ChemTransforms.h File Reference
`#include <RDGeneral/export.h>`
`#include <boost/smart_ptr.hpp>`
`#include <vector>`
`#include <iostream>`
`#include <GraphMol/Substruct/SubstructMatch.h>`
`#include "MolFragmenter.h"`

Go to the source code of this file.

## Namespaces

| RDKit
| Std stuff.

## Typedefs

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 boost::shared_ptr< ROMol > | RDKit::ROMOL_SPTR

## Functions

RDKIT_CHEMTRANSFORMS_EXPORT ROMol * | RDKit::deleteSubstructs (const ROMol &mol, const ROMol &query, bool onlyFrags=false, bool useChirality=false)
| Returns a copy of an ROMol with the atoms and bonds that match a pattern removed. More...
RDKIT_CHEMTRANSFORMS_EXPORT std::vector< ROMOL_SPTR > | RDKit::replaceSubstructs (const ROMol &mol, const ROMol &query, const ROMol &replacement, bool replaceAll=false, unsigned int replacementConnectionPoint=0, bool useChirality=false)
| Returns a list of copies of an ROMol with the atoms and bonds that match a pattern replaced with the atoms contained in another molecule. More...
RDKIT_CHEMTRANSFORMS_EXPORT ROMol * | RDKit::replaceSidechains (const ROMol &mol, const ROMol &coreQuery, bool useChirality=false)
| Returns a copy of an ROMol with the atoms and bonds that don't fall within a substructure match removed. More...
RDKIT_CHEMTRANSFORMS_EXPORT ROMol * | RDKit::replaceCore (const ROMol &mol, const ROMol &core, const MatchVectType &matchVect, bool replaceDummies=true, bool labelByIndex=false, bool requireDummyMatch=false)
| Returns a copy of an ROMol with the atoms and bonds that are referenced by the MatchVector removed. MatchVector must be defined between mol and the specified core. More...
RDKIT_CHEMTRANSFORMS_EXPORT ROMol * | RDKit::replaceCore (const ROMol &mol, const ROMol &coreQuery, bool replaceDummies=true, bool labelByIndex=false, bool requireDummyMatch=false, bool useChirality=false)
| Returns a copy of an ROMol with the atoms and bonds that do fall within a substructure match removed. More...
RDKIT_CHEMTRANSFORMS_EXPORT ROMol * | RDKit::MurckoDecompose (const ROMol &mol)
| Carries out a Murcko decomposition on the molecule provided. More...
RDKIT_CHEMTRANSFORMS_EXPORT ROMol * | RDKit::combineMols (const ROMol &mol1, const ROMol &mol2, RDGeom::Point3D offset=RDGeom::Point3D(0, 0, 0))
| Combined two molecules to create a new one. More...
RDKIT_CHEMTRANSFORMS_EXPORT void | RDKit::addRecursiveQueries (ROMol &mol, const std::map< std::string, ROMOL_SPTR > &queries, const std::string &propName, std::vector< std::pair< unsigned int, std::string >> *reactantLabels=NULL)
| Adds named recursive queries to a molecule's atoms based on atom. More...
RDKIT_CHEMTRANSFORMS_EXPORT void | RDKit::parseQueryDefFile (const std::string &filename, std::map< std::string, ROMOL_SPTR > &queryDefs, bool standardize=true, const std::string &delimiter="\t", const std::string &comment="//", unsigned int nameColumn=0, unsigned int smartsColumn=1)
| parses a query definition file and sets up a set of definitions suitable for use by addRecursiveQueries() More...
RDKIT_CHEMTRANSFORMS_EXPORT void | RDKit::parseQueryDefFile (std::istream *inStream, std::map< std::string, ROMOL_SPTR > &queryDefs, bool standardize=true, const std::string &delimiter="\t", const std::string &comment="//", unsigned int nameColumn=0, unsigned int smartsColumn=1)
| This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. More...
RDKIT_CHEMTRANSFORMS_EXPORT void | RDKit::parseQueryDefText (const std::string &queryDefText, std::map< std::string, ROMOL_SPTR > &queryDefs, bool standardize=true, const std::string &delimiter="\t", const std::string &comment="//", unsigned int nameColumn=0, unsigned int smartsColumn=1)
| equivalent to parseQueryDefFile() but the query definitions are More...