RDKit: ROMol.h File Reference

| RDKit Open-source cheminformatics and machine learning.

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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.