RDKit
Open-source cheminformatics and machine learning.
ChemTransforms.h File Reference
#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

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

Functions

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...
 
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...
 
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...
 
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...
 
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...
 
ROMol * RDKit::MurckoDecompose (const ROMol &mol)
 Carries out a Murcko decomposition on the molecule provided. More...
 
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...
 
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...
 
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...
 
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)
 
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...