ROMol.h File Reference

Defines the primary molecule class ROMol as well as associated typedefs. More...

#include <RDGeneral/export.h>
#include <cstddef>
#include <iterator>
#include <utility>
#include <map>
#include <RDGeneral/BoostStartInclude.h>
#include <boost/graph/adjacency_list.hpp>
#include <boost/smart_ptr.hpp>
#include <boost/dynamic_bitset.hpp>
#include <RDGeneral/BoostEndInclude.h>
#include <RDGeneral/types.h>
#include <RDGeneral/RDProps.h>
#include "Atom.h"
#include "Bond.h"
#include "Conformer.h"
#include "SubstanceGroup.h"
#include "StereoGroup.h"
#include "RingInfo.h"

Go to the source code of this file.

Classes
struct	RDKit::CXXAtomIterator< Graph, Vertex, Iterator >
struct	RDKit::CXXAtomIterator< Graph, Vertex, Iterator >::CXXAtomIter
struct	RDKit::CXXBondIterator< Graph, Edge, Iterator >
struct	RDKit::CXXBondIterator< Graph, Edge, Iterator >::CXXBondIter
class	RDKit::ROMol

Namespaces
namespace	RDKit
	Std stuff.

Typedefs
typedef boost::adjacency_list< boost::vecS, boost::vecS, boost::undirectedS, Atom *, Bond * >	RDKit::MolGraph
	This is the BGL type used to store the topology:
C++11 Iterators
ROMol is a molecule class that is intended to have a fixed topology This is the primary class for most molecule operations. If you need to be manipulating the molecule (e.g. adding or deleting atoms or bonds, use an RWMol instead. Notes: each ROMol maintains a Dict of properties: Each property is keyed by name and can store an arbitrary type. Properties can be marked as calculated, in which case they will be cleared when the clearComputedProps() method is called. Because they have no impact upon chemistry, all property operations are const, this allows extra flexibility for clients who need to store extra data on ROMol objects. each ROMol has collections of bookmarks for Atoms and Bonds: the Atom bookmarks and Bond bookmarks are stored separately from each other each bookmark, an integer, can map to more than one Atom or Bond these are currently used in molecule construction, but could also be useful for reaction mapping and the like information about rings (SSSR and the like) is stored in the molecule's RingInfo pointer.
typedef std::vector< ROMol >	RDKit::MOL_VECT
typedef std::vector< ROMol * >	RDKit::MOL_PTR_VECT
typedef MOL_PTR_VECT::const_iterator	RDKit::MOL_PTR_VECT_CI
typedef MOL_PTR_VECT::iterator	RDKit::MOL_PTR_VECT_I

Variables
RDKIT_GRAPHMOL_EXPORT const int	RDKit::ci_RIGHTMOST_ATOM
RDKIT_GRAPHMOL_EXPORT const int	RDKit::ci_LEADING_BOND
RDKIT_GRAPHMOL_EXPORT const int	RDKit::ci_ATOM_HOLDER

Detailed Description

Defines the primary molecule class ROMol as well as associated typedefs.

Definition in file ROMol.h.