RDKit
Open-source cheminformatics and machine learning.
types.h
Go to the documentation of this file.
1//
2// Copyright 2001-2021 Greg Landrum and other RDKit contributors
3//
4// @@ All Rights Reserved @@
5// This file is part of the RDKit.
6// The contents are covered by the terms of the BSD license
7// which is included in the file license.txt, found at the root
8// of the RDKit source tree.
9//
10
11#include <RDGeneral/export.h>
12#ifndef RD_TYPES_H
13#define RD_TYPES_H
14
15#ifdef WIN32
16#ifndef _USE_MATH_DEFINES
17#define _USE_MATH_DEFINES
18#define _DEFINED_USE_MATH_DEFINES
19#endif
20#endif
21#include <cmath>
22#ifdef _DEFINED_USE_MATH_DEFINES
23#undef _DEFINED_USE_MATH_DEFINES
24#undef _USE_MATH_DEFINES
25#endif
26
27#include "Invariant.h"
28#include "Dict.h"
29
30#include <vector>
31#include <deque>
32#include <map>
33#include <set>
34#include <string>
35#include <algorithm>
36#include <numeric>
37#include <list>
38#include <limits>
39
40#include <cstring>
42#include <boost/any.hpp>
43#include <boost/lexical_cast.hpp>
45
46namespace RDKit {
47
48namespace detail {
49// used in various places for computed properties
50RDKIT_RDGENERAL_EXPORT extern const std::string computedPropName;
51} // namespace detail
52
53namespace common_properties {
54///////////////////////////////////////////////////////////////
55// Molecule Props
56RDKIT_RDGENERAL_EXPORT extern const std::string _Name; // string
57RDKIT_RDGENERAL_EXPORT extern const std::string MolFileInfo; // string
58RDKIT_RDGENERAL_EXPORT extern const std::string MolFileComments; // string
59RDKIT_RDGENERAL_EXPORT extern const std::string
60 _2DConf; // int (combine into dimension?)
61RDKIT_RDGENERAL_EXPORT extern const std::string _3DConf; // int
62RDKIT_RDGENERAL_EXPORT extern const std::string
63 _doIsoSmiles; // int (should probably be removed)
64RDKIT_RDGENERAL_EXPORT extern const std::string extraRings; // vec<vec<int> >
65RDKIT_RDGENERAL_EXPORT extern const std::string
66 _smilesAtomOutputOrder; // vec<int> computed
67RDKIT_RDGENERAL_EXPORT extern const std::string
68 _smilesBondOutputOrder; // vec<int> computed
69RDKIT_RDGENERAL_EXPORT extern const std::string _StereochemDone; // int
70RDKIT_RDGENERAL_EXPORT extern const std::string _NeedsQueryScan; // int (bool)
71RDKIT_RDGENERAL_EXPORT extern const std::string _fragSMARTS; // std::string
72RDKIT_RDGENERAL_EXPORT extern const std::string
73 maxAttachIdx; // int TemplEnumTools.cpp
74RDKIT_RDGENERAL_EXPORT extern const std::string origNoImplicit; // int (bool)
75RDKIT_RDGENERAL_EXPORT extern const std::string
76 ringMembership; //? unused (molopstest.cpp)
77
78// Computed Values
79// ConnectivityDescriptors
80RDKIT_RDGENERAL_EXPORT extern const std::string
81 _connectivityHKDeltas; // std::vector<double> computed
82RDKIT_RDGENERAL_EXPORT extern const std::string
83 _connectivityNVals; // std::vector<double> computed
84
85RDKIT_RDGENERAL_EXPORT extern const std::string
86 _crippenLogP; // double computed
87RDKIT_RDGENERAL_EXPORT extern const std::string
88 _crippenLogPContribs; // std::vector<double> computed
89
90RDKIT_RDGENERAL_EXPORT extern const std::string _crippenMR; // double computed
91RDKIT_RDGENERAL_EXPORT extern const std::string
92 _crippenMRContribs; // std::vector<double> computed
93
94RDKIT_RDGENERAL_EXPORT extern const std::string _labuteASA; // double computed
95RDKIT_RDGENERAL_EXPORT extern const std::string
96 _labuteAtomContribs; // vec<double> computed
97RDKIT_RDGENERAL_EXPORT extern const std::string
98 _labuteAtomHContrib; // double computed
99
100RDKIT_RDGENERAL_EXPORT extern const std::string _tpsa; // double computed
101RDKIT_RDGENERAL_EXPORT extern const std::string
102 _tpsaAtomContribs; // vec<double> computed
103
104RDKIT_RDGENERAL_EXPORT extern const std::string
105 numArom; // int computed (only uses in tests?)
106RDKIT_RDGENERAL_EXPORT extern const std::string
107 _MMFFSanitized; // int (bool) computed
108
109RDKIT_RDGENERAL_EXPORT extern const std::string
110 _CrippenLogP; // Unused (in the basement)
111RDKIT_RDGENERAL_EXPORT extern const std::string
112 _CrippenMR; // Unused (in the basement)
113RDKIT_RDGENERAL_EXPORT extern const std::string
114 _GasteigerCharge; // used to hold partial charges
115RDKIT_RDGENERAL_EXPORT extern const std::string
116 _GasteigerHCharge; // used to hold partial charges from implicit Hs
117
118///////////////////////////////////////////////////////////////
119// Atom Props
120
121// Chirality stuff
122RDKIT_RDGENERAL_EXPORT extern const std::string
123 _BondsPotentialStereo; // int (or bool) COMPUTED
124RDKIT_RDGENERAL_EXPORT extern const std::string
125 _CIPCode; // std::string COMPUTED
126RDKIT_RDGENERAL_EXPORT extern const std::string _CIPRank; // int COMPUTED
127RDKIT_RDGENERAL_EXPORT extern const std::string _ChiralityPossible; // int
128RDKIT_RDGENERAL_EXPORT extern const std::string
129 _UnknownStereo; // int (bool) AddHs/Chirality
130RDKIT_RDGENERAL_EXPORT extern const std::string
131 _ringStereoAtoms; // int vect Canon/Chiral/MolHash/MolOps//Renumber//RWmol
132RDKIT_RDGENERAL_EXPORT extern const std::string
133 _ringStereochemCand; // chirality bool COMPUTED
134RDKIT_RDGENERAL_EXPORT extern const std::string
135 _ringStereoWarning; // obsolete ?
136RDKIT_RDGENERAL_EXPORT extern const std::string _chiralPermutation; // int
137
138// Smiles parsing
139RDKIT_RDGENERAL_EXPORT extern const std::string _SmilesStart; // int
140RDKIT_RDGENERAL_EXPORT extern const std::string
141 _TraversalBondIndexOrder; // ? unused
142RDKIT_RDGENERAL_EXPORT extern const std::string
143 _TraversalRingClosureBond; // unsigned int
144RDKIT_RDGENERAL_EXPORT extern const std::string _TraversalStartPoint; // bool
145RDKIT_RDGENERAL_EXPORT extern const std::string
146 _queryRootAtom; // int SLNParse/SubstructMatch
147RDKIT_RDGENERAL_EXPORT extern const std::string _hasMassQuery; // atom bool
148RDKIT_RDGENERAL_EXPORT extern const std::string _protected; // atom int (bool)
149RDKIT_RDGENERAL_EXPORT extern const std::string
150 _supplementalSmilesLabel; // atom string (SmilesWrite)
151RDKIT_RDGENERAL_EXPORT extern const std::string
152 _unspecifiedOrder; // atom int (bool) smarts/smiles
153RDKIT_RDGENERAL_EXPORT extern const std::string
154 _RingClosures; // INT_VECT smarts/smiles/canon
155RDKIT_RDGENERAL_EXPORT extern const std::string
156 atomLabel; // atom string from CXSMILES
157
158// MDL Style Properties (MolFileParser)
159RDKIT_RDGENERAL_EXPORT extern const std::string molAtomMapNumber; // int
160RDKIT_RDGENERAL_EXPORT extern const std::string molFileAlias; // string
161RDKIT_RDGENERAL_EXPORT extern const std::string molFileValue; // string
162RDKIT_RDGENERAL_EXPORT extern const std::string molInversionFlag; // int
163RDKIT_RDGENERAL_EXPORT extern const std::string molParity; // int
164RDKIT_RDGENERAL_EXPORT extern const std::string molStereoCare; // int
165RDKIT_RDGENERAL_EXPORT extern const std::string molRxnComponent; // int
166RDKIT_RDGENERAL_EXPORT extern const std::string molRxnRole; // int
167RDKIT_RDGENERAL_EXPORT extern const std::string molTotValence; // int
168RDKIT_RDGENERAL_EXPORT extern const std::string molSubstCount; // int
169RDKIT_RDGENERAL_EXPORT extern const std::string molAttachPoint; // int
170RDKIT_RDGENERAL_EXPORT extern const std::string molAttachOrder; // int
171RDKIT_RDGENERAL_EXPORT extern const std::string molAtomClass; // string
172RDKIT_RDGENERAL_EXPORT extern const std::string molAtomSeqId; // int
173RDKIT_RDGENERAL_EXPORT extern const std::string molRxnExactChange; // int
174RDKIT_RDGENERAL_EXPORT extern const std::string molReactStatus; // int
175RDKIT_RDGENERAL_EXPORT extern const std::string molFileLinkNodes; // string
176
177RDKIT_RDGENERAL_EXPORT extern const std::string _MolFileRLabel; // unsigned int
178RDKIT_RDGENERAL_EXPORT extern const std::string _MolFileChiralFlag; // int
179RDKIT_RDGENERAL_EXPORT extern const std::string _MolFileAtomQuery; // int
180RDKIT_RDGENERAL_EXPORT extern const std::string _MolFileBondQuery; // int
181RDKIT_RDGENERAL_EXPORT extern const std::string _MolFileBondEndPts; // string
182RDKIT_RDGENERAL_EXPORT extern const std::string _MolFileBondAttach; // string
183RDKIT_RDGENERAL_EXPORT extern const std::string
184 _MolFileBondType; // unsigned int
185RDKIT_RDGENERAL_EXPORT extern const std::string
186 _MolFileBondStereo; // unsigned int
187RDKIT_RDGENERAL_EXPORT extern const std::string
188 _MolFileBondCfg; // unsigned int
189
190RDKIT_RDGENERAL_EXPORT extern const std::string
191 MRV_SMA; // smarts string from Marvin
192RDKIT_RDGENERAL_EXPORT extern const std::string dummyLabel; // atom string
193
194RDKIT_RDGENERAL_EXPORT extern const std::string
195 _QueryAtomGenericLabel; // string
196
197// Reaction Information (Reactions.cpp)
198RDKIT_RDGENERAL_EXPORT extern const std::string _QueryFormalCharge; // int
199RDKIT_RDGENERAL_EXPORT extern const std::string _QueryHCount; // int
200RDKIT_RDGENERAL_EXPORT extern const std::string _QueryIsotope; // int
201RDKIT_RDGENERAL_EXPORT extern const std::string
202 _QueryMass; // int = round(float * 1000)
203RDKIT_RDGENERAL_EXPORT extern const std::string
204 _ReactionDegreeChanged; // int (bool)
205RDKIT_RDGENERAL_EXPORT extern const std::string NullBond; // int (bool)
206RDKIT_RDGENERAL_EXPORT extern const std::string _rgroupAtomMaps;
207RDKIT_RDGENERAL_EXPORT extern const std::string _rgroupBonds;
208RDKIT_RDGENERAL_EXPORT extern const std::string reactantAtomIdx;
209RDKIT_RDGENERAL_EXPORT extern const std::string reactionMapNum;
210
211// SLN
212RDKIT_RDGENERAL_EXPORT extern const std::string
213 _AtomID; // unsigned int SLNParser
214RDKIT_RDGENERAL_EXPORT extern const std::string
215 _starred; // atom int COMPUTED (SLN)
216RDKIT_RDGENERAL_EXPORT extern const std::string
217 _SLN_s; // string SLNAttribs (chiral info)
218RDKIT_RDGENERAL_EXPORT extern const std::string _Unfinished_SLN_; // int (bool)
219
220// Smarts Smiles
221RDKIT_RDGENERAL_EXPORT extern const std::string _brokenChirality; // atom bool
222RDKIT_RDGENERAL_EXPORT extern const std::string isImplicit; // atom int (bool)
223RDKIT_RDGENERAL_EXPORT extern const std::string
224 smilesSymbol; // atom string (only used in test?)
225
226// Tripos
227RDKIT_RDGENERAL_EXPORT extern const std::string
228 _TriposAtomType; // string Mol2FileParser
229// missing defs for _TriposAtomName//_TriposPartialCharge...
230
231// molecule drawing
232RDKIT_RDGENERAL_EXPORT extern const std::string _displayLabel; // string
233RDKIT_RDGENERAL_EXPORT extern const std::string _displayLabelW; // string
234
235///////////////////////////////////////////////////////////////
236// misc props
237RDKIT_RDGENERAL_EXPORT extern const std::string
238 TWOD; // need THREED -> confusing using in TDTMol supplier
239 // converge with _2DConf?
240RDKIT_RDGENERAL_EXPORT extern const std::string BalabanJ; // mol double
241RDKIT_RDGENERAL_EXPORT extern const std::string BalanbanJ; // typo!! fix...
242
243RDKIT_RDGENERAL_EXPORT extern const std::string Discrims; // FragCatalog Entry
244// Subgraphs::DiscrimTuple (uint32,uint32,uint32)
245RDKIT_RDGENERAL_EXPORT extern const std::string
246 DistanceMatrix_Paths; // boost::shared_array<double>
247// - note, confusing creation of names in
248// - getDistanceMat
249RDKIT_RDGENERAL_EXPORT extern const std::string internalRgroupSmiles;
250RDKIT_RDGENERAL_EXPORT extern const std::string molNote;
251RDKIT_RDGENERAL_EXPORT extern const std::string atomNote;
252RDKIT_RDGENERAL_EXPORT extern const std::string bondNote;
253RDKIT_RDGENERAL_EXPORT extern const std::string _isotopicHs;
254
255} // namespace common_properties
256#ifndef WIN32
257typedef long long int LONGINT;
258#else
259typedef __int64 LONGINT;
260#endif
261#ifdef max
262#undef max // FUCK I hate this nonsense
263#endif
264#ifdef min
265#undef min // FUCK I hate this nonsense
266#endif
267
268RDKIT_RDGENERAL_EXPORT extern const double MAX_DOUBLE;
269RDKIT_RDGENERAL_EXPORT extern const double EPS_DOUBLE;
270RDKIT_RDGENERAL_EXPORT extern const double SMALL_DOUBLE;
271RDKIT_RDGENERAL_EXPORT extern const double MAX_INT;
272RDKIT_RDGENERAL_EXPORT extern const double MAX_LONGINT;
273
274typedef unsigned int UINT;
275typedef unsigned short USHORT;
276typedef unsigned char UCHAR;
277
278typedef std::vector<int> INT_VECT;
279typedef INT_VECT::iterator INT_VECT_I;
280typedef INT_VECT::const_iterator INT_VECT_CI;
281typedef INT_VECT::reverse_iterator INT_VECT_RI;
282typedef INT_VECT::const_reverse_iterator INT_VECT_CRI;
283
284typedef std::list<int> INT_LIST;
285typedef INT_LIST::iterator INT_LIST_I;
286typedef INT_LIST::const_iterator INT_LIST_CI;
287
288typedef std::list<INT_VECT> LIST_INT_VECT;
289typedef LIST_INT_VECT::iterator LIST_INT_VECT_I;
290typedef LIST_INT_VECT::const_iterator LIST_INT_VECT_CI;
291
292typedef std::vector<INT_VECT> VECT_INT_VECT;
293typedef VECT_INT_VECT::iterator VECT_INT_VECT_I;
294typedef VECT_INT_VECT::const_iterator VECT_INT_VECT_CI;
295
296typedef std::vector<UINT>::const_iterator UINT_VECT_CI;
297typedef std::vector<UINT> UINT_VECT;
298
299typedef std::vector<std::string>::const_iterator STR_VECT_CI;
300typedef std::vector<std::string>::iterator STR_VECT_I;
301typedef std::vector<std::string> STR_VECT;
302
303typedef std::vector<double> DOUBLE_VECT;
304typedef DOUBLE_VECT::iterator DOUBLE_VECT_I;
305typedef DOUBLE_VECT::const_iterator DOUBLE_VECT_CI;
306typedef std::vector<DOUBLE_VECT> VECT_DOUBLE_VECT;
307typedef VECT_DOUBLE_VECT::iterator VECT_DOUBLE_VECT_I;
308typedef VECT_DOUBLE_VECT::const_iterator VECT_DOUBLE_VECT_CI;
309
310typedef std::map<std::string, UINT> STR_UINT_MAP;
311typedef std::map<std::string, UINT>::const_iterator STR_UINT_MAP_CI;
312
313typedef std::map<int, INT_VECT> INT_INT_VECT_MAP;
314typedef INT_INT_VECT_MAP::const_iterator INT_INT_VECT_MAP_CI;
315
316typedef std::map<int, int> INT_MAP_INT;
317typedef INT_MAP_INT::iterator INT_MAP_INT_I;
318typedef INT_MAP_INT::const_iterator INT_MAP_INT_CI;
319
320typedef std::deque<int> INT_DEQUE;
321typedef INT_DEQUE::iterator INT_DEQUE_I;
322typedef INT_DEQUE::const_iterator INT_DEQUE_CI;
323
324typedef std::map<int, INT_DEQUE> INT_INT_DEQ_MAP;
325typedef INT_INT_DEQ_MAP::const_iterator INT_INT_DEQ_MAP_CI;
326
327typedef std::set<int> INT_SET;
328typedef INT_SET::iterator INT_SET_I;
329typedef INT_SET::const_iterator INT_SET_CI;
330
331//! functor to compare two doubles with a tolerance
333 public:
335 bool operator()(double d1, double d2) const {
336 if (fabs(d1 - d2) < _tol) {
337 return false;
338 } else {
339 return (d1 < d2);
340 }
341 }
342
343 private:
344 double _tol{1.0e-8};
345};
346
347//! std::map from double to integer.
348typedef std::map<double, int, ltDouble> DOUBLE_INT_MAP;
349
350//! functor for returning the larger of two values
351template <typename T>
353 T operator()(T arg1, T arg2) { return arg1 > arg2 ? arg1 : arg2; }
354};
355
356//! functor for comparing two strings
358 bool operator()(const char *s1, const char *s2) const {
359 // std::cout << s1 << " " << s2 << " " << strcmp(s1, s2) << "\n";
360
361 return strcmp(s1, s2) < 0;
362 }
363};
364
365//! \brief calculate the union of two INT_VECTs and put the results in a
366//! third vector
368 INT_VECT &res);
369
370//! \brief calculate the intersection of two INT_VECTs and put the results in a
371//! third vector
373 INT_VECT &res);
374
375//! calculating the union of the INT_VECT's in a VECT_INT_VECT
376/*!
377 \param rings the INT_VECT's to consider
378 \param res used to return results
379 \param exclude any values in this optional INT_VECT will be excluded
380 from the union.
381*/
383 const INT_VECT *exclude = nullptr);
384
385//! given a current combination of numbers change it to the next possible
386// combination
387/*!
388 \param comb the <b>sorted</b> vector to consider
389 \param tot the maximum number possible in the vector
390
391 \return -1 on failure, the index of the last number changed on success.
392 Example:
393 for all combinations 3 of numbers between 0 and tot=5
394 given (0,1,2) the function wil return (0,1,3) etc.
395
396
397*/
399
400}; // namespace RDKit
401
402#endif
Defines the Dict class.
#define RDKIT_RDGENERAL_EXPORT
Definition: export.h:369
RDKIT_RDGENERAL_EXPORT const std::string _ringStereoWarning
RDKIT_RDGENERAL_EXPORT const std::string _MolFileBondQuery
RDKIT_RDGENERAL_EXPORT const std::string smilesSymbol
RDKIT_RDGENERAL_EXPORT const std::string _TriposAtomType
RDKIT_RDGENERAL_EXPORT const std::string _RingClosures
RDKIT_RDGENERAL_EXPORT const std::string bondNote
RDKIT_RDGENERAL_EXPORT const std::string _QueryHCount
RDKIT_RDGENERAL_EXPORT const std::string _labuteASA
RDKIT_RDGENERAL_EXPORT const std::string _supplementalSmilesLabel
RDKIT_RDGENERAL_EXPORT const std::string molStereoCare
RDKIT_RDGENERAL_EXPORT const std::string MolFileComments
RDKIT_RDGENERAL_EXPORT const std::string molInversionFlag
RDKIT_RDGENERAL_EXPORT const std::string DistanceMatrix_Paths
RDKIT_RDGENERAL_EXPORT const std::string maxAttachIdx
RDKIT_RDGENERAL_EXPORT const std::string _3DConf
RDKIT_RDGENERAL_EXPORT const std::string _NeedsQueryScan
RDKIT_RDGENERAL_EXPORT const std::string atomNote
RDKIT_RDGENERAL_EXPORT const std::string reactionMapNum
RDKIT_RDGENERAL_EXPORT const std::string _ChiralityPossible
RDKIT_RDGENERAL_EXPORT const std::string isImplicit
RDKIT_RDGENERAL_EXPORT const std::string _2DConf
RDKIT_RDGENERAL_EXPORT const std::string dummyLabel
RDKIT_RDGENERAL_EXPORT const std::string _doIsoSmiles
RDKIT_RDGENERAL_EXPORT const std::string _QueryMass
RDKIT_RDGENERAL_EXPORT const std::string _QueryFormalCharge
RDKIT_RDGENERAL_EXPORT const std::string _labuteAtomHContrib
RDKIT_RDGENERAL_EXPORT const std::string _connectivityNVals
RDKIT_RDGENERAL_EXPORT const std::string BalanbanJ
RDKIT_RDGENERAL_EXPORT const std::string _unspecifiedOrder
RDKIT_RDGENERAL_EXPORT const std::string _ringStereoAtoms
RDKIT_RDGENERAL_EXPORT const std::string molRxnRole
RDKIT_RDGENERAL_EXPORT const std::string _SmilesStart
RDKIT_RDGENERAL_EXPORT const std::string _MolFileBondType
RDKIT_RDGENERAL_EXPORT const std::string molFileValue
RDKIT_RDGENERAL_EXPORT const std::string _fragSMARTS
RDKIT_RDGENERAL_EXPORT const std::string molTotValence
RDKIT_RDGENERAL_EXPORT const std::string _connectivityHKDeltas
RDKIT_RDGENERAL_EXPORT const std::string _crippenLogP
RDKIT_RDGENERAL_EXPORT const std::string _QueryAtomGenericLabel
RDKIT_RDGENERAL_EXPORT const std::string _TraversalStartPoint
RDKIT_RDGENERAL_EXPORT const std::string _GasteigerCharge
RDKIT_RDGENERAL_EXPORT const std::string molAttachPoint
RDKIT_RDGENERAL_EXPORT const std::string molAtomClass
RDKIT_RDGENERAL_EXPORT const std::string _MolFileAtomQuery
RDKIT_RDGENERAL_EXPORT const std::string TWOD
RDKIT_RDGENERAL_EXPORT const std::string _protected
RDKIT_RDGENERAL_EXPORT const std::string _displayLabelW
RDKIT_RDGENERAL_EXPORT const std::string _TraversalRingClosureBond
RDKIT_RDGENERAL_EXPORT const std::string _Unfinished_SLN_
RDKIT_RDGENERAL_EXPORT const std::string _CrippenMR
RDKIT_RDGENERAL_EXPORT const std::string _brokenChirality
RDKIT_RDGENERAL_EXPORT const std::string ringMembership
RDKIT_RDGENERAL_EXPORT const std::string molFileLinkNodes
RDKIT_RDGENERAL_EXPORT const std::string _MolFileRLabel
RDKIT_RDGENERAL_EXPORT const std::string _MolFileBondAttach
RDKIT_RDGENERAL_EXPORT const std::string molRxnComponent
RDKIT_RDGENERAL_EXPORT const std::string MRV_SMA
RDKIT_RDGENERAL_EXPORT const std::string _MolFileBondEndPts
RDKIT_RDGENERAL_EXPORT const std::string _queryRootAtom
RDKIT_RDGENERAL_EXPORT const std::string numArom
RDKIT_RDGENERAL_EXPORT const std::string origNoImplicit
RDKIT_RDGENERAL_EXPORT const std::string _rgroupBonds
RDKIT_RDGENERAL_EXPORT const std::string MolFileInfo
RDKIT_RDGENERAL_EXPORT const std::string molNote
RDKIT_RDGENERAL_EXPORT const std::string _crippenMR
RDKIT_RDGENERAL_EXPORT const std::string _GasteigerHCharge
RDKIT_RDGENERAL_EXPORT const std::string _UnknownStereo
RDKIT_RDGENERAL_EXPORT const std::string _smilesBondOutputOrder
RDKIT_RDGENERAL_EXPORT const std::string _TraversalBondIndexOrder
RDKIT_RDGENERAL_EXPORT const std::string _rgroupAtomMaps
RDKIT_RDGENERAL_EXPORT const std::string _CIPCode
RDKIT_RDGENERAL_EXPORT const std::string _BondsPotentialStereo
RDKIT_RDGENERAL_EXPORT const std::string _Name
RDKIT_RDGENERAL_EXPORT const std::string _QueryIsotope
RDKIT_RDGENERAL_EXPORT const std::string molAtomMapNumber
RDKIT_RDGENERAL_EXPORT const std::string _CIPRank
RDKIT_RDGENERAL_EXPORT const std::string _hasMassQuery
RDKIT_RDGENERAL_EXPORT const std::string _ReactionDegreeChanged
RDKIT_RDGENERAL_EXPORT const std::string molParity
RDKIT_RDGENERAL_EXPORT const std::string _CrippenLogP
RDKIT_RDGENERAL_EXPORT const std::string molRxnExactChange
RDKIT_RDGENERAL_EXPORT const std::string _displayLabel
RDKIT_RDGENERAL_EXPORT const std::string molAttachOrder
RDKIT_RDGENERAL_EXPORT const std::string molAtomSeqId
RDKIT_RDGENERAL_EXPORT const std::string BalabanJ
RDKIT_RDGENERAL_EXPORT const std::string extraRings
RDKIT_RDGENERAL_EXPORT const std::string atomLabel
RDKIT_RDGENERAL_EXPORT const std::string _isotopicHs
RDKIT_RDGENERAL_EXPORT const std::string _MMFFSanitized
RDKIT_RDGENERAL_EXPORT const std::string _labuteAtomContribs
RDKIT_RDGENERAL_EXPORT const std::string _tpsa
RDKIT_RDGENERAL_EXPORT const std::string _MolFileBondStereo
RDKIT_RDGENERAL_EXPORT const std::string molFileAlias
RDKIT_RDGENERAL_EXPORT const std::string _StereochemDone
RDKIT_RDGENERAL_EXPORT const std::string _ringStereochemCand
RDKIT_RDGENERAL_EXPORT const std::string _MolFileBondCfg
RDKIT_RDGENERAL_EXPORT const std::string _SLN_s
RDKIT_RDGENERAL_EXPORT const std::string molSubstCount
RDKIT_RDGENERAL_EXPORT const std::string _chiralPermutation
RDKIT_RDGENERAL_EXPORT const std::string _MolFileChiralFlag
RDKIT_RDGENERAL_EXPORT const std::string _crippenMRContribs
RDKIT_RDGENERAL_EXPORT const std::string reactantAtomIdx
RDKIT_RDGENERAL_EXPORT const std::string Discrims
RDKIT_RDGENERAL_EXPORT const std::string _smilesAtomOutputOrder
RDKIT_RDGENERAL_EXPORT const std::string _AtomID
RDKIT_RDGENERAL_EXPORT const std::string molReactStatus
RDKIT_RDGENERAL_EXPORT const std::string NullBond
RDKIT_RDGENERAL_EXPORT const std::string internalRgroupSmiles
RDKIT_RDGENERAL_EXPORT const std::string _starred
RDKIT_RDGENERAL_EXPORT const std::string _tpsaAtomContribs
RDKIT_RDGENERAL_EXPORT const std::string _crippenLogPContribs
RDKIT_RDGENERAL_EXPORT const std::string computedPropName
Std stuff.
Definition: Abbreviations.h:19
INT_MAP_INT::iterator INT_MAP_INT_I
Definition: types.h:317
VECT_DOUBLE_VECT::const_iterator VECT_DOUBLE_VECT_CI
Definition: types.h:308
std::list< int > INT_LIST
Definition: types.h:284
std::list< INT_VECT > LIST_INT_VECT
Definition: types.h:288
std::vector< std::string > STR_VECT
Definition: Dict.h:29
std::set< int > INT_SET
Definition: types.h:327
INT_VECT::const_iterator INT_VECT_CI
Definition: types.h:280
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
INT_INT_DEQ_MAP::const_iterator INT_INT_DEQ_MAP_CI
Definition: types.h:325
std::vector< int > INT_VECT
Definition: types.h:278
unsigned char UCHAR
Definition: types.h:276
long long int LONGINT
Definition: types.h:257
INT_SET::const_iterator INT_SET_CI
Definition: types.h:329
RDKIT_RDGENERAL_EXPORT int nextCombination(INT_VECT &comb, int tot)
given a current combination of numbers change it to the next possible
std::vector< std::string >::iterator STR_VECT_I
Definition: types.h:300
INT_VECT::const_reverse_iterator INT_VECT_CRI
Definition: types.h:282
std::map< int, int > INT_MAP_INT
Definition: types.h:316
std::vector< INT_VECT > VECT_INT_VECT
Definition: types.h:292
std::deque< int > INT_DEQUE
Definition: types.h:320
std::map< std::string, UINT > STR_UINT_MAP
Definition: types.h:310
RDKIT_RDGENERAL_EXPORT const double EPS_DOUBLE
std::map< int, INT_VECT > INT_INT_VECT_MAP
Definition: types.h:313
std::map< int, INT_DEQUE > INT_INT_DEQ_MAP
Definition: types.h:324
std::vector< DOUBLE_VECT > VECT_DOUBLE_VECT
Definition: types.h:306
RDKIT_RDGENERAL_EXPORT const double MAX_LONGINT
INT_DEQUE::iterator INT_DEQUE_I
Definition: types.h:321
INT_LIST::const_iterator INT_LIST_CI
Definition: types.h:286
INT_DEQUE::const_iterator INT_DEQUE_CI
Definition: types.h:322
unsigned short USHORT
Definition: types.h:275
INT_INT_VECT_MAP::const_iterator INT_INT_VECT_MAP_CI
Definition: types.h:314
RDKIT_RDGENERAL_EXPORT const double MAX_INT
std::map< double, int, ltDouble > DOUBLE_INT_MAP
std::map from double to integer.
Definition: types.h:348
INT_VECT::reverse_iterator INT_VECT_RI
Definition: types.h:281
INT_SET::iterator INT_SET_I
Definition: types.h:328
std::vector< UINT >::const_iterator UINT_VECT_CI
Definition: types.h:296
INT_MAP_INT::const_iterator INT_MAP_INT_CI
Definition: types.h:318
VECT_DOUBLE_VECT::iterator VECT_DOUBLE_VECT_I
Definition: types.h:307
std::map< std::string, UINT >::const_iterator STR_UINT_MAP_CI
Definition: types.h:311
DOUBLE_VECT::const_iterator DOUBLE_VECT_CI
Definition: types.h:305
unsigned int UINT
Definition: types.h:274
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
INT_LIST::iterator INT_LIST_I
Definition: types.h:285
std::vector< std::string >::const_iterator STR_VECT_CI
Definition: types.h:299
LIST_INT_VECT::const_iterator LIST_INT_VECT_CI
Definition: types.h:290
std::vector< double > DOUBLE_VECT
Definition: types.h:303
VECT_INT_VECT::iterator VECT_INT_VECT_I
Definition: types.h:293
DOUBLE_VECT::iterator DOUBLE_VECT_I
Definition: types.h:304
RDKIT_RDGENERAL_EXPORT const double SMALL_DOUBLE
RDKIT_RDGENERAL_EXPORT const double MAX_DOUBLE
VECT_INT_VECT::const_iterator VECT_INT_VECT_CI
Definition: types.h:294
LIST_INT_VECT::iterator LIST_INT_VECT_I
Definition: types.h:289
INT_VECT::iterator INT_VECT_I
Definition: types.h:279
std::vector< UINT > UINT_VECT
Definition: types.h:297
functor for comparing two strings
Definition: types.h:357
bool operator()(const char *s1, const char *s2) const
Definition: types.h:358
functor for returning the larger of two values
Definition: types.h:352
T operator()(T arg1, T arg2)
Definition: types.h:353
functor to compare two doubles with a tolerance
Definition: types.h:332
bool operator()(double d1, double d2) const
Definition: types.h:335