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types.h
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//
// Copyright 2001-2021 Greg Landrum and other RDKit contributors
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include <RDGeneral/export.h>
#ifndef RD_TYPES_H
#define RD_TYPES_H
#ifdef WIN32
#ifndef _USE_MATH_DEFINES
#define _USE_MATH_DEFINES
#define _DEFINED_USE_MATH_DEFINES
#endif
#endif
#include <cmath>
#ifdef _DEFINED_USE_MATH_DEFINES
#undef _DEFINED_USE_MATH_DEFINES
#undef _USE_MATH_DEFINES
#endif
#include "Invariant.h"
#include "Dict.h"
#include <vector>
#include <deque>
#include <map>
#include <set>
#include <string>
#include <algorithm>
#include <numeric>
#include <list>
#include <limits>
#include <cstring>
#include <any>
#include <RDGeneral/BoostStartInclude.h>
#include <boost/lexical_cast.hpp>
#include <RDGeneral/BoostEndInclude.h>
namespace RDKit {
namespace detail {
// used in various places for computed properties
RDKIT_RDGENERAL_EXPORT extern const std::string computedPropName;
} // namespace detail
namespace common_properties {
///////////////////////////////////////////////////////////////
// Molecule Props
RDKIT_RDGENERAL_EXPORT extern const std::string _Name; // string
RDKIT_RDGENERAL_EXPORT extern const std::string MolFileInfo; // string
RDKIT_RDGENERAL_EXPORT extern const std::string MolFileComments; // string
RDKIT_RDGENERAL_EXPORT extern const std::string
_2DConf; // int (combine into dimension?)
RDKIT_RDGENERAL_EXPORT extern const std::string _3DConf; // int
RDKIT_RDGENERAL_EXPORT extern const std::string
_doIsoSmiles; // int (should probably be removed)
RDKIT_RDGENERAL_EXPORT extern const std::string extraRings; // vec<vec<int> >
RDKIT_RDGENERAL_EXPORT extern const std::string
_smilesAtomOutputOrder; // vec<int> computed
RDKIT_RDGENERAL_EXPORT extern const std::string
_smilesBondOutputOrder; // vec<int> computed
RDKIT_RDGENERAL_EXPORT extern const std::string _StereochemDone; // int
RDKIT_RDGENERAL_EXPORT extern const std::string _NeedsQueryScan; // int (bool)
RDKIT_RDGENERAL_EXPORT extern const std::string _fragSMARTS; // std::string
RDKIT_RDGENERAL_EXPORT extern const std::string
maxAttachIdx; // int TemplEnumTools.cpp
RDKIT_RDGENERAL_EXPORT extern const std::string
ringMembership; //? unused (molopstest.cpp)
// Computed Values
// ConnectivityDescriptors
RDKIT_RDGENERAL_EXPORT extern const std::string
_connectivityHKDeltas; // std::vector<double> computed
RDKIT_RDGENERAL_EXPORT extern const std::string
_connectivityNVals; // std::vector<double> computed
RDKIT_RDGENERAL_EXPORT extern const std::string
_crippenLogP; // double computed
RDKIT_RDGENERAL_EXPORT extern const std::string
_crippenLogPContribs; // std::vector<double> computed
RDKIT_RDGENERAL_EXPORT extern const std::string _crippenMR; // double computed
RDKIT_RDGENERAL_EXPORT extern const std::string
_crippenMRContribs; // std::vector<double> computed
RDKIT_RDGENERAL_EXPORT extern const std::string _labuteASA; // double computed
RDKIT_RDGENERAL_EXPORT extern const std::string
_labuteAtomContribs; // vec<double> computed
RDKIT_RDGENERAL_EXPORT extern const std::string
_labuteAtomHContrib; // double computed
RDKIT_RDGENERAL_EXPORT extern const std::string _tpsa; // double computed
RDKIT_RDGENERAL_EXPORT extern const std::string
_tpsaAtomContribs; // vec<double> computed
RDKIT_RDGENERAL_EXPORT extern const std::string
numArom; // int computed (only uses in tests?)
RDKIT_RDGENERAL_EXPORT extern const std::string
_MMFFSanitized; // int (bool) computed
RDKIT_RDGENERAL_EXPORT extern const std::string
_CrippenLogP; // Unused (in the basement)
RDKIT_RDGENERAL_EXPORT extern const std::string
_CrippenMR; // Unused (in the basement)
RDKIT_RDGENERAL_EXPORT extern const std::string
_GasteigerCharge; // used to hold partial charges
RDKIT_RDGENERAL_EXPORT extern const std::string
_GasteigerHCharge; // used to hold partial charges from implicit Hs
///////////////////////////////////////////////////////////////
// Atom Props
// Chirality stuff
RDKIT_RDGENERAL_EXPORT extern const std::string
_BondsPotentialStereo; // int (or bool) COMPUTED
RDKIT_RDGENERAL_EXPORT extern const std::string
_CIPCode; // std::string COMPUTED
RDKIT_RDGENERAL_EXPORT extern const std::string _CIPRank; // int COMPUTED
RDKIT_RDGENERAL_EXPORT extern const std::string
_CanonicalRankingNumber; // unsigned int
RDKIT_RDGENERAL_EXPORT extern const std::string _ChiralityPossible; // int
RDKIT_RDGENERAL_EXPORT extern const std::string
_UnknownStereo; // int (bool) AddHs/Chirality
RDKIT_RDGENERAL_EXPORT extern const std::string
_ringStereoAtoms; // int vect Canon/Chiral/MolHash/MolOps//Renumber//RWmol
RDKIT_RDGENERAL_EXPORT extern const std::string
_ringStereochemCand; // chirality bool COMPUTED
RDKIT_RDGENERAL_EXPORT extern const std::string
_ringStereoWarning; // obsolete ?
RDKIT_RDGENERAL_EXPORT extern const std::string _chiralPermutation; // int
RDKIT_RDGENERAL_EXPORT extern const std::string _ringStereoOtherAtom; // int
RDKIT_RDGENERAL_EXPORT extern const std::string _mesoOtherAtom; // int
// Smiles parsing
RDKIT_RDGENERAL_EXPORT extern const std::string _SmilesStart; // int
RDKIT_RDGENERAL_EXPORT extern const std::string
_TraversalBondIndexOrder; // ? unused
RDKIT_RDGENERAL_EXPORT extern const std::string
_TraversalRingClosureBond; // unsigned int
RDKIT_RDGENERAL_EXPORT extern const std::string _TraversalStartPoint; // bool
RDKIT_RDGENERAL_EXPORT extern const std::string
_queryRootAtom; // int SLNParse/SubstructMatch
RDKIT_RDGENERAL_EXPORT extern const std::string _hasMassQuery; // atom bool
RDKIT_RDGENERAL_EXPORT extern const std::string _protected; // atom int (bool)
RDKIT_RDGENERAL_EXPORT extern const std::string
_ChiralAtomRank; // atom rank (unsigned int)
RDKIT_RDGENERAL_EXPORT extern const std::string
_supplementalSmilesLabel; // atom string (SmilesWrite)
RDKIT_RDGENERAL_EXPORT extern const std::string
_unspecifiedOrder; // atom int (bool) smarts/smiles
RDKIT_RDGENERAL_EXPORT extern const std::string
_RingClosures; // INT_VECT smarts/smiles/canon
RDKIT_RDGENERAL_EXPORT extern const std::string
atomLabel; // atom string from CXSMILES
RDKIT_RDGENERAL_EXPORT extern const std::string OxidationNumber; // int
// MDL Style Properties (MolFileParser)
RDKIT_RDGENERAL_EXPORT extern const std::string molAtomMapNumber; // int
RDKIT_RDGENERAL_EXPORT extern const std::string molFileAlias; // string
RDKIT_RDGENERAL_EXPORT extern const std::string molFileValue; // string
RDKIT_RDGENERAL_EXPORT extern const std::string molInversionFlag; // int
RDKIT_RDGENERAL_EXPORT extern const std::string molParity; // int
RDKIT_RDGENERAL_EXPORT extern const std::string molStereoCare; // int
RDKIT_RDGENERAL_EXPORT extern const std::string molRxnComponent; // int
RDKIT_RDGENERAL_EXPORT extern const std::string molRxnRole; // int
RDKIT_RDGENERAL_EXPORT extern const std::string molTotValence; // int
RDKIT_RDGENERAL_EXPORT extern const std::string molRingBondCount; // int
RDKIT_RDGENERAL_EXPORT extern const std::string molSubstCount; // int
RDKIT_RDGENERAL_EXPORT extern const std::string molAttachPoint; // int
RDKIT_RDGENERAL_EXPORT extern const std::string molAttachOrder; // int
RDKIT_RDGENERAL_EXPORT extern const std::string molAtomClass; // string
RDKIT_RDGENERAL_EXPORT extern const std::string molAtomSeqId; // int
RDKIT_RDGENERAL_EXPORT extern const std::string molRxnExactChange; // int
RDKIT_RDGENERAL_EXPORT extern const std::string molReactStatus; // int
RDKIT_RDGENERAL_EXPORT extern const std::string molFileLinkNodes; // string
RDKIT_RDGENERAL_EXPORT extern const std::string _fromAttachPoint; // int
RDKIT_RDGENERAL_EXPORT extern const std::string _MolFileRLabel; // unsigned int
RDKIT_RDGENERAL_EXPORT extern const std::string _MolFileChiralFlag; // int
RDKIT_RDGENERAL_EXPORT extern const std::string _MolFileAtomQuery; // int
RDKIT_RDGENERAL_EXPORT extern const std::string _MolFileBondQuery; // int
RDKIT_RDGENERAL_EXPORT extern const std::string _MolFileBondEndPts; // string
RDKIT_RDGENERAL_EXPORT extern const std::string _MolFileBondAttach; // string
RDKIT_RDGENERAL_EXPORT extern const std::string
_MolFileBondType; // unsigned int
RDKIT_RDGENERAL_EXPORT extern const std::string
_MolFileBondStereo; // unsigned int
RDKIT_RDGENERAL_EXPORT extern const std::string
_MolFileBondCfg; // unsigned int
RDKIT_RDGENERAL_EXPORT extern const std::string
MRV_SMA; // smarts string from Marvin
// flag indicating that the chirality wasn't specified in the input,
// but was calculated from 3D coordinates in the input
RDKIT_RDGENERAL_EXPORT extern const std::string _NonExplicit3DChirality; // int
RDKIT_RDGENERAL_EXPORT extern const std::string dummyLabel; // atom string
RDKIT_RDGENERAL_EXPORT extern const std::string
_QueryAtomGenericLabel; // string
// Reaction Information (Reactions.cpp)
RDKIT_RDGENERAL_EXPORT extern const std::string _QueryFormalCharge; // int
RDKIT_RDGENERAL_EXPORT extern const std::string _QueryHCount; // int
RDKIT_RDGENERAL_EXPORT extern const std::string _QueryIsotope; // int
RDKIT_RDGENERAL_EXPORT extern const std::string
_QueryMass; // int = round(float * 1000)
RDKIT_RDGENERAL_EXPORT extern const std::string
_ReactionDegreeChanged; // int (bool)
RDKIT_RDGENERAL_EXPORT extern const std::string NullBond; // int (bool)
RDKIT_RDGENERAL_EXPORT extern const std::string _rgroupAtomMaps;
RDKIT_RDGENERAL_EXPORT extern const std::string _rgroupBonds;
RDKIT_RDGENERAL_EXPORT extern const std::string _rgroupTargetAtoms;
RDKIT_RDGENERAL_EXPORT extern const std::string _rgroupTargetBonds;
RDKIT_RDGENERAL_EXPORT extern const std::string reactantAtomIdx;
RDKIT_RDGENERAL_EXPORT extern const std::string reactionMapNum;
RDKIT_RDGENERAL_EXPORT extern const std::string reactantIdx;
// SLN
RDKIT_RDGENERAL_EXPORT extern const std::string
_AtomID; // unsigned int SLNParser
RDKIT_RDGENERAL_EXPORT extern const std::string
_starred; // atom int COMPUTED (SLN)
RDKIT_RDGENERAL_EXPORT extern const std::string
_SLN_s; // string SLNAttribs (chiral info)
RDKIT_RDGENERAL_EXPORT extern const std::string _Unfinished_SLN_; // int (bool)
// Smarts Smiles
RDKIT_RDGENERAL_EXPORT extern const std::string _brokenChirality; // atom bool
RDKIT_RDGENERAL_EXPORT extern const std::string isImplicit; // atom int (bool)
RDKIT_RDGENERAL_EXPORT extern const std::string
smilesSymbol; // atom string (only used in test?)
// Tripos
RDKIT_RDGENERAL_EXPORT extern const std::string
_TriposAtomType; // string Mol2FileParser
// missing defs for _TriposAtomName//_TriposPartialCharge...
// molecule drawing
RDKIT_RDGENERAL_EXPORT extern const std::string _displayLabel; // string
RDKIT_RDGENERAL_EXPORT extern const std::string _displayLabelW; // string
///////////////////////////////////////////////////////////////
// misc props
RDKIT_RDGENERAL_EXPORT extern const std::string
TWOD; // need THREED -> confusing using in TDTMol supplier
// converge with _2DConf?
RDKIT_RDGENERAL_EXPORT extern const std::string BalabanJ; // mol double
RDKIT_RDGENERAL_EXPORT extern const std::string BalanbanJ; // typo!! fix...
RDKIT_RDGENERAL_EXPORT extern const std::string Discrims; // FragCatalog Entry
// Subgraphs::DiscrimTuple (uint32,uint32,uint32)
RDKIT_RDGENERAL_EXPORT extern const std::string
DistanceMatrix_Paths; // boost::shared_array<double>
// - note, confusing creation of names in
// - getDistanceMat
RDKIT_RDGENERAL_EXPORT extern const std::string internalRgroupSmiles;
RDKIT_RDGENERAL_EXPORT extern const std::string molNote;
RDKIT_RDGENERAL_EXPORT extern const std::string atomNote;
RDKIT_RDGENERAL_EXPORT extern const std::string bondNote;
RDKIT_RDGENERAL_EXPORT extern const std::string _isotopicHs;
} // namespace common_properties
#ifndef WIN32
typedef long long int LONGINT;
#else
typedef __int64 LONGINT;
#endif
#ifdef max
#undef max // FUCK I hate this nonsense
#endif
#ifdef min
#undef min // FUCK I hate this nonsense
#endif
RDKIT_RDGENERAL_EXPORT extern const double MAX_DOUBLE;
RDKIT_RDGENERAL_EXPORT extern const double EPS_DOUBLE;
RDKIT_RDGENERAL_EXPORT extern const double SMALL_DOUBLE;
RDKIT_RDGENERAL_EXPORT extern const double MAX_INT;
RDKIT_RDGENERAL_EXPORT extern const double MAX_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;
//! functor to compare two doubles with a tolerance
struct RDKIT_RDGENERAL_EXPORT ltDouble {
public:
ltDouble() {}
bool operator()(double d1, double d2) const {
if (fabs(d1 - d2) < _tol) {
return false;
} else {
return (d1 < d2);
}
}
private:
double _tol{1.0e-8};
};
//! std::map from double to integer.
typedef std::map<double, int, ltDouble> DOUBLE_INT_MAP;
//! functor for returning the larger of two values
template <typename T>
struct RDKIT_RDGENERAL_EXPORT larger_of {
T operator()(T arg1, T arg2) { return arg1 > arg2 ? arg1 : arg2; }
};
//! functor for comparing two strings
struct RDKIT_RDGENERAL_EXPORT charptr_functor {
bool operator()(const char *s1, const char *s2) const {
// std::cout << s1 << " " << s2 << " " << strcmp(s1, s2) << "\n";
return strcmp(s1, s2) < 0;
}
};
//! \brief calculate the union of two INT_VECTs and put the results in a
//! third vector
RDKIT_RDGENERAL_EXPORT void Union(const INT_VECT &r1, const INT_VECT &r2,
INT_VECT &res);
//! \brief calculate the intersection of two INT_VECTs and put the results in a
//! third vector
RDKIT_RDGENERAL_EXPORT void Intersect(const INT_VECT &r1, const INT_VECT &r2,
INT_VECT &res);
//! calculating the union of the INT_VECT's in a VECT_INT_VECT
/*!
\param rings the INT_VECT's to consider
\param res used to return results
\param exclude any values in this optional INT_VECT will be excluded
from the union.
*/
RDKIT_RDGENERAL_EXPORT void Union(const VECT_INT_VECT &rings, INT_VECT &res,
const INT_VECT *exclude = nullptr);
//! given a current combination of numbers change it to the next possible
// combination
/*!
\param comb the <b>sorted</b> vector to consider
\param tot the maximum number possible in the vector
\return -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.
*/
RDKIT_RDGENERAL_EXPORT int nextCombination(INT_VECT &comb, int tot);
}; // namespace RDKit
#endif
BoostEndInclude.h
BoostStartInclude.h
Dict.h
Defines the Dict class.
Invariant.h
export.h
RDKIT_RDGENERAL_EXPORT
#define RDKIT_RDGENERAL_EXPORT
Definition export.h:409
RDKit::common_properties::_ringStereoWarning
RDKIT_RDGENERAL_EXPORT const std::string _ringStereoWarning
RDKit::common_properties::_MolFileBondQuery
RDKIT_RDGENERAL_EXPORT const std::string _MolFileBondQuery
RDKit::common_properties::smilesSymbol
RDKIT_RDGENERAL_EXPORT const std::string smilesSymbol
RDKit::common_properties::_TriposAtomType
RDKIT_RDGENERAL_EXPORT const std::string _TriposAtomType
RDKit::common_properties::_RingClosures
RDKIT_RDGENERAL_EXPORT const std::string _RingClosures
RDKit::common_properties::bondNote
RDKIT_RDGENERAL_EXPORT const std::string bondNote
RDKit::common_properties::_QueryHCount
RDKIT_RDGENERAL_EXPORT const std::string _QueryHCount
RDKit::common_properties::molRingBondCount
RDKIT_RDGENERAL_EXPORT const std::string molRingBondCount
RDKit::common_properties::_labuteASA
RDKIT_RDGENERAL_EXPORT const std::string _labuteASA
RDKit::common_properties::_supplementalSmilesLabel
RDKIT_RDGENERAL_EXPORT const std::string _supplementalSmilesLabel
RDKit::common_properties::molStereoCare
RDKIT_RDGENERAL_EXPORT const std::string molStereoCare
RDKit::common_properties::MolFileComments
RDKIT_RDGENERAL_EXPORT const std::string MolFileComments
RDKit::common_properties::molInversionFlag
RDKIT_RDGENERAL_EXPORT const std::string molInversionFlag
RDKit::common_properties::DistanceMatrix_Paths
RDKIT_RDGENERAL_EXPORT const std::string DistanceMatrix_Paths
RDKit::common_properties::maxAttachIdx
RDKIT_RDGENERAL_EXPORT const std::string maxAttachIdx
RDKit::common_properties::_3DConf
RDKIT_RDGENERAL_EXPORT const std::string _3DConf
RDKit::common_properties::_NeedsQueryScan
RDKIT_RDGENERAL_EXPORT const std::string _NeedsQueryScan
RDKit::common_properties::atomNote
RDKIT_RDGENERAL_EXPORT const std::string atomNote
RDKit::common_properties::reactionMapNum
RDKIT_RDGENERAL_EXPORT const std::string reactionMapNum
RDKit::common_properties::reactantIdx
RDKIT_RDGENERAL_EXPORT const std::string reactantIdx
RDKit::common_properties::_ChiralityPossible
RDKIT_RDGENERAL_EXPORT const std::string _ChiralityPossible
RDKit::common_properties::isImplicit
RDKIT_RDGENERAL_EXPORT const std::string isImplicit
RDKit::common_properties::_2DConf
RDKIT_RDGENERAL_EXPORT const std::string _2DConf
RDKit::common_properties::dummyLabel
RDKIT_RDGENERAL_EXPORT const std::string dummyLabel
RDKit::common_properties::_fromAttachPoint
RDKIT_RDGENERAL_EXPORT const std::string _fromAttachPoint
RDKit::common_properties::_rgroupTargetAtoms
RDKIT_RDGENERAL_EXPORT const std::string _rgroupTargetAtoms
RDKit::common_properties::_doIsoSmiles
RDKIT_RDGENERAL_EXPORT const std::string _doIsoSmiles
RDKit::common_properties::_QueryMass
RDKIT_RDGENERAL_EXPORT const std::string _QueryMass
RDKit::common_properties::_QueryFormalCharge
RDKIT_RDGENERAL_EXPORT const std::string _QueryFormalCharge
RDKit::common_properties::_labuteAtomHContrib
RDKIT_RDGENERAL_EXPORT const std::string _labuteAtomHContrib
RDKit::common_properties::_connectivityNVals
RDKIT_RDGENERAL_EXPORT const std::string _connectivityNVals
RDKit::common_properties::BalanbanJ
RDKIT_RDGENERAL_EXPORT const std::string BalanbanJ
RDKit::common_properties::_unspecifiedOrder
RDKIT_RDGENERAL_EXPORT const std::string _unspecifiedOrder
RDKit::common_properties::_ringStereoAtoms
RDKIT_RDGENERAL_EXPORT const std::string _ringStereoAtoms
RDKit::common_properties::_NonExplicit3DChirality
RDKIT_RDGENERAL_EXPORT const std::string _NonExplicit3DChirality
RDKit::common_properties::molRxnRole
RDKIT_RDGENERAL_EXPORT const std::string molRxnRole
RDKit::common_properties::_SmilesStart
RDKIT_RDGENERAL_EXPORT const std::string _SmilesStart
RDKit::common_properties::_MolFileBondType
RDKIT_RDGENERAL_EXPORT const std::string _MolFileBondType
RDKit::common_properties::molFileValue
RDKIT_RDGENERAL_EXPORT const std::string molFileValue
RDKit::common_properties::_CanonicalRankingNumber
RDKIT_RDGENERAL_EXPORT const std::string _CanonicalRankingNumber
RDKit::common_properties::_fragSMARTS
RDKIT_RDGENERAL_EXPORT const std::string _fragSMARTS
RDKit::common_properties::molTotValence
RDKIT_RDGENERAL_EXPORT const std::string molTotValence
RDKit::common_properties::_connectivityHKDeltas
RDKIT_RDGENERAL_EXPORT const std::string _connectivityHKDeltas
RDKit::common_properties::_crippenLogP
RDKIT_RDGENERAL_EXPORT const std::string _crippenLogP
RDKit::common_properties::_QueryAtomGenericLabel
RDKIT_RDGENERAL_EXPORT const std::string _QueryAtomGenericLabel
RDKit::common_properties::_TraversalStartPoint
RDKIT_RDGENERAL_EXPORT const std::string _TraversalStartPoint
RDKit::common_properties::_GasteigerCharge
RDKIT_RDGENERAL_EXPORT const std::string _GasteigerCharge
RDKit::common_properties::molAttachPoint
RDKIT_RDGENERAL_EXPORT const std::string molAttachPoint
RDKit::common_properties::molAtomClass
RDKIT_RDGENERAL_EXPORT const std::string molAtomClass
RDKit::common_properties::_MolFileAtomQuery
RDKIT_RDGENERAL_EXPORT const std::string _MolFileAtomQuery
RDKit::common_properties::TWOD
RDKIT_RDGENERAL_EXPORT const std::string TWOD
RDKit::common_properties::_protected
RDKIT_RDGENERAL_EXPORT const std::string _protected
RDKit::common_properties::_displayLabelW
RDKIT_RDGENERAL_EXPORT const std::string _displayLabelW
RDKit::common_properties::_TraversalRingClosureBond
RDKIT_RDGENERAL_EXPORT const std::string _TraversalRingClosureBond
RDKit::common_properties::_Unfinished_SLN_
RDKIT_RDGENERAL_EXPORT const std::string _Unfinished_SLN_
RDKit::common_properties::_CrippenMR
RDKIT_RDGENERAL_EXPORT const std::string _CrippenMR
RDKit::common_properties::_brokenChirality
RDKIT_RDGENERAL_EXPORT const std::string _brokenChirality
RDKit::common_properties::ringMembership
RDKIT_RDGENERAL_EXPORT const std::string ringMembership
RDKit::common_properties::molFileLinkNodes
RDKIT_RDGENERAL_EXPORT const std::string molFileLinkNodes
RDKit::common_properties::_MolFileRLabel
RDKIT_RDGENERAL_EXPORT const std::string _MolFileRLabel
RDKit::common_properties::_MolFileBondAttach
RDKIT_RDGENERAL_EXPORT const std::string _MolFileBondAttach
RDKit::common_properties::molRxnComponent
RDKIT_RDGENERAL_EXPORT const std::string molRxnComponent
RDKit::common_properties::MRV_SMA
RDKIT_RDGENERAL_EXPORT const std::string MRV_SMA
RDKit::common_properties::_ringStereoOtherAtom
RDKIT_RDGENERAL_EXPORT const std::string _ringStereoOtherAtom
RDKit::common_properties::_MolFileBondEndPts
RDKIT_RDGENERAL_EXPORT const std::string _MolFileBondEndPts
RDKit::common_properties::_queryRootAtom
RDKIT_RDGENERAL_EXPORT const std::string _queryRootAtom
RDKit::common_properties::numArom
RDKIT_RDGENERAL_EXPORT const std::string numArom
RDKit::common_properties::_rgroupBonds
RDKIT_RDGENERAL_EXPORT const std::string _rgroupBonds
RDKit::common_properties::MolFileInfo
RDKIT_RDGENERAL_EXPORT const std::string MolFileInfo
RDKit::common_properties::molNote
RDKIT_RDGENERAL_EXPORT const std::string molNote
RDKit::common_properties::_crippenMR
RDKIT_RDGENERAL_EXPORT const std::string _crippenMR
RDKit::common_properties::_GasteigerHCharge
RDKIT_RDGENERAL_EXPORT const std::string _GasteigerHCharge
RDKit::common_properties::_UnknownStereo
RDKIT_RDGENERAL_EXPORT const std::string _UnknownStereo
RDKit::common_properties::_smilesBondOutputOrder
RDKIT_RDGENERAL_EXPORT const std::string _smilesBondOutputOrder
RDKit::common_properties::OxidationNumber
RDKIT_RDGENERAL_EXPORT const std::string OxidationNumber
RDKit::common_properties::_TraversalBondIndexOrder
RDKIT_RDGENERAL_EXPORT const std::string _TraversalBondIndexOrder
RDKit::common_properties::_rgroupAtomMaps
RDKIT_RDGENERAL_EXPORT const std::string _rgroupAtomMaps
RDKit::common_properties::_CIPCode
RDKIT_RDGENERAL_EXPORT const std::string _CIPCode
RDKit::common_properties::_BondsPotentialStereo
RDKIT_RDGENERAL_EXPORT const std::string _BondsPotentialStereo
RDKit::common_properties::_Name
RDKIT_RDGENERAL_EXPORT const std::string _Name
RDKit::common_properties::_QueryIsotope
RDKIT_RDGENERAL_EXPORT const std::string _QueryIsotope
RDKit::common_properties::molAtomMapNumber
RDKIT_RDGENERAL_EXPORT const std::string molAtomMapNumber
RDKit::common_properties::_CIPRank
RDKIT_RDGENERAL_EXPORT const std::string _CIPRank
RDKit::common_properties::_hasMassQuery
RDKIT_RDGENERAL_EXPORT const std::string _hasMassQuery
RDKit::common_properties::_ReactionDegreeChanged
RDKIT_RDGENERAL_EXPORT const std::string _ReactionDegreeChanged
RDKit::common_properties::molParity
RDKIT_RDGENERAL_EXPORT const std::string molParity
RDKit::common_properties::_mesoOtherAtom
RDKIT_RDGENERAL_EXPORT const std::string _mesoOtherAtom
RDKit::common_properties::_rgroupTargetBonds
RDKIT_RDGENERAL_EXPORT const std::string _rgroupTargetBonds
RDKit::common_properties::_CrippenLogP
RDKIT_RDGENERAL_EXPORT const std::string _CrippenLogP
RDKit::common_properties::molRxnExactChange
RDKIT_RDGENERAL_EXPORT const std::string molRxnExactChange
RDKit::common_properties::_displayLabel
RDKIT_RDGENERAL_EXPORT const std::string _displayLabel
RDKit::common_properties::molAttachOrder
RDKIT_RDGENERAL_EXPORT const std::string molAttachOrder
RDKit::common_properties::molAtomSeqId
RDKIT_RDGENERAL_EXPORT const std::string molAtomSeqId
RDKit::common_properties::BalabanJ
RDKIT_RDGENERAL_EXPORT const std::string BalabanJ
RDKit::common_properties::extraRings
RDKIT_RDGENERAL_EXPORT const std::string extraRings
RDKit::common_properties::atomLabel
RDKIT_RDGENERAL_EXPORT const std::string atomLabel
RDKit::common_properties::_isotopicHs
RDKIT_RDGENERAL_EXPORT const std::string _isotopicHs
RDKit::common_properties::_MMFFSanitized
RDKIT_RDGENERAL_EXPORT const std::string _MMFFSanitized
RDKit::common_properties::_labuteAtomContribs
RDKIT_RDGENERAL_EXPORT const std::string _labuteAtomContribs
RDKit::common_properties::_tpsa
RDKIT_RDGENERAL_EXPORT const std::string _tpsa
RDKit::common_properties::_MolFileBondStereo
RDKIT_RDGENERAL_EXPORT const std::string _MolFileBondStereo
RDKit::common_properties::molFileAlias
RDKIT_RDGENERAL_EXPORT const std::string molFileAlias
RDKit::common_properties::_StereochemDone
RDKIT_RDGENERAL_EXPORT const std::string _StereochemDone
RDKit::common_properties::_ringStereochemCand
RDKIT_RDGENERAL_EXPORT const std::string _ringStereochemCand
RDKit::common_properties::_MolFileBondCfg
RDKIT_RDGENERAL_EXPORT const std::string _MolFileBondCfg
RDKit::common_properties::_SLN_s
RDKIT_RDGENERAL_EXPORT const std::string _SLN_s
RDKit::common_properties::molSubstCount
RDKIT_RDGENERAL_EXPORT const std::string molSubstCount
RDKit::common_properties::_chiralPermutation
RDKIT_RDGENERAL_EXPORT const std::string _chiralPermutation
RDKit::common_properties::_MolFileChiralFlag
RDKIT_RDGENERAL_EXPORT const std::string _MolFileChiralFlag
RDKit::common_properties::_crippenMRContribs
RDKIT_RDGENERAL_EXPORT const std::string _crippenMRContribs
RDKit::common_properties::reactantAtomIdx
RDKIT_RDGENERAL_EXPORT const std::string reactantAtomIdx
RDKit::common_properties::_ChiralAtomRank
RDKIT_RDGENERAL_EXPORT const std::string _ChiralAtomRank
RDKit::common_properties::Discrims
RDKIT_RDGENERAL_EXPORT const std::string Discrims
RDKit::common_properties::_smilesAtomOutputOrder
RDKIT_RDGENERAL_EXPORT const std::string _smilesAtomOutputOrder
RDKit::common_properties::_AtomID
RDKIT_RDGENERAL_EXPORT const std::string _AtomID
RDKit::common_properties::molReactStatus
RDKIT_RDGENERAL_EXPORT const std::string molReactStatus
RDKit::common_properties::NullBond
RDKIT_RDGENERAL_EXPORT const std::string NullBond
RDKit::common_properties::internalRgroupSmiles
RDKIT_RDGENERAL_EXPORT const std::string internalRgroupSmiles
RDKit::common_properties::_starred
RDKIT_RDGENERAL_EXPORT const std::string _starred
RDKit::common_properties::_tpsaAtomContribs
RDKIT_RDGENERAL_EXPORT const std::string _tpsaAtomContribs
RDKit::common_properties::_crippenLogPContribs
RDKIT_RDGENERAL_EXPORT const std::string _crippenLogPContribs
RDKit::detail::computedPropName
RDKIT_RDGENERAL_EXPORT const std::string computedPropName
RDKit
Std stuff.
Definition Abbreviations.h:19
RDKit::INT_MAP_INT_I
INT_MAP_INT::iterator INT_MAP_INT_I
Definition types.h:331
RDKit::VECT_DOUBLE_VECT_CI
VECT_DOUBLE_VECT::const_iterator VECT_DOUBLE_VECT_CI
Definition types.h:322
RDKit::INT_LIST
std::list< int > INT_LIST
Definition types.h:298
RDKit::LIST_INT_VECT
std::list< INT_VECT > LIST_INT_VECT
Definition types.h:302
RDKit::STR_VECT
std::vector< std::string > STR_VECT
Definition Dict.h:29
RDKit::INT_SET
std::set< int > INT_SET
Definition types.h:341
RDKit::INT_VECT_CI
INT_VECT::const_iterator INT_VECT_CI
Definition types.h:294
RDKit::Intersect
RDKIT_RDGENERAL_EXPORT 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
RDKit::INT_INT_DEQ_MAP_CI
INT_INT_DEQ_MAP::const_iterator INT_INT_DEQ_MAP_CI
Definition types.h:339
RDKit::INT_VECT
std::vector< int > INT_VECT
Definition types.h:292
RDKit::UCHAR
unsigned char UCHAR
Definition types.h:290
RDKit::LONGINT
long long int LONGINT
Definition types.h:271
RDKit::rdvalue_is
bool rdvalue_is(const RDValue_cast_t)
Definition RDValue-doublemagic.h:372
RDKit::INT_SET_CI
INT_SET::const_iterator INT_SET_CI
Definition types.h:343
RDKit::nextCombination
RDKIT_RDGENERAL_EXPORT int nextCombination(INT_VECT &comb, int tot)
given a current combination of numbers change it to the next possible
RDKit::STR_VECT_I
std::vector< std::string >::iterator STR_VECT_I
Definition types.h:314
RDKit::INT_VECT_CRI
INT_VECT::const_reverse_iterator INT_VECT_CRI
Definition types.h:296
RDKit::INT_MAP_INT
std::map< int, int > INT_MAP_INT
Definition types.h:330
RDKit::VECT_INT_VECT
std::vector< INT_VECT > VECT_INT_VECT
Definition types.h:306
RDKit::INT_DEQUE
std::deque< int > INT_DEQUE
Definition types.h:334
RDKit::STR_UINT_MAP
std::map< std::string, UINT > STR_UINT_MAP
Definition types.h:324
RDKit::EPS_DOUBLE
RDKIT_RDGENERAL_EXPORT const double EPS_DOUBLE
RDKit::INT_INT_VECT_MAP
std::map< int, INT_VECT > INT_INT_VECT_MAP
Definition types.h:327
RDKit::INT_INT_DEQ_MAP
std::map< int, INT_DEQUE > INT_INT_DEQ_MAP
Definition types.h:338
RDKit::VECT_DOUBLE_VECT
std::vector< DOUBLE_VECT > VECT_DOUBLE_VECT
Definition types.h:320
RDKit::MAX_LONGINT
RDKIT_RDGENERAL_EXPORT const double MAX_LONGINT
RDKit::INT_DEQUE_I
INT_DEQUE::iterator INT_DEQUE_I
Definition types.h:335
RDKit::INT_LIST_CI
INT_LIST::const_iterator INT_LIST_CI
Definition types.h:300
RDKit::INT_DEQUE_CI
INT_DEQUE::const_iterator INT_DEQUE_CI
Definition types.h:336
RDKit::USHORT
unsigned short USHORT
Definition types.h:289
RDKit::INT_INT_VECT_MAP_CI
INT_INT_VECT_MAP::const_iterator INT_INT_VECT_MAP_CI
Definition types.h:328
RDKit::MAX_INT
RDKIT_RDGENERAL_EXPORT const double MAX_INT
RDKit::DOUBLE_INT_MAP
std::map< double, int, ltDouble > DOUBLE_INT_MAP
std::map from double to integer.
Definition types.h:362
RDKit::INT_VECT_RI
INT_VECT::reverse_iterator INT_VECT_RI
Definition types.h:295
RDKit::INT_SET_I
INT_SET::iterator INT_SET_I
Definition types.h:342
RDKit::UINT_VECT_CI
std::vector< UINT >::const_iterator UINT_VECT_CI
Definition types.h:310
RDKit::INT_MAP_INT_CI
INT_MAP_INT::const_iterator INT_MAP_INT_CI
Definition types.h:332
RDKit::VECT_DOUBLE_VECT_I
VECT_DOUBLE_VECT::iterator VECT_DOUBLE_VECT_I
Definition types.h:321
RDKit::STR_UINT_MAP_CI
std::map< std::string, UINT >::const_iterator STR_UINT_MAP_CI
Definition types.h:325
RDKit::DOUBLE_VECT_CI
DOUBLE_VECT::const_iterator DOUBLE_VECT_CI
Definition types.h:319
RDKit::UINT
unsigned int UINT
Definition types.h:288
RDKit::Union
RDKIT_RDGENERAL_EXPORT 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
RDKit::INT_LIST_I
INT_LIST::iterator INT_LIST_I
Definition types.h:299
RDKit::STR_VECT_CI
std::vector< std::string >::const_iterator STR_VECT_CI
Definition types.h:313
RDKit::LIST_INT_VECT_CI
LIST_INT_VECT::const_iterator LIST_INT_VECT_CI
Definition types.h:304
RDKit::DOUBLE_VECT
std::vector< double > DOUBLE_VECT
Definition types.h:317
RDKit::VECT_INT_VECT_I
VECT_INT_VECT::iterator VECT_INT_VECT_I
Definition types.h:307
RDKit::DOUBLE_VECT_I
DOUBLE_VECT::iterator DOUBLE_VECT_I
Definition types.h:318
RDKit::SMALL_DOUBLE
RDKIT_RDGENERAL_EXPORT const double SMALL_DOUBLE
RDKit::MAX_DOUBLE
RDKIT_RDGENERAL_EXPORT const double MAX_DOUBLE
RDKit::VECT_INT_VECT_CI
VECT_INT_VECT::const_iterator VECT_INT_VECT_CI
Definition types.h:308
RDKit::LIST_INT_VECT_I
LIST_INT_VECT::iterator LIST_INT_VECT_I
Definition types.h:303
RDKit::INT_VECT_I
INT_VECT::iterator INT_VECT_I
Definition types.h:293
RDKit::UINT_VECT
std::vector< UINT > UINT_VECT
Definition types.h:311
RDKit::charptr_functor
functor for comparing two strings
Definition types.h:371
RDKit::charptr_functor::operator()
bool operator()(const char *s1, const char *s2) const
Definition types.h:372
RDKit::larger_of
functor for returning the larger of two values
Definition types.h:366
RDKit::larger_of::operator()
T operator()(T arg1, T arg2)
Definition types.h:367
RDKit::ltDouble
functor to compare two doubles with a tolerance
Definition types.h:346
RDKit::ltDouble::ltDouble
ltDouble()
Definition types.h:348
RDKit::ltDouble::operator()
bool operator()(double d1, double d2) const
Definition types.h:349