RDKit
Open-source cheminformatics and machine learning.
RGroupUtils.h
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1//
2// Copyright (C) 2017 Novartis Institutes for BioMedical Research
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 RGROUP_UTILS
11#define RGROUP_UTILS
12
13#include <GraphMol/RDKitBase.h>
14#include "RGroupDecomp.h"
15
16#include <map>
17namespace RDKit {
18
19RDKIT_RGROUPDECOMPOSITION_EXPORT extern const std::string RLABEL;
20RDKIT_RGROUPDECOMPOSITION_EXPORT extern const std::string RLABEL_TYPE;
23RDKIT_RGROUPDECOMPOSITION_EXPORT extern const std::string done;
24RDKIT_RGROUPDECOMPOSITION_EXPORT extern const std::string
26RDKIT_RGROUPDECOMPOSITION_EXPORT extern const std::string
28
29const unsigned int EMPTY_CORE_LABEL = -100000;
30
31// Various places where rgroups can be labeled
32// the order of precedence
33enum class Labelling {
40};
41
42//! return the user friendly name for the given labelling
43std::string labellingToString(Labelling type);
44
45//! Get the RLabels,atom mapping for the current molecule
46std::map<int, Atom *> getRlabels(const RWMol &mol);
47
48//! Remove the user labels from the atom
50
51//! Set the rgroup label for the current atom, this also sets the
52/// appropriate MDL or other label
53bool setLabel(Atom *atom, int label, std::set<int> &labels, int &maxLabel,
54 bool relabel, Labelling type);
55
56//! Returns true if the core has a dummy atom
57bool hasDummy(const RWMol &core);
58
59//! Returns true if the core atom is either an atom with multiple
60/// connections or an atom with a single connection that has no user
61/// defined rgroup label
63
64//! Return true if the atom has a user-defined R group label
65bool isUserRLabel(const Atom &atom);
66
67// ! Return true if the atom is a terminal dummy R group (user labelled or
68// unlabelled)
69bool isDummyRGroupAttachment(const Atom &atom);
70
71//! Returns true if the core atom is either a dummy atom with multiple
72/// connections or a dummy atom with a single connection that has no user
73/// defined rgroup label
75 if (atom.getAtomicNum()) {
76 return false;
77 }
79}
80
81//! Returns a JSON form
82/// The prefix argument is added to each line in the output
84 const RGroupRow &rgr, const std::string &prefix = "");
85//! Returns a JSON form
86/// The prefix argument is added to each line in the output
88 const RGroupRows &rgr, const std::string &prefix = "");
89//! Returns a JSON form
90/// The prefix argument is added to each line in the output
92 const RGroupColumn &rgr, const std::string &prefix = "");
93//! Returns a JSON form
94/// The prefix argument is added to each line in the output
96 const RGroupColumns &rgr, const std::string &prefix = "");
97
98} // namespace RDKit
99
100#endif
pulls in the core RDKit functionality
The class for representing atoms.
Definition: Atom.h:68
int getAtomicNum() const
returns our atomic number
Definition: Atom.h:126
RWMol is a molecule class that is intended to be edited.
Definition: RWMol.h:32
#define RDKIT_RGROUPDECOMPOSITION_EXPORT
Definition: export.h:401
Std stuff.
Definition: Abbreviations.h:19
RDKIT_RGROUPDECOMPOSITION_EXPORT const std::string RLABEL_CORE_INDEX
std::string labellingToString(Labelling type)
return the user friendly name for the given labelling
RDKIT_RGROUPDECOMPOSITION_EXPORT const std::string done
RDKIT_RGROUPDECOMPOSITION_EXPORT const std::string MISSING_RGROUP
std::map< std::string, ROMOL_SPTR > RGroupRow
Definition: RGroupDecomp.h:137
std::vector< ROMOL_SPTR > RGroupColumn
Definition: RGroupDecomp.h:138
bool isDummyRGroupAttachment(const Atom &atom)
bool setLabel(Atom *atom, int label, std::set< int > &labels, int &maxLabel, bool relabel, Labelling type)
void clearInputLabels(Atom *atom)
Remove the user labels from the atom.
std::map< std::string, RGroupColumn > RGroupColumns
Definition: RGroupDecomp.h:141
bool isAtomWithMultipleNeighborsOrNotDummyRGroupAttachment(const Atom &atom)
RDKIT_RGROUPDECOMPOSITION_EXPORT const std::string RLABEL
bool hasDummy(const RWMol &core)
Returns true if the core has a dummy atom.
RDKIT_RGROUPDECOMPOSITION_EXPORT const std::string SIDECHAIN_RLABELS
RDKIT_RGROUPDECOMPOSITION_EXPORT std::string toJSON(const RGroupRow &rgr, const std::string &prefix="")
RDKIT_RGROUPDECOMPOSITION_EXPORT const std::string UNLABELLED_CORE_ATTACHMENT
bool isAnyAtomWithMultipleNeighborsOrNotUserRLabel(const Atom &atom)
Definition: RGroupUtils.h:74
RDKIT_RGROUPDECOMPOSITION_EXPORT const std::string RLABEL_TYPE
const unsigned int EMPTY_CORE_LABEL
Definition: RGroupUtils.h:29
bool isUserRLabel(const Atom &atom)
Return true if the atom has a user-defined R group label.
std::vector< RGroupRow > RGroupRows
Definition: RGroupDecomp.h:140
std::map< int, Atom * > getRlabels(const RWMol &mol)
Get the RLabels,atom mapping for the current molecule.