RDKit
Open-source cheminformatics and machine learning.
FragCatalogUtils.h
Go to the documentation of this file.
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
27  int nToRead = -1);
28 
29 // REVIEW: should this return a vector of pairs or a map?
30 // mark the functional groups of interest on the molecule
31 // and return a vector os std::pair <aid, fid>
32 // aid - is the atom id in mol that connect to a functional (fid)
33 // fid - the functional groups in the list maintained in params
34 // ARGUMENTS:
35 // mol - molecule of interest
36 // params - fragment catalog paramter object (contains a list of functional
37 // groups of interest
38 // fgBonds - container for bondIds in mol that are part of the functional
39 // groups
40 // the connection bond is included. these need to be chopped from
41 // the molecule later
42 
44  const ROMol &mol, const FragCatParams *params, INT_VECT &fgBonds);
45 
46 // This functions is called before either adding the fragments from a molecule
47 // to a fragment catalog or generating the fincgerprint for this molecule
48 // using a fragment catalog. These are the things this function does
49 // - recognize the function groups (and their location) on the molecule
50 // - chop these functional groups of the molecule to create a core molecule
51 // "coreMol"
52 // - map the function group locations onto this "coreMol" (bacause the atom ids
53 // on coreMol are different from the original molecule
54 // - return coreMol to the caller of this function and the enter the atom ids to
55 // func
56 // group ids mapping into aToFmap argument
57 RDKIT_FRAGCATALOG_EXPORT ROMol *prepareMol(const ROMol &mol,
58  const FragCatParams *fparams,
59  MatchVectType &aToFmap);
60 } // namespace RDKit
61 
62 #endif
RDKit::INT_VECT
std::vector< int > INT_VECT
Definition: types.h:254
RDKit::prepareMol
RDKIT_FRAGCATALOG_EXPORT ROMol * prepareMol(const ROMol &mol, const FragCatParams *fparams, MatchVectType &aToFmap)
RDKitBase.h
pulls in the core RDKit functionality
RDKit::MOL_SPTR_VECT
std::vector< boost::shared_ptr< ROMol > > MOL_SPTR_VECT
Definition: FragCatParams.h:20
FragCatParams.h
RDKit
Std stuff.
Definition: Atom.h:30
RDKit::readFuncGroups
RDKIT_FRAGCATALOG_EXPORT MOL_SPTR_VECT readFuncGroups(std::string fileName)
RDKit::findFuncGroupsOnMol
RDKIT_FRAGCATALOG_EXPORT MatchVectType findFuncGroupsOnMol(const ROMol &mol, const FragCatParams *params, INT_VECT &fgBonds)
RDKIT_FRAGCATALOG_EXPORT
#define RDKIT_FRAGCATALOG_EXPORT
Definition: export.h:281
Subgraphs.h
functionality for finding subgraphs and paths in molecules
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
SubstructMatch.h
export.h