RDKit
Open-source cheminformatics and machine learning.
Loading...
Searching...
No Matches
RDKit::v1 Namespace Reference

Classes

class  ForwardSDMolSupplier
 
class  MolSupplier
 
class  SDMolSupplier
 
struct  SmartsParserParams
 
class  SmilesMolSupplier
 lazy file parser for Smiles tables More...
 
struct  SmilesParserParams
 
class  TDTMolSupplier
 lazy file parser for TDT files More...
 

Functions

ChemicalReactionRxnBlockToChemicalReaction (const std::string &rxnBlock, bool sanitize=false, bool removeHs=false, bool strictParsing=true)
 Parse a text block in MDL rxn format into a ChemicalReaction.
 
ChemicalReactionRxnFileToChemicalReaction (const std::string &fileName, bool sanitize=false, bool removeHs=false, bool strictParsing=true)
 Parse a file in MDL rxn format into a ChemicalReaction.
 
ChemicalReactionRxnDataStreamToChemicalReaction (std::istream &rxnStream, unsigned int &line, bool sanitize=false, bool removeHs=false, bool strictParsing=true)
 Parse a text stream in MDL rxn format into a ChemicalReaction.
 
ChemicalReactionPNGStreamToChemicalReaction (std::istream &pngStream)
 constructs a ChemicalReaction from the metadata in a PNG stream
 
ChemicalReactionPNGStringToChemicalReaction (const std::string &data)
 constructs a ChemicalReaction from the metadata in a PNG string See PNGStreamToChemicalReaction() for more details
 
ChemicalReactionPNGFileToChemicalReaction (const std::string &fname)
 constructs a ChemicalReaction from the metadata in a PNG file See PNGStreamToChemicalReaction() for more details
 
std::vector< std::unique_ptr< RWMol > > CDXMLDataStreamToMols (std::istream &inStream, bool sanitize=true, bool removeHs=true)
 construct molecules from a CDXML file Note that the CDXML format is large and complex, the RDKit doesn't support full functionality, just the base ones required for molecule and reaction parsing.
 
std::vector< std::unique_ptr< RWMol > > CDXMLFileToMols (const std::string &filename, bool sanitize=true, bool removeHs=true)
 construct molecules from a CDXML file Note that the CDXML format is large and complex, the RDKit doesn't support full functionality, just the base ones required for molecule and reaction parsing.
 
std::vector< std::unique_ptr< RWMol > > CDXMLToMols (const std::string &cdxml, bool sanitize=true, bool removeHs=true)
 construct molecules from a CDXML file Note that the CDXML format is large and complex, the RDKit doesn't support full functionality, just the base ones required for molecule and reaction parsing.
 
RWMolMolDataStreamToMol (std::istream *inStream, unsigned int &line, bool sanitize=true, bool removeHs=true, bool strictParsing=true)
 
RWMolMolDataStreamToMol (std::istream &inStream, unsigned int &line, bool sanitize=true, bool removeHs=true, bool strictParsing=true)
 
RWMolMolBlockToMol (const std::string &molBlock, bool sanitize=true, bool removeHs=true, bool strictParsing=true)
 
RWMolMolFileToMol (const std::string &fName, bool sanitize=true, bool removeHs=true, bool strictParsing=true)
 
RWMolTPLDataStreamToMol (std::istream *inStream, unsigned int &line, bool sanitize=true, bool skipFirstConf=false)
 translate TPL data (BioCad format) into a multi-conf molecule
 
RWMolTPLFileToMol (const std::string &fName, bool sanitize=true, bool skipFirstConf=false)
 construct a multi-conf molecule from a TPL (BioCad format) file
 
RWMolMol2FileToMol (const std::string &fName, bool sanitize=true, bool removeHs=true, Mol2Type variant=Mol2Type::CORINA, bool cleanupSubstructures=true)
 
RWMolMol2DataStreamToMol (std::istream &inStream, bool sanitize=true, bool removeHs=true, Mol2Type variant=Mol2Type::CORINA, bool cleanupSubstructures=true)
 
RWMolMol2DataStreamToMol (std::istream *inStream, bool sanitize=true, bool removeHs=true, Mol2Type variant=Mol2Type::CORINA, bool cleanupSubstructures=true)
 
RWMolMol2BlockToMol (const std::string &molBlock, bool sanitize=true, bool removeHs=true, Mol2Type variant=Mol2Type::CORINA, bool cleanupSubstructures=true)
 
RWMolXYZDataStreamToMol (std::istream &inStream)
 
RWMolXYZBlockToMol (const std::string &xyzBlock)
 
RWMolXYZFileToMol (const std::string &fName)
 
RWMolPDBBlockToMol (const std::string &str, bool sanitize=true, bool removeHs=true, unsigned int flavor=0, bool proximityBonding=true)
 
RWMolPDBBlockToMol (const char *str, bool sanitize=true, bool removeHs=true, unsigned int flavor=0, bool proximityBonding=true)
 
RWMolPDBFileToMol (const std::string &fname, bool sanitize=true, bool removeHs=true, unsigned int flavor=0, bool proximityBonding=true)
 
RWMolPDBDataStreamToMol (std::istream &inStream, bool sanitize=true, bool removeHs=true, unsigned int flavor=0, bool proximityBonding=true)
 
RWMolPDBDataStreamToMol (std::istream *inStream, bool sanitize=true, bool removeHs=true, unsigned int flavor=0, bool proximityBonding=true)
 
bool MrvFileIsReaction (const std::string &fname)
 
bool MrvDataStreamIsReaction (std::istream *inStream)
 
bool MrvDataStreamIsReaction (std::istream &inStream)
 
bool MrvBlockIsReaction (const std::string &molmrvText)
 
RWMolMrvDataStreamToMol (std::istream *inStream, bool sanitize=false, bool removeHs=false)
 
RWMolMrvDataStreamToMol (std::istream &inStream, bool sanitize=false, bool removeHs=false)
 
RWMolMrvBlockToMol (const std::string &molmrvText, bool sanitize=false, bool removeHs=false)
 
RWMolMrvFileToMol (const std::string &fName, bool sanitize=false, bool removeHs=false)
 
ChemicalReactionMrvDataStreamToChemicalReaction (std::istream *inStream, bool sanitize=false, bool removeHs=false)
 
ChemicalReactionMrvDataStreamToChemicalReaction (std::istream &inStream, bool sanitize=false, bool removeHs=false)
 
ChemicalReactionMrvBlockToChemicalReaction (const std::string &molmrvText, bool sanitize=false, bool removeHs=false)
 
ChemicalReactionMrvFileToChemicalReaction (const std::string &fName, bool sanitize=false, bool removeHs=false)
 
RDKit::RWMolSmilesToMol (const std::string &smi, const SmilesParserParams &ps)
 
AtomSmilesToAtom (const std::string &smi)
 
BondSmilesToBond (const std::string &smi)
 
RWMolSmilesToMol (const std::string &smi, int debugParse=0, bool sanitize=true, std::map< std::string, std::string > *replacements=nullptr)
 Construct a molecule from a SMILES string.
 
RWMolSmartsToMol (const std::string &sma, const SmartsParserParams &ps)
 
RWMolSmartsToMol (const std::string &sma, int debugParse=0, bool mergeHs=false, std::map< std::string, std::string > *replacements=nullptr)
 Construct a molecule from a SMARTS string.
 
AtomSmartsToAtom (const std::string &sma)
 
BondSmartsToBond (const std::string &sma)
 
Reaction SMARTS/SMILES Support
ChemicalReactionRxnSmartsToChemicalReaction (const std::string &text, std::map< std::string, std::string > *replacements=nullptr, bool useSmiles=false, bool allowCXSMILES=true)
 Parse a string containing "Reaction SMARTS" into a ChemicalReaction.
 

Function Documentation

◆ CDXMLDataStreamToMols()

std::vector< std::unique_ptr< RWMol > > RDKit::v1::CDXMLDataStreamToMols ( std::istream &  inStream,
bool  sanitize = true,
bool  removeHs = true 
)
inline

construct molecules from a CDXML file Note that the CDXML format is large and complex, the RDKit doesn't support full functionality, just the base ones required for molecule and reaction parsing.

Parameters
inStream- string containing the mol block
sanitize- toggles sanitization and stereochemistry perception of the molecule
removeHs- toggles removal of Hs from the molecule. H removal is only done if the molecule is sanitized correctness of the contents.

Definition at line 82 of file CDXMLParser.h.

◆ CDXMLFileToMols()

std::vector< std::unique_ptr< RWMol > > RDKit::v1::CDXMLFileToMols ( const std::string &  filename,
bool  sanitize = true,
bool  removeHs = true 
)
inline

construct molecules from a CDXML file Note that the CDXML format is large and complex, the RDKit doesn't support full functionality, just the base ones required for molecule and reaction parsing.

Parameters
fileName- cdxml fileName
sanitize- toggles sanitization and stereochemistry perception of the molecule
removeHs- toggles removal of Hs from the molecule. H removal is only done if the molecule is sanitized correctness of the contents.

Definition at line 102 of file CDXMLParser.h.

◆ CDXMLToMols()

std::vector< std::unique_ptr< RWMol > > RDKit::v1::CDXMLToMols ( const std::string &  cdxml,
bool  sanitize = true,
bool  removeHs = true 
)
inline

construct molecules from a CDXML file Note that the CDXML format is large and complex, the RDKit doesn't support full functionality, just the base ones required for molecule and reaction parsing.

Parameters
cdxml- string containing the mol block
sanitize- toggles sanitization and stereochemistry perception of the molecule
removeHs- toggles removal of Hs from the molecule. H removal is only done if the molecule is sanitized correctness of the contents.

Definition at line 122 of file CDXMLParser.h.

◆ Mol2BlockToMol()

RWMol * RDKit::v1::Mol2BlockToMol ( const std::string &  molBlock,
bool  sanitize = true,
bool  removeHs = true,
Mol2Type  variant = Mol2Type::CORINA,
bool  cleanupSubstructures = true 
)
inline
Parameters
molBlock- string containing the mol block
sanitize- toggles sanitization of the molecule
removeHs- toggles removal of Hs from the molecule. H removal is only done if the molecule is sanitized
variant- the atom type definitions to use
cleanupSubstructures- toggles recognition and cleanup of common substructures

Definition at line 310 of file FileParsers.h.

◆ Mol2DataStreamToMol() [1/2]

RWMol * RDKit::v1::Mol2DataStreamToMol ( std::istream &  inStream,
bool  sanitize = true,
bool  removeHs = true,
Mol2Type  variant = Mol2Type::CORINA,
bool  cleanupSubstructures = true 
)
inline
Parameters
inStream- stream containing the data
sanitize- toggles sanitization of the molecule
removeHs- toggles removal of Hs from the molecule. H removal is only done if the molecule is sanitized
variant- the atom type definitions to use
cleanupSubstructures- toggles recognition and cleanup of common substructures

Definition at line 280 of file FileParsers.h.

◆ Mol2DataStreamToMol() [2/2]

RWMol * RDKit::v1::Mol2DataStreamToMol ( std::istream *  inStream,
bool  sanitize = true,
bool  removeHs = true,
Mol2Type  variant = Mol2Type::CORINA,
bool  cleanupSubstructures = true 
)
inline

Definition at line 292 of file FileParsers.h.

◆ Mol2FileToMol()

RWMol * RDKit::v1::Mol2FileToMol ( const std::string &  fName,
bool  sanitize = true,
bool  removeHs = true,
Mol2Type  variant = Mol2Type::CORINA,
bool  cleanupSubstructures = true 
)
inline
Parameters
fName- string containing the file name
sanitize- toggles sanitization of the molecule
removeHs- toggles removal of Hs from the molecule. H removal is only done if the molecule is sanitized
variant- the atom type definitions to use
cleanupSubstructures- toggles recognition and cleanup of common substructures

Definition at line 258 of file FileParsers.h.

◆ MolBlockToMol()

RWMol * RDKit::v1::MolBlockToMol ( const std::string &  molBlock,
bool  sanitize = true,
bool  removeHs = true,
bool  strictParsing = true 
)
inline
Parameters
molBlock- string containing the mol block
sanitize- toggles sanitization and stereochemistry perception of the molecule
removeHs- toggles removal of Hs from the molecule. H removal is only done if the molecule is sanitized
strictParsing- if set to false, the parser is more lax about correctness of the contents.

Definition at line 112 of file FileParsers.h.

◆ MolDataStreamToMol() [1/2]

RWMol * RDKit::v1::MolDataStreamToMol ( std::istream &  inStream,
unsigned int line,
bool  sanitize = true,
bool  removeHs = true,
bool  strictParsing = true 
)
inline

Definition at line 97 of file FileParsers.h.

◆ MolDataStreamToMol() [2/2]

RWMol * RDKit::v1::MolDataStreamToMol ( std::istream *  inStream,
unsigned int line,
bool  sanitize = true,
bool  removeHs = true,
bool  strictParsing = true 
)
inline
Parameters
inStream- stream containing the data
line- current line number (used for error reporting)
sanitize- toggles sanitization and stereochemistry perception of the molecule
removeHs- toggles removal of Hs from the molecule. H removal is only done if the molecule is sanitized
line- current line number (used for error reporting)
strictParsing- if set to false, the parser is more lax about correctness of the contents.

Definition at line 87 of file FileParsers.h.

◆ MolFileToMol()

RWMol * RDKit::v1::MolFileToMol ( const std::string &  fName,
bool  sanitize = true,
bool  removeHs = true,
bool  strictParsing = true 
)
inline
Parameters
fName- string containing the file name
sanitize- toggles sanitization and stereochemistry perception of the molecule
removeHs- toggles removal of Hs from the molecule. H removal is only done if the molecule is sanitized
strictParsing- if set to false, the parser is more lax about correctness of the contents.

Definition at line 131 of file FileParsers.h.

◆ MrvBlockIsReaction()

bool RDKit::v1::MrvBlockIsReaction ( const std::string &  molmrvText)
inline

Definition at line 67 of file MarvinParser.h.

◆ MrvBlockToChemicalReaction()

ChemicalReaction * RDKit::v1::MrvBlockToChemicalReaction ( const std::string &  molmrvText,
bool  sanitize = false,
bool  removeHs = false 
)
inline

Definition at line 116 of file MarvinParser.h.

◆ MrvBlockToMol()

RWMol * RDKit::v1::MrvBlockToMol ( const std::string &  molmrvText,
bool  sanitize = false,
bool  removeHs = false 
)
inline

Definition at line 85 of file MarvinParser.h.

◆ MrvDataStreamIsReaction() [1/2]

bool RDKit::v1::MrvDataStreamIsReaction ( std::istream &  inStream)
inline

Definition at line 64 of file MarvinParser.h.

◆ MrvDataStreamIsReaction() [2/2]

bool RDKit::v1::MrvDataStreamIsReaction ( std::istream *  inStream)
inline

Definition at line 60 of file MarvinParser.h.

◆ MrvDataStreamToChemicalReaction() [1/2]

ChemicalReaction * RDKit::v1::MrvDataStreamToChemicalReaction ( std::istream &  inStream,
bool  sanitize = false,
bool  removeHs = false 
)
inline

Definition at line 108 of file MarvinParser.h.

◆ MrvDataStreamToChemicalReaction() [2/2]

ChemicalReaction * RDKit::v1::MrvDataStreamToChemicalReaction ( std::istream *  inStream,
bool  sanitize = false,
bool  removeHs = false 
)
inline

Definition at line 100 of file MarvinParser.h.

◆ MrvDataStreamToMol() [1/2]

RWMol * RDKit::v1::MrvDataStreamToMol ( std::istream &  inStream,
bool  sanitize = false,
bool  removeHs = false 
)
inline

Definition at line 78 of file MarvinParser.h.

◆ MrvDataStreamToMol() [2/2]

RWMol * RDKit::v1::MrvDataStreamToMol ( std::istream *  inStream,
bool  sanitize = false,
bool  removeHs = false 
)
inline

Definition at line 71 of file MarvinParser.h.

◆ MrvFileIsReaction()

bool RDKit::v1::MrvFileIsReaction ( const std::string &  fname)
inline

Definition at line 57 of file MarvinParser.h.

◆ MrvFileToChemicalReaction()

ChemicalReaction * RDKit::v1::MrvFileToChemicalReaction ( const std::string &  fName,
bool  sanitize = false,
bool  removeHs = false 
)
inline

Definition at line 124 of file MarvinParser.h.

◆ MrvFileToMol()

RWMol * RDKit::v1::MrvFileToMol ( const std::string &  fName,
bool  sanitize = false,
bool  removeHs = false 
)
inline

Definition at line 92 of file MarvinParser.h.

◆ PDBBlockToMol() [1/2]

RWMol * RDKit::v1::PDBBlockToMol ( const char str,
bool  sanitize = true,
bool  removeHs = true,
unsigned int  flavor = 0,
bool  proximityBonding = true 
)
inline

Definition at line 395 of file FileParsers.h.

◆ PDBBlockToMol() [2/2]

RWMol * RDKit::v1::PDBBlockToMol ( const std::string &  str,
bool  sanitize = true,
bool  removeHs = true,
unsigned int  flavor = 0,
bool  proximityBonding = true 
)
inline

Definition at line 385 of file FileParsers.h.

◆ PDBDataStreamToMol() [1/2]

RWMol * RDKit::v1::PDBDataStreamToMol ( std::istream &  inStream,
bool  sanitize = true,
bool  removeHs = true,
unsigned int  flavor = 0,
bool  proximityBonding = true 
)
inline

Definition at line 411 of file FileParsers.h.

◆ PDBDataStreamToMol() [2/2]

RWMol * RDKit::v1::PDBDataStreamToMol ( std::istream *  inStream,
bool  sanitize = true,
bool  removeHs = true,
unsigned int  flavor = 0,
bool  proximityBonding = true 
)
inline

Definition at line 421 of file FileParsers.h.

◆ PDBFileToMol()

RWMol * RDKit::v1::PDBFileToMol ( const std::string &  fname,
bool  sanitize = true,
bool  removeHs = true,
unsigned int  flavor = 0,
bool  proximityBonding = true 
)
inline

Definition at line 401 of file FileParsers.h.

◆ PNGFileToChemicalReaction()

ChemicalReaction * RDKit::v1::PNGFileToChemicalReaction ( const std::string &  fname)
inline

constructs a ChemicalReaction from the metadata in a PNG file See PNGStreamToChemicalReaction() for more details

Definition at line 344 of file ReactionParser.h.

◆ PNGStreamToChemicalReaction()

ChemicalReaction * RDKit::v1::PNGStreamToChemicalReaction ( std::istream &  pngStream)
inline

constructs a ChemicalReaction from the metadata in a PNG stream

Looks through the metadata in the PNG to find the first tag that matches one of the tags in RDKit::PNGData. A reaction is constructed from this chunk.

Throws a FileParseException if no suitable tag is found.

The caller is responsible for the returned pointer.

Definition at line 334 of file ReactionParser.h.

◆ PNGStringToChemicalReaction()

ChemicalReaction * RDKit::v1::PNGStringToChemicalReaction ( const std::string &  data)
inline

constructs a ChemicalReaction from the metadata in a PNG string See PNGStreamToChemicalReaction() for more details

Definition at line 339 of file ReactionParser.h.

◆ RxnBlockToChemicalReaction()

ChemicalReaction * RDKit::v1::RxnBlockToChemicalReaction ( const std::string &  rxnBlock,
bool  sanitize = false,
bool  removeHs = false,
bool  strictParsing = true 
)
inline

Parse a text block in MDL rxn format into a ChemicalReaction.

Definition at line 216 of file ReactionParser.h.

◆ RxnDataStreamToChemicalReaction()

ChemicalReaction * RDKit::v1::RxnDataStreamToChemicalReaction ( std::istream &  rxnStream,
unsigned int line,
bool  sanitize = false,
bool  removeHs = false,
bool  strictParsing = true 
)
inline

Parse a text stream in MDL rxn format into a ChemicalReaction.

Definition at line 238 of file ReactionParser.h.

◆ RxnFileToChemicalReaction()

ChemicalReaction * RDKit::v1::RxnFileToChemicalReaction ( const std::string &  fileName,
bool  sanitize = false,
bool  removeHs = false,
bool  strictParsing = true 
)
inline

Parse a file in MDL rxn format into a ChemicalReaction.

Definition at line 227 of file ReactionParser.h.

◆ RxnSmartsToChemicalReaction()

ChemicalReaction * RDKit::v1::RxnSmartsToChemicalReaction ( const std::string &  text,
std::map< std::string, std::string > *  replacements = nullptr,
bool  useSmiles = false,
bool  allowCXSMILES = true 
)
inline

Parse a string containing "Reaction SMARTS" into a ChemicalReaction.

Our definition of Reaction SMARTS is something that looks a lot like reaction SMILES, except that SMARTS queries are allowed on the reactant side and that atom-map numbers are required (at least for now)

Parameters
textthe SMARTS to convert
replacementsa string->string map of replacement strings.
See also
SmilesToMol for more information about replacements
Parameters
useSmilesif set, the SMILES parser will be used instead of the SMARTS parserfor the individual components
allowCXSMILESif set, any CXSMILES extensions present will be parsed, otherwise it will be ignored

Definition at line 114 of file ReactionParser.h.

◆ SmartsToAtom()

Atom * RDKit::v1::SmartsToAtom ( const std::string &  sma)
inline

Definition at line 229 of file SmilesParse.h.

◆ SmartsToBond()

Bond * RDKit::v1::SmartsToBond ( const std::string &  sma)
inline

Definition at line 232 of file SmilesParse.h.

◆ SmartsToMol() [1/2]

RWMol * RDKit::v1::SmartsToMol ( const std::string &  sma,
const SmartsParserParams ps 
)
inline

Definition at line 189 of file SmilesParse.h.

◆ SmartsToMol() [2/2]

RWMol * RDKit::v1::SmartsToMol ( const std::string &  sma,
int  debugParse = 0,
bool  mergeHs = false,
std::map< std::string, std::string > *  replacements = nullptr 
)
inline

Construct a molecule from a SMARTS string.

Parameters
smathe SMARTS to convert
debugParsetoggles verbose debugging information from the parser
mergeHstoggles merging H atoms in the SMARTS into neighboring atoms
replacementsa string->string map of replacement strings.
See also
SmilesToMol for more information about replacements
Returns
a pointer to the new molecule; the caller is responsible for free'ing this.

Definition at line 217 of file SmilesParse.h.

◆ SmilesToAtom()

Atom * RDKit::v1::SmilesToAtom ( const std::string &  smi)
inline

Definition at line 135 of file SmilesParse.h.

◆ SmilesToBond()

Bond * RDKit::v1::SmilesToBond ( const std::string &  smi)
inline

Definition at line 140 of file SmilesParse.h.

◆ SmilesToMol() [1/2]

RDKit::RWMol * RDKit::v1::SmilesToMol ( const std::string &  smi,
const SmilesParserParams ps 
)
inline

Definition at line 118 of file SmilesParse.h.

◆ SmilesToMol() [2/2]

RWMol * RDKit::v1::SmilesToMol ( const std::string &  smi,
int  debugParse = 0,
bool  sanitize = true,
std::map< std::string, std::string > *  replacements = nullptr 
)
inline

Construct a molecule from a SMILES string.

Parameters
smithe SMILES to convert
debugParsetoggles verbose debugging information from the parser
sanitizetoggles H removal and sanitization of the molecule
replacementsa string->string map of replacement strings. See below for more information about replacements.
Returns
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:

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
bool rdvalue_is(const RDValue_cast_t)

Definition at line 171 of file SmilesParse.h.

◆ TPLDataStreamToMol()

RWMol * RDKit::v1::TPLDataStreamToMol ( std::istream *  inStream,
unsigned int line,
bool  sanitize = true,
bool  skipFirstConf = false 
)
inline

translate TPL data (BioCad format) into a multi-conf molecule

Parameters
inStreamthe stream from which to read
lineused to track the line number of errors
sanitizetoggles sanitization and stereochemistry perception of the molecule
skipFirstConfaccording to the TPL format description, the atomic coords in the atom-information block describe the first conformation and the first conf block describes second conformation. The CombiCode, on the other hand, writes the first conformation data both to the atom-information block and to the first conf block. We want to be able to read CombiCode-style tpls, so we'll allow this mis-feature to be parsed when this flag is set.

Definition at line 179 of file FileParsers.h.

◆ TPLFileToMol()

RWMol * RDKit::v1::TPLFileToMol ( const std::string &  fName,
bool  sanitize = true,
bool  skipFirstConf = false 
)
inline

construct a multi-conf molecule from a TPL (BioCad format) file

Parameters
fNamethe name of the file from which to read
sanitizetoggles sanitization and stereochemistry perception of the molecule
skipFirstConfaccording to the TPL format description, the atomic coords in the atom-information block describe the first conformation and the first conf block describes second conformation. The CombiCode, on the other hand, writes the first conformation data both to the atom-information block and to the first conf block. We want to be able to read CombiCode-style tpls, so we'll allow this mis-feature to be parsed when this flag is set.

Definition at line 203 of file FileParsers.h.

◆ XYZBlockToMol()

RWMol * RDKit::v1::XYZBlockToMol ( const std::string &  xyzBlock)
inline
Parameters
xyzBlock- string containing the xyz block

Definition at line 350 of file FileParsers.h.

◆ XYZDataStreamToMol()

RWMol * RDKit::v1::XYZDataStreamToMol ( std::istream &  inStream)
inline

Definition at line 343 of file FileParsers.h.

◆ XYZFileToMol()

RWMol * RDKit::v1::XYZFileToMol ( const std::string &  fName)
inline
Parameters
fName- string containing the file name

Definition at line 357 of file FileParsers.h.