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>
17 namespace RDKit {
18 
19 RDKIT_RGROUPDECOMPOSITION_EXPORT extern const std::string RLABEL;
20 RDKIT_RGROUPDECOMPOSITION_EXPORT extern const std::string RLABEL_TYPE;
23 RDKIT_RGROUPDECOMPOSITION_EXPORT extern const std::string done;
24 RDKIT_RGROUPDECOMPOSITION_EXPORT extern const std::string
26 RDKIT_RGROUPDECOMPOSITION_EXPORT extern const std::string
28 
29 const unsigned int EMPTY_CORE_LABEL = -100000;
30 
31 // Various places where rgroups can be labeled
32 // the order of precedence
33 enum class Labelling {
40 };
41 
42 //! return the user friendly name for the given labelling
43 std::string labellingToString(Labelling type);
44 
45 //! Get the RLabels,atom mapping for the current molecule
46 std::map<int, Atom *> getRlabels(const RWMol &mol);
47 
48 //! Remove the user labels from the atom
49 void clearInputLabels(Atom *atom);
50 
51 //! Set the rgroup label for the current atom, this also sets the
52 /// appropriate MDL or other label
53 bool 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
57 bool 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
65 bool isUserRLabel(const Atom &atom);
66 
67 // ! Return true if the atom is a terminal dummy R group (user labelled or
68 // unlabelled)
69 bool 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::map< int, Atom * > getRlabels(const RWMol &mol)
Get the RLabels,atom mapping for the current molecule.
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