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SmilesParse.h
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//
// 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
SanitException.h
RDKit::Atom
The class for representing atoms.
Definition Atom.h:75
RDKit::Bond
class for representing a bond
Definition Bond.h:47
RDKit::MolSanitizeException
class for flagging sanitization errors
Definition SanitException.h:28
RDKit::RWMol
RWMol is a molecule class that is intended to be edited.
Definition RWMol.h:32
RDKit::SmilesParse::SmilesParseException
Definition SmilesParse.h:26
RDKit::SmilesParse::SmilesParseException::SmilesParseException
SmilesParseException(const std::string msg)
Definition SmilesParse.h:29
RDKit::SmilesParse::SmilesParseException::SmilesParseException
SmilesParseException(const char *msg)
Definition SmilesParse.h:28
RDKit::SmilesParse::SmilesParseException::~SmilesParseException
~SmilesParseException() noexcept override=default
RDKit::SmilesParse::SmilesParseException::what
const char * what() const noexcept override
Definition SmilesParse.h:30
export.h
RDKIT_SMILESPARSE_EXPORT
#define RDKIT_SMILESPARSE_EXPORT
Definition export.h:537
RDKit::SmilesParse
Definition SmilesParse.h:25
RDKit::v1
Definition ReactionParser.h:92
RDKit::v1::SmilesToAtom
Atom * SmilesToAtom(const std::string &smi)
Definition SmilesParse.h:135
RDKit::v1::SmilesToBond
Bond * SmilesToBond(const std::string &smi)
Definition SmilesParse.h:140
RDKit::v1::SmartsToMol
RWMol * SmartsToMol(const std::string &sma, const SmartsParserParams &ps)
Definition SmilesParse.h:189
RDKit::v1::SmartsToBond
Bond * SmartsToBond(const std::string &sma)
Definition SmilesParse.h:232
RDKit::v1::SmilesToMol
RDKit::RWMol * SmilesToMol(const std::string &smi, const SmilesParserParams &ps)
Definition SmilesParse.h:118
RDKit::v1::SmartsToAtom
Atom * SmartsToAtom(const std::string &sma)
Definition SmilesParse.h:229
RDKit::v2::SmilesParse
Definition SmilesParse.h:40
RDKit::v2::SmilesParse::AtomFromSmiles
RDKIT_SMILESPARSE_EXPORT std::unique_ptr< RDKit::Atom > AtomFromSmiles(const std::string &smi)
RDKit::v2::SmilesParse::MolFromSmiles
RDKIT_SMILESPARSE_EXPORT std::unique_ptr< RDKit::RWMol > MolFromSmiles(const std::string &smi, const SmilesParserParams &params=SmilesParserParams())
RDKit::v2::SmilesParse::BondFromSmiles
RDKIT_SMILESPARSE_EXPORT std::unique_ptr< RDKit::Bond > BondFromSmiles(const std::string &smi)
RDKit::v2::SmilesParse::AtomFromSmarts
RDKIT_SMILESPARSE_EXPORT std::unique_ptr< RDKit::Atom > AtomFromSmarts(const std::string &sma)
RDKit::v2::SmilesParse::BondFromSmarts
RDKIT_SMILESPARSE_EXPORT std::unique_ptr< RDKit::Bond > BondFromSmarts(const std::string &sma)
RDKit::v2::SmilesParse::MolFromSmarts
RDKIT_SMILESPARSE_EXPORT std::unique_ptr< RDKit::RWMol > MolFromSmarts(const std::string &sma, const SmartsParserParams &params=SmartsParserParams())
RDKit::v2
Definition ReactionParser.h:72
RDKit
Std stuff.
Definition Abbreviations.h:19
RDKit::SmartsParserParams
Definition SmilesParse.h:105
RDKit::v1::SmartsParserParams::replacements
std::map< std::string, std::string > * replacements
Definition SmilesParse.h:107
RDKit::v1::SmartsParserParams::parseName
bool parseName
Definition SmilesParse.h:112
RDKit::v1::SmartsParserParams::skipCleanup
bool skipCleanup
Definition SmilesParse.h:115
RDKit::v1::SmartsParserParams::allowCXSMILES
bool allowCXSMILES
Definition SmilesParse.h:109
RDKit::v1::SmartsParserParams::strictCXSMILES
bool strictCXSMILES
Definition SmilesParse.h:110
RDKit::v1::SmartsParserParams::debugParse
int debugParse
Definition SmilesParse.h:106
RDKit::v1::SmartsParserParams::mergeHs
bool mergeHs
Definition SmilesParse.h:113
RDKit::SmilesParserParams
Definition SmilesParse.h:92
RDKit::v1::SmilesParserParams::replacements
std::map< std::string, std::string > * replacements
Definition SmilesParse.h:95
RDKit::v1::SmilesParserParams::sanitize
bool sanitize
Definition SmilesParse.h:94
RDKit::v1::SmilesParserParams::removeHs
bool removeHs
Definition SmilesParse.h:101
RDKit::v1::SmilesParserParams::allowCXSMILES
bool allowCXSMILES
Definition SmilesParse.h:97
RDKit::v1::SmilesParserParams::strictCXSMILES
bool strictCXSMILES
Definition SmilesParse.h:98
RDKit::v1::SmilesParserParams::skipCleanup
bool skipCleanup
Definition SmilesParse.h:102
RDKit::v1::SmilesParserParams::debugParse
int debugParse
Definition SmilesParse.h:93
RDKit::v1::SmilesParserParams::parseName
bool parseName
Definition SmilesParse.h:100
RDKit::v2::SmilesParse::SmartsParserParams
Definition SmilesParse.h:56
RDKit::v2::SmilesParse::SmartsParserParams::parseName
bool parseName
Definition SmilesParse.h:60
RDKit::v2::SmilesParse::SmartsParserParams::strictCXSMILES
bool strictCXSMILES
Definition SmilesParse.h:58
RDKit::v2::SmilesParse::SmartsParserParams::allowCXSMILES
bool allowCXSMILES
Definition SmilesParse.h:57
RDKit::v2::SmilesParse::SmartsParserParams::skipCleanup
bool skipCleanup
Definition SmilesParse.h:63
RDKit::v2::SmilesParse::SmartsParserParams::mergeHs
bool mergeHs
Definition SmilesParse.h:61
RDKit::v2::SmilesParse::SmartsParserParams::replacements
std::map< std::string, std::string > replacements
Definition SmilesParse.h:66
RDKit::v2::SmilesParse::SmartsParserParams::debugParse
bool debugParse
Definition SmilesParse.h:64
RDKit::v2::SmilesParse::SmilesParserParams
Definition SmilesParse.h:43
RDKit::v2::SmilesParse::SmilesParserParams::parseName
bool parseName
Definition SmilesParse.h:48
RDKit::v2::SmilesParse::SmilesParserParams::strictCXSMILES
bool strictCXSMILES
Definition SmilesParse.h:46
RDKit::v2::SmilesParse::SmilesParserParams::debugParse
bool debugParse
Definition SmilesParse.h:51
RDKit::v2::SmilesParse::SmilesParserParams::allowCXSMILES
bool allowCXSMILES
Definition SmilesParse.h:45
RDKit::v2::SmilesParse::SmilesParserParams::skipCleanup
bool skipCleanup
Definition SmilesParse.h:50
RDKit::v2::SmilesParse::SmilesParserParams::sanitize
bool sanitize
Definition SmilesParse.h:44
RDKit::v2::SmilesParse::SmilesParserParams::replacements
std::map< std::string, std::string > replacements
Definition SmilesParse.h:53
RDKit::v2::SmilesParse::SmilesParserParams::removeHs
bool removeHs
Definition SmilesParse.h:49