11 #ifndef _RD_MOLPICKLE_H 12 #define _RD_MOLPICKLE_H 20 #include <boost/utility/binary.hpp> 40 const char *
message()
const {
return _msg.c_str(); };
47 namespace PicklerOps {
141 static unsigned int getDefaultPickleProperties();
142 static void setDefaultPickleProperties(
unsigned int);
148 static void pickleMol(
const ROMol *mol, std::ostream &ss);
149 static void pickleMol(
const ROMol *mol, std::ostream &ss,
150 unsigned int propertyFlags);
152 static void pickleMol(
const ROMol &mol, std::ostream &ss);
155 unsigned int propertyFlags) {
160 static void pickleMol(
const ROMol *mol, std::string &res);
161 static void pickleMol(
const ROMol *mol, std::string &res,
162 unsigned int propertyFlags);
163 static void pickleMol(
const ROMol &mol, std::string &res);
165 unsigned int propertyFlags) {
170 static void molFromPickle(
const std::string &
pickle,
ROMol *mol);
176 static void molFromPickle(std::istream &ss,
ROMol *mol);
183 static std::int32_t _pickleAtomData(std::ostream &tss,
const Atom *atom);
185 static void _unpickleAtomData(std::istream &tss,
Atom *atom,
int version);
187 static void _pickleQueryAtomData(std::ostream &tss,
const Atom *atom);
190 template <
typename T>
191 static void _pickle(
const ROMol *mol, std::ostream &ss,
192 unsigned int propertyFlags);
195 template <
typename T>
196 static void _pickleAtom(std::ostream &ss,
const Atom *atom);
199 template <
typename T>
200 static void _pickleBond(std::ostream &ss,
const Bond *bond,
201 std::map<int, int> &atomIdxMap);
204 template <
typename T>
205 static void _pickleSSSR(std::ostream &ss,
const RingInfo *ringInfo,
206 std::map<int, int> &atomIdxMap);
209 template <
typename T>
210 static void _pickleSubstanceGroup(std::ostream &ss,
212 std::map<int, int> &atomIdxMap,
213 std::map<int, int> &bondIdxMap);
216 template <
typename T>
217 static void _pickleStereo(std::ostream &ss,
218 const std::vector<StereoGroup> &groups,
219 std::map<int, int> &atomIdxMap);
222 template <
typename T>
223 static void _pickleConformer(std::ostream &ss,
const Conformer *conf);
226 template <
typename T>
227 static void _depickle(std::istream &ss,
ROMol *mol,
int version,
232 template <
typename T>
233 static Atom *_addAtomFromPickle(std::istream &ss,
ROMol *mol,
235 bool directMap =
false);
238 template <
typename T>
239 static Bond *_addBondFromPickle(std::istream &ss,
ROMol *mol,
int version,
240 bool directMap =
false);
244 template <
typename T>
245 static void _addRingInfoFromPickle(std::istream &ss,
ROMol *mol,
int version,
246 bool directMap =
false);
249 template <
typename T>
250 static SubstanceGroup _getSubstanceGroupFromPickle(std::istream &ss,
251 ROMol *mol,
int version);
253 template <
typename T>
254 static void _depickleStereo(std::istream &ss,
ROMol *mol,
int version);
257 template <
typename T>
258 static Conformer *_conformerFromPickle(std::istream &ss,
int version);
261 static void _pickleProperties(std::ostream &ss,
const RDProps &props,
262 unsigned int pickleFlags);
264 static void _unpickleProperties(std::istream &ss,
RDProps &props);
267 static void _pickleV1(
const ROMol *mol, std::ostream &ss);
269 static void _depickleV1(std::istream &ss,
ROMol *mol);
271 static void _addAtomFromPickleV1(std::istream &ss,
ROMol *mol);
273 static void _addBondFromPickleV1(std::istream &ss,
ROMol *mol);
static void pickleMol(const ROMol *mol, std::ostream &ss)
pickles a molecule and sends the results to stream ss
MolPicklerException(const char *msg)
The class for representing SubstanceGroups.
static void pickleMol(const ROMol &mol, std::string &res, unsigned int propertyFlags)
Tags
mark the endian-ness of the pickle
std::vector< std::shared_ptr< const CustomPropHandler > > CustomPropHandlerVec
static const std::int32_t versionMinor
mark the pickle minor version
static const std::int32_t versionMajor
mark the pickle major version
RDKIT_CHEMREACTIONS_EXPORT void pickle(const boost::shared_ptr< EnumerationStrategyBase > &enumerator, std::ostream &ss)
pickles a EnumerationStrategy and adds the results to a stream ss
const char * message() const
#define RDKIT_GRAPHMOL_EXPORT
static const std::int32_t versionPatch
mark the pickle patch version
static void molFromPickle(const std::string &pickle, ROMol &mol)
static const std::int32_t endianId
A class to store information about a molecule's rings.
used to indicate exceptions whilst pickling (serializing) molecules
class for representing a bond
MolPicklerException(const std::string msg)
handles pickling (serializing) molecules
static void molFromPickle(const std::string &pickle, ROMol *mol)
constructs a molecule from a pickle stored in a string
static void molFromPickle(std::istream &ss, ROMol &mol)
Defines the Atom class and associated typedefs.
static void pickleMol(const ROMol &mol, std::ostream &ss, unsigned int propertyFlags)
The class for representing atoms.