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FragCatalogUtils.h
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//
// Copyright (C) 2003-2006 Rational Discovery LLC
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include <RDGeneral/export.h>
#ifndef _RD_FRAG_CATALOG_UTILS_H_
#define _RD_FRAG_CATALOG_UTILS_H_
#include <GraphMol/Subgraphs/Subgraphs.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/Substruct/SubstructMatch.h>
#include "FragCatParams.h"
namespace RDKit {
// get the functional groups from file or stream
// each functional groups is read in as a molecule with queryatoms and
// querybonds
RDKIT_FRAGCATALOG_EXPORT MOL_SPTR_VECT readFuncGroups(std::string fileName);
RDKIT_FRAGCATALOG_EXPORT MOL_SPTR_VECT readFuncGroups(std::istream &inStream,
int nToRead = -1);
// REVIEW: should this return a vector of pairs or a map?
// mark the functional groups of interest on the molecule
// and return a vector os std::pair <aid, fid>
// aid - is the atom id in mol that connect to a functional (fid)
// fid - the functional groups in the list maintained in params
// ARGUMENTS:
// mol - molecule of interest
// params - fragment catalog parameter object (contains a list of functional
// groups of interest
// fgBonds - container for bondIds in mol that are part of the functional
// groups
// the connection bond is included. these need to be chopped from
// the molecule later
RDKIT_FRAGCATALOG_EXPORT MatchVectType findFuncGroupsOnMol(
const ROMol &mol, const FragCatParams *params, INT_VECT &fgBonds);
// This functions is called before either adding the fragments from a molecule
// to a fragment catalog or generating the fingerprint for this molecule
// using a fragment catalog. These are the things this function does
// - recognize the function groups (and their location) on the molecule
// - chop these functional groups of the molecule to create a core molecule
// "coreMol"
// - map the function group locations onto this "coreMol" (because the atom ids
// on coreMol are different from the original molecule
// - return coreMol to the caller of this function and the enter the atom ids to
// func
// group ids mapping into aToFmap argument
RDKIT_FRAGCATALOG_EXPORT ROMol *prepareMol(const ROMol &mol,
const FragCatParams *fparams,
MatchVectType &aToFmap);
} // namespace RDKit
#endif
FragCatParams.h
RDKitBase.h
pulls in the core RDKit functionality
Subgraphs.h
functionality for finding subgraphs and paths in molecules
SubstructMatch.h
RDKit::FragCatParams
container for user parameters used to create a fragment catalog
Definition FragCatParams.h:24
RDKit::ROMol
Definition ROMol.h:285
export.h
RDKIT_FRAGCATALOG_EXPORT
#define RDKIT_FRAGCATALOG_EXPORT
Definition export.h:217
RDKit
Std stuff.
Definition Abbreviations.h:19
RDKit::prepareMol
RDKIT_FRAGCATALOG_EXPORT ROMol * prepareMol(const ROMol &mol, const FragCatParams *fparams, MatchVectType &aToFmap)
RDKit::findFuncGroupsOnMol
RDKIT_FRAGCATALOG_EXPORT MatchVectType findFuncGroupsOnMol(const ROMol &mol, const FragCatParams *params, INT_VECT &fgBonds)
RDKit::INT_VECT
std::vector< int > INT_VECT
Definition types.h:226
RDKit::MatchVectType
std::vector< std::pair< int, int > > MatchVectType
used to return matches from substructure searching, The format is (queryAtomIdx, molAtomIdx)
Definition FragFPGenerator.h:24
RDKit::MOL_SPTR_VECT
std::vector< boost::shared_ptr< ROMol > > MOL_SPTR_VECT
Definition FragCatParams.h:21
RDKit::readFuncGroups
RDKIT_FRAGCATALOG_EXPORT MOL_SPTR_VECT readFuncGroups(std::string fileName)