

class	Dihedral

class	EntityImpl

class	FragmentImpl

struct	GenProp

class	LogicOPNode

class	Node

class	pointer_it

class	QueryImpl

class	QueryLexer

class	QueryToken

class	ResidueImpl

struct	SelItem

class	SelNode

struct	SelStmt

class	StringOrRegexParam

class	SurfaceImpl

class	TorsionImpl

class	WithinParam

Typedefs
typedef std::vector< AtomGroupEntry >	AtomGroupEntryList

typedef std::map< String, AtomGroup >	AtomEntryGroups

typedef boost::shared_ptr< AtomImpl >	AtomImplPtr

typedef std::vector< AtomImplPtr >	AtomImplList

typedef boost::weak_ptr< AtomImpl >	AtomImplW

typedef std::vector< AtomImplW >	AtomImplWList

typedef boost::shared_ptr< ChainImpl >	ChainImplPtr

typedef boost::weak_ptr< ChainImpl >	ChainImplW

typedef boost::shared_ptr< ConnectorImpl >	ConnectorImplP

typedef boost::weak_ptr< ConnectorImpl >	ConnectorImplW

typedef std::list< ConnectorImplP >	ConnectorImplList

typedef std::map< AtomImpl *, AtomImplPtr >	AtomImplMap

typedef std::map< ResidueImpl *, ResidueImplPtr >	ResidueImplMap

typedef std::vector< ChainImplPtr >	ChainImplList

typedef std::map< ConnectorImpl *, ConnectorImplP >	ConnectorImplMap

typedef std::map< TorsionImpl *, TorsionImplP >	TorsionImplMap

typedef std::vector< FragmentImplP >	FragmentImplList

typedef std::map< EntityObserver *, EntityObserverPtr >	EntityObserverMap

typedef SpatialOrganizer< AtomImplPtr >	SpatialAtomOrganizer

typedef boost::shared_ptr< EntityImpl >	EntityImplPtr

typedef boost::weak_ptr< EntityImpl >	EntityImplW

typedef boost::shared_ptr< FragmentImpl >	FragmentImplP

typedef boost::variant< int, Real, WithinParam, StringOrRegexParam >	ParamType

typedef std::vector< SelItem >	SelStack

typedef std::vector< SelStmt >	SelStmts

typedef boost::shared_ptr< QueryImpl >	QueryImplP

typedef boost::shared_ptr< ResidueImpl >	ResidueImplPtr

typedef boost::weak_ptr< ResidueImpl >	ResidueImplW

typedef std::vector< ResidueImplPtr >	ResidueImplList

typedef SpatialOrganizer< SurfaceVertexID >	SpatialSurfaceVertexOrganizer

typedef boost::shared_ptr< SurfaceImpl >	SurfaceImplP

typedef boost::shared_ptr< TorsionImpl >	TorsionImplP

typedef std::vector< TorsionImplP >	TorsionImplList

Enumerations
enum	EntityDirtyFlags { DirtyICS =1 , DirtyXCS =2 , DirtyTrace =DirtyICS+4 , DirtyOrganizer =8 , DisableICS =16 }

enum	LogicOP { LOP_OR , LOP_AND }

enum	CompOP { COP_EQ , COP_NEQ , COP_GE , COP_LE , COP_LT , COP_GT }

enum	SelItemType { LOGIC , VALUE }

Functions
std::ostream &	operator<< (std::ostream &o, const AtomImplPtr ap)

bool	ConnectorExists (const AtomImplPtr &a, const AtomImplPtr &b)

ConnectorImplP	GetConnector (const AtomImplPtr &a, const AtomImplPtr &b)

template<typename T >
pointer_it< T >	begin (const std::vector< T > &values)

template<typename T >
pointer_it< T >	end (const std::vector< T > &values)

Typedef Documentation

◆ AtomEntryGroups

typedef std::map<String, AtomGroup> AtomEntryGroups

Definition at line 48 of file atom_group.hh.

◆ AtomGroupEntryList

typedef std::vector<AtomGroupEntry> AtomGroupEntryList

Definition at line 41 of file atom_group.hh.

◆ AtomImplList

typedef std::vector<AtomImplPtr> AtomImplList

Definition at line 38 of file atom_impl_fw.hh.

◆ AtomImplMap

typedef std::map<AtomImpl*,AtomImplPtr> AtomImplMap

Definition at line 54 of file entity_impl.hh.

◆ AtomImplPtr

typedef boost::shared_ptr<AtomImpl> AtomImplPtr

Definition at line 36 of file atom_impl_fw.hh.

◆ AtomImplW

typedef boost::weak_ptr<AtomImpl> AtomImplW

Definition at line 40 of file atom_impl_fw.hh.

◆ AtomImplWList

typedef std::vector<AtomImplW> AtomImplWList

Definition at line 42 of file atom_impl_fw.hh.

◆ ChainImplList

typedef std::vector<ChainImplPtr> ChainImplList

Definition at line 58 of file entity_impl.hh.

◆ ChainImplPtr

typedef boost::shared_ptr<ChainImpl> ChainImplPtr

Definition at line 29 of file chain_impl_fw.hh.

◆ ChainImplW

typedef boost::weak_ptr<ChainImpl> ChainImplW

Definition at line 30 of file chain_impl_fw.hh.

◆ ConnectorImplList

typedef std::list<ConnectorImplP> ConnectorImplList

Definition at line 30 of file connector_impl_fw.hh.

◆ ConnectorImplMap

typedef std::map<ConnectorImpl*,ConnectorImplP> ConnectorImplMap

Definition at line 60 of file entity_impl.hh.

◆ ConnectorImplP

typedef boost::shared_ptr<ConnectorImpl> ConnectorImplP

Definition at line 28 of file connector_impl_fw.hh.

◆ ConnectorImplW

typedef boost::weak_ptr<ConnectorImpl> ConnectorImplW

Definition at line 29 of file connector_impl_fw.hh.

◆ EntityImplPtr

typedef boost::shared_ptr<EntityImpl> EntityImplPtr

Definition at line 30 of file entity_impl_fw.hh.

◆ EntityImplW

typedef boost::weak_ptr<EntityImpl> EntityImplW

Definition at line 32 of file entity_impl_fw.hh.

◆ EntityObserverMap

typedef std::map<EntityObserver*,EntityObserverPtr> EntityObserverMap

Definition at line 66 of file entity_impl.hh.

◆ FragmentImplList

typedef std::vector<FragmentImplP> FragmentImplList

Definition at line 64 of file entity_impl.hh.

◆ FragmentImplP

typedef boost::shared_ptr<FragmentImpl> FragmentImplP

Definition at line 29 of file fragment_impl_fw.hh.

◆ ParamType

typedef boost::variant<int, Real, WithinParam, StringOrRegexParam> ParamType

Definition at line 71 of file query_ast.hh.

◆ QueryImplP

typedef boost::shared_ptr<QueryImpl> QueryImplP

Definition at line 29 of file query_impl_fw.hh.

◆ ResidueImplList

typedef std::vector<ResidueImplPtr> ResidueImplList

Definition at line 37 of file residue_impl_fw.hh.

◆ ResidueImplMap

typedef std::map<ResidueImpl*,ResidueImplPtr> ResidueImplMap

Definition at line 56 of file entity_impl.hh.

◆ ResidueImplPtr

typedef boost::shared_ptr<ResidueImpl> ResidueImplPtr

Definition at line 31 of file residue_impl_fw.hh.

◆ ResidueImplW

typedef boost::weak_ptr<ResidueImpl> ResidueImplW

Definition at line 34 of file residue_impl_fw.hh.

◆ SelStack

typedef std::vector<SelItem> SelStack

Definition at line 157 of file query_impl.hh.

◆ SelStmts

typedef std::vector<SelStmt> SelStmts

Definition at line 160 of file query_impl.hh.

◆ SpatialAtomOrganizer

typedef SpatialOrganizer<AtomImplPtr> SpatialAtomOrganizer

Definition at line 68 of file entity_impl.hh.

◆ SpatialSurfaceVertexOrganizer

typedef SpatialOrganizer<SurfaceVertexID> SpatialSurfaceVertexOrganizer

Definition at line 32 of file surface_impl.hh.

◆ SurfaceImplP

typedef boost::shared_ptr<SurfaceImpl> SurfaceImplP

Definition at line 27 of file surface_impl_fw.hh.

◆ TorsionImplList

typedef std::vector<TorsionImplP> TorsionImplList

Definition at line 33 of file torsion_impl_fw.hh.

◆ TorsionImplMap

typedef std::map<TorsionImpl*,TorsionImplP> TorsionImplMap

Definition at line 62 of file entity_impl.hh.

◆ TorsionImplP

typedef boost::shared_ptr<TorsionImpl> TorsionImplP

Definition at line 30 of file torsion_impl_fw.hh.

Enumeration Type Documentation

◆ CompOP

enum CompOP

Enumerator
COP_EQ
COP_NEQ
COP_GE
COP_LE
COP_LT
COP_GT

Definition at line 34 of file query_ast_fw.hh.

◆ EntityDirtyFlags

enum EntityDirtyFlags

Enumerator
DirtyICS
DirtyXCS
DirtyTrace
DirtyOrganizer
DisableICS

Definition at line 71 of file entity_impl.hh.

◆ LogicOP

enum LogicOP

Enumerator
LOP_OR
LOP_AND

Definition at line 30 of file query_ast_fw.hh.

◆ SelItemType

enum SelItemType

Enumerator
LOGIC
VALUE

Definition at line 135 of file query_impl.hh.

Function Documentation

◆ begin()

template<typename T >

pointer_it< T > begin ( const std::vector< T > & values )

inline

Definition at line 73 of file pointer_iterator.hh.

◆ ConnectorExists()

bool ConnectorExists	(	const AtomImplPtr &	a,
		const AtomImplPtr &	b
	)

◆ end()