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 _MolFileBondType; // unsigned int
171 RDKIT_RDGENERAL_EXPORT extern const std::string
172  _MolFileBondStereo; // unsigned int
173 RDKIT_RDGENERAL_EXPORT extern const std::string
174  _MolFileBondCfg; // unsigned int
175 
176 RDKIT_RDGENERAL_EXPORT extern const std::string
177  MRV_SMA; // smarts string from Marvin
178 RDKIT_RDGENERAL_EXPORT extern const std::string dummyLabel; // atom string
179 
180 // Reaction Information (Reactions.cpp)
181 RDKIT_RDGENERAL_EXPORT extern const std::string _QueryFormalCharge; // int
182 RDKIT_RDGENERAL_EXPORT extern const std::string _QueryHCount; // int
183 RDKIT_RDGENERAL_EXPORT extern const std::string _QueryIsotope; // int
184 RDKIT_RDGENERAL_EXPORT extern const std::string
185  _QueryMass; // int = round(float * 1000)
186 RDKIT_RDGENERAL_EXPORT extern const std::string
187  _ReactionDegreeChanged; // int (bool)
188 RDKIT_RDGENERAL_EXPORT extern const std::string NullBond; // int (bool)
189 RDKIT_RDGENERAL_EXPORT extern const std::string _rgroupAtomMaps;
190 RDKIT_RDGENERAL_EXPORT extern const std::string _rgroupBonds;
191 RDKIT_RDGENERAL_EXPORT extern const std::string reactantAtomIdx;
192 RDKIT_RDGENERAL_EXPORT extern const std::string reactionMapNum;
193 
194 // SLN
195 RDKIT_RDGENERAL_EXPORT extern const std::string
196  _AtomID; // unsigned int SLNParser
197 RDKIT_RDGENERAL_EXPORT extern const std::string
198  _starred; // atom int COMPUTED (SLN)
199 RDKIT_RDGENERAL_EXPORT extern const std::string
200  _SLN_s; // string SLNAttribs (chiral info)
201 RDKIT_RDGENERAL_EXPORT extern const std::string _Unfinished_SLN_; // int (bool)
202 
203 // Smarts Smiles
204 RDKIT_RDGENERAL_EXPORT extern const std::string _brokenChirality; // atom bool
205 RDKIT_RDGENERAL_EXPORT extern const std::string isImplicit; // atom int (bool)
206 RDKIT_RDGENERAL_EXPORT extern const std::string
207  smilesSymbol; // atom string (only used in test?)
208 
209 // Tripos
210 RDKIT_RDGENERAL_EXPORT extern const std::string
211  _TriposAtomType; // string Mol2FileParser
212 // missing defs for _TriposAtomName//_TriposPartialCharge...
213 
214 ///////////////////////////////////////////////////////////////
215 // misc props
216 RDKIT_RDGENERAL_EXPORT extern const std::string
217  TWOD; // need THREED -> confusing using in TDTMol supplier
218  // converge with _2DConf?
219 RDKIT_RDGENERAL_EXPORT extern const std::string BalabanJ; // mol double
220 RDKIT_RDGENERAL_EXPORT extern const std::string BalanbanJ; // typo!! fix...
221 
222 RDKIT_RDGENERAL_EXPORT extern const std::string Discrims; // FragCatalog Entry
223 // Subgraphs::DiscrimTuple (uint32,uint32,uint32)
224 RDKIT_RDGENERAL_EXPORT extern const std::string
225  DistanceMatrix_Paths; // boost::shared_array<double>
226 // - note, confusing creation of names in
227 // - getDistanceMat
228 RDKIT_RDGENERAL_EXPORT extern const std::string internalRgroupSmiles;
229 
230 } // namespace common_properties
231 #ifndef WIN32
232 typedef long long int LONGINT;
233 #else
234 typedef __int64 LONGINT;
235 #endif
236 #ifdef max
237 #undef max // FUCK I hate this nonsense
238 #endif
239 #ifdef min
240 #undef min // FUCK I hate this nonsense
241 #endif
242 
243 RDKIT_RDGENERAL_EXPORT extern const double MAX_DOUBLE;
244 RDKIT_RDGENERAL_EXPORT extern const double EPS_DOUBLE;
245 RDKIT_RDGENERAL_EXPORT extern const double SMALL_DOUBLE;
246 RDKIT_RDGENERAL_EXPORT extern const double MAX_INT;
247 RDKIT_RDGENERAL_EXPORT extern const double MAX_LONGINT;
248 
249 typedef unsigned int UINT;
250 typedef unsigned short USHORT;
251 typedef unsigned char UCHAR;
252 
253 typedef std::vector<int> INT_VECT;
254 typedef INT_VECT::iterator INT_VECT_I;
255 typedef INT_VECT::const_iterator INT_VECT_CI;
256 typedef INT_VECT::reverse_iterator INT_VECT_RI;
257 typedef INT_VECT::const_reverse_iterator INT_VECT_CRI;
258 
259 typedef std::list<int> INT_LIST;
260 typedef INT_LIST::iterator INT_LIST_I;
261 typedef INT_LIST::const_iterator INT_LIST_CI;
262 
263 typedef std::list<INT_VECT> LIST_INT_VECT;
264 typedef LIST_INT_VECT::iterator LIST_INT_VECT_I;
265 typedef LIST_INT_VECT::const_iterator LIST_INT_VECT_CI;
266 
267 typedef std::vector<INT_VECT> VECT_INT_VECT;
268 typedef VECT_INT_VECT::iterator VECT_INT_VECT_I;
269 typedef VECT_INT_VECT::const_iterator VECT_INT_VECT_CI;
270 
271 typedef std::vector<UINT>::const_iterator UINT_VECT_CI;
272 typedef std::vector<UINT> UINT_VECT;
273 
274 typedef std::vector<std::string>::const_iterator STR_VECT_CI;
275 typedef std::vector<std::string>::iterator STR_VECT_I;
276 typedef std::vector<std::string> STR_VECT;
277 
278 typedef std::vector<double> DOUBLE_VECT;
279 typedef DOUBLE_VECT::iterator DOUBLE_VECT_I;
280 typedef DOUBLE_VECT::const_iterator DOUBLE_VECT_CI;
281 typedef std::vector<DOUBLE_VECT> VECT_DOUBLE_VECT;
282 typedef VECT_DOUBLE_VECT::iterator VECT_DOUBLE_VECT_I;
283 typedef VECT_DOUBLE_VECT::const_iterator VECT_DOUBLE_VECT_CI;
284 
285 typedef std::map<std::string, UINT> STR_UINT_MAP;
286 typedef std::map<std::string, UINT>::const_iterator STR_UINT_MAP_CI;
287 
288 typedef std::map<int, INT_VECT> INT_INT_VECT_MAP;
289 typedef INT_INT_VECT_MAP::const_iterator INT_INT_VECT_MAP_CI;
290 
291 typedef std::map<int, int> INT_MAP_INT;
292 typedef INT_MAP_INT::iterator INT_MAP_INT_I;
293 typedef INT_MAP_INT::const_iterator INT_MAP_INT_CI;
294 
295 typedef std::deque<int> INT_DEQUE;
296 typedef INT_DEQUE::iterator INT_DEQUE_I;
297 typedef INT_DEQUE::const_iterator INT_DEQUE_CI;
298 
299 typedef std::map<int, INT_DEQUE> INT_INT_DEQ_MAP;
300 typedef INT_INT_DEQ_MAP::const_iterator INT_INT_DEQ_MAP_CI;
301 
302 typedef std::set<int> INT_SET;
303 typedef INT_SET::iterator INT_SET_I;
304 typedef INT_SET::const_iterator INT_SET_CI;
305 
306 //! functor to compare two doubles with a tolerance
308  public:
309  ltDouble() : _tol(1.0e-8){};
310  bool operator()(double d1, double d2) const {
311  if (fabs(d1 - d2) < _tol) {
312  return false;
313  } else {
314  return (d1 < d2);
315  }
316  }
317 
318  private:
319  double _tol;
320 };
321 
322 //! std::map from double to integer.
323 typedef std::map<double, int, ltDouble> DOUBLE_INT_MAP;
324 
325 //! functor for returning the larger of two values
326 template <typename T>
328  T operator()(T arg1, T arg2) { return arg1 > arg2 ? arg1 : arg2; };
329 };
330 
331 //! functor for comparing two strings
333  bool operator()(const char *s1, const char *s2) const {
334  // std::cout << s1 << " " << s2 << " " << strcmp(s1, s2) << "\n";
335 
336  return strcmp(s1, s2) < 0;
337  };
338 };
339 
340 //! \brief calculate the union of two INT_VECTs and put the results in a
341 //! third vector
342 RDKIT_RDGENERAL_EXPORT void Union(const INT_VECT &r1, const INT_VECT &r2,
343  INT_VECT &res);
344 
345 //! \brief calculate the intersection of two INT_VECTs and put the results in a
346 //! third vector
347 RDKIT_RDGENERAL_EXPORT void Intersect(const INT_VECT &r1, const INT_VECT &r2,
348  INT_VECT &res);
349 
350 //! calculating the union of the INT_VECT's in a VECT_INT_VECT
351 /*!
352  \param rings the INT_VECT's to consider
353  \param res used to return results
354  \param exclude any values in this optional INT_VECT will be excluded
355  from the union.
356 */
357 RDKIT_RDGENERAL_EXPORT void Union(const VECT_INT_VECT &rings, INT_VECT &res,
358  const INT_VECT *exclude = NULL);
359 
360 //! given a current combination of numbers change it to the next possible
361 // combination
362 /*!
363  \param comb the <b>sorted</b> vector to consider
364  \param tot the maximum number possible in the vector
365 
366  \return -1 on failure, the index of the last number changed on success.
367  Example:
368  for all combinations 3 of numbers between 0 and tot=5
369  given (0,1,2) the function wil return (0,1,3) etc.
370 
371 
372 */
373 RDKIT_RDGENERAL_EXPORT int nextCombination(INT_VECT &comb, int tot);
374 
375 //! rounds a value to the closest int
376 RDKIT_RDGENERAL_EXPORT double round(double v);
377 
378 }; // namespace RDKit
379 
380 #endif
RDKIT_RDGENERAL_EXPORT const std::string _tpsaAtomContribs
std::list< int > INT_LIST
Definition: types.h:259
RDKIT_RDGENERAL_EXPORT const std::string _MolFileAtomQuery
unsigned short USHORT
Definition: types.h:250
RDKIT_RDGENERAL_EXPORT const std::string _CrippenMR
bool operator()(double d1, double d2) const
Definition: types.h:310
RDKIT_RDGENERAL_EXPORT const std::string _rgroupAtomMaps
VECT_DOUBLE_VECT::iterator VECT_DOUBLE_VECT_I
Definition: types.h:282
DOUBLE_VECT::const_iterator DOUBLE_VECT_CI
Definition: types.h:280
RDKIT_RDGENERAL_EXPORT const std::string _MolFileBondStereo
RDKIT_RDGENERAL_EXPORT const std::string _smilesAtomOutputOrder
RDKIT_RDGENERAL_EXPORT const std::string molAtomMapNumber
RDKIT_RDGENERAL_EXPORT const std::string _QueryMass
RDKIT_RDGENERAL_EXPORT const std::string _CrippenLogP
RDKIT_RDGENERAL_EXPORT const std::string _RingClosures
RDKIT_RDGENERAL_EXPORT const std::string _MolFileBondCfg
VECT_INT_VECT::iterator VECT_INT_VECT_I
Definition: types.h:268
functor to compare two doubles with a tolerance
Definition: types.h:307
#define RDKIT_RDGENERAL_EXPORT
Definition: export.h:502
RDKIT_RDGENERAL_EXPORT const std::string _doIsoSmiles
RDKIT_RDGENERAL_EXPORT const std::string _rgroupBonds
RDKIT_RDGENERAL_EXPORT const std::string _protected
std::map< std::string, UINT >::const_iterator STR_UINT_MAP_CI
Definition: types.h:286
std::vector< UINT >::const_iterator UINT_VECT_CI
Definition: types.h:271
std::vector< double > DOUBLE_VECT
Definition: types.h:278
RDKIT_RDGENERAL_EXPORT const std::string _QueryIsotope
RDKIT_RDGENERAL_EXPORT const std::string BalanbanJ
INT_MAP_INT::const_iterator INT_MAP_INT_CI
Definition: types.h:293
RDKIT_RDGENERAL_EXPORT const std::string origNoImplicit
RDKIT_RDGENERAL_EXPORT const std::string _Name
T operator()(T arg1, T arg2)
Definition: types.h:328
RDKIT_RDGENERAL_EXPORT const std::string _NeedsQueryScan
INT_SET::iterator INT_SET_I
Definition: types.h:303
unsigned char UCHAR
Definition: types.h:251
RDKIT_RDGENERAL_EXPORT const std::string _ringStereochemCand
RDKIT_RDGENERAL_EXPORT const std::string _CIPCode
INT_DEQUE::const_iterator INT_DEQUE_CI
Definition: types.h:297
INT_LIST::iterator INT_LIST_I
Definition: types.h:260
RDKIT_RDGENERAL_EXPORT const std::string _MMFFSanitized
RDKIT_RDGENERAL_EXPORT const std::string _SLN_s
RDKIT_RDGENERAL_EXPORT const std::string Discrims
RDKIT_RDGENERAL_EXPORT const std::string numArom
RDKIT_RDGENERAL_EXPORT const std::string molFileAlias
RDKIT_RDGENERAL_EXPORT const std::string _QueryFormalCharge
std::vector< DOUBLE_VECT > VECT_DOUBLE_VECT
Definition: types.h:281
VECT_DOUBLE_VECT::const_iterator VECT_DOUBLE_VECT_CI
Definition: types.h:283
DOUBLE_VECT::iterator DOUBLE_VECT_I
Definition: types.h:279
INT_INT_DEQ_MAP::const_iterator INT_INT_DEQ_MAP_CI
Definition: types.h:300
RDKIT_RDGENERAL_EXPORT const std::string BalabanJ
RDKIT_RDGENERAL_EXPORT const std::string _supplementalSmilesLabel
RDKIT_RDGENERAL_EXPORT const std::string _TraversalStartPoint
RDKIT_RDGENERAL_EXPORT const std::string DistanceMatrix_Paths
Defines the Dict class.
RDKIT_RDGENERAL_EXPORT const std::string molRxnComponent
RDKIT_RDGENERAL_EXPORT const std::string molParity
RDKIT_RDGENERAL_EXPORT const std::string _unspecifiedOrder
RDKIT_RDGENERAL_EXPORT const std::string internalRgroupSmiles
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_SET::const_iterator INT_SET_CI
Definition: types.h:304
RDKIT_RDGENERAL_EXPORT const double MAX_INT
functor for returning the larger of two values
Definition: types.h:327
RDKIT_RDGENERAL_EXPORT const std::string molFileValue
RDKIT_RDGENERAL_EXPORT const std::string computedPropName
INT_MAP_INT::iterator INT_MAP_INT_I
Definition: types.h:292
RDKIT_RDGENERAL_EXPORT const std::string MolFileComments
INT_VECT::const_reverse_iterator INT_VECT_CRI
Definition: types.h:257
std::vector< INT_VECT > VECT_INT_VECT
Definition: types.h:267
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_RDGENERAL_EXPORT const std::string _MolFileRLabel
RDKIT_RDGENERAL_EXPORT const std::string isImplicit
RDKIT_RDGENERAL_EXPORT const std::string atomLabel
RDKIT_RDGENERAL_EXPORT const std::string reactantAtomIdx
RDKIT_RDGENERAL_EXPORT const std::string _SmilesStart
RDKIT_RDGENERAL_EXPORT const std::string _hasMassQuery
long long int LONGINT
Definition: types.h:232
RDKIT_RDGENERAL_EXPORT const std::string _labuteAtomContribs
RDKIT_RDGENERAL_EXPORT const std::string maxAttachIdx
RDKIT_RDGENERAL_EXPORT const std::string _crippenMRContribs
functor for comparing two strings
Definition: types.h:332
RDKIT_RDGENERAL_EXPORT const std::string _Unfinished_SLN_
std::map< std::string, UINT > STR_UINT_MAP
Definition: types.h:285
RDKIT_RDGENERAL_EXPORT const std::string molRxnRole
RDKIT_RDGENERAL_EXPORT const std::string _crippenLogPContribs
RDKIT_RDGENERAL_EXPORT const std::string _MolFileChiralFlag
std::vector< int > INT_VECT
Definition: types.h:253
RDKIT_RDGENERAL_EXPORT const std::string _starred
std::set< int > INT_SET
Definition: types.h:302
INT_VECT::reverse_iterator INT_VECT_RI
Definition: types.h:256
RDKIT_RDGENERAL_EXPORT const std::string _2DConf
RDKIT_RDGENERAL_EXPORT const std::string _ReactionDegreeChanged
std::vector< std::string >::const_iterator STR_VECT_CI
Definition: types.h:274
RDKIT_RDGENERAL_EXPORT const std::string _MolFileBondType
bool operator()(const char *s1, const char *s2) const
Definition: types.h:333
RDKIT_RDGENERAL_EXPORT const std::string _fragSMARTS
Std stuff.
Definition: Atom.h:30
unsigned int UINT
Definition: types.h:249
INT_VECT::iterator INT_VECT_I
Definition: types.h:254
LIST_INT_VECT::iterator LIST_INT_VECT_I
Definition: types.h:264
RDKIT_RDGENERAL_EXPORT const std::string _ringStereoAtoms
RDKIT_RDGENERAL_EXPORT const std::string smilesSymbol
RDKIT_RDGENERAL_EXPORT const std::string extraRings
INT_VECT::const_iterator INT_VECT_CI
Definition: types.h:255
RDKIT_RDGENERAL_EXPORT const std::string MRV_SMA
VECT_INT_VECT::const_iterator VECT_INT_VECT_CI
Definition: types.h:269
RDKIT_RDGENERAL_EXPORT const std::string _brokenChirality
RDKIT_RDGENERAL_EXPORT const std::string _TriposAtomType
RDKIT_RDGENERAL_EXPORT const std::string _labuteASA
RDKIT_RDGENERAL_EXPORT const std::string dummyLabel
RDKIT_RDGENERAL_EXPORT const std::string _labuteAtomHContrib
std::map< double, int, ltDouble > DOUBLE_INT_MAP
std::map from double to integer.
Definition: types.h:323
RDKIT_RDGENERAL_EXPORT const std::string _GasteigerCharge
RDKIT_RDGENERAL_EXPORT const double MAX_DOUBLE
RDKIT_RDGENERAL_EXPORT const std::string _crippenLogP
INT_DEQUE::iterator INT_DEQUE_I
Definition: types.h:296
RDKIT_RDGENERAL_EXPORT double round(double v)
rounds a value to the closest int
RDKIT_RDGENERAL_EXPORT const std::string _GasteigerHCharge
RDKIT_RDGENERAL_EXPORT const std::string _BondsPotentialStereo
RDKIT_RDGENERAL_EXPORT const std::string _StereochemDone
RDKIT_RDGENERAL_EXPORT const std::string _QueryHCount
RDKIT_RDGENERAL_EXPORT const std::string NullBond
RDKIT_RDGENERAL_EXPORT const std::string ringMembership
std::map< int, int > INT_MAP_INT
Definition: types.h:291
RDKIT_RDGENERAL_EXPORT const std::string _TraversalBondIndexOrder
std::list< INT_VECT > LIST_INT_VECT
Definition: types.h:263
RDKIT_RDGENERAL_EXPORT const std::string _MolFileBondAttach
INT_LIST::const_iterator INT_LIST_CI
Definition: types.h:261
RDKIT_RDGENERAL_EXPORT const std::string _crippenMR
RDKIT_RDGENERAL_EXPORT const std::string _UnknownStereo
RDKIT_RDGENERAL_EXPORT const std::string _connectivityNVals
std::map< int, INT_DEQUE > INT_INT_DEQ_MAP
Definition: types.h:299
std::map< int, INT_VECT > INT_INT_VECT_MAP
Definition: types.h:288
std::vector< UINT > UINT_VECT
Definition: types.h:272
RDKIT_RDGENERAL_EXPORT const std::string _tpsa
RDKIT_RDGENERAL_EXPORT const std::string TWOD
RDKIT_RDGENERAL_EXPORT const std::string _connectivityHKDeltas
INT_INT_VECT_MAP::const_iterator INT_INT_VECT_MAP_CI
Definition: types.h:289
std::deque< int > INT_DEQUE
Definition: types.h:295
RDKIT_RDGENERAL_EXPORT const std::string _ringStereoWarning
RDKIT_RDGENERAL_EXPORT const double SMALL_DOUBLE
std::vector< std::string >::iterator STR_VECT_I
Definition: types.h:275
RDKIT_RDGENERAL_EXPORT const std::string _ChiralityPossible
RDKIT_RDGENERAL_EXPORT const std::string _MolFileBondEndPts
RDKIT_RDGENERAL_EXPORT int nextCombination(INT_VECT &comb, int tot)
given a current combination of numbers change it to the next possible
RDKIT_RDGENERAL_EXPORT const std::string _CIPRank
RDKIT_RDGENERAL_EXPORT const std::string _TraversalRingClosureBond
RDKIT_RDGENERAL_EXPORT const std::string _AtomID
RDKIT_RDGENERAL_EXPORT const std::string _3DConf
RDKIT_RDGENERAL_EXPORT const double EPS_DOUBLE
RDKIT_RDGENERAL_EXPORT const std::string reactionMapNum
RDKIT_RDGENERAL_EXPORT const std::string MolFileInfo
RDKIT_RDGENERAL_EXPORT const std::string _MolFileBondQuery
LIST_INT_VECT::const_iterator LIST_INT_VECT_CI
Definition: types.h:265
RDKIT_RDGENERAL_EXPORT const std::string molTotValence
std::vector< std::string > STR_VECT
Definition: Dict.h:29
RDKIT_RDGENERAL_EXPORT const std::string _queryRootAtom
RDKIT_RDGENERAL_EXPORT const std::string molInversionFlag
RDKIT_RDGENERAL_EXPORT const double MAX_LONGINT