RDKit
Open-source cheminformatics and machine learning.
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>
42 #include <boost/any.hpp>
43 #include <boost/lexical_cast.hpp>
45 
46 namespace RDKit {
47 
48 namespace 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 origNoImplicit; // int (bool)
75 RDKIT_RDGENERAL_EXPORT extern const std::string
76  ringMembership; //? unused (molopstest.cpp)
77 
78 // Computed Values
79 // ConnectivityDescriptors
80 RDKIT_RDGENERAL_EXPORT extern const std::string
81  _connectivityHKDeltas; // std::vector<double> computed
82 RDKIT_RDGENERAL_EXPORT extern const std::string
83  _connectivityNVals; // std::vector<double> computed
84 
85 RDKIT_RDGENERAL_EXPORT extern const std::string
86  _crippenLogP; // double computed
87 RDKIT_RDGENERAL_EXPORT extern const std::string
88  _crippenLogPContribs; // std::vector<double> computed
89 
90 RDKIT_RDGENERAL_EXPORT extern const std::string _crippenMR; // double computed
91 RDKIT_RDGENERAL_EXPORT extern const std::string
92  _crippenMRContribs; // std::vector<double> computed
93 
94 RDKIT_RDGENERAL_EXPORT extern const std::string _labuteASA; // double computed
95 RDKIT_RDGENERAL_EXPORT extern const std::string
96  _labuteAtomContribs; // vec<double> computed
97 RDKIT_RDGENERAL_EXPORT extern const std::string
98  _labuteAtomHContrib; // double computed
99 
100 RDKIT_RDGENERAL_EXPORT extern const std::string _tpsa; // double computed
101 RDKIT_RDGENERAL_EXPORT extern const std::string
102  _tpsaAtomContribs; // vec<double> computed
103 
104 RDKIT_RDGENERAL_EXPORT extern const std::string
105  numArom; // int computed (only uses in tests?)
106 RDKIT_RDGENERAL_EXPORT extern const std::string
107  _MMFFSanitized; // int (bool) computed
108 
109 RDKIT_RDGENERAL_EXPORT extern const std::string
110  _CrippenLogP; // Unused (in the basement)
111 RDKIT_RDGENERAL_EXPORT extern const std::string
112  _CrippenMR; // Unused (in the basement)
113 RDKIT_RDGENERAL_EXPORT extern const std::string
114  _GasteigerCharge; // used to hold partial charges
115 RDKIT_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
122 RDKIT_RDGENERAL_EXPORT extern const std::string
123  _BondsPotentialStereo; // int (or bool) COMPUTED
124 RDKIT_RDGENERAL_EXPORT extern const std::string
125  _CIPCode; // std::string COMPUTED
126 RDKIT_RDGENERAL_EXPORT extern const std::string _CIPRank; // int COMPUTED
127 RDKIT_RDGENERAL_EXPORT extern const std::string _ChiralityPossible; // int
128 RDKIT_RDGENERAL_EXPORT extern const std::string
129  _UnknownStereo; // int (bool) AddHs/Chirality
130 RDKIT_RDGENERAL_EXPORT extern const std::string
131  _ringStereoAtoms; // int vect Canon/Chiral/MolHash/MolOps//Renumber//RWmol
132 RDKIT_RDGENERAL_EXPORT extern const std::string
133  _ringStereochemCand; // chirality bool COMPUTED
134 RDKIT_RDGENERAL_EXPORT extern const std::string
135  _ringStereoWarning; // obsolete ?
136 
137 // Smiles parsing
138 RDKIT_RDGENERAL_EXPORT extern const std::string _SmilesStart; // int
139 RDKIT_RDGENERAL_EXPORT extern const std::string
140  _TraversalBondIndexOrder; // ? unused
141 RDKIT_RDGENERAL_EXPORT extern const std::string
142  _TraversalRingClosureBond; // unsigned int
143 RDKIT_RDGENERAL_EXPORT extern const std::string _TraversalStartPoint; // bool
144 RDKIT_RDGENERAL_EXPORT extern const std::string
145  _queryRootAtom; // int SLNParse/SubstructMatch
146 RDKIT_RDGENERAL_EXPORT extern const std::string _hasMassQuery; // atom bool
147 RDKIT_RDGENERAL_EXPORT extern const std::string _protected; // atom int (bool)
148 RDKIT_RDGENERAL_EXPORT extern const std::string
149  _supplementalSmilesLabel; // atom string (SmilesWrite)
150 RDKIT_RDGENERAL_EXPORT extern const std::string
151  _unspecifiedOrder; // atom int (bool) smarts/smiles
152 RDKIT_RDGENERAL_EXPORT extern const std::string
153  _RingClosures; // INT_VECT smarts/smiles/canon
154 RDKIT_RDGENERAL_EXPORT extern const std::string
155  atomLabel; // atom string from CXSMILES
156 
157 // MDL Style Properties (MolFileParser)
158 RDKIT_RDGENERAL_EXPORT extern const std::string molAtomMapNumber; // int
159 RDKIT_RDGENERAL_EXPORT extern const std::string molFileAlias; // string
160 RDKIT_RDGENERAL_EXPORT extern const std::string molFileValue; // string
161 RDKIT_RDGENERAL_EXPORT extern const std::string molInversionFlag; // int
162 RDKIT_RDGENERAL_EXPORT extern const std::string molParity; // int
163 RDKIT_RDGENERAL_EXPORT extern const std::string molStereoCare; // int
164 RDKIT_RDGENERAL_EXPORT extern const std::string molRxnComponent; // int
165 RDKIT_RDGENERAL_EXPORT extern const std::string molRxnRole; // int
166 RDKIT_RDGENERAL_EXPORT extern const std::string molTotValence; // int
167 RDKIT_RDGENERAL_EXPORT extern const std::string molSubstCount; // int
168 RDKIT_RDGENERAL_EXPORT extern const std::string molAttachPoint; // int
169 RDKIT_RDGENERAL_EXPORT extern const std::string molAttachOrder; // int
170 RDKIT_RDGENERAL_EXPORT extern const std::string molAtomClass; // string
171 RDKIT_RDGENERAL_EXPORT extern const std::string molAtomSeqId; // int
172 RDKIT_RDGENERAL_EXPORT extern const std::string molRxnExactChange; // int
173 RDKIT_RDGENERAL_EXPORT extern const std::string molReactStatus; // int
174 RDKIT_RDGENERAL_EXPORT extern const std::string molFileLinkNodes; // string
175 
176 RDKIT_RDGENERAL_EXPORT extern const std::string _MolFileRLabel; // unsigned int
177 RDKIT_RDGENERAL_EXPORT extern const std::string _MolFileChiralFlag; // int
178 RDKIT_RDGENERAL_EXPORT extern const std::string _MolFileAtomQuery; // int
179 RDKIT_RDGENERAL_EXPORT extern const std::string _MolFileBondQuery; // int
180 RDKIT_RDGENERAL_EXPORT extern const std::string _MolFileBondEndPts; // string
181 RDKIT_RDGENERAL_EXPORT extern const std::string _MolFileBondAttach; // string
182 RDKIT_RDGENERAL_EXPORT extern const std::string
183  _MolFileBondType; // unsigned int
184 RDKIT_RDGENERAL_EXPORT extern const std::string
185  _MolFileBondStereo; // unsigned int
186 RDKIT_RDGENERAL_EXPORT extern const std::string
187  _MolFileBondCfg; // unsigned int
188 
189 RDKIT_RDGENERAL_EXPORT extern const std::string
190  MRV_SMA; // smarts string from Marvin
191 RDKIT_RDGENERAL_EXPORT extern const std::string dummyLabel; // atom string
192 
193 RDKIT_RDGENERAL_EXPORT extern const std::string
194  _QueryAtomGenericLabel; // string
195 
196 // Reaction Information (Reactions.cpp)
197 RDKIT_RDGENERAL_EXPORT extern const std::string _QueryFormalCharge; // int
198 RDKIT_RDGENERAL_EXPORT extern const std::string _QueryHCount; // int
199 RDKIT_RDGENERAL_EXPORT extern const std::string _QueryIsotope; // int
200 RDKIT_RDGENERAL_EXPORT extern const std::string
201  _QueryMass; // int = round(float * 1000)
202 RDKIT_RDGENERAL_EXPORT extern const std::string
203  _ReactionDegreeChanged; // int (bool)
204 RDKIT_RDGENERAL_EXPORT extern const std::string NullBond; // int (bool)
205 RDKIT_RDGENERAL_EXPORT extern const std::string _rgroupAtomMaps;
206 RDKIT_RDGENERAL_EXPORT extern const std::string _rgroupBonds;
207 RDKIT_RDGENERAL_EXPORT extern const std::string reactantAtomIdx;
208 RDKIT_RDGENERAL_EXPORT extern const std::string reactionMapNum;
209 
210 // SLN
211 RDKIT_RDGENERAL_EXPORT extern const std::string
212  _AtomID; // unsigned int SLNParser
213 RDKIT_RDGENERAL_EXPORT extern const std::string
214  _starred; // atom int COMPUTED (SLN)
215 RDKIT_RDGENERAL_EXPORT extern const std::string
216  _SLN_s; // string SLNAttribs (chiral info)
217 RDKIT_RDGENERAL_EXPORT extern const std::string _Unfinished_SLN_; // int (bool)
218 
219 // Smarts Smiles
220 RDKIT_RDGENERAL_EXPORT extern const std::string _brokenChirality; // atom bool
221 RDKIT_RDGENERAL_EXPORT extern const std::string isImplicit; // atom int (bool)
222 RDKIT_RDGENERAL_EXPORT extern const std::string
223  smilesSymbol; // atom string (only used in test?)
224 
225 // Tripos
226 RDKIT_RDGENERAL_EXPORT extern const std::string
227  _TriposAtomType; // string Mol2FileParser
228 // missing defs for _TriposAtomName//_TriposPartialCharge...
229 
230 // molecule drawing
231 RDKIT_RDGENERAL_EXPORT extern const std::string _displayLabel; // string
232 RDKIT_RDGENERAL_EXPORT extern const std::string _displayLabelW; // string
233 
234 ///////////////////////////////////////////////////////////////
235 // misc props
236 RDKIT_RDGENERAL_EXPORT extern const std::string
237  TWOD; // need THREED -> confusing using in TDTMol supplier
238  // converge with _2DConf?
239 RDKIT_RDGENERAL_EXPORT extern const std::string BalabanJ; // mol double
240 RDKIT_RDGENERAL_EXPORT extern const std::string BalanbanJ; // typo!! fix...
241 
242 RDKIT_RDGENERAL_EXPORT extern const std::string Discrims; // FragCatalog Entry
243 // Subgraphs::DiscrimTuple (uint32,uint32,uint32)
244 RDKIT_RDGENERAL_EXPORT extern const std::string
245  DistanceMatrix_Paths; // boost::shared_array<double>
246 // - note, confusing creation of names in
247 // - getDistanceMat
248 RDKIT_RDGENERAL_EXPORT extern const std::string internalRgroupSmiles;
249 RDKIT_RDGENERAL_EXPORT extern const std::string molNote;
250 RDKIT_RDGENERAL_EXPORT extern const std::string atomNote;
251 RDKIT_RDGENERAL_EXPORT extern const std::string bondNote;
252 RDKIT_RDGENERAL_EXPORT extern const std::string _isotopicHs;
253 
254 } // namespace common_properties
255 #ifndef WIN32
256 typedef long long int LONGINT;
257 #else
258 typedef __int64 LONGINT;
259 #endif
260 #ifdef max
261 #undef max // FUCK I hate this nonsense
262 #endif
263 #ifdef min
264 #undef min // FUCK I hate this nonsense
265 #endif
266 
267 RDKIT_RDGENERAL_EXPORT extern const double MAX_DOUBLE;
268 RDKIT_RDGENERAL_EXPORT extern const double EPS_DOUBLE;
269 RDKIT_RDGENERAL_EXPORT extern const double SMALL_DOUBLE;
270 RDKIT_RDGENERAL_EXPORT extern const double MAX_INT;
271 RDKIT_RDGENERAL_EXPORT extern const double MAX_LONGINT;
272 
273 typedef unsigned int UINT;
274 typedef unsigned short USHORT;
275 typedef unsigned char UCHAR;
276 
277 typedef std::vector<int> INT_VECT;
278 typedef INT_VECT::iterator INT_VECT_I;
279 typedef INT_VECT::const_iterator INT_VECT_CI;
280 typedef INT_VECT::reverse_iterator INT_VECT_RI;
281 typedef INT_VECT::const_reverse_iterator INT_VECT_CRI;
282 
283 typedef std::list<int> INT_LIST;
284 typedef INT_LIST::iterator INT_LIST_I;
285 typedef INT_LIST::const_iterator INT_LIST_CI;
286 
287 typedef std::list<INT_VECT> LIST_INT_VECT;
288 typedef LIST_INT_VECT::iterator LIST_INT_VECT_I;
289 typedef LIST_INT_VECT::const_iterator LIST_INT_VECT_CI;
290 
291 typedef std::vector<INT_VECT> VECT_INT_VECT;
292 typedef VECT_INT_VECT::iterator VECT_INT_VECT_I;
293 typedef VECT_INT_VECT::const_iterator VECT_INT_VECT_CI;
294 
295 typedef std::vector<UINT>::const_iterator UINT_VECT_CI;
296 typedef std::vector<UINT> UINT_VECT;
297 
298 typedef std::vector<std::string>::const_iterator STR_VECT_CI;
299 typedef std::vector<std::string>::iterator STR_VECT_I;
300 typedef std::vector<std::string> STR_VECT;
301 
302 typedef std::vector<double> DOUBLE_VECT;
303 typedef DOUBLE_VECT::iterator DOUBLE_VECT_I;
304 typedef DOUBLE_VECT::const_iterator DOUBLE_VECT_CI;
305 typedef std::vector<DOUBLE_VECT> VECT_DOUBLE_VECT;
306 typedef VECT_DOUBLE_VECT::iterator VECT_DOUBLE_VECT_I;
307 typedef VECT_DOUBLE_VECT::const_iterator VECT_DOUBLE_VECT_CI;
308 
309 typedef std::map<std::string, UINT> STR_UINT_MAP;
310 typedef std::map<std::string, UINT>::const_iterator STR_UINT_MAP_CI;
311 
312 typedef std::map<int, INT_VECT> INT_INT_VECT_MAP;
313 typedef INT_INT_VECT_MAP::const_iterator INT_INT_VECT_MAP_CI;
314 
315 typedef std::map<int, int> INT_MAP_INT;
316 typedef INT_MAP_INT::iterator INT_MAP_INT_I;
317 typedef INT_MAP_INT::const_iterator INT_MAP_INT_CI;
318 
319 typedef std::deque<int> INT_DEQUE;
320 typedef INT_DEQUE::iterator INT_DEQUE_I;
321 typedef INT_DEQUE::const_iterator INT_DEQUE_CI;
322 
323 typedef std::map<int, INT_DEQUE> INT_INT_DEQ_MAP;
324 typedef INT_INT_DEQ_MAP::const_iterator INT_INT_DEQ_MAP_CI;
325 
326 typedef std::set<int> INT_SET;
327 typedef INT_SET::iterator INT_SET_I;
328 typedef INT_SET::const_iterator INT_SET_CI;
329 
330 //! functor to compare two doubles with a tolerance
332  public:
333  ltDouble() {}
334  bool operator()(double d1, double d2) const {
335  if (fabs(d1 - d2) < _tol) {
336  return false;
337  } else {
338  return (d1 < d2);
339  }
340  }
341 
342  private:
343  double _tol{1.0e-8};
344 };
345 
346 //! std::map from double to integer.
347 typedef std::map<double, int, ltDouble> DOUBLE_INT_MAP;
348 
349 //! functor for returning the larger of two values
350 template <typename T>
352  T operator()(T arg1, T arg2) { return arg1 > arg2 ? arg1 : arg2; }
353 };
354 
355 //! functor for comparing two strings
357  bool operator()(const char *s1, const char *s2) const {
358  // std::cout << s1 << " " << s2 << " " << strcmp(s1, s2) << "\n";
359 
360  return strcmp(s1, s2) < 0;
361  }
362 };
363 
364 //! \brief calculate the union of two INT_VECTs and put the results in a
365 //! third vector
366 RDKIT_RDGENERAL_EXPORT void Union(const INT_VECT &r1, const INT_VECT &r2,
367  INT_VECT &res);
368 
369 //! \brief calculate the intersection of two INT_VECTs and put the results in a
370 //! third vector
372  INT_VECT &res);
373 
374 //! calculating the union of the INT_VECT's in a VECT_INT_VECT
375 /*!
376  \param rings the INT_VECT's to consider
377  \param res used to return results
378  \param exclude any values in this optional INT_VECT will be excluded
379  from the union.
380 */
382  const INT_VECT *exclude = nullptr);
383 
384 //! given a current combination of numbers change it to the next possible
385 // combination
386 /*!
387  \param comb the <b>sorted</b> vector to consider
388  \param tot the maximum number possible in the vector
389 
390  \return -1 on failure, the index of the last number changed on success.
391  Example:
392  for all combinations 3 of numbers between 0 and tot=5
393  given (0,1,2) the function wil return (0,1,3) etc.
394 
395 
396 */
398 
399 }; // namespace RDKit
400 
401 #endif
Defines the Dict class.
#define RDKIT_RDGENERAL_EXPORT
Definition: export.h:361
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 _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:18
INT_MAP_INT::iterator INT_MAP_INT_I
Definition: types.h:316
VECT_DOUBLE_VECT::const_iterator VECT_DOUBLE_VECT_CI
Definition: types.h:307
std::list< int > INT_LIST
Definition: types.h:283
std::list< INT_VECT > LIST_INT_VECT
Definition: types.h:287
std::vector< std::string > STR_VECT
Definition: Dict.h:29
std::set< int > INT_SET
Definition: types.h:326
INT_VECT::const_iterator INT_VECT_CI
Definition: types.h:279
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:324
std::vector< int > INT_VECT
Definition: types.h:277
unsigned char UCHAR
Definition: types.h:275
long long int LONGINT
Definition: types.h:256
INT_SET::const_iterator INT_SET_CI
Definition: types.h:328
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:299
INT_VECT::const_reverse_iterator INT_VECT_CRI
Definition: types.h:281
std::map< int, int > INT_MAP_INT
Definition: types.h:315
std::vector< INT_VECT > VECT_INT_VECT
Definition: types.h:291
std::deque< int > INT_DEQUE
Definition: types.h:319
std::map< std::string, UINT > STR_UINT_MAP
Definition: types.h:309
RDKIT_RDGENERAL_EXPORT const double EPS_DOUBLE
std::map< std::string, UINT >::const_iterator STR_UINT_MAP_CI
Definition: types.h:310
std::map< int, INT_VECT > INT_INT_VECT_MAP
Definition: types.h:312
std::map< int, INT_DEQUE > INT_INT_DEQ_MAP
Definition: types.h:323
std::vector< DOUBLE_VECT > VECT_DOUBLE_VECT
Definition: types.h:305
RDKIT_RDGENERAL_EXPORT const double MAX_LONGINT
INT_DEQUE::iterator INT_DEQUE_I
Definition: types.h:320
INT_LIST::const_iterator INT_LIST_CI
Definition: types.h:285
INT_DEQUE::const_iterator INT_DEQUE_CI
Definition: types.h:321
unsigned short USHORT
Definition: types.h:274
INT_INT_VECT_MAP::const_iterator INT_INT_VECT_MAP_CI
Definition: types.h:313
RDKIT_RDGENERAL_EXPORT const double MAX_INT
std::map< double, int, ltDouble > DOUBLE_INT_MAP
std::map from double to integer.
Definition: types.h:347
INT_VECT::reverse_iterator INT_VECT_RI
Definition: types.h:280
INT_SET::iterator INT_SET_I
Definition: types.h:327
std::vector< UINT >::const_iterator UINT_VECT_CI
Definition: types.h:295
INT_MAP_INT::const_iterator INT_MAP_INT_CI
Definition: types.h:317
VECT_DOUBLE_VECT::iterator VECT_DOUBLE_VECT_I
Definition: types.h:306
DOUBLE_VECT::const_iterator DOUBLE_VECT_CI
Definition: types.h:304
unsigned int UINT
Definition: types.h:273
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:284
std::vector< std::string >::const_iterator STR_VECT_CI
Definition: types.h:298
LIST_INT_VECT::const_iterator LIST_INT_VECT_CI
Definition: types.h:289
std::vector< double > DOUBLE_VECT
Definition: types.h:302
VECT_INT_VECT::iterator VECT_INT_VECT_I
Definition: types.h:292
DOUBLE_VECT::iterator DOUBLE_VECT_I
Definition: types.h:303
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:293
LIST_INT_VECT::iterator LIST_INT_VECT_I
Definition: types.h:288
INT_VECT::iterator INT_VECT_I
Definition: types.h:278
std::vector< UINT > UINT_VECT
Definition: types.h:296
functor for comparing two strings
Definition: types.h:356
bool operator()(const char *s1, const char *s2) const
Definition: types.h:357
functor for returning the larger of two values
Definition: types.h:351
T operator()(T arg1, T arg2)
Definition: types.h:352
functor to compare two doubles with a tolerance
Definition: types.h:331
bool operator()(double d1, double d2) const
Definition: types.h:334