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 
25 const unsigned int EMPTY_CORE_LABEL = -100000;
26 
27 // Various places where rgroups can be labeled
28 // the order of precedence
29 enum class Labelling {
36 };
37 
38 //! return the user friendly name for the given labelling
39 std::string labellingToString(Labelling type);
40 
41 //! Get the RLabels,atom mapping for the current molecule
42 std::map<int, Atom *> getRlabels(const RWMol &mol);
43 
44 //! Remove the user labels from the atom
45 void clearInputLabels(Atom *atom);
46 
47 //! Set the rgroup label for the current atom, this also sets the
48 /// appropriate MDL or other label
49 bool 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
53 bool 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
61 bool 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::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
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