RDKit
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SmilesParse.h
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1 //
2 // Copyright (C) 2001-2021 Greg Landrum and other RDKit contributors
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 #include <RDGeneral/export.h>
11 #ifndef RD_SMILESPARSE_H
12 #define RD_SMILESPARSE_H
13 
14 #include <GraphMol/RWMol.h>
16 #include <string>
17 #include <exception>
18 #include <map>
19 
20 namespace RDKit {
21 
23  int debugParse = 0; /**< enable debugging in the SMILES parser*/
24  bool sanitize = true; /**< sanitize the molecule after building it */
25  std::map<std::string, std::string> *replacements =
26  nullptr; /**< allows SMILES "macros" */
27  bool allowCXSMILES = true; /**< recognize and parse CXSMILES*/
28  bool strictCXSMILES =
29  true; /**< throw an exception if the CXSMILES parsing fails */
30  bool parseName = true; /**< parse (and set) the molecule name as well */
31  bool removeHs = true; /**< remove Hs after constructing the molecule */
32  bool useLegacyStereo =
33  true; /**< use the legacy stereochemistry perception code */
34  bool skipCleanup =
35  false; /**< skip the final cleanup stage (for internal use) */
36 };
37 RDKIT_SMILESPARSE_EXPORT RWMol *SmilesToMol(const std::string &smi,
38  const SmilesParserParams &params);
39 
40 RDKIT_SMILESPARSE_EXPORT Atom *SmilesToAtom(const std::string &smi);
41 RDKIT_SMILESPARSE_EXPORT Bond *SmilesToBond(const std::string &smi);
42 
43 //! Construct a molecule from a SMILES string
44 /*!
45  \param smi the SMILES to convert
46  \param debugParse toggles verbose debugging information from the parser
47  \param sanitize toggles H removal and sanitization of the molecule
48  \param replacements a string->string map of replacement strings. See below
49  for more information about replacements.
50 
51  \return a pointer to the new molecule; the caller is responsible for free'ing
52  this.
53 
54  The optional replacements map can be used to do string substitution of
55  abbreviations
56  in the input SMILES. The set of substitutions is repeatedly looped through
57  until
58  the string no longer changes. It is the responsibility of the caller to make
59  sure
60  that substitutions results in legal and sensible SMILES.
61 
62  Examples of substitutions:
63  \code
64  CC{Q}C with {"{Q}":"OCCO"} -> CCOCCOC
65  C{A}C{Q}C with {"{Q}":"OCCO", "{A}":"C1(CC1)"} -> CC1(CC1)COCCOC
66  C{A}C{Q}C with {"{Q}":"{X}CC{X}", "{A}":"C1CC1", "{X}":"N"} -> CC1CC1CNCCNC
67  \endcode
68 
69  */
71  const std::string &smi, int debugParse = 0, bool sanitize = true,
72  std::map<std::string, std::string> *replacements = nullptr) {
73  SmilesParserParams params;
74  params.debugParse = debugParse;
75  params.replacements = replacements;
76  if (sanitize) {
77  params.sanitize = true;
78  params.removeHs = true;
79  } else {
80  params.sanitize = false;
81  params.removeHs = false;
82  }
83  return SmilesToMol(smi, params);
84 };
85 
87  int debugParse = 0; /**< enable debugging in the SMARTS parser*/
88  std::map<std::string, std::string> *replacements =
89  nullptr; /**< allows SMARTS "macros" */
90  bool allowCXSMILES = true; /**< recognize and parse CXSMILES extensions */
91  bool strictCXSMILES =
92  true; /**< throw an exception if the CXSMILES parsing fails */
93  bool parseName = true; /**< parse (and set) the molecule name as well */
94  bool mergeHs =
95  true; /**< toggles merging H atoms in the SMARTS into neighboring atoms*/
96  bool skipCleanup =
97  false; /**< skip the final cleanup stage (for internal use) */
98 };
99 RDKIT_SMILESPARSE_EXPORT RWMol *SmartsToMol(const std::string &sma,
100  const SmartsParserParams &ps);
101 
102 //! Construct a molecule from a SMARTS string
103 /*!
104  \param sma the SMARTS to convert
105  \param debugParse toggles verbose debugging information from the parser
106  \param mergeHs toggles merging H atoms in the SMARTS into neighboring
107  atoms
108  \param replacements a string->string map of replacement strings.
109  \see SmilesToMol for more information about replacements
110 
111  \return a pointer to the new molecule; the caller is responsible for free'ing
112  this.
113  */
115  const std::string &sma, int debugParse = 0, bool mergeHs = false,
116  std::map<std::string, std::string> *replacements = nullptr) {
118  ps.debugParse = debugParse;
119  ps.mergeHs = mergeHs;
120  ps.replacements = replacements;
121  return SmartsToMol(sma, ps);
122 };
123 
124 RDKIT_SMILESPARSE_EXPORT Atom *SmartsToAtom(const std::string &sma);
125 RDKIT_SMILESPARSE_EXPORT Bond *SmartsToBond(const std::string &sma);
126 
127 class RDKIT_SMILESPARSE_EXPORT SmilesParseException : public std::exception {
128  public:
129  SmilesParseException(const char *msg) : _msg(msg) {}
130  SmilesParseException(const std::string msg) : _msg(msg) {}
131  const char *what() const noexcept override { return _msg.c_str(); }
132  ~SmilesParseException() noexcept override = default;
133 
134  private:
135  std::string _msg;
136 };
137 
138 inline std::unique_ptr<RDKit::RWMol> operator"" _smiles(const char *text,
139  size_t len) {
140  std::string smi(text, len);
141  RWMol *ptr = nullptr;
142  try {
143  ptr = SmilesToMol(smi);
144  } catch (const RDKit::MolSanitizeException &) {
145  ptr = nullptr;
146  }
147  return std::unique_ptr<RWMol>(ptr);
148 }
149 inline std::unique_ptr<RDKit::RWMol> operator"" _smarts(const char *text,
150  size_t len) {
151  std::string smi(text, len);
152  // no need for exception handling here: SmartsToMol() doesn't do
153  // sanitization
154  RWMol *ptr = SmartsToMol(smi);
155  return std::unique_ptr<RWMol>(ptr);
156 }
157 
158 } // namespace RDKit
159 
160 #endif
Defines the editable molecule class RWMol.
The class for representing atoms.
Definition: Atom.h:68
class for representing a bond
Definition: Bond.h:47
class for flagging sanitization errors
RWMol is a molecule class that is intended to be edited.
Definition: RWMol.h:32
SmilesParseException(const std::string msg)
Definition: SmilesParse.h:130
SmilesParseException(const char *msg)
Definition: SmilesParse.h:129
const char * what() const noexcept override
Definition: SmilesParse.h:131
~SmilesParseException() noexcept override=default
#define RDKIT_SMILESPARSE_EXPORT
Definition: export.h:449
RDKIT_GRAPHMOL_EXPORT ROMol * removeHs(const ROMol &mol, bool implicitOnly=false, bool updateExplicitCount=false, bool sanitize=true)
returns a copy of a molecule with hydrogens removed
Std stuff.
Definition: Abbreviations.h:18
RDKIT_SMILESPARSE_EXPORT Atom * SmartsToAtom(const std::string &sma)
RDKIT_SMILESPARSE_EXPORT RWMol * SmartsToMol(const std::string &sma, const SmartsParserParams &ps)
RDKIT_SMILESPARSE_EXPORT Atom * SmilesToAtom(const std::string &smi)
RDKIT_SMILESPARSE_EXPORT Bond * SmilesToBond(const std::string &smi)
RDKIT_SMILESPARSE_EXPORT Bond * SmartsToBond(const std::string &sma)
RDKIT_SMILESPARSE_EXPORT RWMol * SmilesToMol(const std::string &smi, const SmilesParserParams &params)
std::map< std::string, std::string > * replacements
Definition: SmilesParse.h:88
std::map< std::string, std::string > * replacements
Definition: SmilesParse.h:25