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 molRxnComponent; // int
162 RDKIT_RDGENERAL_EXPORT extern const std::string molRxnRole; // int
163 RDKIT_RDGENERAL_EXPORT extern const std::string molTotValence; // int
164 RDKIT_RDGENERAL_EXPORT extern const std::string _MolFileRLabel; // unsigned int
165 RDKIT_RDGENERAL_EXPORT extern const std::string _MolFileChiralFlag; // int
166 RDKIT_RDGENERAL_EXPORT extern const std::string _MolFileAtomQuery; // int
167 RDKIT_RDGENERAL_EXPORT extern const std::string _MolFileBondQuery; // int
168 RDKIT_RDGENERAL_EXPORT extern const std::string _MolFileBondEndPts; // string
169 RDKIT_RDGENERAL_EXPORT extern const std::string _MolFileBondAttach; // string
170 RDKIT_RDGENERAL_EXPORT extern const std::string
171  _MolFileBondType; // unsigned int
172 RDKIT_RDGENERAL_EXPORT extern const std::string
173  _MolFileBondStereo; // unsigned int
174 RDKIT_RDGENERAL_EXPORT extern const std::string
175  _MolFileBondCfg; // unsigned int
176 
177 RDKIT_RDGENERAL_EXPORT extern const std::string
178  MRV_SMA; // smarts string from Marvin
179 RDKIT_RDGENERAL_EXPORT extern const std::string dummyLabel; // atom string
180 
181 // Reaction Information (Reactions.cpp)
182 RDKIT_RDGENERAL_EXPORT extern const std::string _QueryFormalCharge; // int
183 RDKIT_RDGENERAL_EXPORT extern const std::string _QueryHCount; // int
184 RDKIT_RDGENERAL_EXPORT extern const std::string _QueryIsotope; // int
185 RDKIT_RDGENERAL_EXPORT extern const std::string
186  _QueryMass; // int = round(float * 1000)
187 RDKIT_RDGENERAL_EXPORT extern const std::string
188  _ReactionDegreeChanged; // int (bool)
189 RDKIT_RDGENERAL_EXPORT extern const std::string NullBond; // int (bool)
190 RDKIT_RDGENERAL_EXPORT extern const std::string _rgroupAtomMaps;
191 RDKIT_RDGENERAL_EXPORT extern const std::string _rgroupBonds;
192 RDKIT_RDGENERAL_EXPORT extern const std::string reactantAtomIdx;
193 RDKIT_RDGENERAL_EXPORT extern const std::string reactionMapNum;
194 
195 // SLN
196 RDKIT_RDGENERAL_EXPORT extern const std::string
197  _AtomID; // unsigned int SLNParser
198 RDKIT_RDGENERAL_EXPORT extern const std::string
199  _starred; // atom int COMPUTED (SLN)
200 RDKIT_RDGENERAL_EXPORT extern const std::string
201  _SLN_s; // string SLNAttribs (chiral info)
202 RDKIT_RDGENERAL_EXPORT extern const std::string _Unfinished_SLN_; // int (bool)
203 
204 // Smarts Smiles
205 RDKIT_RDGENERAL_EXPORT extern const std::string _brokenChirality; // atom bool
206 RDKIT_RDGENERAL_EXPORT extern const std::string isImplicit; // atom int (bool)
207 RDKIT_RDGENERAL_EXPORT extern const std::string
208  smilesSymbol; // atom string (only used in test?)
209 
210 // Tripos
211 RDKIT_RDGENERAL_EXPORT extern const std::string
212  _TriposAtomType; // string Mol2FileParser
213 // missing defs for _TriposAtomName//_TriposPartialCharge...
214 
215 ///////////////////////////////////////////////////////////////
216 // misc props
217 RDKIT_RDGENERAL_EXPORT extern const std::string
218  TWOD; // need THREED -> confusing using in TDTMol supplier
219  // converge with _2DConf?
220 RDKIT_RDGENERAL_EXPORT extern const std::string BalabanJ; // mol double
221 RDKIT_RDGENERAL_EXPORT extern const std::string BalanbanJ; // typo!! fix...
222 
223 RDKIT_RDGENERAL_EXPORT extern const std::string Discrims; // FragCatalog Entry
224 // Subgraphs::DiscrimTuple (uint32,uint32,uint32)
225 RDKIT_RDGENERAL_EXPORT extern const std::string
226  DistanceMatrix_Paths; // boost::shared_array<double>
227 // - note, confusing creation of names in
228 // - getDistanceMat
229 RDKIT_RDGENERAL_EXPORT extern const std::string internalRgroupSmiles;
230 
231 } // namespace common_properties
232 #ifndef WIN32
233 typedef long long int LONGINT;
234 #else
235 typedef __int64 LONGINT;
236 #endif
237 #ifdef max
238 #undef max // FUCK I hate this nonsense
239 #endif
240 #ifdef min
241 #undef min // FUCK I hate this nonsense
242 #endif
243 
244 RDKIT_RDGENERAL_EXPORT extern const double MAX_DOUBLE;
245 RDKIT_RDGENERAL_EXPORT extern const double EPS_DOUBLE;
246 RDKIT_RDGENERAL_EXPORT extern const double SMALL_DOUBLE;
247 RDKIT_RDGENERAL_EXPORT extern const double MAX_INT;
248 RDKIT_RDGENERAL_EXPORT extern const double MAX_LONGINT;
249 
250 typedef unsigned int UINT;
251 typedef unsigned short USHORT;
252 typedef unsigned char UCHAR;
253 
254 typedef std::vector<int> INT_VECT;
255 typedef INT_VECT::iterator INT_VECT_I;
256 typedef INT_VECT::const_iterator INT_VECT_CI;
257 typedef INT_VECT::reverse_iterator INT_VECT_RI;
258 typedef INT_VECT::const_reverse_iterator INT_VECT_CRI;
259 
260 typedef std::list<int> INT_LIST;
261 typedef INT_LIST::iterator INT_LIST_I;
262 typedef INT_LIST::const_iterator INT_LIST_CI;
263 
264 typedef std::list<INT_VECT> LIST_INT_VECT;
265 typedef LIST_INT_VECT::iterator LIST_INT_VECT_I;
266 typedef LIST_INT_VECT::const_iterator LIST_INT_VECT_CI;
267 
268 typedef std::vector<INT_VECT> VECT_INT_VECT;
269 typedef VECT_INT_VECT::iterator VECT_INT_VECT_I;
270 typedef VECT_INT_VECT::const_iterator VECT_INT_VECT_CI;
271 
272 typedef std::vector<UINT>::const_iterator UINT_VECT_CI;
273 typedef std::vector<UINT> UINT_VECT;
274 
275 typedef std::vector<std::string>::const_iterator STR_VECT_CI;
276 typedef std::vector<std::string>::iterator STR_VECT_I;
277 typedef std::vector<std::string> STR_VECT;
278 
279 typedef std::vector<double> DOUBLE_VECT;
280 typedef DOUBLE_VECT::iterator DOUBLE_VECT_I;
281 typedef DOUBLE_VECT::const_iterator DOUBLE_VECT_CI;
282 typedef std::vector<DOUBLE_VECT> VECT_DOUBLE_VECT;
283 typedef VECT_DOUBLE_VECT::iterator VECT_DOUBLE_VECT_I;
284 typedef VECT_DOUBLE_VECT::const_iterator VECT_DOUBLE_VECT_CI;
285 
286 typedef std::map<std::string, UINT> STR_UINT_MAP;
287 typedef std::map<std::string, UINT>::const_iterator STR_UINT_MAP_CI;
288 
289 typedef std::map<int, INT_VECT> INT_INT_VECT_MAP;
290 typedef INT_INT_VECT_MAP::const_iterator INT_INT_VECT_MAP_CI;
291 
292 typedef std::map<int, int> INT_MAP_INT;
293 typedef INT_MAP_INT::iterator INT_MAP_INT_I;
294 typedef INT_MAP_INT::const_iterator INT_MAP_INT_CI;
295 
296 typedef std::deque<int> INT_DEQUE;
297 typedef INT_DEQUE::iterator INT_DEQUE_I;
298 typedef INT_DEQUE::const_iterator INT_DEQUE_CI;
299 
300 typedef std::map<int, INT_DEQUE> INT_INT_DEQ_MAP;
301 typedef INT_INT_DEQ_MAP::const_iterator INT_INT_DEQ_MAP_CI;
302 
303 typedef std::set<int> INT_SET;
304 typedef INT_SET::iterator INT_SET_I;
305 typedef INT_SET::const_iterator INT_SET_CI;
306 
307 //! functor to compare two doubles with a tolerance
309  public:
310  ltDouble() : _tol(1.0e-8){};
311  bool operator()(double d1, double d2) const {
312  if (fabs(d1 - d2) < _tol) {
313  return false;
314  } else {
315  return (d1 < d2);
316  }
317  }
318 
319  private:
320  double _tol;
321 };
322 
323 //! std::map from double to integer.
324 typedef std::map<double, int, ltDouble> DOUBLE_INT_MAP;
325 
326 //! functor for returning the larger of two values
327 template <typename T>
329  T operator()(T arg1, T arg2) { return arg1 > arg2 ? arg1 : arg2; };
330 };
331 
332 //! functor for comparing two strings
334  bool operator()(const char *s1, const char *s2) const {
335  // std::cout << s1 << " " << s2 << " " << strcmp(s1, s2) << "\n";
336 
337  return strcmp(s1, s2) < 0;
338  };
339 };
340 
341 //! \brief calculate the union of two INT_VECTs and put the results in a
342 //! third vector
343 RDKIT_RDGENERAL_EXPORT void Union(const INT_VECT &r1, const INT_VECT &r2,
344  INT_VECT &res);
345 
346 //! \brief calculate the intersection of two INT_VECTs and put the results in a
347 //! third vector
348 RDKIT_RDGENERAL_EXPORT void Intersect(const INT_VECT &r1, const INT_VECT &r2,
349  INT_VECT &res);
350 
351 //! calculating the union of the INT_VECT's in a VECT_INT_VECT
352 /*!
353  \param rings the INT_VECT's to consider
354  \param res used to return results
355  \param exclude any values in this optional INT_VECT will be excluded
356  from the union.
357 */
358 RDKIT_RDGENERAL_EXPORT void Union(const VECT_INT_VECT &rings, INT_VECT &res,
359  const INT_VECT *exclude = NULL);
360 
361 //! given a current combination of numbers change it to the next possible
362 // combination
363 /*!
364  \param comb the <b>sorted</b> vector to consider
365  \param tot the maximum number possible in the vector
366 
367  \return -1 on failure, the index of the last number changed on success.
368  Example:
369  for all combinations 3 of numbers between 0 and tot=5
370  given (0,1,2) the function wil return (0,1,3) etc.
371 
372 
373 */
375 
376 //! rounds a value to the closest int
377 RDKIT_RDGENERAL_EXPORT double round(double v);
378 
379 }; // namespace RDKit
380 
381 #endif
RDKit::common_properties::_hasMassQuery
const RDKIT_RDGENERAL_EXPORT std::string _hasMassQuery
RDKit::common_properties::_AtomID
const RDKIT_RDGENERAL_EXPORT std::string _AtomID
RDKit::common_properties::_crippenLogPContribs
const RDKIT_RDGENERAL_EXPORT std::string _crippenLogPContribs
RDKit::common_properties::_QueryMass
const RDKIT_RDGENERAL_EXPORT std::string _QueryMass
RDKit::LIST_INT_VECT_CI
LIST_INT_VECT::const_iterator LIST_INT_VECT_CI
Definition: types.h:266
RDKit::common_properties::_MolFileBondEndPts
const RDKIT_RDGENERAL_EXPORT std::string _MolFileBondEndPts
RDKit::UCHAR
unsigned char UCHAR
Definition: types.h:252
RDKit::VECT_INT_VECT
std::vector< INT_VECT > VECT_INT_VECT
Definition: types.h:268
RDKit::common_properties::reactionMapNum
const RDKIT_RDGENERAL_EXPORT std::string reactionMapNum
RDKit::charptr_functor
functor for comparing two strings
Definition: types.h:333
RDKit::common_properties::_NeedsQueryScan
const RDKIT_RDGENERAL_EXPORT std::string _NeedsQueryScan
RDKit::INT_INT_VECT_MAP
std::map< int, INT_VECT > INT_INT_VECT_MAP
Definition: types.h:289
RDKit::common_properties::_CIPRank
const RDKIT_RDGENERAL_EXPORT std::string _CIPRank
RDKit::INT_VECT
std::vector< int > INT_VECT
Definition: types.h:254
RDKit::STR_UINT_MAP_CI
std::map< std::string, UINT >::const_iterator STR_UINT_MAP_CI
Definition: types.h:287
RDKit::common_properties::_queryRootAtom
const RDKIT_RDGENERAL_EXPORT std::string _queryRootAtom
RDKit::STR_VECT_CI
std::vector< std::string >::const_iterator STR_VECT_CI
Definition: types.h:275
RDKit::common_properties::_crippenMRContribs
const RDKIT_RDGENERAL_EXPORT std::string _crippenMRContribs
BoostStartInclude.h
RDKit::common_properties::BalanbanJ
const RDKIT_RDGENERAL_EXPORT std::string BalanbanJ
RDKit::common_properties::_RingClosures
const RDKIT_RDGENERAL_EXPORT std::string _RingClosures
RDKit::common_properties::_tpsaAtomContribs
const RDKIT_RDGENERAL_EXPORT std::string _tpsaAtomContribs
RDKit::common_properties::_ReactionDegreeChanged
const RDKIT_RDGENERAL_EXPORT std::string _ReactionDegreeChanged
RDKit::common_properties::_2DConf
const RDKIT_RDGENERAL_EXPORT std::string _2DConf
RDKit::common_properties::_brokenChirality
const RDKIT_RDGENERAL_EXPORT std::string _brokenChirality
RDKit::ltDouble::operator()
bool operator()(double d1, double d2) const
Definition: types.h:311
RDKit::common_properties::TWOD
const RDKIT_RDGENERAL_EXPORT std::string TWOD
RDKit::INT_LIST_CI
INT_LIST::const_iterator INT_LIST_CI
Definition: types.h:262
RDKit::common_properties::_MolFileBondType
const RDKIT_RDGENERAL_EXPORT std::string _MolFileBondType
RDKit::DOUBLE_VECT
std::vector< double > DOUBLE_VECT
Definition: types.h:279
RDKit::common_properties::_Unfinished_SLN_
const RDKIT_RDGENERAL_EXPORT std::string _Unfinished_SLN_
RDKit::charptr_functor::operator()
bool operator()(const char *s1, const char *s2) const
Definition: types.h:334
RDKit::INT_VECT_RI
INT_VECT::reverse_iterator INT_VECT_RI
Definition: types.h:257
RDKit::common_properties::molTotValence
const RDKIT_RDGENERAL_EXPORT std::string molTotValence
RDKit::common_properties::_ringStereoAtoms
const RDKIT_RDGENERAL_EXPORT std::string _ringStereoAtoms
RDKit::common_properties::smilesSymbol
const RDKIT_RDGENERAL_EXPORT std::string smilesSymbol
RDKit::common_properties::_MolFileBondQuery
const RDKIT_RDGENERAL_EXPORT std::string _MolFileBondQuery
RDKit::LIST_INT_VECT_I
LIST_INT_VECT::iterator LIST_INT_VECT_I
Definition: types.h:265
RDKit::DOUBLE_VECT_CI
DOUBLE_VECT::const_iterator DOUBLE_VECT_CI
Definition: types.h:281
RDKit::VECT_DOUBLE_VECT
std::vector< DOUBLE_VECT > VECT_DOUBLE_VECT
Definition: types.h:282
RDKit::LIST_INT_VECT
std::list< INT_VECT > LIST_INT_VECT
Definition: types.h:264
RDKit::common_properties::_MolFileChiralFlag
const RDKIT_RDGENERAL_EXPORT std::string _MolFileChiralFlag
RDKit::INT_SET_I
INT_SET::iterator INT_SET_I
Definition: types.h:304
RDKit::INT_SET
std::set< int > INT_SET
Definition: types.h:303
RDKit::common_properties::DistanceMatrix_Paths
const RDKIT_RDGENERAL_EXPORT std::string DistanceMatrix_Paths
RDKit::DOUBLE_VECT_I
DOUBLE_VECT::iterator DOUBLE_VECT_I
Definition: types.h:280
RDKit::STR_VECT
std::vector< std::string > STR_VECT
Definition: Dict.h:29
RDKit::common_properties::_labuteAtomContribs
const RDKIT_RDGENERAL_EXPORT std::string _labuteAtomContribs
RDKit::common_properties::_protected
const RDKIT_RDGENERAL_EXPORT std::string _protected
BoostEndInclude.h
RDKit::common_properties::_labuteASA
const RDKIT_RDGENERAL_EXPORT std::string _labuteASA
RDKit::common_properties::_ringStereoWarning
const RDKIT_RDGENERAL_EXPORT std::string _ringStereoWarning
RDKit::common_properties::_ringStereochemCand
const RDKIT_RDGENERAL_EXPORT std::string _ringStereochemCand
RDKit::VECT_DOUBLE_VECT_I
VECT_DOUBLE_VECT::iterator VECT_DOUBLE_VECT_I
Definition: types.h:283
RDKit::common_properties::isImplicit
const RDKIT_RDGENERAL_EXPORT std::string isImplicit
RDKit::common_properties::MRV_SMA
const RDKIT_RDGENERAL_EXPORT std::string MRV_SMA
RDKit::common_properties::_StereochemDone
const RDKIT_RDGENERAL_EXPORT std::string _StereochemDone
RDKit::common_properties::_TriposAtomType
const RDKIT_RDGENERAL_EXPORT std::string _TriposAtomType
RDKit::common_properties::_MolFileAtomQuery
const RDKIT_RDGENERAL_EXPORT std::string _MolFileAtomQuery
RDKit::MAX_INT
const RDKIT_RDGENERAL_EXPORT double MAX_INT
RDKit::common_properties::_MMFFSanitized
const RDKIT_RDGENERAL_EXPORT std::string _MMFFSanitized
RDKit::UINT
unsigned int UINT
Definition: types.h:250
RDKit::STR_UINT_MAP
std::map< std::string, UINT > STR_UINT_MAP
Definition: types.h:286
RDKit::common_properties::BalabanJ
const RDKIT_RDGENERAL_EXPORT std::string BalabanJ
RDKit::common_properties::_CrippenMR
const RDKIT_RDGENERAL_EXPORT std::string _CrippenMR
RDKit::INT_MAP_INT_I
INT_MAP_INT::iterator INT_MAP_INT_I
Definition: types.h:293
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::molFileAlias
const RDKIT_RDGENERAL_EXPORT std::string molFileAlias
RDKit::common_properties::origNoImplicit
const RDKIT_RDGENERAL_EXPORT std::string origNoImplicit
RDKit::common_properties::_smilesAtomOutputOrder
const RDKIT_RDGENERAL_EXPORT std::string _smilesAtomOutputOrder
RDKit::common_properties::_BondsPotentialStereo
const RDKIT_RDGENERAL_EXPORT std::string _BondsPotentialStereo
RDKit::common_properties::_SmilesStart
const RDKIT_RDGENERAL_EXPORT std::string _SmilesStart
RDKit::INT_DEQUE
std::deque< int > INT_DEQUE
Definition: types.h:296
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:233
RDKit::common_properties::_UnknownStereo
const RDKIT_RDGENERAL_EXPORT std::string _UnknownStereo
RDKit::UINT_VECT
std::vector< UINT > UINT_VECT
Definition: types.h:273
RDKit::common_properties::extraRings
const RDKIT_RDGENERAL_EXPORT std::string extraRings
RDKit::common_properties::reactantAtomIdx
const RDKIT_RDGENERAL_EXPORT std::string reactantAtomIdx
RDKit::INT_VECT_I
INT_VECT::iterator INT_VECT_I
Definition: types.h:255
RDKit::common_properties::_TraversalRingClosureBond
const RDKIT_RDGENERAL_EXPORT std::string _TraversalRingClosureBond
RDKit::common_properties::_QueryHCount
const RDKIT_RDGENERAL_EXPORT std::string _QueryHCount
RDKit::detail::computedPropName
const RDKIT_RDGENERAL_EXPORT std::string computedPropName
RDKit::larger_of
functor for returning the larger of two values
Definition: types.h:328
RDKit::common_properties::_TraversalStartPoint
const RDKIT_RDGENERAL_EXPORT std::string _TraversalStartPoint
RDKit::common_properties::_MolFileBondAttach
const RDKIT_RDGENERAL_EXPORT std::string _MolFileBondAttach
RDKit::common_properties::_ChiralityPossible
const RDKIT_RDGENERAL_EXPORT std::string _ChiralityPossible
RDKit::INT_LIST_I
INT_LIST::iterator INT_LIST_I
Definition: types.h:261
RDKit::common_properties::_Name
const RDKIT_RDGENERAL_EXPORT std::string _Name
RDKit::UINT_VECT_CI
std::vector< UINT >::const_iterator UINT_VECT_CI
Definition: types.h:272
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::common_properties::_connectivityNVals
const RDKIT_RDGENERAL_EXPORT std::string _connectivityNVals
RDKit::INT_DEQUE_CI
INT_DEQUE::const_iterator INT_DEQUE_CI
Definition: types.h:298
Invariant.h
RDKit::common_properties::_CIPCode
const RDKIT_RDGENERAL_EXPORT std::string _CIPCode
RDKit::common_properties::internalRgroupSmiles
const RDKIT_RDGENERAL_EXPORT std::string internalRgroupSmiles
RDKit::common_properties::_MolFileBondCfg
const RDKIT_RDGENERAL_EXPORT std::string _MolFileBondCfg
RDKit::SMALL_DOUBLE
const RDKIT_RDGENERAL_EXPORT double SMALL_DOUBLE
RDKit::round
RDKIT_RDGENERAL_EXPORT double round(double v)
rounds a value to the closest int
RDKit::common_properties::_TraversalBondIndexOrder
const RDKIT_RDGENERAL_EXPORT std::string _TraversalBondIndexOrder
RDKit::common_properties::_MolFileRLabel
const RDKIT_RDGENERAL_EXPORT std::string _MolFileRLabel
RDKit::INT_DEQUE_I
INT_DEQUE::iterator INT_DEQUE_I
Definition: types.h:297
RDKit::common_properties::_starred
const RDKIT_RDGENERAL_EXPORT std::string _starred
RDKit::common_properties::_unspecifiedOrder
const RDKIT_RDGENERAL_EXPORT std::string _unspecifiedOrder
RDKit::common_properties::dummyLabel
const RDKIT_RDGENERAL_EXPORT std::string dummyLabel
RDKit::common_properties::_labuteAtomHContrib
const RDKIT_RDGENERAL_EXPORT std::string _labuteAtomHContrib
RDKit::common_properties::_tpsa
const RDKIT_RDGENERAL_EXPORT std::string _tpsa
RDKit
Std stuff.
Definition: Atom.h:30
RDKit::common_properties::molRxnComponent
const RDKIT_RDGENERAL_EXPORT std::string molRxnComponent
RDKit::ltDouble
functor to compare two doubles with a tolerance
Definition: types.h:308
RDKit::common_properties::maxAttachIdx
const RDKIT_RDGENERAL_EXPORT std::string maxAttachIdx
RDKit::common_properties::molParity
const RDKIT_RDGENERAL_EXPORT std::string molParity
RDKit::common_properties::_crippenLogP
const RDKIT_RDGENERAL_EXPORT std::string _crippenLogP
RDKit::common_properties::molInversionFlag
const RDKIT_RDGENERAL_EXPORT std::string molInversionFlag
RDKit::MAX_LONGINT
const RDKIT_RDGENERAL_EXPORT double MAX_LONGINT
RDKit::VECT_INT_VECT_I
VECT_INT_VECT::iterator VECT_INT_VECT_I
Definition: types.h:269
RDKit::common_properties::_MolFileBondStereo
const RDKIT_RDGENERAL_EXPORT std::string _MolFileBondStereo
RDKit::common_properties::_connectivityHKDeltas
const RDKIT_RDGENERAL_EXPORT std::string _connectivityHKDeltas
RDKit::USHORT
unsigned short USHORT
Definition: types.h:251
RDKit::INT_MAP_INT
std::map< int, int > INT_MAP_INT
Definition: types.h:292
RDKit::MAX_DOUBLE
const RDKIT_RDGENERAL_EXPORT double MAX_DOUBLE
RDKit::common_properties::_supplementalSmilesLabel
const RDKIT_RDGENERAL_EXPORT std::string _supplementalSmilesLabel
RDKit::INT_VECT_CRI
INT_VECT::const_reverse_iterator INT_VECT_CRI
Definition: types.h:258
RDKit::common_properties::_QueryFormalCharge
const RDKIT_RDGENERAL_EXPORT std::string _QueryFormalCharge
RDKit::INT_INT_VECT_MAP_CI
INT_INT_VECT_MAP::const_iterator INT_INT_VECT_MAP_CI
Definition: types.h:290
RDKit::VECT_DOUBLE_VECT_CI
VECT_DOUBLE_VECT::const_iterator VECT_DOUBLE_VECT_CI
Definition: types.h:284
RDKit::INT_LIST
std::list< int > INT_LIST
Definition: types.h:260
RDKit::common_properties::_rgroupAtomMaps
const RDKIT_RDGENERAL_EXPORT std::string _rgroupAtomMaps
RDKit::common_properties::numArom
const RDKIT_RDGENERAL_EXPORT std::string numArom
RDKit::common_properties::_SLN_s
const RDKIT_RDGENERAL_EXPORT std::string _SLN_s
RDKit::common_properties::MolFileComments
const RDKIT_RDGENERAL_EXPORT std::string MolFileComments
RDKit::common_properties::_CrippenLogP
const RDKIT_RDGENERAL_EXPORT std::string _CrippenLogP
RDKit::common_properties::_rgroupBonds
const RDKIT_RDGENERAL_EXPORT std::string _rgroupBonds
RDKit::common_properties::atomLabel
const RDKIT_RDGENERAL_EXPORT std::string atomLabel
RDKit::common_properties::molRxnRole
const RDKIT_RDGENERAL_EXPORT std::string molRxnRole
RDKit::common_properties::_QueryIsotope
const RDKIT_RDGENERAL_EXPORT std::string _QueryIsotope
RDKit::common_properties::_3DConf
const RDKIT_RDGENERAL_EXPORT std::string _3DConf
RDKit::STR_VECT_I
std::vector< std::string >::iterator STR_VECT_I
Definition: types.h:276
RDKit::EPS_DOUBLE
const RDKIT_RDGENERAL_EXPORT double EPS_DOUBLE
RDKit::common_properties::molFileValue
const RDKIT_RDGENERAL_EXPORT std::string molFileValue
RDKit::common_properties::ringMembership
const RDKIT_RDGENERAL_EXPORT std::string ringMembership
RDKIT_RDGENERAL_EXPORT
#define RDKIT_RDGENERAL_EXPORT
Definition: export.h:502
RDKit::common_properties::_crippenMR
const RDKIT_RDGENERAL_EXPORT std::string _crippenMR
RDKit::common_properties::NullBond
const RDKIT_RDGENERAL_EXPORT std::string NullBond
Dict.h
Defines the Dict class.
RDKit::common_properties::_fragSMARTS
const RDKIT_RDGENERAL_EXPORT std::string _fragSMARTS
RDKit::common_properties::_doIsoSmiles
const RDKIT_RDGENERAL_EXPORT std::string _doIsoSmiles
RDKit::DOUBLE_INT_MAP
std::map< double, int, ltDouble > DOUBLE_INT_MAP
std::map from double to integer.
Definition: types.h:324
RDKit::common_properties::MolFileInfo
const RDKIT_RDGENERAL_EXPORT std::string MolFileInfo
RDKit::VECT_INT_VECT_CI
VECT_INT_VECT::const_iterator VECT_INT_VECT_CI
Definition: types.h:270
RDKit::common_properties::Discrims
const RDKIT_RDGENERAL_EXPORT std::string Discrims
RDKit::larger_of::operator()
T operator()(T arg1, T arg2)
Definition: types.h:329
RDKit::ltDouble::ltDouble
ltDouble()
Definition: types.h:310
RDKit::INT_VECT_CI
INT_VECT::const_iterator INT_VECT_CI
Definition: types.h:256
RDKit::common_properties::molAtomMapNumber
const RDKIT_RDGENERAL_EXPORT std::string molAtomMapNumber
RDKit::common_properties::_GasteigerCharge
const RDKIT_RDGENERAL_EXPORT std::string _GasteigerCharge
RDKit::INT_MAP_INT_CI
INT_MAP_INT::const_iterator INT_MAP_INT_CI
Definition: types.h:294
RDKit::INT_INT_DEQ_MAP
std::map< int, INT_DEQUE > INT_INT_DEQ_MAP
Definition: types.h:300
RDKit::INT_INT_DEQ_MAP_CI
INT_INT_DEQ_MAP::const_iterator INT_INT_DEQ_MAP_CI
Definition: types.h:301
RDKit::common_properties::_GasteigerHCharge
const RDKIT_RDGENERAL_EXPORT std::string _GasteigerHCharge
RDKit::INT_SET_CI
INT_SET::const_iterator INT_SET_CI
Definition: types.h:305
export.h