RDKit Namespace Reference

Includes a bunch of functionality for handling Atom and Bond queries. More...

Classes

class Atom

The class for representing atoms. More...

class atomicData

class AtomIterator_

A general random access iterator. More...

class HeteroatomIterator_

Iterate over heteroatoms, this is bidirectional. More...

class AromaticAtomIterator_

Iterate over aromatic atoms, this is bidirectional. More...

class QueryAtomIterator_

Iterate over atoms matching a query. This is bidirectional. More...

struct vertex_atom_t

class Bond

class for representing a bond More...

class BondIterator_

iterator for a molecule's bonds, currently BiDirectional, but it theoretically ought to be RandomAccess. More...

class ConstBondIterator_

const iterator for a molecule's bonds, currently BiDirectional, but it theoretically ought to be RandomAccess. More...

struct edge_bond_t

struct edge_wght_t

class ChemicalReactionException

used to indicate an error in the chemical reaction engine More...

class ChemicalReaction

This is a class for storing and applying general chemical reactions. More...

class ChemicalReactionParserException

used to indicate an error in parsing reaction data More...

class ConformerException

used to indicate errors from incorrect confomer access More...

class Conformer

The class for representing 2D or 3D conformation of a molecule. More...

class MolSupplier

class SDMolSupplier

class SmilesMolSupplier

lazy file parser for Smiles tables More...

class TDTMolSupplier

lazy file parser for TDT files More...

class MolWriter

class SmilesWriter

class SDWriter

class TDTWriter

class FragCatalogEntry

class FragCatGenerator

class FragCatParams

container for user parameters used to create a fragment catalog More...

class FragFPGenerator

class MolCatalogEntry

This class is used to store ROMol objects in a MolCatalog. More...

class MolCatalogParams

container for user parameters used to create a mol catalog More...

class FeatureFileParseException

class used to indicate errors in parsing feature definition files. More...

class MolChemicalFeature

class MolChemicalFeatureDef

class MolChemicalFeatureFactory

The class for finding chemical features in molecules. More...

class MolPicklerException

used to indicate exceptions whilst pickling (serializing) molecules More...

class MolPickler

handles pickling (serializing) molecules More...

class GasteigerParams

class PeriodicTable

singleton class for retrieving information about atoms More...

class QueryAtom

Class for storing atomic queries. More...

class QueryBond

Class for storing Bond queries. More...

class AtomRingQuery

class RecursiveStructureQuery

allows use of recursive structure queries (e.g. recursive SMARTS) More...

class RingInfo

A class to store information about a molecule's rings. More...

class ROMol

ROMol is a molecule class that is intended to have a fixed topology. More...

class RWMol

RWMol is a molecule class that is intended to be edited. More...

class MolSanitizeException

class for flagging sanitization errors More...

class SmilesParseException

class DiscreteDistMat

class DiscreteValueVect

a class for efficiently storing vectors of discrete values More...

class SparseIntVect

a class for efficiently storing sparse vectors of ints More...

class BadFileException

used by various file parsing classes to indicate a bad file More...

class Dict

The Dict class can be used to store objects of arbitrary type keyed by strings. More...

class FileParseException

used by various file parsing classes to indicate a parse error More...

struct ltDouble

functor to compare two doubles with a tolerance More...

struct larger_of

functor for returning the larger of two values More...

struct charptr_functor

functor for comparing two strings More...

Namespaces

namespace Descriptors

namespace DGeomHelpers

namespace FeatTrees

namespace Local

namespace MolAlign

namespace MolOps

namespace MolShapes

namespace SmartsWrite

namespace SmilesWrite

namespace Subgraphs

namespace UFF

Typedefs

typedef
boost::shared_ptr
< Atom > ATOM_SPTR

typedef
boost::property
< vertex_atom_t,
Atom * > AtomProperty

typedef std::vector
< int > INT_VECT

typedef
boost::shared_ptr
< Atom > ATOM_SPTR

typedef
boost::shared_ptr
< Bond > BOND_SPTR

typedef
boost::property
< edge_wght_t,
double > BondWeight

typedef
boost::property
< edge_bond_t, Bond *,
BondWeight > BondProperty

typedef
boost::shared_ptr
< ROMol > ROMOL_SPTR

typedef
boost::shared_ptr
< Conformer > CONFORMER_SPTR

typedef std::vector
< RWMOL_SPTR > RWMOL_SPTR_VECT

typedef
RDCatalog::HierarchCatalog
< FragCatalogEntry,
FragCatParams, int > FragCatalog

typedef std::vector
< boost::shared_ptr
< ROMol > > MOL_SPTR_VECT

typedef
RDCatalog::HierarchCatalog
< FragCatalogEntry,
FragCatParams, int > FragCatalog

typedef std::vector
< std::pair< int,
int > > MatchVectType

typedef std::vector
< std::pair< int,
int > > MatchVectType

typedef
RDCatalog::HierarchCatalog
< MolCatalogEntry,
MolCatalogParams,
int > MolCatalog

a hierarchical catalog for holding molecules

typedef
boost::shared_ptr
< MolChemicalFeature > FeatSPtr

typedef std::list
< FeatSPtr > FeatSPtrList

typedef
FeatSPtrList::iterator FeatSPtrList_I

typedef std::vector
< double > INVAR_VECT

typedef
INVAR_VECT::iterator INVAR_VECT_I

typedef
INVAR_VECT::const_iterator INVAR_VECT_CI

typedef
boost::tuples::tuple
< double, double,
double > DiscrimTuple

used to return atomic discriminators (three doubles)

typedef
Queries::Query< bool,
Atom const *, true > ATOM_BOOL_QUERY

typedef
Queries::Query< bool,
Bond const *, true > BOND_BOOL_QUERY

typedef
Queries::AndQuery
< int, Atom const *,
true > ATOM_AND_QUERY

typedef
Queries::AndQuery
< int, Bond const *,
true > BOND_AND_QUERY

typedef
Queries::OrQuery
< int, Atom const *,
true > ATOM_OR_QUERY

typedef
Queries::OrQuery
< int, Bond const *,
true > BOND_OR_QUERY

typedef
Queries::XOrQuery
< int, Atom const *,
true > ATOM_XOR_QUERY

typedef
Queries::XOrQuery
< int, Bond const *,
true > BOND_XOR_QUERY

typedef
Queries::EqualityQuery
< int, Atom const *,
true > ATOM_EQUALS_QUERY

typedef
Queries::EqualityQuery
< int, Bond const *,
true > BOND_EQUALS_QUERY

typedef
Queries::GreaterQuery
< int, Atom const *,
true > ATOM_GREATER_QUERY

typedef
Queries::GreaterQuery
< int, Bond const *,
true > BOND_GREATER_QUERY

typedef
Queries::GreaterEqualQuery
< int, Atom const *,
true > ATOM_GREATEREQUAL_QUERY

typedef
Queries::GreaterEqualQuery
< int, Bond const *,
true > BOND_GREATEREQUAL_QUERY

typedef
Queries::LessQuery
< int, Atom const *,
true > ATOM_LESS_QUERY

typedef
Queries::LessQuery
< int, Bond const *,
true > BOND_LESS_QUERY

typedef
Queries::LessEqualQuery
< int, Atom const *,
true > ATOM_LESSEQUAL_QUERY

typedef
Queries::LessEqualQuery
< int, Bond const *,
true > BOND_LESSEQUAL_QUERY

typedef
Queries::RangeQuery
< int, Atom const *,
true > ATOM_RANGE_QUERY

typedef
Queries::RangeQuery
< int, Bond const *,
true > BOND_RANGE_QUERY

typedef
Queries::SetQuery
< int, Atom const *,
true > ATOM_SET_QUERY

typedef
Queries::SetQuery
< int, Bond const *,
true > BOND_SET_QUERY

typedef
Queries::Query< int,
Bond const *, true > BOND_NULL_QUERY

typedef
Queries::Query< int,
Atom const *, true > ATOM_NULL_QUERY

typedef Atom const * ConstAtomPtr

typedef
boost::adjacency_list
< boost::vecS,
boost::vecS,
boost::undirectedS,
AtomProperty,
BondProperty > MolGraph

This is the BGL type used to store the topology:.

typedef
boost::shared_ptr
< Atom > ATOM_SPTR

typedef
boost::shared_ptr
< Bond > BOND_SPTR

typedef std::vector
< ROMol > MOL_VECT

typedef
boost::shared_ptr
< ROMol > ROMOL_SPTR

typedef std::vector
< ROMol * > MOL_PTR_VECT

typedef std::vector
< ROMOL_SPTR > MOL_SPTR_VECT

typedef
MOL_PTR_VECT::const_iterator MOL_PTR_VECT_CI

typedef
MOL_PTR_VECT::iterator MOL_PTR_VECT_I

typedef
boost::shared_ptr
< RWMol > RWMOL_SPTR

typedef std::vector
< RWMOL_SPTR > RWMOL_SPTR_VECT

typedef std::vector
< int > PATH_TYPE

typedef std::list
< PATH_TYPE > PATH_LIST

typedef
PATH_LIST::const_iterator PATH_LIST_CI

typedef std::map
< int, PATH_LIST > INT_PATH_LIST_MAP

typedef
INT_PATH_LIST_MAP::const_iterator INT_PATH_LIST_MAP_CI

typedef
INT_PATH_LIST_MAP::iterator INT_PATH_LIST_MAP_I

typedef std::vector
< std::pair< int,
int > > MatchVectType

used to return matches from substructure searching, The format is (queryAtomIdx, molAtomIdx)

typedef VF2MonoState MatcherState

typedef ARGraph
< const Atom, const
Bond > AR_MOLGRAPH

typedef std::vector
< std::string > STR_VECT

typedef long long int LONGINT

typedef unsigned int UINT

typedef unsigned short USHORT

typedef unsigned char UCHAR

typedef std::vector
< int > INT_VECT

typedef
INT_VECT::iterator INT_VECT_I

typedef
INT_VECT::const_iterator INT_VECT_CI

typedef
INT_VECT::reverse_iterator INT_VECT_RI

typedef
INT_VECT::const_reverse_iterator INT_VECT_CRI

typedef std::list< int > INT_LIST

typedef
INT_LIST::iterator INT_LIST_I

typedef
INT_LIST::const_iterator INT_LIST_CI

typedef std::list
< INT_VECT > LIST_INT_VECT

typedef
LIST_INT_VECT::iterator LIST_INT_VECT_I

typedef
LIST_INT_VECT::const_iterator LIST_INT_VECT_CI

typedef std::vector
< INT_VECT > VECT_INT_VECT

typedef
VECT_INT_VECT::iterator VECT_INT_VECT_I

typedef
VECT_INT_VECT::const_iterator VECT_INT_VECT_CI

typedef std::vector
< UINT >
::const_iterator UINT_VECT_CI

typedef std::vector
< UINT > UINT_VECT

typedef std::vector
< std::string >
::const_iterator STR_VECT_CI

typedef std::vector
< std::string >
::iterator STR_VECT_I

typedef std::vector
< std::string > STR_VECT

typedef std::vector
< double > DOUBLE_VECT

typedef
DOUBLE_VECT::iterator DOUBLE_VECT_I

typedef
DOUBLE_VECT::const_iterator DOUBLE_VECT_CI

typedef std::vector
< DOUBLE_VECT > VECT_DOUBLE_VECT

typedef
VECT_DOUBLE_VECT::iterator VECT_DOUBLE_VECT_I

typedef
VECT_DOUBLE_VECT::const_iterator VECT_DOUBLE_VECT_CI

typedef std::map
< std::string, UINT > STR_UINT_MAP

typedef std::map
< std::string, UINT >
::const_iterator STR_UINT_MAP_CI

typedef std::map
< int, INT_VECT > INT_INT_VECT_MAP

typedef
INT_INT_VECT_MAP::const_iterator INT_INT_VECT_MAP_CI

typedef std::map
< int, int > INT_MAP_INT

typedef
INT_MAP_INT::iterator INT_MAP_INT_I

typedef
INT_MAP_INT::const_iterator INT_MAP_INT_CI

typedef std::deque< int > INT_DEQUE

typedef
INT_DEQUE::iterator INT_DEQUE_I

typedef
INT_DEQUE::const_iterator INT_DEQUE_CI

typedef std::map
< int, INT_DEQUE > INT_INT_DEQ_MAP

typedef
INT_INT_DEQ_MAP::const_iterator INT_INT_DEQ_MAP_CI

typedef std::set< int > INT_SET

typedef INT_SET::iterator INT_SET_I

typedef
INT_SET::const_iterator INT_SET_CI

typedef std::map
< double, int,
ltDouble > DOUBLE_INT_MAP

std::map from double to integer.

typedef
boost::minstd_rand rng_type

typedef
boost::uniform_int uniform_int

typedef
boost::uniform_real uniform_double

typedef
boost::variate_generator
< rng_type &,
uniform_int > int_source_type

typedef
boost::variate_generator
< rng_type &,
uniform_double > double_source_type

Enumerations

enum AtomInvariantType { ComprehensiveInvariants, ChiralSearchInvariants }

used to request particular types of atom invariants More...

Functions

ChemicalReaction * RxnBlockToChemicalReaction (const std::string &rxnBlock)

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

ChemicalReaction * RxnFileToChemicalReaction (const std::string &fileName)

Parse a file in MDL rxn format into a ChemicalReaction.

ChemicalReaction * RxnDataStreamToChemicalReaction (std::istream &rxnStream, unsigned int &line)

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

ChemicalReaction * RxnSmartsToChemicalReaction (const std::string &text)

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

ROMol * deleteSubstructs (const ROMol &mol, const ROMol &query, bool replaceAll=false)

Returns a copy of an ROMol with the atoms and bonds that match a pattern removed.

std::vector< ROMOL_SPTR > replaceSubstructs (const ROMol &mol, const ROMol &query, const ROMol &replacement, bool replaceAll=false)

Returns a list of copies of an ROMol with the atoms and bonds that match a pattern replaced with the atoms contained in another molecule.

ROMol * replaceSidechains (const ROMol &mol, const ROMol &coreQuery)

Returns a copy of an ROMol with the atoms and bonds that don't fall within a substructure match removed.

ROMol * replaceCore (const ROMol &mol, const ROMol &coreQuery, bool replaceDummies=true)

Returns a copy of an ROMol with the atoms and bonds that do fall within a substructure match removed.

int Add2DCoordsToMol (ROMol &mol, bool useDLL=false)

std::string strip (const std::string &orig)

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

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

RWMol * MolBlockToMol (const std::string &molBlock, bool sanitize=true, bool removeHs=true)

RWMol * MolFileToMol (std::string fName, bool sanitize=true, bool removeHs=true)

std::string MolToMolBlock (const ROMol &mol, bool includeStereo=true, int confId=-1)

void MolToMolFile (const ROMol &mol, std::string fName, bool includeStereo=true, int confId=-1)

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

RWMol * TPLFileToMol (std::string fName, bool sanitize=true, bool skipFirstConf=false)

std::string MolToTPLText (const ROMol &mol, std::string partialChargeProp="_GasteigerCharge", bool writeFirstConfTwice=false)

void MolToTPLFile (const ROMol &mol, std::string fName, std::string partialChargeProp="_GasteigerCharge", bool writeFirstConfTwice=false)

void DetectAtomStereoChemistry (RWMol &mol, const Conformer *conf)

void DetectBondStereoChemistry (ROMol &mol, const Conformer *conf)

void WedgeMolBonds (ROMol &mol, const Conformer *conf)

INT_MAP_INT pickBondsToWedge (const ROMol &mol)

Bond::BondDir DetermineBondWedgeState (const Bond *bond, const INT_MAP_INT &wedgeBonds, const Conformer *conf)

ExplicitBitVect * DaylightFingerprintMol (const ROMol &mol, unsigned int minPath=1, unsigned int maxPath=7, unsigned int fpSize=2048, unsigned int nBitsPerHash=4, bool useHs=true, double tgtDensity=0.0, unsigned int minSize=128)

ExplicitBitVect * RDKFingerprintMol (const ROMol &mol, unsigned int minPath=1, unsigned int maxPath=7, unsigned int fpSize=2048, unsigned int nBitsPerHash=4, bool useHs=true, double tgtDensity=0.0, unsigned int minSize=128)

Generates a topological (Daylight like) fingerprint for a molecule using an alternate (faster) hashing algorithm.

MOL_SPTR_VECT readFuncGroups (std::string fileName)

MOL_SPTR_VECT readFuncGroups (std::istream &inStream, int nToRead=-1)

MatchVectType findFuncGroupsOnMol (const ROMol &mol, const FragCatParams *params, INT_VECT &fgBonds)

ROMol * prepareMol (const ROMol &mol, const FragCatParams *fparams, MatchVectType &aToFmap)

int parseFeatureData (const std::string &defnText, MolChemicalFeatureDef::CollectionType &featDefs)

int parseFeatureData (std::istream &istream, MolChemicalFeatureDef::CollectionType &featDefs)

int parseFeatureFile (const std::string &fileName, MolChemicalFeatureDef::CollectionType &featDefs)

MolChemicalFeatureFactory * buildFeatureFactory (std::istream &inStream)

constructs a MolChemicalFeatureFactory from the data in a stream

MolChemicalFeatureFactory * buildFeatureFactory (const std::string &featureData)

constructs a MolChemicalFeatureFactory from the data in a string

void computeGasteigerCharges (const ROMol *mol, int nIter=12, bool throwOnParamFailure=false)

static int queryAtomAromatic (Atom const *at)

static int queryAtomAliphatic (Atom const *at)

static int queryAtomExplicitDegree (Atom const *at)

static int queryAtomTotalDegree (Atom const *at)

static int queryAtomHeavyAtomDegree (Atom const *at)

static int queryAtomHCount (Atom const *at)

static int queryAtomImplicitValence (Atom const *at)

static int queryAtomTotalValence (Atom const *at)

static int queryAtomUnsaturated (Atom const *at)

static int queryAtomNum (Atom const *at)

static int queryAtomMass (Atom const *at)

static int queryAtomFormalCharge (Atom const *at)

static int queryAtomHybridization (Atom const *at)

unsigned int queryAtomBondProduct (Atom const *at)

unsigned int queryAtomAllBondProduct (Atom const *at)

static int queryBondOrder (Bond const *bond)

static int queryBondDir (Bond const *bond)

static int queryIsBondInNRings (Bond const *at)

static int queryIsAtomInNRings (Atom const *at)

static int queryIsAtomInRing (Atom const *at)

static int queryIsBondInRing (Bond const *bond)

static int queryAtomMinRingSize (Atom const *at)

static int queryBondMinRingSize (Bond const *bond)

static int queryAtomRingBondCount (Atom const *at)

template<int tgt>

int queryAtomIsInRingOfSize (Atom const *at)

template<int tgt>

int queryBondIsInRingOfSize (Bond const *bond)

ATOM_EQUALS_QUERY * makeAtomNumEqualsQuery (int what)

returns a Query for matching atomic number

ATOM_EQUALS_QUERY * makeAtomImplicitValenceQuery (int what)

returns a Query for matching implicit valence

ATOM_EQUALS_QUERY * makeAtomTotalValenceQuery (int what)

returns a Query for matching total valence

ATOM_EQUALS_QUERY * makeAtomExplicitDegreeQuery (int what)

returns a Query for matching explicit valence

ATOM_EQUALS_QUERY * makeAtomTotalDegreeQuery (int what)

returns a Query for matching atomic degree

ATOM_EQUALS_QUERY * makeAtomHCountQuery (int what)

returns a Query for matching hydrogen count

ATOM_EQUALS_QUERY * makeAtomAromaticQuery ()

returns a Query for matching the isAromatic flag

ATOM_EQUALS_QUERY * makeAtomAliphaticQuery ()

returns a Query for matching aliphatic atoms

ATOM_EQUALS_QUERY * makeAtomMassQuery (int what)

returns a Query for matching atoms with a particular mass (for isotopes)

ATOM_EQUALS_QUERY * makeAtomFormalChargeQuery (int what)

returns a Query for matching formal charge

ATOM_EQUALS_QUERY * makeAtomHybridizationQuery (int what)

returns a Query for matching hybridization

ATOM_EQUALS_QUERY * makeAtomUnsaturatedQuery ()

returns a Query for matching atoms with unsaturation:

ATOM_EQUALS_QUERY * makeAtomInRingQuery ()

returns a Query for matching ring atoms

ATOM_EQUALS_QUERY * makeAtomInNRingsQuery (int what)

returns a Query for matching atoms in a particular number of rings

ATOM_EQUALS_QUERY * makeAtomInRingOfSizeQuery (int tgt)

returns a Query for matching atoms in rings of a particular size

ATOM_EQUALS_QUERY * makeAtomMinRingSizeQuery (int tgt)

returns a Query for matching an atom's minimum ring size

ATOM_EQUALS_QUERY * makeAtomRingBondCountQuery (int what)

returns a Query for matching atoms with a particular number of ring bonds

BOND_EQUALS_QUERY * makeBondOrderEqualsQuery (Bond::BondType what)

returns a Query for matching bond orders

BOND_EQUALS_QUERY * makeBondDirEqualsQuery (Bond::BondDir what)

returns a Query for matching bond directions

BOND_EQUALS_QUERY * makeBondIsInRingQuery ()

returns a Query for matching ring bonds

BOND_EQUALS_QUERY * makeBondInRingOfSizeQuery (int what)

returns a Query for matching bonds in rings of a particular size

BOND_EQUALS_QUERY * makeBondMinRingSizeQuery (int what)

returns a Query for matching a bond's minimum ring size

BOND_EQUALS_QUERY * makeBondInNRingsQuery (int tgt)

returns a Query for matching bonds in a particular number of rings

BOND_NULL_QUERY * makeBondNullQuery ()

returns a Query for matching any bond

ATOM_NULL_QUERY * makeAtomNullQuery ()

returns a Query for matching any atom

static int queryAtomRingMembership (Atom const *at)

template<typename T>

int nullDataFun (T arg)

template<typename T>

bool nullQueryFun (T arg)

std::string MolToSmarts (ROMol &mol, bool doIsomericSmarts=false)

returns the SMARTS for a molecule

RWMol * SmilesToMol (std::string smi, int debugParse=0, bool sanitize=1)

RWMol * SmartsToMol (std::string sma, int debugParse=0, bool mergeHs=false)

std::string MolToSmiles (ROMol &mol, bool doIsomericSmiles=false, bool doKekule=false, int rootedAtAtom=-1)

INT_PATH_LIST_MAP findAllSubgraphsOfLengthsMtoN (const ROMol &mol, unsigned int lowerLen, unsigned int upperLen, bool useHs=false)

PATH_LIST findAllSubgraphsOfLengthN (const ROMol &mol, unsigned int targetLen, bool useHs=false)

PATH_LIST findUniqueSubgraphsOfLengthN (const ROMol &mol, unsigned int targetLen, bool useHs=false, bool useBO=true)

PATH_LIST findAllPathsOfLengthN (const ROMol &mol, unsigned int targetLen, bool useBonds=true, bool useHs=false)

AR_MOLGRAPH * getMolGraph (const ROMol &mol, bool registerIt=false)

Internal Use Only.

bool SubstructMatch (const ROMol &mol, const ROMol &query, MatchVectType &matchVect, bool recursionPossible=true, bool useChirality=false, bool registerQuery=false)

Find a substructure match for a query in a molecule.

bool SubstructMatch (AR_MOLGRAPH *molG, const ROMol &query, MatchVectType &matchVect, bool recursionPossible=true, bool useChirality=false, bool registerQuery=false)

unsigned int SubstructMatch (const ROMol &mol, const ROMol &query, std::vector< MatchVectType > &matchVect, bool uniquify=true, bool recursionPossible=true, bool useChirality=false, bool registerQuery=false)

Find all substructure matches for a query in a molecule.

unsigned int SubstructMatch (AR_MOLGRAPH *molG, const ROMol &query, std::vector< MatchVectType > &matchVect, bool uniquify=true, bool recursionPossible=true, bool useChirality=false, bool registerQuery=false)

bool atomCompat (Atom const *a1, Atom const *a2)

bool chiralAtomCompat (Atom const *a1, Atom const *a2)

bool bondCompat (Bond const *b1, Bond const *b2)

void MolToVFGraph (const ROMol &mol, ARGEdit *vgEd)

bool substructVisitor (int n, node_id ni1[], node_id ni2[], void *mvp)

bool substructHeadVisitor (int n, node_id ni1[], node_id ni2[], void *mvp)

double toPrime (const MatchVectType &v)

void removeDuplicates (std::vector< MatchVectType > &v)

DiscreteDistMat * getDiscreteDistMat ()

unsigned int computeL1Norm (const DiscreteValueVect &v1, const DiscreteValueVect &v2)

DiscreteValueVect operator+ (const DiscreteValueVect &p1, const DiscreteValueVect &p2)

DiscreteValueVect operator- (const DiscreteValueVect &p1, const DiscreteValueVect &p2)

template<typename IndexType, typename SequenceType>

void updateFromSequence (SparseIntVect< IndexType > &vect, const SequenceType &seq)

template<typename IndexType>

double DiceSimilarity (const SparseIntVect< IndexType > &v1, const SparseIntVect< IndexType > &v2, bool returnDistance=false, double bounds=0.0)

void appendPackedIntToStream (std::stringstream &ss, unsigned int num)

Packs an integer and outputs it to a stream.

unsigned int readPackedIntFromStream (std::stringstream &ss)

Reads an integer from a stream in packed format and returns the result.

unsigned int pullPackedIntFromString (const char *&text)

template<typename T>

void streamWrite (std::ostream &ss, const T &val)

does a binary write of an object to a stream

template<typename T>

void streamRead (std::istream &ss, T &loc)

does a binary read of an object from a stream

std::string getLine (std::istream *inStream)

grabs the next line from an instream and returns it.

std::string getLine (std::istream &inStream)

grabs the next line from an instream and returns it.

void Union (const INT_VECT &r1, const INT_VECT &r2, INT_VECT &res)

calculate the union of two INT_VECTs and put the results in a third vector

void Intersect (const INT_VECT &r1, const INT_VECT &r2, INT_VECT &res)

calculate the intersection of two INT_VECTs and put the results in a third vector

void Union (const VECT_INT_VECT &rings, INT_VECT &res, const INT_VECT *exclude=NULL)

calculating the union of the INT_VECT's in a VECT_INT_VECT

int nextCombination (INT_VECT &comb, int tot)

given a current combination of numbers change it to the next possible combination

double round (double v)

rounds a value to the closest int

double computeIntVectPrimesProduct (const INT_VECT &ring)

compute the product of the set of primes corresponding to the values in an INT_VECT

bool feq (double v1, double v2, double tol=1e-4)

floating point comparison with a tolerance

rng_type & getRandomGenerator (int seed=-1)

Optionally seed and return a reference to the global (Boost) random generator.

double getRandomVal (int seed=-1)

Variables

const std::string periodicTableAtomData

const int MOLFILE_MAXLINE = 256

static int defaultConfId = -1

std::string paramData

const double IONXH = 20.02

const double DAMP_SCALE = 0.5

const double DAMP = 0.5

const int ci_RIGHTMOST_ATOM

const int ci_LEADING_BOND

const int ci_ATOM_HOLDER

const int NUM_PRIMES_AVAIL = 1000

int firstThousandPrimes [NUM_PRIMES_AVAIL]

const unsigned int BITS_PER_INT = 32

const double MAX_DOUBLE = std::numeric_limits<double>::max()

const double EPS_DOUBLE = std::numeric_limits<double>::epsilon()

const double SMALL_DOUBLE = 1.0e-8

const double MAX_INT = static_cast<double>(std::numeric_limits<int>::max())

const double MAX_LONGINT = static_cast<double>(std::numeric_limits<LONGINT>::max())

const double PI = 3.1415926535897931

const int NUM_PRIMES_AVAIL = 1000

the number of primes available and stored

int firstThousandPrimes [NUM_PRIMES_AVAIL]

const int FILE_MAXLINE = 256

an assumed maximum length for lines read from files

Detailed Description

Includes a bunch of functionality for handling Atom and Bond queries.

Std stuff.

Typedef Documentation

typedef ARGraph<const Atom, const Bond> RDKit::AR_MOLGRAPH

Definition at line 28 of file SubstructMatch.h.

typedef Queries::AndQuery<int,Atom const *,true> RDKit::ATOM_AND_QUERY

Definition at line 21 of file QueryOps.h.

typedef Queries::Query<bool,Atom const *,true> RDKit::ATOM_BOOL_QUERY

Definition at line 18 of file QueryOps.h.

typedef Queries::EqualityQuery<int,Atom const *,true> RDKit::ATOM_EQUALS_QUERY

Definition at line 30 of file QueryOps.h.

typedef Queries::GreaterQuery<int,Atom const *,true> RDKit::ATOM_GREATER_QUERY

Definition at line 33 of file QueryOps.h.

typedef Queries::GreaterEqualQuery<int,Atom const *,true> RDKit::ATOM_GREATEREQUAL_QUERY

Definition at line 36 of file QueryOps.h.

typedef Queries::LessQuery<int,Atom const *,true> RDKit::ATOM_LESS_QUERY

Definition at line 39 of file QueryOps.h.

typedef Queries::LessEqualQuery<int,Atom const *,true> RDKit::ATOM_LESSEQUAL_QUERY

Definition at line 42 of file QueryOps.h.

typedef Queries::Query<int,Atom const *,true> RDKit::ATOM_NULL_QUERY

Definition at line 52 of file QueryOps.h.

typedef Queries::OrQuery<int,Atom const *,true> RDKit::ATOM_OR_QUERY

Definition at line 24 of file QueryOps.h.

typedef Queries::RangeQuery<int,Atom const *,true> RDKit::ATOM_RANGE_QUERY

Definition at line 45 of file QueryOps.h.

typedef Queries::SetQuery<int,Atom const *,true> RDKit::ATOM_SET_QUERY

Definition at line 48 of file QueryOps.h.

typedef boost::shared_ptr<Atom> RDKit::ATOM_SPTR

Definition at line 52 of file ROMol.h.

typedef boost::shared_ptr<Atom> RDKit::ATOM_SPTR

Definition at line 20 of file Bond.h.

typedef boost::shared_ptr<Atom> RDKit::ATOM_SPTR

Definition at line 21 of file AtomProps.h.

typedef Queries::XOrQuery<int,Atom const *,true> RDKit::ATOM_XOR_QUERY

Definition at line 27 of file QueryOps.h.

typedef boost::property<vertex_atom_t,Atom *> RDKit::AtomProperty

Definition at line 29 of file AtomProps.h.

typedef Queries::AndQuery<int,Bond const *,true> RDKit::BOND_AND_QUERY

Definition at line 22 of file QueryOps.h.

typedef Queries::Query<bool,Bond const *,true> RDKit::BOND_BOOL_QUERY

Definition at line 19 of file QueryOps.h.

typedef Queries::EqualityQuery<int,Bond const *,true> RDKit::BOND_EQUALS_QUERY

Definition at line 31 of file QueryOps.h.

typedef Queries::GreaterQuery<int,Bond const *,true> RDKit::BOND_GREATER_QUERY

Definition at line 34 of file QueryOps.h.

typedef Queries::GreaterEqualQuery<int,Bond const *,true> RDKit::BOND_GREATEREQUAL_QUERY

Definition at line 37 of file QueryOps.h.

typedef Queries::LessQuery<int,Bond const *,true> RDKit::BOND_LESS_QUERY

Definition at line 40 of file QueryOps.h.

typedef Queries::LessEqualQuery<int,Bond const *,true> RDKit::BOND_LESSEQUAL_QUERY

Definition at line 43 of file QueryOps.h.

typedef Queries::Query<int,Bond const *,true> RDKit::BOND_NULL_QUERY

Definition at line 51 of file QueryOps.h.

typedef Queries::OrQuery<int,Bond const *,true> RDKit::BOND_OR_QUERY

Definition at line 25 of file QueryOps.h.

typedef Queries::RangeQuery<int,Bond const *,true> RDKit::BOND_RANGE_QUERY

Definition at line 46 of file QueryOps.h.

typedef Queries::SetQuery<int,Bond const *,true> RDKit::BOND_SET_QUERY

Definition at line 49 of file QueryOps.h.

typedef boost::shared_ptr<Bond> RDKit::BOND_SPTR

Definition at line 55 of file ROMol.h.

typedef boost::shared_ptr<Bond> RDKit::BOND_SPTR

Definition at line 23 of file BondProps.h.

typedef Queries::XOrQuery<int,Bond const *,true> RDKit::BOND_XOR_QUERY

Definition at line 28 of file QueryOps.h.

typedef boost::property<edge_bond_t,Bond *,BondWeight> RDKit::BondProperty

Definition at line 34 of file BondProps.h.

typedef boost::property<edge_wght_t,double> RDKit::BondWeight

Definition at line 33 of file BondProps.h.

typedef boost::shared_ptr<Conformer> RDKit::CONFORMER_SPTR

Definition at line 131 of file Conformer.h.

typedef Atom const* RDKit::ConstAtomPtr

Definition at line 202 of file QueryOps.h.

typedef boost::tuples::tuple<double,double,double> RDKit::DiscrimTuple

used to return atomic discriminators (three doubles)

Definition at line 29 of file MolOps.h.

typedef std::map<double, int, ltDouble> RDKit::DOUBLE_INT_MAP

std::map from double to integer.

Definition at line 131 of file types.h.

typedef boost::variate_generator<rng_type &,uniform_double> RDKit::double_source_type

Definition at line 31 of file utils.h.

typedef std::vector<double> RDKit::DOUBLE_VECT

Definition at line 86 of file types.h.

typedef DOUBLE_VECT::const_iterator RDKit::DOUBLE_VECT_CI

Definition at line 88 of file types.h.

typedef DOUBLE_VECT::iterator RDKit::DOUBLE_VECT_I

Definition at line 87 of file types.h.

typedef boost::shared_ptr<MolChemicalFeature> RDKit::FeatSPtr

Definition at line 14 of file MolChemicalFeatureFactory.h.

typedef std::list< FeatSPtr > RDKit::FeatSPtrList

Definition at line 16 of file MolChemicalFeatureFactory.h.

typedef FeatSPtrList::iterator RDKit::FeatSPtrList_I

Definition at line 17 of file MolChemicalFeatureFactory.h.

typedef RDCatalog::HierarchCatalog<FragCatalogEntry, FragCatParams, int> RDKit::FragCatalog

Definition at line 16 of file FragFPGenerator.h.

typedef RDCatalog::HierarchCatalog<FragCatalogEntry, FragCatParams, int> RDKit::FragCatalog

Definition at line 15 of file FragCatGenerator.h.

typedef std::deque<int> RDKit::INT_DEQUE

Definition at line 103 of file types.h.

typedef INT_DEQUE::const_iterator RDKit::INT_DEQUE_CI

Definition at line 105 of file types.h.

typedef INT_DEQUE::iterator RDKit::INT_DEQUE_I

Definition at line 104 of file types.h.

typedef std::map<int, INT_DEQUE> RDKit::INT_INT_DEQ_MAP

Definition at line 107 of file types.h.

typedef INT_INT_DEQ_MAP::const_iterator RDKit::INT_INT_DEQ_MAP_CI

Definition at line 108 of file types.h.

typedef std::map<int, INT_VECT> RDKit::INT_INT_VECT_MAP

Definition at line 96 of file types.h.

typedef INT_INT_VECT_MAP::const_iterator RDKit::INT_INT_VECT_MAP_CI

Definition at line 97 of file types.h.

typedef std::list<int> RDKit::INT_LIST

Definition at line 66 of file types.h.

typedef INT_LIST::const_iterator RDKit::INT_LIST_CI

Definition at line 68 of file types.h.

typedef INT_LIST::iterator RDKit::INT_LIST_I

Definition at line 67 of file types.h.

typedef std::map<int, int> RDKit::INT_MAP_INT

Definition at line 99 of file types.h.

typedef INT_MAP_INT::const_iterator RDKit::INT_MAP_INT_CI

Definition at line 101 of file types.h.

typedef INT_MAP_INT::iterator RDKit::INT_MAP_INT_I

Definition at line 100 of file types.h.

typedef std::map<int, PATH_LIST> RDKit::INT_PATH_LIST_MAP

Definition at line 41 of file Subgraphs.h.

typedef INT_PATH_LIST_MAP::const_iterator RDKit::INT_PATH_LIST_MAP_CI

Definition at line 42 of file Subgraphs.h.

typedef INT_PATH_LIST_MAP::iterator RDKit::INT_PATH_LIST_MAP_I

Definition at line 43 of file Subgraphs.h.

typedef std::set<int> RDKit::INT_SET

Definition at line 110 of file types.h.

typedef INT_SET::const_iterator RDKit::INT_SET_CI

Definition at line 112 of file types.h.

typedef INT_SET::iterator RDKit::INT_SET_I

Definition at line 111 of file types.h.

typedef boost::variate_generator<rng_type &,uniform_int> RDKit::int_source_type

Definition at line 30 of file utils.h.

typedef std::vector<int> RDKit::INT_VECT

Definition at line 60 of file types.h.

typedef std::vector<int> RDKit::INT_VECT

Definition at line 21 of file FeatTreeUtils.h.

typedef INT_VECT::const_iterator RDKit::INT_VECT_CI

Definition at line 62 of file types.h.

typedef INT_VECT::const_reverse_iterator RDKit::INT_VECT_CRI

Definition at line 64 of file types.h.

typedef INT_VECT::iterator RDKit::INT_VECT_I

Definition at line 61 of file types.h.

typedef INT_VECT::reverse_iterator RDKit::INT_VECT_RI

Definition at line 63 of file types.h.

typedef std::vector<double> RDKit::INVAR_VECT

Definition at line 17 of file MolOps.h.

typedef INVAR_VECT::const_iterator RDKit::INVAR_VECT_CI

Definition at line 20 of file MolOps.h.

typedef INVAR_VECT::iterator RDKit::INVAR_VECT_I

Definition at line 19 of file MolOps.h.

typedef std::list<INT_VECT> RDKit::LIST_INT_VECT

Definition at line 70 of file types.h.

typedef LIST_INT_VECT::const_iterator RDKit::LIST_INT_VECT_CI

Definition at line 72 of file types.h.

typedef LIST_INT_VECT::iterator RDKit::LIST_INT_VECT_I

Definition at line 71 of file types.h.

typedef long long int RDKit::LONGINT

Definition at line 38 of file types.h.

typedef VF2MonoState RDKit::MatcherState

Definition at line 26 of file SubstructMatch.h.

typedef std::vector< std::pair<int,int> > RDKit::MatchVectType

used to return matches from substructure searching, The format is (queryAtomIdx, molAtomIdx)

Definition at line 20 of file SubstructMatch.h.

typedef std::vector< std::pair<int,int> > RDKit::MatchVectType

Definition at line 14 of file AlignMolecules.h.

typedef std::vector< std::pair<int,int> > RDKit::MatchVectType

Definition at line 18 of file FragFPGenerator.h.

typedef std::vector<ROMol *> RDKit::MOL_PTR_VECT

Definition at line 682 of file ROMol.h.

typedef MOL_PTR_VECT::const_iterator RDKit::MOL_PTR_VECT_CI

Definition at line 685 of file ROMol.h.

typedef MOL_PTR_VECT::iterator RDKit::MOL_PTR_VECT_I

Definition at line 686 of file ROMol.h.

typedef std::vector<ROMOL_SPTR> RDKit::MOL_SPTR_VECT

Definition at line 683 of file ROMol.h.

typedef std::vector< boost::shared_ptr<ROMol> > RDKit::MOL_SPTR_VECT

Definition at line 16 of file FragCatParams.h.

typedef std::vector<ROMol> RDKit::MOL_VECT

Definition at line 680 of file ROMol.h.

typedef RDCatalog::HierarchCatalog<MolCatalogEntry, MolCatalogParams, int> RDKit::MolCatalog

a hierarchical catalog for holding molecules

Definition at line 15 of file MolCatalog.h.

typedef boost::adjacency_list< boost::vecS, boost::vecS, boost::undirectedS, AtomProperty, BondProperty> RDKit::MolGraph

This is the BGL type used to store the topology:.

Definition at line 34 of file ROMol.h.

typedef std::list< PATH_TYPE > RDKit::PATH_LIST

Definition at line 38 of file Subgraphs.h.

typedef PATH_LIST::const_iterator RDKit::PATH_LIST_CI

Definition at line 39 of file Subgraphs.h.

typedef std::vector<int> RDKit::PATH_TYPE

Definition at line 33 of file Subgraphs.h.

typedef boost::minstd_rand RDKit::rng_type

Definition at line 27 of file utils.h.

typedef boost::shared_ptr<ROMol> RDKit::ROMOL_SPTR

Definition at line 681 of file ROMol.h.

typedef boost::shared_ptr<ROMol> RDKit::ROMOL_SPTR

Definition at line 13 of file ChemTransforms.h.

typedef boost::shared_ptr<RWMol> RDKit::RWMOL_SPTR

Definition at line 152 of file RWMol.h.

typedef std::vector< RWMOL_SPTR > RDKit::RWMOL_SPTR_VECT

Definition at line 153 of file RWMol.h.

typedef std::vector< RWMOL_SPTR > RDKit::RWMOL_SPTR_VECT

Definition at line 26 of file FileParsers.h.

typedef std::map<std::string, UINT> RDKit::STR_UINT_MAP

Definition at line 93 of file types.h.

typedef std::map<std::string, UINT>::const_iterator RDKit::STR_UINT_MAP_CI

Definition at line 94 of file types.h.

typedef std::vector<std::string> RDKit::STR_VECT

Definition at line 83 of file types.h.

typedef std::vector<std::string> RDKit::STR_VECT

Definition at line 22 of file Dict.h.

typedef std::vector<std::string>::const_iterator RDKit::STR_VECT_CI

Definition at line 81 of file types.h.

typedef std::vector<std::string>::iterator RDKit::STR_VECT_I

Definition at line 82 of file types.h.

typedef unsigned char RDKit::UCHAR

Definition at line 58 of file types.h.

typedef unsigned int RDKit::UINT

Definition at line 56 of file types.h.

typedef std::vector<UINT> RDKit::UINT_VECT

Definition at line 79 of file types.h.

typedef std::vector<UINT>::const_iterator RDKit::UINT_VECT_CI

Definition at line 78 of file types.h.

typedef boost::uniform_real RDKit::uniform_double

Definition at line 29 of file utils.h.

typedef boost::uniform_int RDKit::uniform_int

Definition at line 28 of file utils.h.

typedef unsigned short RDKit::USHORT

Definition at line 57 of file types.h.

typedef std::vector<DOUBLE_VECT> RDKit::VECT_DOUBLE_VECT

Definition at line 89 of file types.h.

typedef VECT_DOUBLE_VECT::const_iterator RDKit::VECT_DOUBLE_VECT_CI

Definition at line 91 of file types.h.

typedef VECT_DOUBLE_VECT::iterator RDKit::VECT_DOUBLE_VECT_I

Definition at line 90 of file types.h.

typedef std::vector<INT_VECT> RDKit::VECT_INT_VECT

Definition at line 74 of file types.h.

typedef VECT_INT_VECT::const_iterator RDKit::VECT_INT_VECT_CI

Definition at line 76 of file types.h.

typedef VECT_INT_VECT::iterator RDKit::VECT_INT_VECT_I

Definition at line 75 of file types.h.

Enumeration Type Documentation

enum RDKit::AtomInvariantType

used to request particular types of atom invariants

Enumerator:

ComprehensiveInvariants	for general atomic ranking
ChiralSearchInvariants	for ranking atoms for calculating CIP codes

Definition at line 23 of file MolOps.h.

Function Documentation

int RDKit::Add2DCoordsToMol	(	ROMol &	mol,
		bool	useDLL = `false`
	)

void RDKit::appendPackedIntToStream	(	std::stringstream &	ss,
		unsigned int	num
	)			`[inline]`

Packs an integer and outputs it to a stream.

Definition at line 19 of file StreamOps.h.

References CHECK_INVARIANT.

bool RDKit::atomCompat	(	Atom const *	a1,
		Atom const *	a2
	)

bool RDKit::bondCompat	(	Bond const *	b1,
		Bond const *	b2
	)

MolChemicalFeatureFactory* RDKit::buildFeatureFactory ( const std::string & featureData )

constructs a MolChemicalFeatureFactory from the data in a string

MolChemicalFeatureFactory* RDKit::buildFeatureFactory ( std::istream & inStream )

constructs a MolChemicalFeatureFactory from the data in a stream

bool RDKit::chiralAtomCompat	(	Atom const *	a1,
		Atom const *	a2
	)

void RDKit::computeGasteigerCharges	(	const ROMol *	mol,
		int	nIter = `12`,
		bool	throwOnParamFailure = `false`
	)

double RDKit::computeIntVectPrimesProduct ( const INT_VECT & ring )

compute the product of the set of primes corresponding to the values in an INT_VECT

unsigned int RDKit::computeL1Norm	(	const DiscreteValueVect &	v1,
		const DiscreteValueVect &	v2
	)

ExplicitBitVect* RDKit::DaylightFingerprintMol	(	const ROMol &	mol,
		unsigned int	minPath = `1`,
		unsigned int	maxPath = `7`,
		unsigned int	fpSize = `2048`,
		unsigned int	nBitsPerHash = `4`,
		bool	useHs = `true`,
		double	tgtDensity = `0.0`,
		unsigned int	minSize = `128`
	)

Generates a topological (Daylight like) fingerprint for a molecule

Parameters:

	mol,:	the molecule to be fingerprinted
	minPath,:	the minimum path length (in bonds) to be included
	maxPath,:	the minimum path length (in bonds) to be included
	fpSize,:	the size of the fingerprint
	nBitsPerHash,:	the number of bits to be set by each path
	useHs,:	toggles inclusion of Hs in distinguishing paths from each other.
	tgtDensity,:	if the generated fingerprint is below this density, it will be folded until the density is reached.
	minSize,:	the minimum size to which the fingerprint will be folded

Returns:: the molecular fingerprint, as an ExplicitBitVect

Notes:

the caller is responsible for deleteing the result

ROMol* RDKit::deleteSubstructs	(	const ROMol &	mol,
		const ROMol &	query,
		bool	replaceAll = `false`
	)

Returns a copy of an ROMol with the atoms and bonds that match a pattern removed.

Parameters:

	mol	the ROMol of interest
	query	the query ROMol
	replaceAll	if this is set all matches of the query to the substructure will be removed. Default is to only remove the first.

Returns:: a copy of mol with the matching atoms and bonds (if any) removed.

void RDKit::DetectAtomStereoChemistry	(	RWMol &	mol,
		const Conformer *	conf
	)

void RDKit::DetectBondStereoChemistry	(	ROMol &	mol,
		const Conformer *	conf
	)

Bond::BondDir RDKit::DetermineBondWedgeState	(	const Bond *	bond,
		const INT_MAP_INT &	wedgeBonds,
		const Conformer *	conf
	)

template<typename IndexType>

double RDKit::DiceSimilarity	(	const SparseIntVect< IndexType > &	v1,
		const SparseIntVect< IndexType > &	v2,
		bool	returnDistance = `false`,
		double	bounds = `0.0`
	)			`[inline]`

Definition at line 337 of file SparseIntVect.h.

References RDKit::SparseIntVect< IndexType >::getLength(), RDKit::SparseIntVect< IndexType >::getNonzeroElements(), and RDKit::SparseIntVect< IndexType >::getTotalVal().

bool RDKit::feq	(	double	v1,
		double	v2,
		double	tol = `1e-4`
	)

floating point comparison with a tolerance

Referenced by RDPickers::MaxMinPicker::lazyPick().

PATH_LIST RDKit::findAllPathsOfLengthN	(	const ROMol &	mol,
		unsigned int	targetLen,
		bool	useBonds = `true`,
		bool	useHs = `false`
	)

find all paths of a particular size

Parameters:

	mol	- the molecule to be considered
	targetLen	- the length of the paths to be returned
	useBonds	- if set, the path indices will be bond indices, not atom indices
	useHs	- if set, hydrogens in the graph will be considered eligible to be in paths. NOTE: this will not add Hs to the graph.

PATH_LIST RDKit::findAllSubgraphsOfLengthN	(	const ROMol &	mol,
		unsigned int	targetLen,
		bool	useHs = `false`
	)

find all subgraphs of a particular size

Parameters:

	mol	- the molecule to be considered
	targetLen	- the length of the subgraphs to be returned
	useHs	- if set, hydrogens in the graph will be considered eligible to be in paths. NOTE: this will not add Hs to the graph.

INT_PATH_LIST_MAP RDKit::findAllSubgraphsOfLengthsMtoN	(	const ROMol &	mol,
		unsigned int	lowerLen,
		unsigned int	upperLen,
		bool	useHs = `false`
	)

find all subgraphs in a range of sizes

Parameters:

	mol	- the molecule to be considered
	lowerLen	- the minimum subgraph size to find
	upperLen	- the maximum subgraph size to find
	useHs	- if set, hydrogens in the graph will be considered eligible to be in paths. NOTE: this will not add Hs to the graph.

MatchVectType RDKit::findFuncGroupsOnMol	(	const ROMol &	mol,
		const FragCatParams *	params,
		INT_VECT &	fgBonds
	)

PATH_LIST RDKit::findUniqueSubgraphsOfLengthN	(	const ROMol &	mol,
		unsigned int	targetLen,
		bool	useHs = `false`,
		bool	useBO = `true`
	)

find unique subgraphs of a particular size

Parameters:

	mol	- the molecule to be considered
	targetLen	- the length of the subgraphs to be returned
	useHs	- if set, hydrogens in the graph will be considered eligible to be in paths. NOTE: this will not add Hs to the graph.
	useBO	- if set, bond orders will be considered when uniquifying the paths

DiscreteDistMat* RDKit::getDiscreteDistMat ( )

std::string RDKit::getLine ( std::istream & inStream ) [inline]

grabs the next line from an instream and returns it.

Definition at line 169 of file StreamOps.h.

References getLine().

std::string RDKit::getLine ( std::istream * inStream ) [inline]

grabs the next line from an instream and returns it.

Definition at line 160 of file StreamOps.h.

Referenced by getLine().

AR_MOLGRAPH* RDKit::getMolGraph	(	const ROMol &	mol,
		bool	registerIt = `false`
	)

Internal Use Only.

rng_type& RDKit::getRandomGenerator ( int seed = -1 )

Optionally seed and return a reference to the global (Boost) random generator.

double RDKit::getRandomVal ( int seed = -1 )

Return a random double value between 0.0 and 1.0 Optionally seed the random number generator

void RDKit::Intersect	(	const INT_VECT &	r1,
		const INT_VECT &	r2,
		INT_VECT &	res
	)

calculate the intersection of two INT_VECTs and put the results in a third vector

ATOM_EQUALS_QUERY* RDKit::makeAtomAliphaticQuery ( )

returns a Query for matching aliphatic atoms

ATOM_EQUALS_QUERY* RDKit::makeAtomAromaticQuery ( )

returns a Query for matching the isAromatic flag

ATOM_EQUALS_QUERY* RDKit::makeAtomExplicitDegreeQuery ( int what )

returns a Query for matching explicit valence

ATOM_EQUALS_QUERY* RDKit::makeAtomFormalChargeQuery ( int what )

returns a Query for matching formal charge

ATOM_EQUALS_QUERY* RDKit::makeAtomHCountQuery ( int what )

returns a Query for matching hydrogen count

ATOM_EQUALS_QUERY* RDKit::makeAtomHybridizationQuery ( int what )

returns a Query for matching hybridization

ATOM_EQUALS_QUERY* RDKit::makeAtomImplicitValenceQuery ( int what )

returns a Query for matching implicit valence

ATOM_EQUALS_QUERY* RDKit::makeAtomInNRingsQuery ( int what )

returns a Query for matching atoms in a particular number of rings

ATOM_EQUALS_QUERY* RDKit::makeAtomInRingOfSizeQuery ( int tgt )

returns a Query for matching atoms in rings of a particular size

ATOM_EQUALS_QUERY* RDKit::makeAtomInRingQuery ( )

returns a Query for matching ring atoms

ATOM_EQUALS_QUERY* RDKit::makeAtomMassQuery ( int what )

returns a Query for matching atoms with a particular mass (for isotopes)

ATOM_EQUALS_QUERY* RDKit::makeAtomMinRingSizeQuery ( int tgt )

returns a Query for matching an atom's minimum ring size

ATOM_NULL_QUERY* RDKit::makeAtomNullQuery ( )

returns a Query for matching any atom

ATOM_EQUALS_QUERY* RDKit::makeAtomNumEqualsQuery ( int what )

returns a Query for matching atomic number

ATOM_EQUALS_QUERY* RDKit::makeAtomRingBondCountQuery ( int what )

returns a Query for matching atoms with a particular number of ring bonds

ATOM_EQUALS_QUERY* RDKit::makeAtomTotalDegreeQuery ( int what )

returns a Query for matching atomic degree

ATOM_EQUALS_QUERY* RDKit::makeAtomTotalValenceQuery ( int what )

returns a Query for matching total valence

ATOM_EQUALS_QUERY* RDKit::makeAtomUnsaturatedQuery ( )

returns a Query for matching atoms with unsaturation:

BOND_EQUALS_QUERY* RDKit::makeBondDirEqualsQuery ( Bond::BondDir what )

returns a Query for matching bond directions

BOND_EQUALS_QUERY* RDKit::makeBondInNRingsQuery ( int tgt )

returns a Query for matching bonds in a particular number of rings

BOND_EQUALS_QUERY* RDKit::makeBondInRingOfSizeQuery ( int what )

returns a Query for matching bonds in rings of a particular size

BOND_EQUALS_QUERY* RDKit::makeBondIsInRingQuery ( )

returns a Query for matching ring bonds

BOND_EQUALS_QUERY* RDKit::makeBondMinRingSizeQuery ( int what )

returns a Query for matching a bond's minimum ring size

BOND_NULL_QUERY* RDKit::makeBondNullQuery ( )

returns a Query for matching any bond

BOND_EQUALS_QUERY* RDKit::makeBondOrderEqualsQuery ( Bond::BondType what )

returns a Query for matching bond orders

RWMol* RDKit::MolBlockToMol	(	const std::string &	molBlock,
		bool	sanitize = `true`,
		bool	removeHs = `true`
	)

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

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

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

Parameters:

	inStream	- stream containing the data
	line	- current line number (used for error reporting)
	sanitize	- toggles sanitization of the molecule
	removeHs	- toggles removal of Hs from the molecule. H removal is only done if the molecule is sanitized

RWMol* RDKit::MolFileToMol	(	std::string	fName,
		bool	sanitize = `true`,
		bool	removeHs = `true`
	)

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

std::string RDKit::MolToMolBlock	(	const ROMol &	mol,
		bool	includeStereo = `true`,
		int	confId = `-1`
	)

Parameters:

	mol	- the molecule in question
	includeStereo	- toggles inclusion of stereochemistry information
	confId	- selects the conformer to be used

void RDKit::MolToMolFile	(	const ROMol &	mol,
		std::string	fName,
		bool	includeStereo = `true`,
		int	confId = `-1`
	)

Parameters:

	mol	- the molecule in question
	fName	- the name of the file to use
	includeStereo	- toggles inclusion of stereochemistry information
	confId	- selects the conformer to be used

std::string RDKit::MolToSmarts	(	ROMol &	mol,
		bool	doIsomericSmarts = `false`
	)

returns the SMARTS for a molecule

std::string RDKit::MolToSmiles	(	ROMol &	mol,
		bool	doIsomericSmiles = `false`,
		bool	doKekule = `false`,
		int	rootedAtAtom = `-1`
	)

returns canonical SMILES for a molecule

Parameters:

	mol	: the molecule in question. NOTE that the molecule may be modified as part of the canonicalization process.
	doIsomericSmiles	: include stereochemistry and isotope information in the SMILES
	doKekule	: do Kekule smiles (i.e. don't use aromatic bonds)
	rootedAtAtom	: make sure the SMILES starts at the specified atom. The resulting SMILES is not, of course, canonical.

void RDKit::MolToTPLFile	(	const ROMol &	mol,
		std::string	fName,
		std::string	partialChargeProp = `"_GasteigerCharge"`,
		bool	writeFirstConfTwice = `false`
	)

std::string RDKit::MolToTPLText	(	const ROMol &	mol,
		std::string	partialChargeProp = `"_GasteigerCharge"`,
		bool	writeFirstConfTwice = `false`
	)

void RDKit::MolToVFGraph	(	const ROMol &	mol,
		ARGEdit *	vgEd
	)

int RDKit::nextCombination	(	INT_VECT &	comb,
		int	tot
	)

given a current combination of numbers change it to the next possible combination

Parameters:

	comb	the sorted vector to consider
	tot	the maximum number possible in the vector

Returns:: -1 on failure, the index of the last number changed on success. Example: for all combinations 3 of numbers between 0 and tot=5 given (0,1,2) the function wil return (0,1,3) etc.

template<typename T>

int RDKit::nullDataFun ( T arg ) [inline]

Definition at line 296 of file QueryOps.h.

template<typename T>

bool RDKit::nullQueryFun ( T arg ) [inline]

Definition at line 298 of file QueryOps.h.

DiscreteValueVect RDKit::operator+	(	const DiscreteValueVect &	p1,
		const DiscreteValueVect &	p2
	)

DiscreteValueVect RDKit::operator-	(	const DiscreteValueVect &	p1,
		const DiscreteValueVect &	p2
	)

int RDKit::parseFeatureData	(	std::istream &	istream,
		MolChemicalFeatureDef::CollectionType &	featDefs
	)

int RDKit::parseFeatureData	(	const std::string &	defnText,
		MolChemicalFeatureDef::CollectionType &	featDefs
	)

int RDKit::parseFeatureFile	(	const std::string &	fileName,
		MolChemicalFeatureDef::CollectionType &	featDefs
	)

INT_MAP_INT RDKit::pickBondsToWedge ( const ROMol & mol )

ROMol* RDKit::prepareMol	(	const ROMol &	mol,
		const FragCatParams *	fparams,
		MatchVectType &	aToFmap
	)

unsigned int RDKit::pullPackedIntFromString ( const char *& text ) [inline]

Reads an integer from a char * in packed format and returns the result. The argument is advanced

Definition at line 103 of file StreamOps.h.

static int RDKit::queryAtomAliphatic ( Atom const * at ) [static]

Definition at line 58 of file QueryOps.h.

References RDKit::Atom::getIsAromatic().

unsigned int RDKit::queryAtomAllBondProduct ( Atom const * at )

static int RDKit::queryAtomAromatic ( Atom const * at ) [static]

Definition at line 57 of file QueryOps.h.

References RDKit::Atom::getIsAromatic().

unsigned int RDKit::queryAtomBondProduct ( Atom const * at )

static int RDKit::queryAtomExplicitDegree ( Atom const * at ) [static]

Definition at line 59 of file QueryOps.h.

References RDKit::Atom::getDegree().

static int RDKit::queryAtomFormalCharge ( Atom const * at ) [static]

Definition at line 71 of file QueryOps.h.

References RDKit::Atom::getFormalCharge().

static int RDKit::queryAtomHCount ( Atom const * at ) [static]

Definition at line 62 of file QueryOps.h.

References RDKit::Atom::getTotalNumHs().

static int RDKit::queryAtomHeavyAtomDegree ( Atom const * at ) [static]

Definition at line 61 of file QueryOps.h.

References RDKit::Atom::getDegree().

static int RDKit::queryAtomHybridization ( Atom const * at ) [static]

Definition at line 74 of file QueryOps.h.

References RDKit::Atom::getHybridization().

static int RDKit::queryAtomImplicitValence ( Atom const * at ) [static]

Definition at line 63 of file QueryOps.h.

References RDKit::Atom::getImplicitValence().

template<int tgt>

int RDKit::queryAtomIsInRingOfSize ( Atom const * at ) [inline]

Definition at line 123 of file QueryOps.h.

References RDKit::Atom::getIdx(), RDKit::Atom::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::isAtomInRingOfSize().

static int RDKit::queryAtomMass ( Atom const * at ) [static]

Definition at line 67 of file QueryOps.h.

References RDKit::Atom::getMass(), and round().

static int RDKit::queryAtomMinRingSize ( Atom const * at ) [static]

Definition at line 100 of file QueryOps.h.

References RDKit::Atom::getIdx(), RDKit::Atom::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::minAtomRingSize().

static int RDKit::queryAtomNum ( Atom const * at ) [static]

Definition at line 66 of file QueryOps.h.

References RDKit::Atom::getAtomicNum().

static int RDKit::queryAtomRingBondCount ( Atom const * at ) [static]

Definition at line 107 of file QueryOps.h.

References RDKit::ROMol::getAtomBonds(), RDKit::ROMol::getBondPMap(), RDKit::Atom::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::numBondRings().

static int RDKit::queryAtomRingMembership ( Atom const * at ) [static]

Definition at line 194 of file QueryOps.h.

References RDKit::Atom::getIdx(), RDKit::Atom::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::numAtomRings().

Referenced by RDKit::AtomRingQuery::AtomRingQuery().

static int RDKit::queryAtomTotalDegree ( Atom const * at ) [static]

Definition at line 60 of file QueryOps.h.

References RDKit::Atom::getDegree(), and RDKit::Atom::getImplicitValence().

static int RDKit::queryAtomTotalValence ( Atom const * at ) [static]

Definition at line 64 of file QueryOps.h.

References RDKit::Atom::getExplicitValence(), and RDKit::Atom::getImplicitValence().

static int RDKit::queryAtomUnsaturated ( Atom const * at ) [static]

Definition at line 65 of file QueryOps.h.

References RDKit::Atom::getDegree(), and RDKit::Atom::getExplicitValence().

static int RDKit::queryBondDir ( Bond const * bond ) [static]

Definition at line 83 of file QueryOps.h.

References RDKit::Bond::getBondDir().

template<int tgt>

int RDKit::queryBondIsInRingOfSize ( Bond const * bond ) [inline]

Definition at line 131 of file QueryOps.h.

References RDKit::Bond::getIdx(), RDKit::Bond::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::isBondInRingOfSize().

static int RDKit::queryBondMinRingSize ( Bond const * bond ) [static]

Definition at line 103 of file QueryOps.h.

References RDKit::Bond::getIdx(), RDKit::Bond::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::minBondRingSize().

static int RDKit::queryBondOrder ( Bond const * bond ) [static]

Definition at line 82 of file QueryOps.h.

References RDKit::Bond::getBondType().

static int RDKit::queryIsAtomInNRings ( Atom const * at ) [static]

Definition at line 91 of file QueryOps.h.

References RDKit::Atom::getIdx(), RDKit::Atom::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::numAtomRings().

static int RDKit::queryIsAtomInRing ( Atom const * at ) [static]

Definition at line 94 of file QueryOps.h.

References RDKit::Atom::getIdx(), RDKit::Atom::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::numAtomRings().

static int RDKit::queryIsBondInNRings ( Bond const * at ) [static]

Definition at line 84 of file QueryOps.h.

References RDKit::Bond::getIdx(), RDKit::Bond::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::numBondRings().

static int RDKit::queryIsBondInRing ( Bond const * bond ) [static]

Definition at line 97 of file QueryOps.h.

References RDKit::Bond::getIdx(), RDKit::Bond::getOwningMol(), RDKit::ROMol::getRingInfo(), and RDKit::RingInfo::numBondRings().

ExplicitBitVect* RDKit::RDKFingerprintMol	(	const ROMol &	mol,
		unsigned int	minPath = `1`,
		unsigned int	maxPath = `7`,
		unsigned int	fpSize = `2048`,
		unsigned int	nBitsPerHash = `4`,
		bool	useHs = `true`,
		double	tgtDensity = `0.0`,
		unsigned int	minSize = `128`
	)

Generates a topological (Daylight like) fingerprint for a molecule using an alternate (faster) hashing algorithm.

Parameters:

	mol,:	the molecule to be fingerprinted
	minPath,:	the minimum path length (in bonds) to be included
	maxPath,:	the minimum path length (in bonds) to be included
	fpSize,:	the size of the fingerprint
	nBitsPerHash,:	the number of bits to be set by each path
	useHs,:	toggles inclusion of Hs in distinguishing paths from each other.
	tgtDensity,:	if the generated fingerprint is below this density, it will be folded until the density is reached.
	minSize,:	the minimum size to which the fingerprint will be folded

Returns:: the molecular fingerprint, as an ExplicitBitVect

Notes:

the caller is responsible for deleteing the result

MOL_SPTR_VECT RDKit::readFuncGroups	(	std::istream &	inStream,
		int	nToRead = `-1`
	)

MOL_SPTR_VECT RDKit::readFuncGroups ( std::string fileName )

unsigned int RDKit::readPackedIntFromStream ( std::stringstream & ss ) [inline]

Reads an integer from a stream in packed format and returns the result.

Definition at line 63 of file StreamOps.h.

void RDKit::removeDuplicates ( std::vector< MatchVectType > & v )

ROMol* RDKit::replaceCore	(	const ROMol &	mol,
		const ROMol &	coreQuery,
		bool	replaceDummies = `true`
	)

Returns a copy of an ROMol with the atoms and bonds that do fall within a substructure match removed.

dummy atoms are left to indicate attachment points.

Note that this is essentially identical to the replaceSidechains function, except we invert the query and replace the atoms that *do* match the query.

Parameters:

	mol	- the ROMol of interest
	coreQuery	- a query ROMol to be used to match the core
	replaceDummies	- if set, atoms matching dummies in the core will also be replaced

Returns:: a copy of mol with the non-matching atoms and bonds (if any) removed and dummies at the connection points. The client is responsible for deleting this molecule

ROMol* RDKit::replaceSidechains	(	const ROMol &	mol,
		const ROMol &	coreQuery
	)

Returns a copy of an ROMol with the atoms and bonds that don't fall within a substructure match removed.

dummy atoms are left to indicate attachment points.

Parameters:

	mol	the ROMol of interest
	coreQuery	a query ROMol to be used to match the core

Returns:: a copy of mol with the non-matching atoms and bonds (if any) removed and dummies at the connection points.

std::vector<ROMOL_SPTR> RDKit::replaceSubstructs	(	const ROMol &	mol,
		const ROMol &	query,
		const ROMol &	replacement,
		bool	replaceAll = `false`
	)

Returns a list of copies of an ROMol with the atoms and bonds that match a pattern replaced with the atoms contained in another molecule.

Bonds are created between the joining atom in the existing molecule and the atoms in the new molecule. So, using SMILES instead of molecules: replaceSubstructs('OC(=O)NCCNC(=O)O','C(=O)O','[X]') -> ['[X]NCCNC(=O)O','OC(=O)NCCN[X]'] replaceSubstructs('OC(=O)NCCNC(=O)O','C(=O)O','[X]',true) -> ['[X]NCCN[X]'] Chains should be handled "correctly": replaceSubstructs('CC(=O)C','C(=O)','[X]') -> ['C[X]C'] As should rings: replaceSubstructs('C1C(=O)C1','C(=O)','[X]') -> ['C1[X]C1'] And higher order branches: replaceSubstructs('CC(=O)(C)C','C(=O)','[X]') -> ['C[X](C)C'] Note that the client is responsible for making sure that the resulting molecule actually makes sense - this function does not perform sanitization.

Parameters:

	mol	the ROMol of interest
	query	the query ROMol
	replacement	the ROMol to be inserted
	replaceAll	if this is true, only a single result, with all occurances of the substructure replaced, will be returned.

Returns:: a vector of pointers to copies of mol with the matching atoms and bonds (if any) replaced

double RDKit::round ( double v )

rounds a value to the closest int

Referenced by queryAtomMass().

ChemicalReaction* RDKit::RxnBlockToChemicalReaction ( const std::string & rxnBlock )

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

ChemicalReaction* RDKit::RxnDataStreamToChemicalReaction	(	std::istream &	rxnStream,
		unsigned int &	line
	)

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

ChemicalReaction* RDKit::RxnFileToChemicalReaction ( const std::string & fileName )

Parse a file in MDL rxn format into a ChemicalReaction.

ChemicalReaction* RDKit::RxnSmartsToChemicalReaction ( const std::string & text )

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)

RWMol* RDKit::SmartsToMol	(	std::string	sma,
		int	debugParse = `0`,
		bool	mergeHs = `false`
	)

RWMol* RDKit::SmilesToMol	(	std::string	smi,
		int	debugParse = `0`,
		bool	sanitize = `1`
	)

template<typename T>

void RDKit::streamRead	(	std::istream &	ss,
		T &	loc
	)			`[inline]`

does a binary read of an object from a stream

Definition at line 155 of file StreamOps.h.

Referenced by RDCatalog::HierarchCatalog< entryType, paramType, orderType >::initFromStream().

template<typename T>

void RDKit::streamWrite	(	std::ostream &	ss,
		const T &	val
	)			`[inline]`

does a binary write of an object to a stream

Definition at line 150 of file StreamOps.h.

Referenced by RDCatalog::HierarchCatalog< entryType, paramType, orderType >::toStream().

std::string RDKit::strip ( const std::string & orig )

bool RDKit::substructHeadVisitor	(	int	n,
		node_id	ni1[],
		node_id	ni2[],
		void *	mvp
	)

unsigned int RDKit::SubstructMatch	(	AR_MOLGRAPH *	molG,
		const ROMol &	query,
		std::vector< MatchVectType > &	matchVect,
		bool	uniquify = `true`,
		bool	recursionPossible = `true`,
		bool	useChirality = `false`,
		bool	registerQuery = `false`
	)

unsigned int RDKit::SubstructMatch	(	const ROMol &	mol,
		const ROMol &	query,
		std::vector< MatchVectType > &	matchVect,
		bool	uniquify = `true`,
		bool	recursionPossible = `true`,
		bool	useChirality = `false`,
		bool	registerQuery = `false`
	)

Find all substructure matches for a query in a molecule.

Parameters:

	mol	The ROMol to be searched
	query	The query ROMol
	matchVect	Used to return the matches (pre-existing contents will be deleted)
	uniquify	Toggles uniquification (by atom index) of the results
	recursionPossible	flags whether or not recursive matches are allowed
	useChirality	use atomic CIP codes as part of the comparison
	registerQuery	cache the query (uses more memory but speeds up searches)

Returns:: the number of matches found

bool RDKit::SubstructMatch	(	AR_MOLGRAPH *	molG,
		const ROMol &	query,
		MatchVectType &	matchVect,
		bool	recursionPossible = `true`,
		bool	useChirality = `false`,
		bool	registerQuery = `false`
	)

bool RDKit::SubstructMatch	(	const ROMol &	mol,
		const ROMol &	query,
		MatchVectType &	matchVect,
		bool	recursionPossible = `true`,
		bool	useChirality = `false`,
		bool	registerQuery = `false`
	)

Find a substructure match for a query in a molecule.

Parameters:

	mol	The ROMol to be searched
	query	The query ROMol
	matchVect	Used to return the match (pre-existing contents will be deleted)
	recursionPossible	flags whether or not recursive matches are allowed
	useChirality	use atomic CIP codes as part of the comparison
	registerQuery	cache the query (uses more memory but speeds up searches)

Returns:: whether or not a match was found

bool RDKit::substructVisitor	(	int	n,
		node_id	ni1[],
		node_id	ni2[],
		void *	mvp
	)

double RDKit::toPrime ( const MatchVectType & v )

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

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

Parameters:

	inStream,:	the stream from which to read
	line,:	used to track the line number of errors
	sanitize,:	toggles sanitization of the molecule
	skipFirstConf,:	according 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.

RWMol* RDKit::TPLFileToMol	(	std::string	fName,
		bool	sanitize = `true`,
		bool	skipFirstConf = `false`
	)

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

Parameters:

	fName,:	the name of the file from which to read
	sanitize,:	toggles sanitization of the molecule
	skipFirstConf,:	according 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.