RDKit
Open-source cheminformatics and machine learning.
Loading...
Searching...
No Matches
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
20namespace 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 parameter 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 fingerprint 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" (because 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
60} // namespace RDKit
61
62#endif
pulls in the core RDKit functionality
functionality for finding subgraphs and paths in molecules
container for user parameters used to create a fragment catalog
#define RDKIT_FRAGCATALOG_EXPORT
Definition export.h:201
Std stuff.
RDKIT_FRAGCATALOG_EXPORT ROMol * prepareMol(const ROMol &mol, const FragCatParams *fparams, MatchVectType &aToFmap)
RDKIT_FRAGCATALOG_EXPORT MatchVectType findFuncGroupsOnMol(const ROMol &mol, const FragCatParams *params, INT_VECT &fgBonds)
std::vector< int > INT_VECT
Definition types.h:281
std::vector< std::pair< int, int > > MatchVectType
used to return matches from substructure searching, The format is (queryAtomIdx, molAtomIdx)
bool rdvalue_is(const RDValue_cast_t)
std::vector< boost::shared_ptr< ROMol > > MOL_SPTR_VECT
RDKIT_FRAGCATALOG_EXPORT MOL_SPTR_VECT readFuncGroups(std::string fileName)