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RDKit
Open-source cheminformatics and machine learning.
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Typedefs | |
typedef std::map< int, SubstanceGroup > | IDX_TO_SGROUP_MAP |
typedef std::map< int, STR_VECT > | IDX_TO_STR_VECT_MAP |
Functions | |
unsigned int | ParseSGroupIntField (const std::string &text, unsigned int line, unsigned int &pos, bool isFieldCounter=false) |
unsigned int | ParseSGroupIntField (bool &ok, bool strictParsing, const std::string &text, unsigned int line, unsigned int &pos, bool isFieldCounter=false) |
double | ParseSGroupDoubleField (const std::string &text, unsigned int line, unsigned int &pos) |
double | ParseSGroupDoubleField (bool &ok, bool strictParsing, const std::string &text, unsigned int line, unsigned int &pos) |
SubstanceGroup * | FindSgIdx (IDX_TO_SGROUP_MAP &sGroupMap, int sgIdx, unsigned int line) |
template<class Exc = FileParseException> | |
void | SGroupWarnOrThrow (bool strictParsing, const std::string &msg) |
void | ParseSGroupV2000STYLine (IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol, const std::string &text, unsigned int line, bool strictParsing=true) |
void | ParseSGroupV2000VectorDataLine (IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol, const std::string &text, unsigned int line, bool strictParsing=true) |
void | ParseSGroupV2000SDILine (IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol, const std::string &text, unsigned int line, bool strictParsing=true) |
void | ParseSGroupV2000SSTLine (IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol, const std::string &text, unsigned int line, bool strictParsing=true) |
void | ParseSGroupV2000SMTLine (IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol, const std::string &text, unsigned int line, bool strictParsing=true) |
void | ParseSGroupV2000SLBLine (IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol, const std::string &text, unsigned int line, bool strictParsing=true) |
void | ParseSGroupV2000SCNLine (IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol, const std::string &text, unsigned int line, bool strictParsing=true) |
void | ParseSGroupV2000SDSLine (IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol, const std::string &text, unsigned int line, bool strictParsing=true) |
void | ParseSGroupV2000SBVLine (IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol, const std::string &text, unsigned int line, bool strictParsing=true) |
void | ParseSGroupV2000SDTLine (IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol, const std::string &text, unsigned int line, bool strictParsing=true) |
void | ParseSGroupV2000SDDLine (IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol, const std::string &text, unsigned int line, bool strictParsing=true) |
void | ParseSGroupV2000SCDSEDLine (IDX_TO_SGROUP_MAP &sGroupMap, IDX_TO_STR_VECT_MAP &dataFieldsMap, RWMol *mol, const std::string &text, unsigned int line, bool strictParsing, unsigned int &counter, unsigned int &lastDataSGroup, std::ostringstream ¤tDataField) |
void | ParseSGroupV2000SPLLine (IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol, const std::string &text, unsigned int line, bool strictParsing=true) |
void | ParseSGroupV2000SNCLine (IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol, const std::string &text, unsigned int line, bool strictParsing=true) |
void | ParseSGroupV2000SAPLine (IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol, const std::string &text, unsigned int line, bool strictParsing=true) |
void | ParseSGroupV2000SCLLine (IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol, const std::string &text, unsigned int line, bool strictParsing=true) |
void | ParseSGroupV2000SBTLine (IDX_TO_SGROUP_MAP &sGroupMap, RWMol *mol, const std::string &text, unsigned int line, bool strictParsing=true) |
template<class T > | |
RDKIT_FILEPARSERS_EXPORT std::vector< T > | ParseV3000Array (std::stringstream &stream) |
template<class T > | |
std::vector< T > | ParseV3000Array (const std::string &s) |
void | ParseV3000CStateLabel (RWMol *mol, SubstanceGroup &sgroup, std::stringstream &stream, unsigned int line, bool strictParsing=true) |
void | ParseV3000SAPLabel (RWMol *mol, SubstanceGroup &sgroup, std::stringstream &stream, bool strictParsing=true) |
std::string | ParseV3000StringPropLabel (std::stringstream &stream) |
std::string | ParseV3000SGroupsBlock (std::istream *inStream, unsigned int line, unsigned int nSgroups, RWMol *mol, bool strictParsing) |
typedef std::map<int, SubstanceGroup> RDKit::SGroupParsing::IDX_TO_SGROUP_MAP |
Definition at line 20 of file MolSGroupParsing.h.
typedef std::map<int, STR_VECT> RDKit::SGroupParsing::IDX_TO_STR_VECT_MAP |
Definition at line 21 of file MolSGroupParsing.h.
SubstanceGroup* RDKit::SGroupParsing::FindSgIdx | ( | IDX_TO_SGROUP_MAP & | sGroupMap, |
int | sgIdx, | ||
unsigned int | line | ||
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double RDKit::SGroupParsing::ParseSGroupDoubleField | ( | bool & | ok, |
bool | strictParsing, | ||
const std::string & | text, | ||
unsigned int | line, | ||
unsigned int & | pos | ||
) |
double RDKit::SGroupParsing::ParseSGroupDoubleField | ( | const std::string & | text, |
unsigned int | line, | ||
unsigned int & | pos | ||
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unsigned int RDKit::SGroupParsing::ParseSGroupIntField | ( | bool & | ok, |
bool | strictParsing, | ||
const std::string & | text, | ||
unsigned int | line, | ||
unsigned int & | pos, | ||
bool | isFieldCounter = false |
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unsigned int RDKit::SGroupParsing::ParseSGroupIntField | ( | const std::string & | text, |
unsigned int | line, | ||
unsigned int & | pos, | ||
bool | isFieldCounter = false |
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) |
void RDKit::SGroupParsing::ParseSGroupV2000SAPLine | ( | IDX_TO_SGROUP_MAP & | sGroupMap, |
RWMol * | mol, | ||
const std::string & | text, | ||
unsigned int | line, | ||
bool | strictParsing = true |
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if the SAP line is malformed and has no lvIdx and no id, lvIdx is set to mol->getNumAtoms() and id is set to " " the user is responsible for replacing lvIdx with the correct index: if d_bonds.size() == 1, and one of the bond atom indices is aIdx, the other can be safely assigned to lvIdx
void RDKit::SGroupParsing::ParseSGroupV2000SBTLine | ( | IDX_TO_SGROUP_MAP & | sGroupMap, |
RWMol * | mol, | ||
const std::string & | text, | ||
unsigned int | line, | ||
bool | strictParsing = true |
||
) |
void RDKit::SGroupParsing::ParseSGroupV2000SBVLine | ( | IDX_TO_SGROUP_MAP & | sGroupMap, |
RWMol * | mol, | ||
const std::string & | text, | ||
unsigned int | line, | ||
bool | strictParsing = true |
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) |
void RDKit::SGroupParsing::ParseSGroupV2000SCDSEDLine | ( | IDX_TO_SGROUP_MAP & | sGroupMap, |
IDX_TO_STR_VECT_MAP & | dataFieldsMap, | ||
RWMol * | mol, | ||
const std::string & | text, | ||
unsigned int | line, | ||
bool | strictParsing, | ||
unsigned int & | counter, | ||
unsigned int & | lastDataSGroup, | ||
std::ostringstream & | currentDataField | ||
) |
void RDKit::SGroupParsing::ParseSGroupV2000SCLLine | ( | IDX_TO_SGROUP_MAP & | sGroupMap, |
RWMol * | mol, | ||
const std::string & | text, | ||
unsigned int | line, | ||
bool | strictParsing = true |
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) |
void RDKit::SGroupParsing::ParseSGroupV2000SCNLine | ( | IDX_TO_SGROUP_MAP & | sGroupMap, |
RWMol * | mol, | ||
const std::string & | text, | ||
unsigned int | line, | ||
bool | strictParsing = true |
||
) |
void RDKit::SGroupParsing::ParseSGroupV2000SDDLine | ( | IDX_TO_SGROUP_MAP & | sGroupMap, |
RWMol * | mol, | ||
const std::string & | text, | ||
unsigned int | line, | ||
bool | strictParsing = true |
||
) |
void RDKit::SGroupParsing::ParseSGroupV2000SDILine | ( | IDX_TO_SGROUP_MAP & | sGroupMap, |
RWMol * | mol, | ||
const std::string & | text, | ||
unsigned int | line, | ||
bool | strictParsing = true |
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) |
void RDKit::SGroupParsing::ParseSGroupV2000SDSLine | ( | IDX_TO_SGROUP_MAP & | sGroupMap, |
RWMol * | mol, | ||
const std::string & | text, | ||
unsigned int | line, | ||
bool | strictParsing = true |
||
) |
void RDKit::SGroupParsing::ParseSGroupV2000SDTLine | ( | IDX_TO_SGROUP_MAP & | sGroupMap, |
RWMol * | mol, | ||
const std::string & | text, | ||
unsigned int | line, | ||
bool | strictParsing = true |
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) |
void RDKit::SGroupParsing::ParseSGroupV2000SLBLine | ( | IDX_TO_SGROUP_MAP & | sGroupMap, |
RWMol * | mol, | ||
const std::string & | text, | ||
unsigned int | line, | ||
bool | strictParsing = true |
||
) |
void RDKit::SGroupParsing::ParseSGroupV2000SMTLine | ( | IDX_TO_SGROUP_MAP & | sGroupMap, |
RWMol * | mol, | ||
const std::string & | text, | ||
unsigned int | line, | ||
bool | strictParsing = true |
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) |
void RDKit::SGroupParsing::ParseSGroupV2000SNCLine | ( | IDX_TO_SGROUP_MAP & | sGroupMap, |
RWMol * | mol, | ||
const std::string & | text, | ||
unsigned int | line, | ||
bool | strictParsing = true |
||
) |
void RDKit::SGroupParsing::ParseSGroupV2000SPLLine | ( | IDX_TO_SGROUP_MAP & | sGroupMap, |
RWMol * | mol, | ||
const std::string & | text, | ||
unsigned int | line, | ||
bool | strictParsing = true |
||
) |
void RDKit::SGroupParsing::ParseSGroupV2000SSTLine | ( | IDX_TO_SGROUP_MAP & | sGroupMap, |
RWMol * | mol, | ||
const std::string & | text, | ||
unsigned int | line, | ||
bool | strictParsing = true |
||
) |
void RDKit::SGroupParsing::ParseSGroupV2000STYLine | ( | IDX_TO_SGROUP_MAP & | sGroupMap, |
RWMol * | mol, | ||
const std::string & | text, | ||
unsigned int | line, | ||
bool | strictParsing = true |
||
) |
void RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine | ( | IDX_TO_SGROUP_MAP & | sGroupMap, |
RWMol * | mol, | ||
const std::string & | text, | ||
unsigned int | line, | ||
bool | strictParsing = true |
||
) |
std::vector<T> RDKit::SGroupParsing::ParseV3000Array | ( | const std::string & | s | ) |
Definition at line 141 of file MolSGroupParsing.h.
RDKIT_FILEPARSERS_EXPORT std::vector<T> RDKit::SGroupParsing::ParseV3000Array | ( | std::stringstream & | stream | ) |
void RDKit::SGroupParsing::ParseV3000CStateLabel | ( | RWMol * | mol, |
SubstanceGroup & | sgroup, | ||
std::stringstream & | stream, | ||
unsigned int | line, | ||
bool | strictParsing = true |
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) |
void RDKit::SGroupParsing::ParseV3000SAPLabel | ( | RWMol * | mol, |
SubstanceGroup & | sgroup, | ||
std::stringstream & | stream, | ||
bool | strictParsing = true |
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) |
std::string RDKit::SGroupParsing::ParseV3000SGroupsBlock | ( | std::istream * | inStream, |
unsigned int | line, | ||
unsigned int | nSgroups, | ||
RWMol * | mol, | ||
bool | strictParsing | ||
) |
std::string RDKit::SGroupParsing::ParseV3000StringPropLabel | ( | std::stringstream & | stream | ) |
void RDKit::SGroupParsing::SGroupWarnOrThrow | ( | bool | strictParsing, |
const std::string & | msg | ||
) |
Definition at line 45 of file MolSGroupParsing.h.
References BOOST_LOG, and rdWarningLog.