RDKit
Open-source cheminformatics and machine learning.
Loading...
Searching...
No Matches
MolPickler.h
Go to the documentation of this file.
1///
2// Copyright (C) 2001-2021 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#include <RDGeneral/export.h>
11#ifndef RD_MOLPICKLE_H
12#define RD_MOLPICKLE_H
13
14#include <Geometry/point.h>
15#include <GraphMol/Atom.h>
16#include <GraphMol/QueryAtom.h>
17#include <GraphMol/Bond.h>
18#include <GraphMol/QueryBond.h>
19#include <RDGeneral/StreamOps.h>
20#include <boost/utility/binary.hpp>
21#include <boost/variant.hpp>
22#include <Query/QueryObjects.h>
23
24// Std stuff
25#include <iostream>
26#include <string>
27#include <sstream>
28#include <exception>
29#ifdef WIN32
30#include <ios>
31#endif
32#include <cstdint>
33
34namespace RDKit {
35class ROMol;
36class RingInfo;
37
38//! used to indicate exceptions whilst pickling (serializing) molecules
39class RDKIT_GRAPHMOL_EXPORT MolPicklerException : public std::exception {
40 public:
41 MolPicklerException(const char *msg) : _msg(msg) {}
42 MolPicklerException(const std::string msg) : _msg(msg) {}
43 const char *what() const noexcept override { return _msg.c_str(); }
44 ~MolPicklerException() noexcept override = default;
45
46 private:
47 std::string _msg;
48};
49
50namespace PicklerOps {
51typedef enum {
52 NoProps = 0, // no data pickled (default pickling, single-precision coords)
53 MolProps = 0x1, // only public non computed properties
54 AtomProps = 0x2,
55 BondProps = 0x4,
56 QueryAtomData =
57 0x2, // n.b. DEPRECATED and set to AtomProps (does the same work)
58 PrivateProps = 0x10,
59 ComputedProps = 0x20,
60 AllProps = 0x0000FFFF, // all data pickled
61 CoordsAsDouble = 0x00010000, // save coordinates in double precision
62 NoConformers =
63 0x00020000 // do not include conformers or associated properties
64} PropertyPickleOptions;
65} // namespace PicklerOps
66
67//! handles pickling (serializing) molecules
69 public:
70 static const std::int32_t versionMajor; //!< mark the pickle major version
71 static const std::int32_t versionMinor; //!< mark the pickle minor version
72 static const std::int32_t versionPatch; //!< mark the pickle patch version
73 static const std::int32_t endianId; //!< mark the endian-ness of the pickle
74
75 //! the pickle format is tagged using these tags:
76 //! NOTE: if you add to this list, be sure to put new entries AT THE BOTTOM,
77 /// otherwise
78 //! you will break old pickles.
149
150 static unsigned int getDefaultPickleProperties();
151 static void setDefaultPickleProperties(unsigned int);
152
154 static void addCustomPropHandler(const CustomPropHandler &handler);
155
156 //! pickles a molecule and sends the results to stream \c ss
157 static void pickleMol(const ROMol *mol, std::ostream &ss);
158 static void pickleMol(const ROMol *mol, std::ostream &ss,
159 unsigned int propertyFlags);
160
161 static void pickleMol(const ROMol &mol, std::ostream &ss);
162
163 static void pickleMol(const ROMol &mol, std::ostream &ss,
164 unsigned int propertyFlags) {
165 MolPickler::pickleMol(&mol, ss, propertyFlags);
166 }
167
168 //! pickles a molecule and adds the results to string \c res
169 static void pickleMol(const ROMol *mol, std::string &res);
170 static void pickleMol(const ROMol *mol, std::string &res,
171 unsigned int propertyFlags);
172 static void pickleMol(const ROMol &mol, std::string &res);
173 static void pickleMol(const ROMol &mol, std::string &res,
174 unsigned int propertyFlags) {
175 MolPickler::pickleMol(&mol, res, propertyFlags);
176 }
177
178 //! constructs a molecule from a pickle stored in a string
179 static void molFromPickle(const std::string &pickle, ROMol *mol,
180 unsigned int propertyFlags);
181 static void molFromPickle(const std::string &pickle, ROMol &mol,
182 unsigned int propertyFlags) {
183 MolPickler::molFromPickle(pickle, &mol, propertyFlags);
184 }
185 static void molFromPickle(const std::string &pickle, ROMol *mol) {
186 MolPickler::molFromPickle(pickle, mol, PicklerOps::AllProps);
187 }
188 static void molFromPickle(const std::string &pickle, ROMol &mol) {
189 MolPickler::molFromPickle(pickle, &mol, PicklerOps::AllProps);
190 }
191
192 //! constructs a molecule from a pickle stored in a stream
193 static void molFromPickle(std::istream &ss, ROMol *mol,
194 unsigned int propertyFlags);
195 static void molFromPickle(std::istream &ss, ROMol &mol,
196 unsigned int propertyFlags) {
197 MolPickler::molFromPickle(ss, &mol, propertyFlags);
198 }
199 static void molFromPickle(std::istream &ss, ROMol *mol) {
200 MolPickler::molFromPickle(ss, mol, PicklerOps::AllProps);
201 }
202 static void molFromPickle(std::istream &ss, ROMol &mol) {
203 MolPickler::molFromPickle(ss, &mol, PicklerOps::AllProps);
204 }
205
206 private:
207 //! Pickle nonquery atom data
208 static std::int32_t _pickleAtomData(std::ostream &tss, const Atom *atom);
209 //! depickle nonquery atom data
210 static void _unpickleAtomData(std::istream &tss, Atom *atom, int version);
211
212 static void _pickleQueryAtomData(std::ostream &tss, const Atom *atom);
213
214 //! do the actual work of pickling a molecule
215 template <typename T>
216 static void _pickle(const ROMol *mol, std::ostream &ss,
217 unsigned int propertyFlags);
218
219 //! do the actual work of pickling an Atom
220 template <typename T>
221 static void _pickleAtom(std::ostream &ss, const Atom *atom);
222
223 //! do the actual work of pickling a Bond
224 template <typename T>
225 static void _pickleBond(std::ostream &ss, const Bond *bond,
226 std::map<int, int> &atomIdxMap);
227
228 //! do the actual work of pickling an SSSR structure
229 template <typename T>
230 static void _pickleSSSR(std::ostream &ss, const RingInfo *ringInfo,
231 std::map<int, int> &atomIdxMap);
232
233 //! do the actual work of pickling a SubstanceGroup
234 template <typename T>
235 static void _pickleSubstanceGroup(std::ostream &ss,
236 const SubstanceGroup &sgroup,
237 std::map<int, int> &atomIdxMap,
238 std::map<int, int> &bondIdxMap);
239
240 //! do the actual work of pickling Stereo Group data
241 template <typename T>
242 static void _pickleStereo(std::ostream &ss, std::vector<StereoGroup> groups,
243 std::map<int, int> &atomIdxMap);
244
245 //! do the actual work of pickling a Conformer
246 template <typename T, typename C>
247 static void _pickleConformer(std::ostream &ss, const Conformer *conf);
248
249 //! do the actual work of de-pickling a molecule
250 template <typename T>
251 static void _depickle(std::istream &ss, ROMol *mol, int version, int numAtoms,
252 unsigned int propertyFlags);
253
254 //! extract atomic data from a pickle and add the resulting Atom to the
255 /// molecule
256 template <typename T>
257 static Atom *_addAtomFromPickle(std::istream &ss, ROMol *mol,
258 RDGeom::Point3D &pos, int version,
259 bool directMap = false);
260
261 //! extract bond data from a pickle and add the resulting Bond to the molecule
262 template <typename T>
263 static Bond *_addBondFromPickle(std::istream &ss, ROMol *mol, int version,
264 bool directMap = false);
265
266 //! extract ring info from a pickle and add the resulting RingInfo to the
267 /// molecule
268 template <typename T>
269 static void _addRingInfoFromPickle(std::istream &ss, ROMol *mol, int version,
270 bool directMap = false);
271
272 //! extract a SubstanceGroup from a pickle
273 template <typename T>
274 static SubstanceGroup _getSubstanceGroupFromPickle(std::istream &ss,
275 ROMol *mol, int version);
276
277 template <typename T>
278 static void _depickleStereo(std::istream &ss, ROMol *mol, int version);
279
280 //! extract a conformation from a pickle
281 template <typename T, typename C>
282 static Conformer *_conformerFromPickle(std::istream &ss, int version);
283
284 //! pickle standard properties
285 static void _pickleProperties(std::ostream &ss, const RDProps &props,
286 unsigned int pickleFlags);
287 //! unpickle standard properties
288 static void _unpickleProperties(std::istream &ss, RDProps &props,
289 int version);
290
291 //! backwards compatibility
292 static void _pickleV1(const ROMol *mol, std::ostream &ss);
293 //! backwards compatibility
294 static void _depickleV1(std::istream &ss, ROMol *mol);
295 //! backwards compatibility
296 static void _addAtomFromPickleV1(std::istream &ss, ROMol *mol);
297 //! backwards compatibility
298 static void _addBondFromPickleV1(std::istream &ss, ROMol *mol);
299};
300
301namespace PicklerOps {
302using QueryDetails = boost::variant<
303 MolPickler::Tags, std::tuple<MolPickler::Tags, int32_t>,
304 std::tuple<MolPickler::Tags, int32_t, int32_t>,
305 std::tuple<MolPickler::Tags, int32_t, int32_t, int32_t, char>,
306 std::tuple<MolPickler::Tags, std::set<int32_t>>>;
307template <class T>
309
310} // namespace PicklerOps
311
312}; // namespace RDKit
313
314#endif
Defines the Atom class and associated typedefs.
Pulls in all the query types.
Base class for all queries.
Definition Query.h:45
The class for representing atoms.
Definition Atom.h:68
class for representing a bond
Definition Bond.h:47
The class for representing 2D or 3D conformation of a molecule.
Definition Conformer.h:46
used to indicate exceptions whilst pickling (serializing) molecules
Definition MolPickler.h:39
~MolPicklerException() noexcept override=default
const char * what() const noexcept override
Definition MolPickler.h:43
MolPicklerException(const std::string msg)
Definition MolPickler.h:42
MolPicklerException(const char *msg)
Definition MolPickler.h:41
handles pickling (serializing) molecules
Definition MolPickler.h:68
static const std::int32_t endianId
mark the endian-ness of the pickle
Definition MolPickler.h:73
static void molFromPickle(std::istream &ss, ROMol *mol)
Definition MolPickler.h:199
static void molFromPickle(const std::string &pickle, ROMol &mol, unsigned int propertyFlags)
Definition MolPickler.h:181
static void molFromPickle(std::istream &ss, ROMol &mol, unsigned int propertyFlags)
Definition MolPickler.h:195
static void pickleMol(const ROMol *mol, std::string &res, unsigned int propertyFlags)
static void molFromPickle(std::istream &ss, ROMol *mol, unsigned int propertyFlags)
constructs a molecule from a pickle stored in a stream
static void molFromPickle(const std::string &pickle, ROMol *mol)
Definition MolPickler.h:185
@ ATOM_PDB_RESIDUE_SECONDARYSTRUCTURE
Definition MolPickler.h:134
static void pickleMol(const ROMol &mol, std::ostream &ss)
static void pickleMol(const ROMol &mol, std::string &res, unsigned int propertyFlags)
Definition MolPickler.h:173
static void pickleMol(const ROMol *mol, std::ostream &ss, unsigned int propertyFlags)
static void molFromPickle(const std::string &pickle, ROMol *mol, unsigned int propertyFlags)
constructs a molecule from a pickle stored in a string
static const CustomPropHandlerVec & getCustomPropHandlers()
static void molFromPickle(const std::string &pickle, ROMol &mol)
Definition MolPickler.h:188
static void setDefaultPickleProperties(unsigned int)
static const std::int32_t versionMajor
mark the pickle major version
Definition MolPickler.h:70
static const std::int32_t versionMinor
mark the pickle minor version
Definition MolPickler.h:71
static void molFromPickle(std::istream &ss, ROMol &mol)
Definition MolPickler.h:202
static void pickleMol(const ROMol &mol, std::ostream &ss, unsigned int propertyFlags)
Definition MolPickler.h:163
static void pickleMol(const ROMol *mol, std::ostream &ss)
pickles a molecule and sends the results to stream ss
static void pickleMol(const ROMol *mol, std::string &res)
pickles a molecule and adds the results to string res
static unsigned int getDefaultPickleProperties()
static void addCustomPropHandler(const CustomPropHandler &handler)
static const std::int32_t versionPatch
mark the pickle patch version
Definition MolPickler.h:72
static void pickleMol(const ROMol &mol, std::string &res)
A class to store information about a molecule's rings.
Definition RingInfo.h:31
The class for representing SubstanceGroups.
#define RDKIT_GRAPHMOL_EXPORT
Definition export.h:233
QueryDetails getQueryDetails(const Queries::Query< int, T const *, true > *query)
boost::variant< MolPickler::Tags, std::tuple< MolPickler::Tags, int32_t >, std::tuple< MolPickler::Tags, int32_t, int32_t >, std::tuple< MolPickler::Tags, int32_t, int32_t, int32_t, char >, std::tuple< MolPickler::Tags, std::set< int32_t > > > QueryDetails
Definition MolPickler.h:306
Std stuff.
std::vector< std::shared_ptr< const CustomPropHandler > > CustomPropHandlerVec
Definition StreamOps.h:382