RDKit
Open-source cheminformatics and machine learning.
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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
26
27const unsigned int EMPTY_CORE_LABEL = -100000;
28
29// Various places where rgroups can be labeled
30// the order of precedence
39
40//! return the user friendly name for the given labelling
41std::string labellingToString(Labelling type);
42
43//! Get the RLabels,atom mapping for the current molecule
44std::map<int, Atom *> getRlabels(const RWMol &mol);
45
46//! Remove the user labels from the atom
48
49//! Set the rgroup label for the current atom, this also sets the
50/// appropriate MDL or other label
51bool setLabel(Atom *atom, int label, std::set<int> &labels, int &maxLabel,
52 bool relabel, Labelling type);
53
54//! Returns true if the core has a dummy atom
55bool hasDummy(const RWMol &core);
56
57//! Returns true if the core atom is either an atom with multiple
58/// connections or an atom with a single connection that has no user
59/// defined rgroup label
61
62//! Return true if the atom has a user-defined R group label
63bool isUserRLabel(const Atom &atom);
64
65// ! Return true if the atom is a terminal dummy R group (user labelled or
66// unlabelled)
67bool isDummyRGroupAttachment(const Atom &atom);
68
69//! Returns true if the core atom is either a dummy atom with multiple
70/// connections or a dummy atom with a single connection that has no user
71/// defined rgroup label
73 if (atom.getAtomicNum()) {
74 return false;
75 }
77}
78
79//! Returns a JSON form
80/// The prefix argument is added to each line in the output
82 const RGroupRow &rgr, const std::string &prefix = "");
83//! Returns a JSON form
84/// The prefix argument is added to each line in the output
86 const RGroupRows &rgr, const std::string &prefix = "");
87//! Returns a JSON form
88/// The prefix argument is added to each line in the output
90 const RGroupColumn &rgr, const std::string &prefix = "");
91//! Returns a JSON form
92/// The prefix argument is added to each line in the output
94 const RGroupColumns &rgr, const std::string &prefix = "");
95
96//! Relabel dummy atoms bearing an R-group mapping (as
97/// atom map number, isotope or MDLRGroup label) such that
98/// they will be displayed by the rendering code as R# rather
99/// than #*, *:#, #*:#, etc. By default, only the MDLRGroup label
100/// is retained on output; this may be configured through the
101/// outputLabels parameter.
102/// In case there are multiple potential R-group mappings,
103/// the priority on input is Atom map number > Isotope > MDLRGroup.
104/// The inputLabels parameter allows to configure which mappings
105/// are taken into consideration.
107 ROMol &mol, unsigned int inputLabels = AtomMap | Isotope | MDLRGroup,
108 unsigned int outputLabels = MDLRGroup);
109
110} // namespace RDKit
111
112#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:417
Std stuff.
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 UNLABELED_CORE_ATTACHMENT
bool rdvalue_is(const RDValue_cast_t)
std::map< std::string, ROMOL_SPTR > RGroupRow
std::vector< ROMOL_SPTR > RGroupColumn
RDKIT_RGROUPDECOMPOSITION_EXPORT void relabelMappedDummies(ROMol &mol, unsigned int inputLabels=AtomMap|Isotope|MDLRGroup, unsigned int outputLabels=MDLRGroup)
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
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="")
bool isAnyAtomWithMultipleNeighborsOrNotUserRLabel(const Atom &atom)
Definition RGroupUtils.h:72
RDKIT_RGROUPDECOMPOSITION_EXPORT const std::string RLABEL_TYPE
const unsigned int EMPTY_CORE_LABEL
Definition RGroupUtils.h:27
bool isUserRLabel(const Atom &atom)
Return true if the atom has a user-defined R group label.
std::vector< RGroupRow > RGroupRows
std::map< int, Atom * > getRlabels(const RWMol &mol)
Get the RLabels,atom mapping for the current molecule.