RDKit
Open-source cheminformatics and machine learning.
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 
15 #include <GraphMol/RDKitBase.h>
17 #include "FragCatParams.h"
18 #include <iostream>
19 
20 namespace RDKit {
21 
22 // get the functional groups from file or stream
23 // each functional groups is read in as a molecule with queryatoms and
24 // querybonds
26 RDKIT_FRAGCATALOG_EXPORT MOL_SPTR_VECT readFuncGroups(std::istream &inStream, 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 paramter 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(const ROMol &mol, const FragCatParams *params,
43  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 fincgerprint 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" (bacause 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, const FragCatParams *fparams,
57  MatchVectType &aToFmap);
58 }
59 
60 #endif
RDKIT_FRAGCATALOG_EXPORT MOL_SPTR_VECT readFuncGroups(std::string fileName)
RDKIT_FRAGCATALOG_EXPORT MatchVectType findFuncGroupsOnMol(const ROMol &mol, const FragCatParams *params, INT_VECT &fgBonds)
std::vector< std::pair< int, int > > MatchVectType
used to return matches from substructure searching, The format is (queryAtomIdx, molAtomIdx) ...
RDKIT_FRAGCATALOG_EXPORT ROMol * prepareMol(const ROMol &mol, const FragCatParams *fparams, MatchVectType &aToFmap)
pulls in the core RDKit functionality
std::vector< boost::shared_ptr< ROMol > > MOL_SPTR_VECT
Definition: FragCatParams.h:20
std::vector< int > INT_VECT
Definition: types.h:247
Std stuff.
Definition: Atom.h:30
functionality for finding subgraphs and paths in molecules
#define RDKIT_FRAGCATALOG_EXPORT
Definition: export.h:268