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 #ifndef _RD_FRAG_CATALOG_UTILS_H_
11 #define _RD_FRAG_CATALOG_UTILS_H_
12 
14 #include <GraphMol/RDKitBase.h>
16 #include "FragCatParams.h"
17 #include <iostream>
18 
19 namespace 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 MOL_SPTR_VECT readFuncGroups(std::string fileName);
25 MOL_SPTR_VECT readFuncGroups(std::istream &inStream, int nToRead = -1);
26 
27 // REVIEW: should this return a vector of pairs or a map?
28 // mark the functional groups of interest on the molecule
29 // and return a vector os std::pair <aid, fid>
30 // aid - is the atom id in mol that connect to a functional (fid)
31 // fid - the functional groups in the list maintained in params
32 // ARGUMENTS:
33 // mol - molecule of interest
34 // params - fragment catalog paramter object (contains a list of functional
35 // groups of interest
36 // fgBonds - container for bondIds in mol that are part of the functional
37 // groups
38 // the connection bond is included. these need to be chopped from
39 // the molecule later
40 
41 MatchVectType findFuncGroupsOnMol(const ROMol &mol, const FragCatParams *params,
42  INT_VECT &fgBonds);
43 
44 // This functions is called before either adding the fragments from a molecule
45 // to a fragment catalog or generating the fincgerprint for this molecule
46 // using a fragment catalog. These are the things this function does
47 // - recognize the function groups (and their location) on the molecule
48 // - chop these functional groups of the molecule to create a core molecule
49 // "coreMol"
50 // - map the function group locations onto this "coreMol" (bacause the atom ids
51 // on coreMol are different from the original molecule
52 // - return coreMol to the caller of this function and the enter the atom ids to
53 // func
54 // group ids mapping into aToFmap argument
55 ROMol *prepareMol(const ROMol &mol, const FragCatParams *fparams,
56  MatchVectType &aToFmap);
57 }
58 
59 #endif
MOL_SPTR_VECT readFuncGroups(std::string fileName)
std::vector< std::pair< int, int > > MatchVectType
used to return matches from substructure searching, The format is (queryAtomIdx, molAtomIdx) ...
pulls in the core RDKit functionality
std::vector< boost::shared_ptr< ROMol > > MOL_SPTR_VECT
Definition: FragCatParams.h:19
std::vector< int > INT_VECT
Definition: types.h:188
MatchVectType findFuncGroupsOnMol(const ROMol &mol, const FragCatParams *params, INT_VECT &fgBonds)
Includes a bunch of functionality for handling Atom and Bond queries.
Definition: Atom.h:29
ROMol * prepareMol(const ROMol &mol, const FragCatParams *fparams, MatchVectType &aToFmap)
functionality for finding subgraphs and paths in molecules