/src/rdkit/Code/GraphMol/SmilesParse/SmilesParse.h

Source
//
//  Copyright (C) 2001-2021 Greg Landrum and other RDKit contributors
//
//   @@ All Rights Reserved @@
//  This file is part of the RDKit.
//  The contents are covered by the terms of the BSD license
//  which is included in the file license.txt, found at the root
//  of the RDKit source tree.
//
#include <RDGeneral/export.h>
#ifndef RD_SMILESPARSE_H
#define RD_SMILESPARSE_H

#include <GraphMol/SanitException.h>
#include <string>
#include <exception>
#include <map>
#include <memory>

namespace RDKit {
class RWMol;
class Atom;
class Bond;

namespace SmilesParse {
class RDKIT_SMILESPARSE_EXPORT SmilesParseException : public std::exception {
 public:
  SmilesParseException(const char *msg) : _msg(msg) {}
  SmilesParseException(const std::string msg) : _msg(msg) {}
  const char *what() const noexcept override { return _msg.c_str(); }
  ~SmilesParseException() noexcept override = default;

 private:
  std::string _msg;
};

}  // namespace SmilesParse

namespace v2 {
namespace SmilesParse {
using RDKit::SmilesParse::SmilesParseException;

struct RDKIT_SMILESPARSE_EXPORT SmilesParserParams {
  bool sanitize = true;      /**< sanitize the molecule after building it */
  bool allowCXSMILES = true; /**< recognize and parse CXSMILES*/
  bool strictCXSMILES =
      true; /**< throw an exception if the CXSMILES parsing fails */
  bool parseName = true;    /**< parse (and set) the molecule name as well */
  bool removeHs = true;     /**< remove Hs after constructing the molecule */
  bool skipCleanup = false; /**<  skip the final cleanup stage */
  bool debugParse = false;  /**< enable debugging in the SMILES parser*/
  std::map<std::string, std::string>
      replacements{}; /**< allows SMILES "macros" */
};

struct RDKIT_SMILESPARSE_EXPORT SmartsParserParams {
  bool allowCXSMILES = true; /**< recognize and parse CXSMILES extensions */
  bool strictCXSMILES =
      true; /**< throw an exception if the CXSMILES parsing fails */
  bool parseName = true; /**< parse (and set) the molecule name as well */
  bool mergeHs =
      false; /**< toggles merging H atoms in the SMARTS into neighboring atoms*/
  bool skipCleanup = false; /**<  skip the final cleanup stage */
  bool debugParse = false;  /**< enable debugging in the SMARTS parser*/
  std::map<std::string, std::string>
      replacements{}; /**< allows SMARTS "macros" */
};

RDKIT_SMILESPARSE_EXPORT std::unique_ptr<RDKit::RWMol> MolFromSmiles(
    const std::string &smi,
    const SmilesParserParams &params = SmilesParserParams());
RDKIT_SMILESPARSE_EXPORT std::unique_ptr<RDKit::RWMol> MolFromSmarts(
    const std::string &sma,
    const SmartsParserParams &params = SmartsParserParams());

RDKIT_SMILESPARSE_EXPORT std::unique_ptr<RDKit::Atom> AtomFromSmiles(
    const std::string &smi);
RDKIT_SMILESPARSE_EXPORT std::unique_ptr<RDKit::Bond> BondFromSmiles(
    const std::string &smi);

RDKIT_SMILESPARSE_EXPORT std::unique_ptr<RDKit::Atom> AtomFromSmarts(
    const std::string &sma);
RDKIT_SMILESPARSE_EXPORT std::unique_ptr<RDKit::Bond> BondFromSmarts(
    const std::string &sma);

}  // namespace SmilesParse
}  // namespace v2

inline namespace v1 {
using RDKit::SmilesParse::SmilesParseException;

struct RDKIT_SMILESPARSE_EXPORT SmilesParserParams {
  int debugParse = 0;   /**< enable debugging in the SMILES parser*/
  bool sanitize = true; /**< sanitize the molecule after building it */
  std::map<std::string, std::string> *replacements =
      nullptr;               /**< allows SMILES "macros" */
  bool allowCXSMILES = true; /**< recognize and parse CXSMILES*/
  bool strictCXSMILES =
      true; /**< throw an exception if the CXSMILES parsing fails */
  bool parseName = true;    /**< parse (and set) the molecule name as well */
  bool removeHs = true;     /**< remove Hs after constructing the molecule */
  bool skipCleanup = false; /**<  skip the final cleanup stage */
};

struct RDKIT_SMILESPARSE_EXPORT SmartsParserParams {
  int debugParse = 0; /**< enable debugging in the SMARTS parser*/
  std::map<std::string, std::string> *replacements =
      nullptr;               /**< allows SMARTS "macros" */
  bool allowCXSMILES = true; /**< recognize and parse CXSMILES extensions */
  bool strictCXSMILES =
      true; /**< throw an exception if the CXSMILES parsing fails */
  bool parseName = true; /**< parse (and set) the molecule name as well */
  bool mergeHs =
      false; /**< toggles merging H atoms in the SMARTS into neighboring atoms*/
  bool skipCleanup = false; /**<  skip the final cleanup stage */
};

inline RDKit::RWMol *SmilesToMol(const std::string &smi,
                                 const SmilesParserParams &ps) {
  RDKit::v2::SmilesParse::SmilesParserParams v2ps;
  v2ps.debugParse = ps.debugParse;
  v2ps.sanitize = ps.sanitize;

  if (ps.replacements) {
    v2ps.replacements = *ps.replacements;
  }
  v2ps.allowCXSMILES = ps.allowCXSMILES;
  v2ps.strictCXSMILES = ps.strictCXSMILES;
  v2ps.parseName = ps.parseName;
  v2ps.removeHs = ps.removeHs;
  v2ps.skipCleanup = ps.skipCleanup;
  return RDKit::v2::SmilesParse::MolFromSmiles(smi, v2ps).release();
}

inline Atom *SmilesToAtom(const std::string &smi) {
  auto res = RDKit::v2::SmilesParse::AtomFromSmiles(smi).release();
  return res;
}

inline Bond *SmilesToBond(const std::string &smi) {
  return RDKit::v2::SmilesParse::BondFromSmiles(smi).release();
}

//! Construct a molecule from a SMILES string
/*!
 \param smi           the SMILES to convert
 \param debugParse    toggles verbose debugging information from the parser
 \param sanitize      toggles H removal and sanitization of the molecule
 \param replacements  a string->string map of replacement strings. See below
                      for more information about replacements.

 \return a pointer to the new molecule; the caller is responsible for free'ing
 this.

 The optional replacements map can be used to do string substitution of
 abbreviations
 in the input SMILES. The set of substitutions is repeatedly looped through
 until
 the string no longer changes. It is the responsibility of the caller to make
 sure
 that substitutions results in legal and sensible SMILES.

 Examples of substitutions:
 \code
   CC{Q}C with {"{Q}":"OCCO"} -> CCOCCOC
   C{A}C{Q}C with {"{Q}":"OCCO", "{A}":"C1(CC1)"} -> CC1(CC1)COCCOC
   C{A}C{Q}C with {"{Q}":"{X}CC{X}", "{A}":"C1CC1", "{X}":"N"} -> CC1CC1CNCCNC
 \endcode

 */
inline RWMol *SmilesToMol(
    const std::string &smi, int debugParse = 0, bool sanitize = true,
    std::map<std::string, std::string> *replacements = nullptr) {
  RDKit::v2::SmilesParse::SmilesParserParams params;
  params.debugParse = debugParse;
  if (replacements) {
    params.replacements = *replacements;
  }
  if (sanitize) {
    params.sanitize = true;
    params.removeHs = true;
  } else {
    params.sanitize = false;
    params.removeHs = false;
  }
  return RDKit::v2::SmilesParse::MolFromSmiles(smi, params).release();
};

inline RWMol *SmartsToMol(const std::string &sma,
                          const SmartsParserParams &ps) {
  RDKit::v2::SmilesParse::SmartsParserParams v2ps;
  v2ps.debugParse = ps.debugParse;
  if (ps.replacements) {
    v2ps.replacements = *ps.replacements;
  }
  v2ps.allowCXSMILES = ps.allowCXSMILES;
  v2ps.strictCXSMILES = ps.strictCXSMILES;
  v2ps.parseName = ps.parseName;
  v2ps.mergeHs = ps.mergeHs;
  v2ps.skipCleanup = ps.skipCleanup;

  return RDKit::v2::SmilesParse::MolFromSmarts(sma, v2ps).release();
}

//! Construct a molecule from a SMARTS string
/*!
 \param sma           the SMARTS to convert
 \param debugParse    toggles verbose debugging information from the parser
 \param mergeHs       toggles merging H atoms in the SMARTS into neighboring
 atoms
 \param replacements  a string->string map of replacement strings.
                      \see SmilesToMol for more information about replacements

 \return a pointer to the new molecule; the caller is responsible for free'ing
 this.
 */
inline RWMol *SmartsToMol(
    const std::string &sma, int debugParse = 0, bool mergeHs = false,
    std::map<std::string, std::string> *replacements = nullptr) {
  RDKit::v2::SmilesParse::SmartsParserParams ps;
  ps.debugParse = debugParse;
  ps.mergeHs = mergeHs;
  if (replacements) {
    ps.replacements = *replacements;
  }
  return RDKit::v2::SmilesParse::MolFromSmarts(sma, ps).release();
};

inline Atom *SmartsToAtom(const std::string &sma) {
  return RDKit::v2::SmilesParse::AtomFromSmarts(sma).release();
}
inline Bond *SmartsToBond(const std::string &sma) {
  return RDKit::v2::SmilesParse::BondFromSmarts(sma).release();
}
}  // namespace v1

inline std::unique_ptr<RDKit::RWMol> operator""_smiles(const char *text,
                                                       size_t len) {
  std::string smi(text, len);
  try {
    return v2::SmilesParse::MolFromSmiles(smi);
  } catch (const RDKit::MolSanitizeException &) {
    return nullptr;
  }
}
inline std::unique_ptr<RDKit::RWMol> operator""_smarts(const char *text,
                                                       size_t len) {
  std::string smi(text, len);
  return v2::SmilesParse::MolFromSmarts(smi);
}

}  // namespace RDKit

#endif

Coverage Report

Created: 2026-11-12 07:33

Line	Count	Source
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/SanitException.h>
15		#include <string>
16		#include <exception>
17		#include <map>
18		#include <memory>
19
20		namespace RDKit {
21		class RWMol;
22		class Atom;
23		class Bond;
24
25		namespace SmilesParse {
26		class RDKIT_SMILESPARSE_EXPORT SmilesParseException : public std::exception {
27		public:
28	820	SmilesParseException(const char *msg) : _msg(msg) {}
29	863	SmilesParseException(const std::string msg) : _msg(msg) {}
30	0	const char *what() const noexcept override { return _msg.c_str(); }
31	1.68k	~SmilesParseException() noexcept override = default;
32
33		private:
34		std::string _msg;
35		};
36
37		} // namespace SmilesParse
38
39		namespace v2 {
40		namespace SmilesParse {
41		using RDKit::SmilesParse::SmilesParseException;
42
43		struct RDKIT_SMILESPARSE_EXPORT SmilesParserParams {
44		bool sanitize = true; /*< sanitize the molecule after building it /
45		bool allowCXSMILES = true; /*< recognize and parse CXSMILES/
46		bool strictCXSMILES =
47		true; /*< throw an exception if the CXSMILES parsing fails /
48		bool parseName = true; /*< parse (and set) the molecule name as well /
49		bool removeHs = true; /*< remove Hs after constructing the molecule /
50		bool skipCleanup = false; /*< skip the final cleanup stage /
51		bool debugParse = false; /*< enable debugging in the SMILES parser/
52		std::map<std::string, std::string>
53		replacements{}; /*< allows SMILES "macros" /
54		};
55
56		struct RDKIT_SMILESPARSE_EXPORT SmartsParserParams {
57		bool allowCXSMILES = true; /*< recognize and parse CXSMILES extensions /
58		bool strictCXSMILES =
59		true; /*< throw an exception if the CXSMILES parsing fails /
60		bool parseName = true; /*< parse (and set) the molecule name as well /
61		bool mergeHs =
62		false; /*< toggles merging H atoms in the SMARTS into neighboring atoms/
63		bool skipCleanup = false; /*< skip the final cleanup stage /
64		bool debugParse = false; /*< enable debugging in the SMARTS parser/
65		std::map<std::string, std::string>
66		replacements{}; /*< allows SMARTS "macros" /
67		};
68
69		RDKIT_SMILESPARSE_EXPORT std::unique_ptr<RDKit::RWMol> MolFromSmiles(
70		const std::string &smi,
71		const SmilesParserParams &params = SmilesParserParams());
72		RDKIT_SMILESPARSE_EXPORT std::unique_ptr<RDKit::RWMol> MolFromSmarts(
73		const std::string &sma,
74		const SmartsParserParams &params = SmartsParserParams());
75
76		RDKIT_SMILESPARSE_EXPORT std::unique_ptr<RDKit::Atom> AtomFromSmiles(
77		const std::string &smi);
78		RDKIT_SMILESPARSE_EXPORT std::unique_ptr<RDKit::Bond> BondFromSmiles(
79		const std::string &smi);
80
81		RDKIT_SMILESPARSE_EXPORT std::unique_ptr<RDKit::Atom> AtomFromSmarts(
82		const std::string &sma);
83		RDKIT_SMILESPARSE_EXPORT std::unique_ptr<RDKit::Bond> BondFromSmarts(
84		const std::string &sma);
85
86		} // namespace SmilesParse
87		} // namespace v2
88
89		inline namespace v1 {
90		using RDKit::SmilesParse::SmilesParseException;
91
92		struct RDKIT_SMILESPARSE_EXPORT SmilesParserParams {
93		int debugParse = 0; /*< enable debugging in the SMILES parser/
94		bool sanitize = true; /*< sanitize the molecule after building it /
95		std::map<std::string, std::string> *replacements =
96		nullptr; /*< allows SMILES "macros" /
97		bool allowCXSMILES = true; /*< recognize and parse CXSMILES/
98		bool strictCXSMILES =
99		true; /*< throw an exception if the CXSMILES parsing fails /
100		bool parseName = true; /*< parse (and set) the molecule name as well /
101		bool removeHs = true; /*< remove Hs after constructing the molecule /
102		bool skipCleanup = false; /*< skip the final cleanup stage /
103		};
104
105		struct RDKIT_SMILESPARSE_EXPORT SmartsParserParams {
106		int debugParse = 0; /*< enable debugging in the SMARTS parser/
107		std::map<std::string, std::string> *replacements =
108		nullptr; /*< allows SMARTS "macros" /
109		bool allowCXSMILES = true; /*< recognize and parse CXSMILES extensions /
110		bool strictCXSMILES =
111		true; /*< throw an exception if the CXSMILES parsing fails /
112		bool parseName = true; /*< parse (and set) the molecule name as well /
113		bool mergeHs =
114		false; /*< toggles merging H atoms in the SMARTS into neighboring atoms/
115		bool skipCleanup = false; /*< skip the final cleanup stage /
116		};
117
118		inline RDKit::RWMol *SmilesToMol(const std::string &smi,
119	0	const SmilesParserParams &ps) {
120	0	RDKit::v2::SmilesParse::SmilesParserParams v2ps;
121	0	v2ps.debugParse = ps.debugParse;
122	0	v2ps.sanitize = ps.sanitize;
123	0
124	0	if (ps.replacements) {
125	0	v2ps.replacements = *ps.replacements;
126	0	}
127	0	v2ps.allowCXSMILES = ps.allowCXSMILES;
128	0	v2ps.strictCXSMILES = ps.strictCXSMILES;
129	0	v2ps.parseName = ps.parseName;
130	0	v2ps.removeHs = ps.removeHs;
131	0	v2ps.skipCleanup = ps.skipCleanup;
132	0	return RDKit::v2::SmilesParse::MolFromSmiles(smi, v2ps).release();
133	0	}
134
135	0	inline Atom *SmilesToAtom(const std::string &smi) {
136	0	auto res = RDKit::v2::SmilesParse::AtomFromSmiles(smi).release();
137	0	return res;
138	0	}
139
140	0	inline Bond *SmilesToBond(const std::string &smi) {
141	0	return RDKit::v2::SmilesParse::BondFromSmiles(smi).release();
142	0	}
143
144		//! Construct a molecule from a SMILES string
145		/*!
146		\param smi the SMILES to convert
147		\param debugParse toggles verbose debugging information from the parser
148		\param sanitize toggles H removal and sanitization of the molecule
149		\param replacements a string->string map of replacement strings. See below
150		for more information about replacements.
151
152		\return a pointer to the new molecule; the caller is responsible for free'ing
153		this.
154
155		The optional replacements map can be used to do string substitution of
156		abbreviations
157		in the input SMILES. The set of substitutions is repeatedly looped through
158		until
159		the string no longer changes. It is the responsibility of the caller to make
160		sure
161		that substitutions results in legal and sensible SMILES.
162
163		Examples of substitutions:
164		\code
165		CC{Q}C with {"{Q}":"OCCO"} -> CCOCCOC
166		C{A}C{Q}C with {"{Q}":"OCCO", "{A}":"C1(CC1)"} -> CC1(CC1)COCCOC
167		C{A}C{Q}C with {"{Q}":"{X}CC{X}", "{A}":"C1CC1", "{X}":"N"} -> CC1CC1CNCCNC
168		\endcode
169
170		*/
171		inline RWMol *SmilesToMol(
172		const std::string &smi, int debugParse = 0, bool sanitize = true,
173	311	std::map<std::string, std::string> *replacements = nullptr) {
174	311	RDKit::v2::SmilesParse::SmilesParserParams params;
175	311	params.debugParse = debugParse;
176	311	if (replacements) {
177	0	params.replacements = *replacements;
178	0	}
179	311	if (sanitize) {
180	223	params.sanitize = true;
181	223	params.removeHs = true;
182	223	} else {
183	88	params.sanitize = false;
184	88	params.removeHs = false;
185	88	}
186	311	return RDKit::v2::SmilesParse::MolFromSmiles(smi, params).release();
187	311	};
188
189		inline RWMol *SmartsToMol(const std::string &sma,
190	0	const SmartsParserParams &ps) {
191	0	RDKit::v2::SmilesParse::SmartsParserParams v2ps;
192	0	v2ps.debugParse = ps.debugParse;
193	0	if (ps.replacements) {
194	0	v2ps.replacements = *ps.replacements;
195	0	}
196	0	v2ps.allowCXSMILES = ps.allowCXSMILES;
197	0	v2ps.strictCXSMILES = ps.strictCXSMILES;
198	0	v2ps.parseName = ps.parseName;
199	0	v2ps.mergeHs = ps.mergeHs;
200	0	v2ps.skipCleanup = ps.skipCleanup;
201	0
202	0	return RDKit::v2::SmilesParse::MolFromSmarts(sma, v2ps).release();
203	0	}
204
205		//! Construct a molecule from a SMARTS string
206		/*!
207		\param sma the SMARTS to convert
208		\param debugParse toggles verbose debugging information from the parser
209		\param mergeHs toggles merging H atoms in the SMARTS into neighboring
210		atoms
211		\param replacements a string->string map of replacement strings.
212		\see SmilesToMol for more information about replacements
213
214		\return a pointer to the new molecule; the caller is responsible for free'ing
215		this.
216		*/
217		inline RWMol *SmartsToMol(
218		const std::string &sma, int debugParse = 0, bool mergeHs = false,
219	33.6k	std::map<std::string, std::string> *replacements = nullptr) {
220	33.6k	RDKit::v2::SmilesParse::SmartsParserParams ps;
221	33.6k	ps.debugParse = debugParse;
222	33.6k	ps.mergeHs = mergeHs;
223	33.6k	if (replacements) {
224	0	ps.replacements = *replacements;
225	0	}
226	33.6k	return RDKit::v2::SmilesParse::MolFromSmarts(sma, ps).release();
227	33.6k	};
228
229	0	inline Atom *SmartsToAtom(const std::string &sma) {
230	0	return RDKit::v2::SmilesParse::AtomFromSmarts(sma).release();
231	0	}
232	0	inline Bond *SmartsToBond(const std::string &sma) {
233	0	return RDKit::v2::SmilesParse::BondFromSmarts(sma).release();
234	0	}
235		} // namespace v1
236
237		inline std::unique_ptr<RDKit::RWMol> operator""_smiles(const char *text,
238	0	size_t len) {
239	0	std::string smi(text, len);
240	0	try {
241	0	return v2::SmilesParse::MolFromSmiles(smi);
242	0	} catch (const RDKit::MolSanitizeException &) {
243	0	return nullptr;
244	0	}
245	0	}
246		inline std::unique_ptr<RDKit::RWMol> operator""_smarts(const char *text,
247	0	size_t len) {
248	0	std::string smi(text, len);
249	0	return v2::SmilesParse::MolFromSmarts(smi);
250	0	}
251
252		} // namespace RDKit
253
254		#endif