RDKit
Open-source cheminformatics and machine learning.
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#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 | |
namespace | RDKit |
Std stuff. | |
namespace | RDKit::details |
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:
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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. | |
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. | |
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. | |
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. | |
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. | |
RDKIT_CHEMTRANSFORMS_EXPORT ROMol * | RDKit::MurckoDecompose (const ROMol &mol) |
Carries out a Murcko decomposition on the molecule provided. | |
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. | |
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=nullptr) |
Adds named recursive queries to a molecule's atoms based on atom labels. | |
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() | |
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. | |
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 explicitly passed in | |
RDKIT_CHEMTRANSFORMS_EXPORT void | RDKit::details::updateSubMolConfs (const ROMol &mol, RWMol &res, boost::dynamic_bitset<> &removedAtoms) |
not recommended for use in other code | |
RDKIT_CHEMTRANSFORMS_EXPORT void | RDKit::details::copyStereoGroups (const std::map< const Atom *, Atom * > &molAtomMap, const ROMol &mol, RWMol &newMol) |