RDKit
Open-source cheminformatics and machine learning.
types.h
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1 //
2 // Copyright (C) 2001-2018 Greg Landrum and Rational Discovery LLC
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 _StereochemDone; // int
68 RDKIT_RDGENERAL_EXPORT extern const std::string _NeedsQueryScan; // int (bool)
69 RDKIT_RDGENERAL_EXPORT extern const std::string _fragSMARTS; // std::string
70 RDKIT_RDGENERAL_EXPORT extern const std::string
71  maxAttachIdx; // int TemplEnumTools.cpp
72 RDKIT_RDGENERAL_EXPORT extern const std::string origNoImplicit; // int (bool)
73 RDKIT_RDGENERAL_EXPORT extern const std::string
74  ringMembership; //? unused (molopstest.cpp)
75 
76 // Computed Values
77 // ConnectivityDescriptors
78 RDKIT_RDGENERAL_EXPORT extern const std::string
79  _connectivityHKDeltas; // std::vector<double> computed
80 RDKIT_RDGENERAL_EXPORT extern const std::string
81  _connectivityNVals; // std::vector<double> computed
82 
83 RDKIT_RDGENERAL_EXPORT extern const std::string
84  _crippenLogP; // double computed
85 RDKIT_RDGENERAL_EXPORT extern const std::string
86  _crippenLogPContribs; // std::vector<double> computed
87 
88 RDKIT_RDGENERAL_EXPORT extern const std::string _crippenMR; // double computed
89 RDKIT_RDGENERAL_EXPORT extern const std::string
90  _crippenMRContribs; // std::vector<double> computed
91 
92 RDKIT_RDGENERAL_EXPORT extern const std::string _labuteASA; // double computed
93 RDKIT_RDGENERAL_EXPORT extern const std::string
94  _labuteAtomContribs; // vec<double> computed
95 RDKIT_RDGENERAL_EXPORT extern const std::string
96  _labuteAtomHContrib; // double computed
97 
98 RDKIT_RDGENERAL_EXPORT extern const std::string _tpsa; // double computed
99 RDKIT_RDGENERAL_EXPORT extern const std::string
100  _tpsaAtomContribs; // vec<double> computed
101 
102 RDKIT_RDGENERAL_EXPORT extern const std::string
103  numArom; // int computed (only uses in tests?)
104 RDKIT_RDGENERAL_EXPORT extern const std::string
105  _MMFFSanitized; // int (bool) computed
106 
107 RDKIT_RDGENERAL_EXPORT extern const std::string
108  _CrippenLogP; // Unused (in the basement)
109 RDKIT_RDGENERAL_EXPORT extern const std::string
110  _CrippenMR; // Unused (in the basement)
111 RDKIT_RDGENERAL_EXPORT extern const std::string
112  _GasteigerCharge; // used to hold partial charges
113 RDKIT_RDGENERAL_EXPORT extern const std::string
114  _GasteigerHCharge; // used to hold partial charges from implicit Hs
115 
116 ///////////////////////////////////////////////////////////////
117 // Atom Props
118 
119 // Chirality stuff
120 RDKIT_RDGENERAL_EXPORT extern const std::string
121  _BondsPotentialStereo; // int (or bool) COMPUTED
122 RDKIT_RDGENERAL_EXPORT extern const std::string
123  _CIPCode; // std::string COMPUTED
124 RDKIT_RDGENERAL_EXPORT extern const std::string _CIPRank; // int COMPUTED
125 RDKIT_RDGENERAL_EXPORT extern const std::string _ChiralityPossible; // int
126 RDKIT_RDGENERAL_EXPORT extern const std::string
127  _UnknownStereo; // int (bool) AddHs/Chirality
128 RDKIT_RDGENERAL_EXPORT extern const std::string
129  _ringStereoAtoms; // int vect Canon/Chiral/MolHash/MolOps//Renumber//RWmol
130 RDKIT_RDGENERAL_EXPORT extern const std::string
131  _ringStereochemCand; // chirality bool COMPUTED
132 RDKIT_RDGENERAL_EXPORT extern const std::string
133  _ringStereoWarning; // obsolete ?
134 
135 // Smiles parsing
136 RDKIT_RDGENERAL_EXPORT extern const std::string _SmilesStart; // int
137 RDKIT_RDGENERAL_EXPORT extern const std::string
138  _TraversalBondIndexOrder; // ? unused
139 RDKIT_RDGENERAL_EXPORT extern const std::string
140  _TraversalRingClosureBond; // unsigned int
141 RDKIT_RDGENERAL_EXPORT extern const std::string _TraversalStartPoint; // bool
142 RDKIT_RDGENERAL_EXPORT extern const std::string
143  _queryRootAtom; // int SLNParse/SubstructMatch
144 RDKIT_RDGENERAL_EXPORT extern const std::string _hasMassQuery; // atom bool
145 RDKIT_RDGENERAL_EXPORT extern const std::string _protected; // atom int (bool)
146 RDKIT_RDGENERAL_EXPORT extern const std::string
147  _supplementalSmilesLabel; // atom string (SmilesWrite)
148 RDKIT_RDGENERAL_EXPORT extern const std::string
149  _unspecifiedOrder; // atom int (bool) smarts/smiles
150 RDKIT_RDGENERAL_EXPORT extern const std::string
151  _RingClosures; // INT_VECT smarts/smiles/canon
152 RDKIT_RDGENERAL_EXPORT extern const std::string
153  atomLabel; // atom string from CXSMILES
154 
155 // MDL Style Properties (MolFileParser)
156 RDKIT_RDGENERAL_EXPORT extern const std::string molAtomMapNumber; // int
157 RDKIT_RDGENERAL_EXPORT extern const std::string molFileAlias; // string
158 RDKIT_RDGENERAL_EXPORT extern const std::string molFileValue; // string
159 RDKIT_RDGENERAL_EXPORT extern const std::string molInversionFlag; // int
160 RDKIT_RDGENERAL_EXPORT extern const std::string molParity; // int
161 RDKIT_RDGENERAL_EXPORT extern const std::string molStereoCare; // int
162 RDKIT_RDGENERAL_EXPORT extern const std::string molRxnComponent; // int
163 RDKIT_RDGENERAL_EXPORT extern const std::string molRxnRole; // int
164 RDKIT_RDGENERAL_EXPORT extern const std::string molTotValence; // int
165 RDKIT_RDGENERAL_EXPORT extern const std::string molSubstCount; // int
166 RDKIT_RDGENERAL_EXPORT extern const std::string molAttachPoint; // int
167 RDKIT_RDGENERAL_EXPORT extern const std::string molAttachOrder; // int
168 RDKIT_RDGENERAL_EXPORT extern const std::string molAtomClass; // string
169 RDKIT_RDGENERAL_EXPORT extern const std::string molAtomSeqId; // int
170 RDKIT_RDGENERAL_EXPORT extern const std::string molRxnExactChange; // int
171 RDKIT_RDGENERAL_EXPORT extern const std::string molReactStatus; // int
172 RDKIT_RDGENERAL_EXPORT extern const std::string molFileLinkNodes; // string
173 
174 RDKIT_RDGENERAL_EXPORT extern const std::string _MolFileRLabel; // unsigned int
175 RDKIT_RDGENERAL_EXPORT extern const std::string _MolFileChiralFlag; // int
176 RDKIT_RDGENERAL_EXPORT extern const std::string _MolFileAtomQuery; // int
177 RDKIT_RDGENERAL_EXPORT extern const std::string _MolFileBondQuery; // int
178 RDKIT_RDGENERAL_EXPORT extern const std::string _MolFileBondEndPts; // string
179 RDKIT_RDGENERAL_EXPORT extern const std::string _MolFileBondAttach; // string
180 RDKIT_RDGENERAL_EXPORT extern const std::string
181  _MolFileBondType; // unsigned int
182 RDKIT_RDGENERAL_EXPORT extern const std::string
183  _MolFileBondStereo; // unsigned int
184 RDKIT_RDGENERAL_EXPORT extern const std::string
185  _MolFileBondCfg; // unsigned int
186 
187 RDKIT_RDGENERAL_EXPORT extern const std::string
188  MRV_SMA; // smarts string from Marvin
189 RDKIT_RDGENERAL_EXPORT extern const std::string dummyLabel; // atom string
190 
191 // Reaction Information (Reactions.cpp)
192 RDKIT_RDGENERAL_EXPORT extern const std::string _QueryFormalCharge; // int
193 RDKIT_RDGENERAL_EXPORT extern const std::string _QueryHCount; // int
194 RDKIT_RDGENERAL_EXPORT extern const std::string _QueryIsotope; // int
195 RDKIT_RDGENERAL_EXPORT extern const std::string
196  _QueryMass; // int = round(float * 1000)
197 RDKIT_RDGENERAL_EXPORT extern const std::string
198  _ReactionDegreeChanged; // int (bool)
199 RDKIT_RDGENERAL_EXPORT extern const std::string NullBond; // int (bool)
200 RDKIT_RDGENERAL_EXPORT extern const std::string _rgroupAtomMaps;
201 RDKIT_RDGENERAL_EXPORT extern const std::string _rgroupBonds;
202 RDKIT_RDGENERAL_EXPORT extern const std::string reactantAtomIdx;
203 RDKIT_RDGENERAL_EXPORT extern const std::string reactionMapNum;
204 
205 // SLN
206 RDKIT_RDGENERAL_EXPORT extern const std::string
207  _AtomID; // unsigned int SLNParser
208 RDKIT_RDGENERAL_EXPORT extern const std::string
209  _starred; // atom int COMPUTED (SLN)
210 RDKIT_RDGENERAL_EXPORT extern const std::string
211  _SLN_s; // string SLNAttribs (chiral info)
212 RDKIT_RDGENERAL_EXPORT extern const std::string _Unfinished_SLN_; // int (bool)
213 
214 // Smarts Smiles
215 RDKIT_RDGENERAL_EXPORT extern const std::string _brokenChirality; // atom bool
216 RDKIT_RDGENERAL_EXPORT extern const std::string isImplicit; // atom int (bool)
217 RDKIT_RDGENERAL_EXPORT extern const std::string
218  smilesSymbol; // atom string (only used in test?)
219 
220 // Tripos
221 RDKIT_RDGENERAL_EXPORT extern const std::string
222  _TriposAtomType; // string Mol2FileParser
223 // missing defs for _TriposAtomName//_TriposPartialCharge...
224 
225 ///////////////////////////////////////////////////////////////
226 // misc props
227 RDKIT_RDGENERAL_EXPORT extern const std::string
228  TWOD; // need THREED -> confusing using in TDTMol supplier
229  // converge with _2DConf?
230 RDKIT_RDGENERAL_EXPORT extern const std::string BalabanJ; // mol double
231 RDKIT_RDGENERAL_EXPORT extern const std::string BalanbanJ; // typo!! fix...
232 
233 RDKIT_RDGENERAL_EXPORT extern const std::string Discrims; // FragCatalog Entry
234 // Subgraphs::DiscrimTuple (uint32,uint32,uint32)
235 RDKIT_RDGENERAL_EXPORT extern const std::string
236  DistanceMatrix_Paths; // boost::shared_array<double>
237 // - note, confusing creation of names in
238 // - getDistanceMat
239 RDKIT_RDGENERAL_EXPORT extern const std::string internalRgroupSmiles;
240 RDKIT_RDGENERAL_EXPORT extern const std::string atomNote;
241 RDKIT_RDGENERAL_EXPORT extern const std::string bondNote;
242 
243 } // namespace common_properties
244 #ifndef WIN32
245 typedef long long int LONGINT;
246 #else
247 typedef __int64 LONGINT;
248 #endif
249 #ifdef max
250 #undef max // FUCK I hate this nonsense
251 #endif
252 #ifdef min
253 #undef min // FUCK I hate this nonsense
254 #endif
255 
256 RDKIT_RDGENERAL_EXPORT extern const double MAX_DOUBLE;
257 RDKIT_RDGENERAL_EXPORT extern const double EPS_DOUBLE;
258 RDKIT_RDGENERAL_EXPORT extern const double SMALL_DOUBLE;
259 RDKIT_RDGENERAL_EXPORT extern const double MAX_INT;
260 RDKIT_RDGENERAL_EXPORT extern const double MAX_LONGINT;
261 
262 typedef unsigned int UINT;
263 typedef unsigned short USHORT;
264 typedef unsigned char UCHAR;
265 
266 typedef std::vector<int> INT_VECT;
267 typedef INT_VECT::iterator INT_VECT_I;
268 typedef INT_VECT::const_iterator INT_VECT_CI;
269 typedef INT_VECT::reverse_iterator INT_VECT_RI;
270 typedef INT_VECT::const_reverse_iterator INT_VECT_CRI;
271 
272 typedef std::list<int> INT_LIST;
273 typedef INT_LIST::iterator INT_LIST_I;
274 typedef INT_LIST::const_iterator INT_LIST_CI;
275 
276 typedef std::list<INT_VECT> LIST_INT_VECT;
277 typedef LIST_INT_VECT::iterator LIST_INT_VECT_I;
278 typedef LIST_INT_VECT::const_iterator LIST_INT_VECT_CI;
279 
280 typedef std::vector<INT_VECT> VECT_INT_VECT;
281 typedef VECT_INT_VECT::iterator VECT_INT_VECT_I;
282 typedef VECT_INT_VECT::const_iterator VECT_INT_VECT_CI;
283 
284 typedef std::vector<UINT>::const_iterator UINT_VECT_CI;
285 typedef std::vector<UINT> UINT_VECT;
286 
287 typedef std::vector<std::string>::const_iterator STR_VECT_CI;
288 typedef std::vector<std::string>::iterator STR_VECT_I;
289 typedef std::vector<std::string> STR_VECT;
290 
291 typedef std::vector<double> DOUBLE_VECT;
292 typedef DOUBLE_VECT::iterator DOUBLE_VECT_I;
293 typedef DOUBLE_VECT::const_iterator DOUBLE_VECT_CI;
294 typedef std::vector<DOUBLE_VECT> VECT_DOUBLE_VECT;
295 typedef VECT_DOUBLE_VECT::iterator VECT_DOUBLE_VECT_I;
296 typedef VECT_DOUBLE_VECT::const_iterator VECT_DOUBLE_VECT_CI;
297 
298 typedef std::map<std::string, UINT> STR_UINT_MAP;
299 typedef std::map<std::string, UINT>::const_iterator STR_UINT_MAP_CI;
300 
301 typedef std::map<int, INT_VECT> INT_INT_VECT_MAP;
302 typedef INT_INT_VECT_MAP::const_iterator INT_INT_VECT_MAP_CI;
303 
304 typedef std::map<int, int> INT_MAP_INT;
305 typedef INT_MAP_INT::iterator INT_MAP_INT_I;
306 typedef INT_MAP_INT::const_iterator INT_MAP_INT_CI;
307 
308 typedef std::deque<int> INT_DEQUE;
309 typedef INT_DEQUE::iterator INT_DEQUE_I;
310 typedef INT_DEQUE::const_iterator INT_DEQUE_CI;
311 
312 typedef std::map<int, INT_DEQUE> INT_INT_DEQ_MAP;
313 typedef INT_INT_DEQ_MAP::const_iterator INT_INT_DEQ_MAP_CI;
314 
315 typedef std::set<int> INT_SET;
316 typedef INT_SET::iterator INT_SET_I;
317 typedef INT_SET::const_iterator INT_SET_CI;
318 
319 //! functor to compare two doubles with a tolerance
321  public:
322  ltDouble() : _tol(1.0e-8){};
323  bool operator()(double d1, double d2) const {
324  if (fabs(d1 - d2) < _tol) {
325  return false;
326  } else {
327  return (d1 < d2);
328  }
329  }
330 
331  private:
332  double _tol;
333 };
334 
335 //! std::map from double to integer.
336 typedef std::map<double, int, ltDouble> DOUBLE_INT_MAP;
337 
338 //! functor for returning the larger of two values
339 template <typename T>
341  T operator()(T arg1, T arg2) { return arg1 > arg2 ? arg1 : arg2; };
342 };
343 
344 //! functor for comparing two strings
346  bool operator()(const char *s1, const char *s2) const {
347  // std::cout << s1 << " " << s2 << " " << strcmp(s1, s2) << "\n";
348 
349  return strcmp(s1, s2) < 0;
350  };
351 };
352 
353 //! \brief calculate the union of two INT_VECTs and put the results in a
354 //! third vector
355 RDKIT_RDGENERAL_EXPORT void Union(const INT_VECT &r1, const INT_VECT &r2,
356  INT_VECT &res);
357 
358 //! \brief calculate the intersection of two INT_VECTs and put the results in a
359 //! third vector
361  INT_VECT &res);
362 
363 //! calculating the union of the INT_VECT's in a VECT_INT_VECT
364 /*!
365  \param rings the INT_VECT's to consider
366  \param res used to return results
367  \param exclude any values in this optional INT_VECT will be excluded
368  from the union.
369 */
371  const INT_VECT *exclude = NULL);
372 
373 //! given a current combination of numbers change it to the next possible
374 // combination
375 /*!
376  \param comb the <b>sorted</b> vector to consider
377  \param tot the maximum number possible in the vector
378 
379  \return -1 on failure, the index of the last number changed on success.
380  Example:
381  for all combinations 3 of numbers between 0 and tot=5
382  given (0,1,2) the function wil return (0,1,3) etc.
383 
384 
385 */
387 
388 }; // namespace RDKit
389 
390 #endif
RDKit::common_properties::_labuteASA
RDKIT_RDGENERAL_EXPORT const std::string _labuteASA
RDKit::LIST_INT_VECT_CI
LIST_INT_VECT::const_iterator LIST_INT_VECT_CI
Definition: types.h:278
RDKit::common_properties::_CIPRank
RDKIT_RDGENERAL_EXPORT const std::string _CIPRank
RDKit::UCHAR
unsigned char UCHAR
Definition: types.h:264
RDKit::common_properties::reactionMapNum
RDKIT_RDGENERAL_EXPORT const std::string reactionMapNum
RDKit::common_properties::_labuteAtomContribs
RDKIT_RDGENERAL_EXPORT const std::string _labuteAtomContribs
RDKit::common_properties::maxAttachIdx
RDKIT_RDGENERAL_EXPORT const std::string maxAttachIdx
RDKit::VECT_INT_VECT
std::vector< INT_VECT > VECT_INT_VECT
Definition: types.h:280
RDKit::common_properties::BalanbanJ
RDKIT_RDGENERAL_EXPORT const std::string BalanbanJ
RDKit::charptr_functor
functor for comparing two strings
Definition: types.h:345
RDKit::common_properties::molTotValence
RDKIT_RDGENERAL_EXPORT const std::string molTotValence
RDKit::common_properties::_Name
RDKIT_RDGENERAL_EXPORT const std::string _Name
RDKit::INT_INT_VECT_MAP
std::map< int, INT_VECT > INT_INT_VECT_MAP
Definition: types.h:301
RDKit::common_properties::_ringStereochemCand
RDKIT_RDGENERAL_EXPORT const std::string _ringStereochemCand
RDKit::INT_VECT
std::vector< int > INT_VECT
Definition: types.h:266
RDKit::STR_UINT_MAP_CI
std::map< std::string, UINT >::const_iterator STR_UINT_MAP_CI
Definition: types.h:299
RDKit::STR_VECT_CI
std::vector< std::string >::const_iterator STR_VECT_CI
Definition: types.h:287
BoostStartInclude.h
RDKit::EPS_DOUBLE
RDKIT_RDGENERAL_EXPORT const double EPS_DOUBLE
RDKit::common_properties::_tpsa
RDKIT_RDGENERAL_EXPORT const std::string _tpsa
RDKit::common_properties::BalabanJ
RDKIT_RDGENERAL_EXPORT const std::string BalabanJ
RDKit::common_properties::NullBond
RDKIT_RDGENERAL_EXPORT const std::string NullBond
RDKit::common_properties::ringMembership
RDKIT_RDGENERAL_EXPORT const std::string ringMembership
RDKit::ltDouble::operator()
bool operator()(double d1, double d2) const
Definition: types.h:323
RDKit::common_properties::atomNote
RDKIT_RDGENERAL_EXPORT const std::string atomNote
RDKit::INT_LIST_CI
INT_LIST::const_iterator INT_LIST_CI
Definition: types.h:274
RDKit::common_properties::molParity
RDKIT_RDGENERAL_EXPORT const std::string molParity
RDKit::common_properties::_connectivityNVals
RDKIT_RDGENERAL_EXPORT const std::string _connectivityNVals
RDKit::common_properties::_CIPCode
RDKIT_RDGENERAL_EXPORT const std::string _CIPCode
RDKit::DOUBLE_VECT
std::vector< double > DOUBLE_VECT
Definition: types.h:291
RDKit::charptr_functor::operator()
bool operator()(const char *s1, const char *s2) const
Definition: types.h:346
RDKit::INT_VECT_RI
INT_VECT::reverse_iterator INT_VECT_RI
Definition: types.h:269
RDKit::common_properties::molReactStatus
RDKIT_RDGENERAL_EXPORT const std::string molReactStatus
RDKit::common_properties::_MolFileAtomQuery
RDKIT_RDGENERAL_EXPORT const std::string _MolFileAtomQuery
RDKit::common_properties::molFileLinkNodes
RDKIT_RDGENERAL_EXPORT const std::string molFileLinkNodes
RDKit::common_properties::_Unfinished_SLN_
RDKIT_RDGENERAL_EXPORT const std::string _Unfinished_SLN_
RDKit::LIST_INT_VECT_I
LIST_INT_VECT::iterator LIST_INT_VECT_I
Definition: types.h:277
RDKit::SMALL_DOUBLE
RDKIT_RDGENERAL_EXPORT const double SMALL_DOUBLE
RDKit::common_properties::_ringStereoAtoms
RDKIT_RDGENERAL_EXPORT const std::string _ringStereoAtoms
RDKit::DOUBLE_VECT_CI
DOUBLE_VECT::const_iterator DOUBLE_VECT_CI
Definition: types.h:293
RDKit::common_properties::_smilesAtomOutputOrder
RDKIT_RDGENERAL_EXPORT const std::string _smilesAtomOutputOrder
RDKit::VECT_DOUBLE_VECT
std::vector< DOUBLE_VECT > VECT_DOUBLE_VECT
Definition: types.h:294
RDKit::common_properties::_queryRootAtom
RDKIT_RDGENERAL_EXPORT const std::string _queryRootAtom
RDKit::LIST_INT_VECT
std::list< INT_VECT > LIST_INT_VECT
Definition: types.h:276
RDKit::common_properties::_crippenLogP
RDKIT_RDGENERAL_EXPORT const std::string _crippenLogP
RDKit::INT_SET_I
INT_SET::iterator INT_SET_I
Definition: types.h:316
RDKit::INT_SET
std::set< int > INT_SET
Definition: types.h:315
RDKit::common_properties::MRV_SMA
RDKIT_RDGENERAL_EXPORT const std::string MRV_SMA
RDKit::common_properties::internalRgroupSmiles
RDKIT_RDGENERAL_EXPORT const std::string internalRgroupSmiles
RDKit::common_properties::_SmilesStart
RDKIT_RDGENERAL_EXPORT const std::string _SmilesStart
RDKit::common_properties::_hasMassQuery
RDKIT_RDGENERAL_EXPORT const std::string _hasMassQuery
RDKit::common_properties::_TriposAtomType
RDKIT_RDGENERAL_EXPORT const std::string _TriposAtomType
RDKit::DOUBLE_VECT_I
DOUBLE_VECT::iterator DOUBLE_VECT_I
Definition: types.h:292
RDKit::STR_VECT
std::vector< std::string > STR_VECT
Definition: Dict.h:29
RDKit::common_properties::molFileValue
RDKIT_RDGENERAL_EXPORT const std::string molFileValue
BoostEndInclude.h
RDKit::VECT_DOUBLE_VECT_I
VECT_DOUBLE_VECT::iterator VECT_DOUBLE_VECT_I
Definition: types.h:295
RDKit::common_properties::_CrippenMR
RDKIT_RDGENERAL_EXPORT const std::string _CrippenMR
RDKit::common_properties::molInversionFlag
RDKIT_RDGENERAL_EXPORT const std::string molInversionFlag
RDKit::common_properties::_StereochemDone
RDKIT_RDGENERAL_EXPORT const std::string _StereochemDone
RDKit::UINT
unsigned int UINT
Definition: types.h:262
RDKit::common_properties::_MMFFSanitized
RDKIT_RDGENERAL_EXPORT const std::string _MMFFSanitized
RDKit::common_properties::MolFileInfo
RDKIT_RDGENERAL_EXPORT const std::string MolFileInfo
RDKit::common_properties::_CrippenLogP
RDKIT_RDGENERAL_EXPORT const std::string _CrippenLogP
RDKit::MAX_INT
RDKIT_RDGENERAL_EXPORT const double MAX_INT
RDKit::STR_UINT_MAP
std::map< std::string, UINT > STR_UINT_MAP
Definition: types.h:298
RDKit::common_properties::_QueryIsotope
RDKIT_RDGENERAL_EXPORT const std::string _QueryIsotope
RDKit::INT_MAP_INT_I
INT_MAP_INT::iterator INT_MAP_INT_I
Definition: types.h:305
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::common_properties::_MolFileBondCfg
RDKIT_RDGENERAL_EXPORT const std::string _MolFileBondCfg
RDKit::common_properties::_MolFileBondAttach
RDKIT_RDGENERAL_EXPORT const std::string _MolFileBondAttach
RDKit::common_properties::molFileAlias
RDKIT_RDGENERAL_EXPORT const std::string molFileAlias
RDKit::common_properties::_NeedsQueryScan
RDKIT_RDGENERAL_EXPORT const std::string _NeedsQueryScan
RDKit::INT_DEQUE
std::deque< int > INT_DEQUE
Definition: types.h:308
RDKit::common_properties::_MolFileBondType
RDKIT_RDGENERAL_EXPORT const std::string _MolFileBondType
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::LONGINT
long long int LONGINT
Definition: types.h:245
RDKit::common_properties::reactantAtomIdx
RDKIT_RDGENERAL_EXPORT const std::string reactantAtomIdx
RDKit::common_properties::_TraversalRingClosureBond
RDKIT_RDGENERAL_EXPORT const std::string _TraversalRingClosureBond
RDKit::MAX_LONGINT
RDKIT_RDGENERAL_EXPORT const double MAX_LONGINT
RDKit::common_properties::_AtomID
RDKIT_RDGENERAL_EXPORT const std::string _AtomID
RDKit::UINT_VECT
std::vector< UINT > UINT_VECT
Definition: types.h:285
RDKit::INT_VECT_I
INT_VECT::iterator INT_VECT_I
Definition: types.h:267
RDKit::larger_of
functor for returning the larger of two values
Definition: types.h:340
RDKit::common_properties::_brokenChirality
RDKIT_RDGENERAL_EXPORT const std::string _brokenChirality
RDKit::common_properties::bondNote
RDKIT_RDGENERAL_EXPORT const std::string bondNote
RDKit::common_properties::_starred
RDKIT_RDGENERAL_EXPORT const std::string _starred
RDKit::common_properties::_MolFileRLabel
RDKIT_RDGENERAL_EXPORT const std::string _MolFileRLabel
RDKit::INT_LIST_I
INT_LIST::iterator INT_LIST_I
Definition: types.h:273
RDKit::common_properties::atomLabel
RDKIT_RDGENERAL_EXPORT const std::string atomLabel
RDKit::common_properties::_fragSMARTS
RDKIT_RDGENERAL_EXPORT const std::string _fragSMARTS
RDKit::UINT_VECT_CI
std::vector< UINT >::const_iterator UINT_VECT_CI
Definition: types.h:284
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::INT_DEQUE_CI
INT_DEQUE::const_iterator INT_DEQUE_CI
Definition: types.h:310
Invariant.h
RDKit::common_properties::dummyLabel
RDKIT_RDGENERAL_EXPORT const std::string dummyLabel
RDKit::common_properties::_supplementalSmilesLabel
RDKIT_RDGENERAL_EXPORT const std::string _supplementalSmilesLabel
RDKit::common_properties::molRxnComponent
RDKIT_RDGENERAL_EXPORT const std::string molRxnComponent
RDKit::common_properties::_GasteigerCharge
RDKIT_RDGENERAL_EXPORT const std::string _GasteigerCharge
RDKit::common_properties::molRxnRole
RDKIT_RDGENERAL_EXPORT const std::string molRxnRole
RDKit::common_properties::_unspecifiedOrder
RDKIT_RDGENERAL_EXPORT const std::string _unspecifiedOrder
RDKit::INT_DEQUE_I
INT_DEQUE::iterator INT_DEQUE_I
Definition: types.h:309
RDKit::common_properties::_protected
RDKIT_RDGENERAL_EXPORT const std::string _protected
RDKit::common_properties::molAtomClass
RDKIT_RDGENERAL_EXPORT const std::string molAtomClass
RDKit
Std stuff.
Definition: Atom.h:30
RDKit::ltDouble
functor to compare two doubles with a tolerance
Definition: types.h:320
RDKit::common_properties::_MolFileChiralFlag
RDKIT_RDGENERAL_EXPORT const std::string _MolFileChiralFlag
RDKit::common_properties::molAttachPoint
RDKIT_RDGENERAL_EXPORT const std::string molAttachPoint
RDKit::common_properties::TWOD
RDKIT_RDGENERAL_EXPORT const std::string TWOD
RDKit::common_properties::_TraversalBondIndexOrder
RDKIT_RDGENERAL_EXPORT const std::string _TraversalBondIndexOrder
RDKit::common_properties::_SLN_s
RDKIT_RDGENERAL_EXPORT const std::string _SLN_s
RDKit::common_properties::_MolFileBondStereo
RDKIT_RDGENERAL_EXPORT const std::string _MolFileBondStereo
RDKit::common_properties::_ReactionDegreeChanged
RDKIT_RDGENERAL_EXPORT const std::string _ReactionDegreeChanged
RDKit::common_properties::_crippenMR
RDKIT_RDGENERAL_EXPORT const std::string _crippenMR
RDKit::VECT_INT_VECT_I
VECT_INT_VECT::iterator VECT_INT_VECT_I
Definition: types.h:281
RDKit::common_properties::_UnknownStereo
RDKIT_RDGENERAL_EXPORT const std::string _UnknownStereo
RDKit::USHORT
unsigned short USHORT
Definition: types.h:263
RDKit::common_properties::smilesSymbol
RDKIT_RDGENERAL_EXPORT const std::string smilesSymbol
RDKit::INT_MAP_INT
std::map< int, int > INT_MAP_INT
Definition: types.h:304
RDKit::INT_VECT_CRI
INT_VECT::const_reverse_iterator INT_VECT_CRI
Definition: types.h:270
RDKit::INT_INT_VECT_MAP_CI
INT_INT_VECT_MAP::const_iterator INT_INT_VECT_MAP_CI
Definition: types.h:302
RDKit::common_properties::origNoImplicit
RDKIT_RDGENERAL_EXPORT const std::string origNoImplicit
RDKit::common_properties::_QueryFormalCharge
RDKIT_RDGENERAL_EXPORT const std::string _QueryFormalCharge
RDKit::VECT_DOUBLE_VECT_CI
VECT_DOUBLE_VECT::const_iterator VECT_DOUBLE_VECT_CI
Definition: types.h:296
RDKit::INT_LIST
std::list< int > INT_LIST
Definition: types.h:272
RDKit::common_properties::_BondsPotentialStereo
RDKIT_RDGENERAL_EXPORT const std::string _BondsPotentialStereo
RDKit::common_properties::_doIsoSmiles
RDKIT_RDGENERAL_EXPORT const std::string _doIsoSmiles
RDKit::common_properties::_connectivityHKDeltas
RDKIT_RDGENERAL_EXPORT const std::string _connectivityHKDeltas
RDKit::common_properties::_rgroupBonds
RDKIT_RDGENERAL_EXPORT const std::string _rgroupBonds
RDKit::common_properties::Discrims
RDKIT_RDGENERAL_EXPORT const std::string Discrims
RDKit::common_properties::_crippenMRContribs
RDKIT_RDGENERAL_EXPORT const std::string _crippenMRContribs
RDKit::common_properties::molAtomSeqId
RDKIT_RDGENERAL_EXPORT const std::string molAtomSeqId
RDKit::common_properties::_3DConf
RDKIT_RDGENERAL_EXPORT const std::string _3DConf
RDKit::common_properties::_QueryMass
RDKIT_RDGENERAL_EXPORT const std::string _QueryMass
RDKit::MAX_DOUBLE
RDKIT_RDGENERAL_EXPORT const double MAX_DOUBLE
RDKit::STR_VECT_I
std::vector< std::string >::iterator STR_VECT_I
Definition: types.h:288
RDKit::common_properties::_RingClosures
RDKIT_RDGENERAL_EXPORT const std::string _RingClosures
RDKit::common_properties::MolFileComments
RDKIT_RDGENERAL_EXPORT const std::string MolFileComments
RDKit::common_properties::_crippenLogPContribs
RDKIT_RDGENERAL_EXPORT const std::string _crippenLogPContribs
RDKit::common_properties::_ringStereoWarning
RDKIT_RDGENERAL_EXPORT const std::string _ringStereoWarning
RDKIT_RDGENERAL_EXPORT
#define RDKIT_RDGENERAL_EXPORT
Definition: export.h:502
RDKit::common_properties::extraRings
RDKIT_RDGENERAL_EXPORT const std::string extraRings
RDKit::common_properties::_MolFileBondQuery
RDKIT_RDGENERAL_EXPORT const std::string _MolFileBondQuery
Dict.h
Defines the Dict class.
RDKit::common_properties::_GasteigerHCharge
RDKIT_RDGENERAL_EXPORT const std::string _GasteigerHCharge
RDKit::common_properties::molRxnExactChange
RDKIT_RDGENERAL_EXPORT const std::string molRxnExactChange
RDKit::common_properties::_rgroupAtomMaps
RDKIT_RDGENERAL_EXPORT const std::string _rgroupAtomMaps
RDKit::common_properties::_tpsaAtomContribs
RDKIT_RDGENERAL_EXPORT const std::string _tpsaAtomContribs
RDKit::DOUBLE_INT_MAP
std::map< double, int, ltDouble > DOUBLE_INT_MAP
std::map from double to integer.
Definition: types.h:336
RDKit::common_properties::molStereoCare
RDKIT_RDGENERAL_EXPORT const std::string molStereoCare
RDKit::common_properties::_2DConf
RDKIT_RDGENERAL_EXPORT const std::string _2DConf
RDKit::common_properties::_TraversalStartPoint
RDKIT_RDGENERAL_EXPORT const std::string _TraversalStartPoint
RDKit::VECT_INT_VECT_CI
VECT_INT_VECT::const_iterator VECT_INT_VECT_CI
Definition: types.h:282
RDKit::common_properties::molSubstCount
RDKIT_RDGENERAL_EXPORT const std::string molSubstCount
RDKit::common_properties::molAttachOrder
RDKIT_RDGENERAL_EXPORT const std::string molAttachOrder
RDKit::larger_of::operator()
T operator()(T arg1, T arg2)
Definition: types.h:341
RDKit::ltDouble::ltDouble
ltDouble()
Definition: types.h:322
RDKit::INT_VECT_CI
INT_VECT::const_iterator INT_VECT_CI
Definition: types.h:268
RDKit::common_properties::molAtomMapNumber
RDKIT_RDGENERAL_EXPORT const std::string molAtomMapNumber
RDKit::common_properties::_labuteAtomHContrib
RDKIT_RDGENERAL_EXPORT const std::string _labuteAtomHContrib
RDKit::INT_MAP_INT_CI
INT_MAP_INT::const_iterator INT_MAP_INT_CI
Definition: types.h:306
RDKit::INT_INT_DEQ_MAP
std::map< int, INT_DEQUE > INT_INT_DEQ_MAP
Definition: types.h:312
RDKit::common_properties::numArom
RDKIT_RDGENERAL_EXPORT const std::string numArom
RDKit::detail::computedPropName
RDKIT_RDGENERAL_EXPORT const std::string computedPropName
RDKit::INT_INT_DEQ_MAP_CI
INT_INT_DEQ_MAP::const_iterator INT_INT_DEQ_MAP_CI
Definition: types.h:313
RDKit::common_properties::_QueryHCount
RDKIT_RDGENERAL_EXPORT const std::string _QueryHCount
RDKit::INT_SET_CI
INT_SET::const_iterator INT_SET_CI
Definition: types.h:317
RDKit::common_properties::isImplicit
RDKIT_RDGENERAL_EXPORT const std::string isImplicit
RDKit::common_properties::DistanceMatrix_Paths
RDKIT_RDGENERAL_EXPORT const std::string DistanceMatrix_Paths
RDKit::common_properties::_ChiralityPossible
RDKIT_RDGENERAL_EXPORT const std::string _ChiralityPossible
RDKit::common_properties::_MolFileBondEndPts
RDKIT_RDGENERAL_EXPORT const std::string _MolFileBondEndPts
export.h