RDKit: types.h Source File

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types.h
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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>
41#include <any>
42#include <RDGeneral/BoostStartInclude.h>
43#include <boost/lexical_cast.hpp>
44#include <RDGeneral/BoostEndInclude.h>
45
46namespace RDKit {
47
48namespace detail {
49// used in various places for computed properties
50 RDKIT_RDGENERAL_EXPORT extern const std::string computedPropName;
51} // namespace detail
52
53 namespace common_properties {
54///////////////////////////////////////////////////////////////
55// Molecule Props
56 RDKIT_RDGENERAL_EXPORT extern const std::string _Name; // string
57 RDKIT_RDGENERAL_EXPORT extern const std::string MolFileInfo; // string
58 RDKIT_RDGENERAL_EXPORT extern const std::string MolFileComments; // string
59 RDKIT_RDGENERAL_EXPORT extern const std::string
60 _2DConf; // int (combine into dimension?)
61 RDKIT_RDGENERAL_EXPORT extern const std::string _3DConf; // int
62 RDKIT_RDGENERAL_EXPORT extern const std::string
63 _doIsoSmiles; // int (should probably be removed)
64 RDKIT_RDGENERAL_EXPORT extern const std::string extraRings; // vec<vec<int> >
65 RDKIT_RDGENERAL_EXPORT extern const std::string
66 _smilesAtomOutputOrder; // vec<int> computed
67 RDKIT_RDGENERAL_EXPORT extern const std::string
68 _smilesBondOutputOrder; // vec<int> computed
69 RDKIT_RDGENERAL_EXPORT extern const std::string _StereochemDone; // int
70 RDKIT_RDGENERAL_EXPORT extern const std::string _NeedsQueryScan; // int (bool)
71 RDKIT_RDGENERAL_EXPORT extern const std::string _fragSMARTS; // std::string
72 RDKIT_RDGENERAL_EXPORT extern const std::string
73 maxAttachIdx; // int TemplEnumTools.cpp
74 RDKIT_RDGENERAL_EXPORT extern const std::string
75 ringMembership; //? unused (molopstest.cpp)
76
77// Computed Values
78// ConnectivityDescriptors
79 RDKIT_RDGENERAL_EXPORT extern const std::string
80 _connectivityHKDeltas; // std::vector<double> computed
81 RDKIT_RDGENERAL_EXPORT extern const std::string
82 _connectivityNVals; // std::vector<double> computed
83
84 RDKIT_RDGENERAL_EXPORT extern const std::string
85 _crippenLogP; // double computed
86 RDKIT_RDGENERAL_EXPORT extern const std::string
87 _crippenLogPContribs; // std::vector<double> computed
88
89 RDKIT_RDGENERAL_EXPORT extern const std::string _crippenMR; // double computed
90 RDKIT_RDGENERAL_EXPORT extern const std::string
91 _crippenMRContribs; // std::vector<double> computed
92
93 RDKIT_RDGENERAL_EXPORT extern const std::string _labuteASA; // double computed
94 RDKIT_RDGENERAL_EXPORT extern const std::string
95 _labuteAtomContribs; // vec<double> computed
96 RDKIT_RDGENERAL_EXPORT extern const std::string
97 _labuteAtomHContrib; // double computed
98
99 RDKIT_RDGENERAL_EXPORT extern const std::string _tpsa; // double computed
100 RDKIT_RDGENERAL_EXPORT extern const std::string
101 _tpsaAtomContribs; // vec<double> computed
102
103 RDKIT_RDGENERAL_EXPORT extern const std::string
104 numArom; // int computed (only uses in tests?)
105 RDKIT_RDGENERAL_EXPORT extern const std::string
106 _MMFFSanitized; // int (bool) computed
107
108 RDKIT_RDGENERAL_EXPORT extern const std::string
109 _CrippenLogP; // Unused (in the basement)
110 RDKIT_RDGENERAL_EXPORT extern const std::string
111 _CrippenMR; // Unused (in the basement)
112 RDKIT_RDGENERAL_EXPORT extern const std::string
113 _GasteigerCharge; // used to hold partial charges
114 RDKIT_RDGENERAL_EXPORT extern const std::string
115 _GasteigerHCharge; // used to hold partial charges from implicit Hs
116
117///////////////////////////////////////////////////////////////
118// Atom Props
119
120// Chirality stuff
121 RDKIT_RDGENERAL_EXPORT extern const std::string
122 _BondsPotentialStereo; // int (or bool) COMPUTED
123 RDKIT_RDGENERAL_EXPORT extern const std::string
124 _CIPCode; // std::string COMPUTED
125 RDKIT_RDGENERAL_EXPORT extern const std::string _CIPRank; // int COMPUTED
126 RDKIT_RDGENERAL_EXPORT extern const std::string
127 _CIPComputed; // int (bool) COMPUTED
128 RDKIT_RDGENERAL_EXPORT extern const std::string _CIPNeighborOrder;
129
130 RDKIT_RDGENERAL_EXPORT extern const std::string
131 _CanonicalRankingNumber; // unsigned int
132 RDKIT_RDGENERAL_EXPORT extern const std::string _ChiralityPossible; // int
133 RDKIT_RDGENERAL_EXPORT extern const std::string
134 _UnknownStereo; // int (bool) AddHs/Chirality
135 RDKIT_RDGENERAL_EXPORT extern const std::string
136 _ringStereoAtoms; // int vect Canon/Chiral/MolHash/MolOps//Renumber//RWmol
137 RDKIT_RDGENERAL_EXPORT extern const std::string
138 _ringStereochemCand; // chirality bool COMPUTED
139 RDKIT_RDGENERAL_EXPORT extern const std::string
140 _ringStereoWarning; // obsolete ?
141 RDKIT_RDGENERAL_EXPORT extern const std::string _chiralPermutation; // int
142 RDKIT_RDGENERAL_EXPORT extern const std::string _ringStereoOtherAtom; // int
143 RDKIT_RDGENERAL_EXPORT extern const std::string _mesoOtherAtom; // int
144
145// Smiles parsing
146 RDKIT_RDGENERAL_EXPORT extern const std::string _SmilesStart; // int
147 RDKIT_RDGENERAL_EXPORT extern const std::string
148 _TraversalBondIndexOrder; // ? unused
149 RDKIT_RDGENERAL_EXPORT extern const std::string
150 _TraversalRingClosureBond; // unsigned int
151 RDKIT_RDGENERAL_EXPORT extern const std::string _TraversalStartPoint; // bool
152 RDKIT_RDGENERAL_EXPORT extern const std::string
153 _queryRootAtom; // int SLNParse/SubstructMatch
154 RDKIT_RDGENERAL_EXPORT extern const std::string _hasMassQuery; // atom bool
155 RDKIT_RDGENERAL_EXPORT extern const std::string _protected; // atom int (bool)
156 RDKIT_RDGENERAL_EXPORT extern const std::string
157 _ChiralAtomRank; // atom rank (unsigned int)
158 RDKIT_RDGENERAL_EXPORT extern const std::string
159 _supplementalSmilesLabel; // atom string (SmilesWrite)
160 RDKIT_RDGENERAL_EXPORT extern const std::string
161 _unspecifiedOrder; // atom int (bool) smarts/smiles
162 RDKIT_RDGENERAL_EXPORT extern const std::string
163 _RingClosures; // INT_VECT smarts/smiles/canon
164 RDKIT_RDGENERAL_EXPORT extern const std::string
165 atomLabel; // atom string from CXSMILES
166 RDKIT_RDGENERAL_EXPORT extern const std::string OxidationNumber; // int
167
168// MDL Style Properties (MolFileParser)
169 RDKIT_RDGENERAL_EXPORT extern const std::string molAtomMapNumber; // int
170 RDKIT_RDGENERAL_EXPORT extern const std::string molFileAlias; // string
171 RDKIT_RDGENERAL_EXPORT extern const std::string molFileValue; // string
172 RDKIT_RDGENERAL_EXPORT extern const std::string molInversionFlag; // int
173 RDKIT_RDGENERAL_EXPORT extern const std::string molParity; // int
174 RDKIT_RDGENERAL_EXPORT extern const std::string molStereoCare; // int
175 RDKIT_RDGENERAL_EXPORT extern const std::string molRxnComponent; // int
176 RDKIT_RDGENERAL_EXPORT extern const std::string molRxnRole; // int
177 RDKIT_RDGENERAL_EXPORT extern const std::string molTotValence; // int
178 RDKIT_RDGENERAL_EXPORT extern const std::string molRingBondCount; // int
179 RDKIT_RDGENERAL_EXPORT extern const std::string molSubstCount; // int
180 RDKIT_RDGENERAL_EXPORT extern const std::string molAttachPoint; // int
181 RDKIT_RDGENERAL_EXPORT extern const std::string molAttachOrder; // int
182 RDKIT_RDGENERAL_EXPORT extern const std::string
183 molAttachOrderTemplate; // std::vector<AtomAttchOrd>
184
185 RDKIT_RDGENERAL_EXPORT extern const std::string molAtomClass; // string
186 RDKIT_RDGENERAL_EXPORT extern const std::string
187 templateNames; // vector of strings
188
189 RDKIT_RDGENERAL_EXPORT extern const std::string molAtomSeqId; // int
190 RDKIT_RDGENERAL_EXPORT extern const std::string molAtomSeqName; // string
191 RDKIT_RDGENERAL_EXPORT extern const std::string molRxnExactChange; // int
192 RDKIT_RDGENERAL_EXPORT extern const std::string molReactStatus; // int
193 RDKIT_RDGENERAL_EXPORT extern const std::string molFileLinkNodes; // string
194 RDKIT_RDGENERAL_EXPORT extern const std::string _fromAttachPoint; // int
195
196 RDKIT_RDGENERAL_EXPORT extern const std::string _MolFileRLabel; // unsigned int
197 RDKIT_RDGENERAL_EXPORT extern const std::string _MolFileChiralFlag; // int
198 RDKIT_RDGENERAL_EXPORT extern const std::string _MolFileAtomQuery; // int
199 RDKIT_RDGENERAL_EXPORT extern const std::string _MolFileBondQuery; // int
200 RDKIT_RDGENERAL_EXPORT extern const std::string _MolFileBondEndPts; // string
201 RDKIT_RDGENERAL_EXPORT extern const std::string _MolFileBondAttach; // string
202 RDKIT_RDGENERAL_EXPORT extern const std::string
203 _MolFileBondType; // unsigned int
204 RDKIT_RDGENERAL_EXPORT extern const std::string
205 _MolFileBondStereo; // unsigned int
206 RDKIT_RDGENERAL_EXPORT extern const std::string
207 _MolFileBondCfg; // unsigned int
208 RDKIT_RDGENERAL_EXPORT extern const std::string
209 MRV_SMA; // smarts string from Marvin
210
211// flag indicating that the chirality wasn't specified in the input,
212// but was calculated from 3D coordinates in the input
213 RDKIT_RDGENERAL_EXPORT extern const std::string _NonExplicit3DChirality; // int
214 RDKIT_RDGENERAL_EXPORT extern const std::string dummyLabel; // atom string
215
216 RDKIT_RDGENERAL_EXPORT extern const std::string
217 _QueryAtomGenericLabel; // string
218
219// Reaction Information (Reactions.cpp)
220 RDKIT_RDGENERAL_EXPORT extern const std::string _QueryFormalCharge; // int
221 RDKIT_RDGENERAL_EXPORT extern const std::string _QueryHCount; // int
222 RDKIT_RDGENERAL_EXPORT extern const std::string _QueryIsotope; // int
223 RDKIT_RDGENERAL_EXPORT extern const std::string
224 _QueryMass; // int = round(float * 1000)
225 RDKIT_RDGENERAL_EXPORT extern const std::string
226 _ReactionDegreeChanged; // int (bool)
227 RDKIT_RDGENERAL_EXPORT extern const std::string NullBond; // int (bool)
228 RDKIT_RDGENERAL_EXPORT extern const std::string _rgroupAtomMaps;
229 RDKIT_RDGENERAL_EXPORT extern const std::string _rgroupBonds;
230 RDKIT_RDGENERAL_EXPORT extern const std::string _rgroupTargetAtoms;
231 RDKIT_RDGENERAL_EXPORT extern const std::string _rgroupTargetBonds;
232 RDKIT_RDGENERAL_EXPORT extern const std::string reactantAtomIdx;
233 RDKIT_RDGENERAL_EXPORT extern const std::string reactionMapNum;
234 RDKIT_RDGENERAL_EXPORT extern const std::string reactantIdx;
235
236// SLN
237 RDKIT_RDGENERAL_EXPORT extern const std::string
238 _AtomID; // unsigned int SLNParser
239 RDKIT_RDGENERAL_EXPORT extern const std::string
240 _starred; // atom int COMPUTED (SLN)
241 RDKIT_RDGENERAL_EXPORT extern const std::string
242 _SLN_s; // string SLNAttribs (chiral info)
243 RDKIT_RDGENERAL_EXPORT extern const std::string _Unfinished_SLN_; // int (bool)
244
245// Smarts Smiles
246 RDKIT_RDGENERAL_EXPORT extern const std::string _brokenChirality; // atom bool
247 RDKIT_RDGENERAL_EXPORT extern const std::string isImplicit; // atom int (bool)
248 RDKIT_RDGENERAL_EXPORT extern const std::string
249 smilesSymbol; // atom string (only used in test?)
250
251// Tripos
252 RDKIT_RDGENERAL_EXPORT extern const std::string
253 _TriposAtomType; // string Mol2FileParser
254// missing defs for _TriposAtomName//_TriposPartialCharge...
255
256// molecule drawing
257 RDKIT_RDGENERAL_EXPORT extern const std::string _displayLabel; // string
258 RDKIT_RDGENERAL_EXPORT extern const std::string _displayLabelW; // string
259
260///////////////////////////////////////////////////////////////
261// misc props
262 RDKIT_RDGENERAL_EXPORT extern const std::string
263 TWOD; // need THREED -> confusing using in TDTMol supplier
264 // converge with _2DConf?
265 RDKIT_RDGENERAL_EXPORT extern const std::string BalabanJ; // mol double
266 RDKIT_RDGENERAL_EXPORT extern const std::string BalanbanJ; // typo!! fix...
267
268 RDKIT_RDGENERAL_EXPORT extern const std::string Discrims; // FragCatalog Entry
269// Subgraphs::DiscrimTuple (uint32,uint32,uint32)
270 RDKIT_RDGENERAL_EXPORT extern const std::string
271 DistanceMatrix_Paths; // boost::shared_array<double>
272// - note, confusing creation of names in
273// - getDistanceMat
274 RDKIT_RDGENERAL_EXPORT extern const std::string internalRgroupSmiles;
275 RDKIT_RDGENERAL_EXPORT extern const std::string molNote;
276 RDKIT_RDGENERAL_EXPORT extern const std::string atomNote;
277 RDKIT_RDGENERAL_EXPORT extern const std::string bondNote;
278 RDKIT_RDGENERAL_EXPORT extern const std::string _isotopicHs;
279
280} // namespace common_properties
281#ifndef WIN32
282 typedef long long int LONGINT;
283#else
284typedef __int64 LONGINT;
285#endif
286#ifdef max
287#undef max // FUCK I hate this nonsense
288#endif
289#ifdef min
290#undef min // FUCK I hate this nonsense
291#endif
292
293 RDKIT_RDGENERAL_EXPORT extern const double MAX_DOUBLE;
294 RDKIT_RDGENERAL_EXPORT extern const double EPS_DOUBLE;
295 RDKIT_RDGENERAL_EXPORT extern const double SMALL_DOUBLE;
296 RDKIT_RDGENERAL_EXPORT extern const double MAX_INT;
297 RDKIT_RDGENERAL_EXPORT extern const double MAX_LONGINT;
298
299 typedef unsigned int UINT;
300 typedef unsigned short USHORT;
301 typedef unsigned char UCHAR;
302
303 typedef std::vector<int> INT_VECT;
304 typedef INT_VECT::iterator INT_VECT_I;
305 typedef INT_VECT::const_iterator INT_VECT_CI;
306 typedef INT_VECT::reverse_iterator INT_VECT_RI;
307 typedef INT_VECT::const_reverse_iterator INT_VECT_CRI;
308
309 typedef std::list<int> INT_LIST;
310 typedef INT_LIST::iterator INT_LIST_I;
311 typedef INT_LIST::const_iterator INT_LIST_CI;
312
313 typedef std::list<INT_VECT> LIST_INT_VECT;
314 typedef LIST_INT_VECT::iterator LIST_INT_VECT_I;
315 typedef LIST_INT_VECT::const_iterator LIST_INT_VECT_CI;
316
317 typedef std::vector<INT_VECT> VECT_INT_VECT;
318 typedef VECT_INT_VECT::iterator VECT_INT_VECT_I;
319 typedef VECT_INT_VECT::const_iterator VECT_INT_VECT_CI;
320
321 typedef std::vector<UINT>::const_iterator UINT_VECT_CI;
322 typedef std::vector<UINT> UINT_VECT;
323
324 typedef std::vector<std::string>::const_iterator STR_VECT_CI;
325 typedef std::vector<std::string>::iterator STR_VECT_I;
326typedef std::vector<std::string> STR_VECT;
327
328 typedef std::vector<double> DOUBLE_VECT;
329 typedef DOUBLE_VECT::iterator DOUBLE_VECT_I;
330 typedef DOUBLE_VECT::const_iterator DOUBLE_VECT_CI;
331 typedef std::vector<DOUBLE_VECT> VECT_DOUBLE_VECT;
332 typedef VECT_DOUBLE_VECT::iterator VECT_DOUBLE_VECT_I;
333 typedef VECT_DOUBLE_VECT::const_iterator VECT_DOUBLE_VECT_CI;
334
335 typedef std::map<std::string, UINT> STR_UINT_MAP;
336 typedef std::map<std::string, UINT>::const_iterator STR_UINT_MAP_CI;
337
338 typedef std::map<int, INT_VECT> INT_INT_VECT_MAP;
339 typedef INT_INT_VECT_MAP::const_iterator INT_INT_VECT_MAP_CI;
340
341 typedef std::map<int, int> INT_MAP_INT;
342 typedef INT_MAP_INT::iterator INT_MAP_INT_I;
343 typedef INT_MAP_INT::const_iterator INT_MAP_INT_CI;
344
345 typedef std::deque<int> INT_DEQUE;
346 typedef INT_DEQUE::iterator INT_DEQUE_I;
347 typedef INT_DEQUE::const_iterator INT_DEQUE_CI;
348
349 typedef std::map<int, INT_DEQUE> INT_INT_DEQ_MAP;
350 typedef INT_INT_DEQ_MAP::const_iterator INT_INT_DEQ_MAP_CI;
351
352 typedef std::set<int> INT_SET;
353 typedef INT_SET::iterator INT_SET_I;
354 typedef INT_SET::const_iterator INT_SET_CI;
355
356//! functor to compare two doubles with a tolerance
357 struct RDKIT_RDGENERAL_EXPORT ltDouble {
358 public:
359 ltDouble() {}
360 bool operator()(double d1, double d2) const {
361 if (fabs(d1 - d2) < _tol) {
362 return false;
363 } else {
364 return (d1 < d2);
365 }
366 }
367
368 private:
369 double _tol{1.0e-8};
370};
371
372//! std::map from double to integer.
373 typedef std::map<double, int, ltDouble> DOUBLE_INT_MAP;
374
375//! functor for returning the larger of two values
376template <typename T>
377 struct RDKIT_RDGENERAL_EXPORT larger_of {
378 T operator()(T arg1, T arg2) { return arg1 > arg2 ? arg1 : arg2; }
379};
380
381//! functor for comparing two strings
382 struct RDKIT_RDGENERAL_EXPORT charptr_functor {
383 bool operator()(const char *s1, const char *s2) const {
384 return strcmp(s1, s2) < 0;
385 }
386};
387
388//! \brief calculate the union of two INT_VECTs and put the results in a
389//! third vector
390 RDKIT_RDGENERAL_EXPORT void Union(const INT_VECT &r1, const INT_VECT &r2,
391 INT_VECT &res);
392
393//! \brief calculate the intersection of two INT_VECTs and put the results in a
394//! third vector
395 RDKIT_RDGENERAL_EXPORT void Intersect(const INT_VECT &r1, const INT_VECT &r2,
396 INT_VECT &res);
397
398//! calculating the union of the INT_VECT's in a VECT_INT_VECT
399/*!
400 \param rings the INT_VECT's to consider
401 \param res used to return results
402 \param exclude any values in this optional INT_VECT will be excluded
403 from the union.
404*/
405 RDKIT_RDGENERAL_EXPORT void Union(const VECT_INT_VECT &rings, INT_VECT &res,
406 const INT_VECT *exclude = nullptr);
407
408//! given a current combination of numbers change it to the next possible
409// combination
410/*!
411 \param comb the <b>sorted</b> vector to consider
412 \param tot the maximum number possible in the vector
413
414 \return -1 on failure, the index of the last number changed on success.
415 Example:
416 for all combinations 3 of numbers between 0 and tot=5
417 given (0,1,2) the function wil return (0,1,3) etc.
418
419
420*/
421 RDKIT_RDGENERAL_EXPORT int nextCombination(INT_VECT &comb, int tot);
422}; // namespace RDKit
423
424#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:441
RDKit::common_properties
Definition types.h:53
RDKit::common_properties::_ringStereoWarning
RDKIT_RDGENERAL_EXPORT const std::string _ringStereoWarning
RDKit::common_properties::_CIPComputed
RDKIT_RDGENERAL_EXPORT const std::string _CIPComputed
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::molAttachOrderTemplate
RDKIT_RDGENERAL_EXPORT const std::string molAttachOrderTemplate
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::templateNames
RDKIT_RDGENERAL_EXPORT const std::string templateNames
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::molAtomSeqName
RDKIT_RDGENERAL_EXPORT const std::string molAtomSeqName
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::_CIPNeighborOrder
RDKIT_RDGENERAL_EXPORT const std::string _CIPNeighborOrder
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
Definition FMCS.h:185
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:342
RDKit::VECT_DOUBLE_VECT_CI
VECT_DOUBLE_VECT::const_iterator VECT_DOUBLE_VECT_CI
Definition types.h:333
RDKit::INT_LIST
std::list< int > INT_LIST
Definition types.h:309
RDKit::LIST_INT_VECT
std::list< INT_VECT > LIST_INT_VECT
Definition types.h:313
RDKit::STR_VECT
std::vector< std::string > STR_VECT
Definition Dict.h:29
RDKit::INT_SET
std::set< int > INT_SET
Definition types.h:352
RDKit::INT_VECT_CI
INT_VECT::const_iterator INT_VECT_CI
Definition types.h:305
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:350
RDKit::INT_VECT
std::vector< int > INT_VECT
Definition types.h:303
RDKit::UCHAR
unsigned char UCHAR
Definition types.h:301
RDKit::LONGINT
long long int LONGINT
Definition types.h:282
RDKit::INT_SET_CI
INT_SET::const_iterator INT_SET_CI
Definition types.h:354
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:325
RDKit::INT_VECT_CRI
INT_VECT::const_reverse_iterator INT_VECT_CRI
Definition types.h:307
RDKit::INT_MAP_INT
std::map< int, int > INT_MAP_INT
Definition types.h:341
RDKit::VECT_INT_VECT
std::vector< INT_VECT > VECT_INT_VECT
Definition types.h:317
RDKit::INT_DEQUE
std::deque< int > INT_DEQUE
Definition types.h:345
RDKit::STR_UINT_MAP
std::map< std::string, UINT > STR_UINT_MAP
Definition types.h:335
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:338
RDKit::INT_INT_DEQ_MAP
std::map< int, INT_DEQUE > INT_INT_DEQ_MAP
Definition types.h:349
RDKit::VECT_DOUBLE_VECT
std::vector< DOUBLE_VECT > VECT_DOUBLE_VECT
Definition types.h:331
RDKit::MAX_LONGINT
RDKIT_RDGENERAL_EXPORT const double MAX_LONGINT
RDKit::INT_DEQUE_I
INT_DEQUE::iterator INT_DEQUE_I
Definition types.h:346
RDKit::INT_LIST_CI
INT_LIST::const_iterator INT_LIST_CI
Definition types.h:311
RDKit::INT_DEQUE_CI
INT_DEQUE::const_iterator INT_DEQUE_CI
Definition types.h:347
RDKit::USHORT
unsigned short USHORT
Definition types.h:300
RDKit::INT_INT_VECT_MAP_CI
INT_INT_VECT_MAP::const_iterator INT_INT_VECT_MAP_CI
Definition types.h:339
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:373
RDKit::INT_VECT_RI
INT_VECT::reverse_iterator INT_VECT_RI
Definition types.h:306
RDKit::INT_SET_I
INT_SET::iterator INT_SET_I
Definition types.h:353
RDKit::UINT_VECT_CI
std::vector< UINT >::const_iterator UINT_VECT_CI
Definition types.h:321
RDKit::INT_MAP_INT_CI
INT_MAP_INT::const_iterator INT_MAP_INT_CI
Definition types.h:343
RDKit::VECT_DOUBLE_VECT_I
VECT_DOUBLE_VECT::iterator VECT_DOUBLE_VECT_I
Definition types.h:332
RDKit::STR_UINT_MAP_CI
std::map< std::string, UINT >::const_iterator STR_UINT_MAP_CI
Definition types.h:336
RDKit::DOUBLE_VECT_CI
DOUBLE_VECT::const_iterator DOUBLE_VECT_CI
Definition types.h:330
RDKit::UINT
unsigned int UINT
Definition types.h:299
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:310
RDKit::STR_VECT_CI
std::vector< std::string >::const_iterator STR_VECT_CI
Definition types.h:324
RDKit::LIST_INT_VECT_CI
LIST_INT_VECT::const_iterator LIST_INT_VECT_CI
Definition types.h:315
RDKit::DOUBLE_VECT
std::vector< double > DOUBLE_VECT
Definition types.h:328
RDKit::VECT_INT_VECT_I
VECT_INT_VECT::iterator VECT_INT_VECT_I
Definition types.h:318
RDKit::DOUBLE_VECT_I
DOUBLE_VECT::iterator DOUBLE_VECT_I
Definition types.h:329
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:319
RDKit::LIST_INT_VECT_I
LIST_INT_VECT::iterator LIST_INT_VECT_I
Definition types.h:314
RDKit::INT_VECT_I
INT_VECT::iterator INT_VECT_I
Definition types.h:304
RDKit::UINT_VECT
std::vector< UINT > UINT_VECT
Definition types.h:322
RDKit::charptr_functor
functor for comparing two strings
Definition types.h:382
RDKit::charptr_functor::operator()
bool operator()(const char *s1, const char *s2) const
Definition types.h:383
RDKit::larger_of
functor for returning the larger of two values
Definition types.h:377
RDKit::larger_of::operator()
T operator()(T arg1, T arg2)
Definition types.h:378
RDKit::ltDouble::ltDouble
ltDouble()
Definition types.h:359
RDKit::ltDouble::operator()
bool operator()(double d1, double d2) const
Definition types.h:360