20#include <boost/utility/binary.hpp>
21#include <boost/variant.hpp>
43 const char *
what() const noexcept
override {
return _msg.c_str(); }
60 AllProps = 0x0000FFFF,
61 CoordsAsDouble = 0x00010000,
64} PropertyPickleOptions;
159 unsigned int propertyFlags);
164 unsigned int propertyFlags) {
165 MolPickler::pickleMol(&mol, ss, propertyFlags);
171 unsigned int propertyFlags);
174 unsigned int propertyFlags) {
175 MolPickler::pickleMol(&mol, res, propertyFlags);
180 unsigned int propertyFlags);
182 unsigned int propertyFlags) {
183 MolPickler::molFromPickle(pickle, &mol, propertyFlags);
186 MolPickler::molFromPickle(pickle, mol, PicklerOps::AllProps);
189 MolPickler::molFromPickle(pickle, &mol, PicklerOps::AllProps);
194 unsigned int propertyFlags);
196 unsigned int propertyFlags) {
197 MolPickler::molFromPickle(ss, &mol, propertyFlags);
200 MolPickler::molFromPickle(ss, mol, PicklerOps::AllProps);
203 MolPickler::molFromPickle(ss, &mol, PicklerOps::AllProps);
208 static std::int32_t _pickleAtomData(std::ostream &tss,
const Atom *atom);
210 static void _unpickleAtomData(std::istream &tss,
Atom *atom,
int version);
212 static void _pickleQueryAtomData(std::ostream &tss,
const Atom *atom);
215 template <
typename T>
216 static void _pickle(
const ROMol *mol, std::ostream &ss,
217 unsigned int propertyFlags);
220 template <
typename T>
221 static void _pickleAtom(std::ostream &ss,
const Atom *atom);
224 template <
typename T>
225 static void _pickleBond(std::ostream &ss,
const Bond *bond,
226 std::map<int, int> &atomIdxMap);
229 template <
typename T>
230 static void _pickleSSSR(std::ostream &ss,
const RingInfo *ringInfo,
231 std::map<int, int> &atomIdxMap);
234 template <
typename T>
235 static void _pickleSubstanceGroup(std::ostream &ss,
237 std::map<int, int> &atomIdxMap,
238 std::map<int, int> &bondIdxMap);
241 template <
typename T>
242 static void _pickleStereo(std::ostream &ss, std::vector<StereoGroup> groups,
243 std::map<int, int> &atomIdxMap);
246 template <
typename T,
typename C>
247 static void _pickleConformer(std::ostream &ss,
const Conformer *conf);
250 template <
typename T>
251 static void _depickle(std::istream &ss,
ROMol *mol,
int version,
int numAtoms,
252 unsigned int propertyFlags);
256 template <
typename T>
257 static Atom *_addAtomFromPickle(std::istream &ss,
ROMol *mol,
259 bool directMap =
false);
262 template <
typename T>
263 static Bond *_addBondFromPickle(std::istream &ss,
ROMol *mol,
int version,
264 bool directMap =
false);
268 template <
typename T>
269 static void _addRingInfoFromPickle(std::istream &ss,
ROMol *mol,
int version,
270 bool directMap =
false);
273 template <
typename T>
274 static SubstanceGroup _getSubstanceGroupFromPickle(std::istream &ss,
275 ROMol *mol,
int version);
277 template <
typename T>
278 static void _depickleStereo(std::istream &ss,
ROMol *mol,
int version);
281 template <
typename T,
typename C>
282 static Conformer *_conformerFromPickle(std::istream &ss,
int version);
285 static void _pickleProperties(std::ostream &ss,
const RDProps &props,
286 unsigned int pickleFlags);
288 static void _unpickleProperties(std::istream &ss,
RDProps &props,
292 static void _pickleV1(
const ROMol *mol, std::ostream &ss);
294 static void _depickleV1(std::istream &ss,
ROMol *mol);
296 static void _addAtomFromPickleV1(std::istream &ss,
ROMol *mol);
298 static void _addBondFromPickleV1(std::istream &ss,
ROMol *mol);
301namespace PicklerOps {
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>>>;
Defines the Atom class and associated typedefs.
Pulls in all the query types.
Base class for all queries.
The class for representing atoms.
class for representing a bond
used to indicate exceptions whilst pickling (serializing) molecules
~MolPicklerException() noexcept override=default
const char * what() const noexcept override
MolPicklerException(const std::string msg)
MolPicklerException(const char *msg)
handles pickling (serializing) molecules
static const std::int32_t endianId
mark the endian-ness of the pickle
static void molFromPickle(std::istream &ss, ROMol *mol)
static void molFromPickle(const std::string &pickle, ROMol &mol, unsigned int propertyFlags)
static void molFromPickle(std::istream &ss, ROMol &mol, unsigned int propertyFlags)
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)
@ ATOM_PDB_RESIDUE_TEMPFACTOR
@ ATOM_PDB_RESIDUE_OCCUPANCY
@ ATOM_PDB_RESIDUE_SERIALNUMBER
@ ATOM_PDB_RESIDUE_INSERTIONCODE
@ ATOM_PDB_RESIDUE_RESIDUENUMBER
@ ATOM_PDB_RESIDUE_SECONDARYSTRUCTURE
@ ATOM_PDB_RESIDUE_SEGMENTNUMBER
@ ATOM_PDB_RESIDUE_RESIDUENAME
@ ATOM_PDB_RESIDUE_ALTLOC
@ ATOM_PDB_RESIDUE_CHAINID
@ ATOM_PDB_RESIDUE_ISHETEROATOM
static void pickleMol(const ROMol &mol, std::ostream &ss)
static void pickleMol(const ROMol &mol, std::string &res, unsigned int propertyFlags)
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)
static void setDefaultPickleProperties(unsigned int)
static const std::int32_t versionMajor
mark the pickle major version
static const std::int32_t versionMinor
mark the pickle minor version
static void molFromPickle(std::istream &ss, ROMol &mol)
static void pickleMol(const ROMol &mol, std::ostream &ss, unsigned int propertyFlags)
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
static void pickleMol(const ROMol &mol, std::string &res)
A class to store information about a molecule's rings.
The class for representing SubstanceGroups.
#define RDKIT_GRAPHMOL_EXPORT
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
std::vector< std::shared_ptr< const CustomPropHandler > > CustomPropHandlerVec