RDKit: FragCatalogUtils.h Source File

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FragCatalogUtils.h
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1//
2// Copyright (C) 2003-2006 Rational Discovery LLC
3//
4// @@ All Rights Reserved @@
5// This file is part of the RDKit.
6// The contents are covered by the terms of the BSD license
7// which is included in the file license.txt, found at the root
8// of the RDKit source tree.
9//
10#include <RDGeneral/export.h>
11#ifndef _RD_FRAG_CATALOG_UTILS_H_
12#define _RD_FRAG_CATALOG_UTILS_H_
13
14#include <GraphMol/Subgraphs/Subgraphs.h>
15#include <GraphMol/RDKitBase.h>
16#include <GraphMol/Substruct/SubstructMatch.h>
17#include "FragCatParams.h"
18
19namespace RDKit {
20
21// get the functional groups from file or stream
22// each functional groups is read in as a molecule with queryatoms and
23// querybonds
24 RDKIT_FRAGCATALOG_EXPORT MOL_SPTR_VECT readFuncGroups(std::string fileName);
25 RDKIT_FRAGCATALOG_EXPORT MOL_SPTR_VECT readFuncGroups(std::istream &inStream,
26 int nToRead = -1);
27
28// REVIEW: should this return a vector of pairs or a map?
29// mark the functional groups of interest on the molecule
30// and return a vector os std::pair <aid, fid>
31// aid - is the atom id in mol that connect to a functional (fid)
32// fid - the functional groups in the list maintained in params
33// ARGUMENTS:
34// mol - molecule of interest
35// params - fragment catalog parameter object (contains a list of functional
36// groups of interest
37// fgBonds - container for bondIds in mol that are part of the functional
38// groups
39// the connection bond is included. these need to be chopped from
40// the molecule later
41
42 RDKIT_FRAGCATALOG_EXPORT MatchVectType findFuncGroupsOnMol(
43 const ROMol &mol, const FragCatParams *params, INT_VECT &fgBonds);
44
45// This functions is called before either adding the fragments from a molecule
46// to a fragment catalog or generating the fingerprint for this molecule
47// using a fragment catalog. These are the things this function does
48// - recognize the function groups (and their location) on the molecule
49// - chop these functional groups of the molecule to create a core molecule
50// "coreMol"
51// - map the function group locations onto this "coreMol" (because the atom ids
52// on coreMol are different from the original molecule
53// - return coreMol to the caller of this function and the enter the atom ids to
54// func
55// group ids mapping into aToFmap argument
56 RDKIT_FRAGCATALOG_EXPORT ROMol *prepareMol(const ROMol &mol,
57 const FragCatParams *fparams,
58 MatchVectType &aToFmap);
59} // namespace RDKit
60
61#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:199
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:303
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)