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;
24
25const unsigned int EMPTY_CORE_LABEL = -100000;
26
27// Various places where rgroups can be labeled
28// the order of precedence
29enum class Labelling {
36};
37
38//! return the user friendly name for the given labelling
39std::string labellingToString(Labelling type);
40
41//! Get the RLabels,atom mapping for the current molecule
42std::map<int, Atom *> getRlabels(const RWMol &mol);
43
44//! Remove the user labels from the atom
46
47//! Set the rgroup label for the current atom, this also sets the
48/// appropriate MDL or other label
49bool setLabel(Atom *atom, int label, std::set<int> &labels, int &maxLabel,
50 bool relabel, Labelling type);
51
52//! Returns true if the core has a dummy atom
53bool hasDummy(const RWMol &core);
54
55//! Returns true if the core atom is either an atom with multiple
56/// connections or an atom with a single connection that has no user
57/// defined rgroup label
59
60//! Return true if the atom has a user-defined R group label
61bool isUserRLabel(const Atom &atom);
62
63//! Returns true if the core atom is either a dummy atom with multiple
64/// connections or a dummy atom with a single connection that has no user
65/// defined rgroup label
67 if (atom.getAtomicNum()) {
68 return false;
69 }
71}
72
73//! Returns a JSON form
74/// The prefix argument is added to each line in the output
76 const RGroupRow &rgr, const std::string &prefix = "");
77//! Returns a JSON form
78/// The prefix argument is added to each line in the output
80 const RGroupRows &rgr, const std::string &prefix = "");
81//! Returns a JSON form
82/// The prefix argument is added to each line in the output
84 const RGroupColumn &rgr, const std::string &prefix = "");
85//! Returns a JSON form
86/// The prefix argument is added to each line in the output
88 const RGroupColumns &rgr, const std::string &prefix = "");
89
90} // namespace RDKit
91
92#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:120
RWMol is a molecule class that is intended to be edited.
Definition: RWMol.h:32
#define RDKIT_RGROUPDECOMPOSITION_EXPORT
Definition: export.h:393
Std stuff.
Definition: Abbreviations.h:18
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
std::map< std::string, ROMOL_SPTR > RGroupRow
Definition: RGroupDecomp.h:132
std::vector< ROMOL_SPTR > RGroupColumn
Definition: RGroupDecomp.h:133
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:136
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="")
bool isAnyAtomWithMultipleNeighborsOrNotUserRLabel(const Atom &atom)
Definition: RGroupUtils.h:66
bool isAtomWithMultipleNeighborsOrNotUserRLabel(const Atom &atom)
RDKIT_RGROUPDECOMPOSITION_EXPORT const std::string RLABEL_TYPE
const unsigned int EMPTY_CORE_LABEL
Definition: RGroupUtils.h:25
bool isUserRLabel(const Atom &atom)
Return true if the atom has a user-defined R group label.
std::vector< RGroupRow > RGroupRows
Definition: RGroupDecomp.h:135
std::map< int, Atom * > getRlabels(const RWMol &mol)
Get the RLabels,atom mapping for the current molecule.