handles pickling (serializing) molecules More...

#include <MolPickler.h>

Public Types
enum	Tags { VERSION = 0 , BEGINATOM , ATOM_INDEX , ATOM_NUMBER , ATOM_POS , ATOM_CHARGE , ATOM_NEXPLICIT , ATOM_CHIRALTAG , ATOM_MASS , ATOM_ISAROMATIC , ENDATOM , BEGINBOND , BOND_INDEX , BOND_BEGATOMIDX , BOND_ENDATOMIDX , BOND_TYPE , BOND_DIR , ENDBOND , BEGINPROPS , ENDPROPS , BEGINSSSR , ENDSSSR , ENDMOL , BEGINCONFS , ATOM_MAPNUMBER , BEGINQUERY , QUERY_VALUE , QUERY_ISNEGATED , QUERY_NUMCHILDREN , QUERY_BOOL , QUERY_AND , QUERY_OR , QUERY_XOR , QUERY_EQUALS , QUERY_GREATER , QUERY_GREATEREQUAL , QUERY_LESS , QUERY_LESSEQUAL , QUERY_RANGE , QUERY_SET , QUERY_NULL , QUERY_ATOMRING , QUERY_RECURSIVE , ENDQUERY , ATOM_DUMMYLABEL , BEGIN_ATOM_MONOMER , ATOM_PDB_RESIDUE_SERIALNUMBER , ATOM_PDB_RESIDUE_ALTLOC , ATOM_PDB_RESIDUE_RESIDUENAME , ATOM_PDB_RESIDUE_CHAINID , ATOM_PDB_RESIDUE_INSERTIONCODE , ATOM_PDB_RESIDUE_OCCUPANCY , ATOM_PDB_RESIDUE_TEMPFACTOR , ATOM_PDB_RESIDUE_ISHETEROATOM , ATOM_PDB_RESIDUE_SECONDARYSTRUCTURE , ATOM_PDB_RESIDUE_RESIDUENUMBER , ATOM_PDB_RESIDUE_SEGMENTNUMBER , END_ATOM_MONOMER , BEGINATOMPROPS , BEGINBONDPROPS , BEGINQUERYATOMDATA , BEGINSGROUP , BEGINSTEREOGROUP , BEGINCONFPROPS , BEGINCONFS_DOUBLE , QUERY_TYPELABEL , BEGINSYMMSSSR , BEGINFASTFIND , BEGINFINDOTHERORUNKNOWN , QUERY_PROPERTY , QUERY_PROPERTY_WITH_VALUE , INVALID_TAG = 255 }

Static Public Member Functions
static unsigned int	getDefaultPickleProperties ()

static void	setDefaultPickleProperties (unsigned int)

static const CustomPropHandlerVec &	getCustomPropHandlers ()

static void	addCustomPropHandler (const CustomPropHandler &handler)

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::ostream &ss, unsigned int propertyFlags)

static void	pickleMol (const ROMol &mol, std::ostream &ss)

static void	pickleMol (const ROMol &mol, std::ostream &ss, unsigned int propertyFlags)

static void	pickleMol (const ROMol *mol, std::string &res)
	pickles a molecule and adds the results to string `res`

static void	pickleMol (const ROMol *mol, std::string &res, unsigned int propertyFlags)

static void	pickleMol (const ROMol &mol, std::string &res)

static void	pickleMol (const ROMol &mol, std::string &res, 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 void	molFromPickle (const std::string &pickle, ROMol &mol, unsigned int propertyFlags)

static void	molFromPickle (const std::string &pickle, ROMol *mol)

static void	molFromPickle (const std::string &pickle, ROMol &mol)

static void	molFromPickle (std::istream &ss, ROMol *mol, unsigned int propertyFlags)
	constructs a molecule from a pickle stored in a stream

static void	molFromPickle (std::istream &ss, ROMol &mol, unsigned int propertyFlags)

static void	molFromPickle (std::istream &ss, ROMol *mol)

static void	molFromPickle (std::istream &ss, ROMol &mol)

Static Public Attributes
static const std::int32_t	versionMajor
	mark the pickle major version

static const std::int32_t	versionMinor
	mark the pickle minor version

static const std::int32_t	versionPatch
	mark the pickle patch version

static const std::int32_t	endianId
	mark the endian-ness of the pickle

Detailed Description

handles pickling (serializing) molecules

Definition at line 67 of file MolPickler.h.

Member Enumeration Documentation

◆ Tags

enum RDKit::MolPickler::Tags

the pickle format is tagged using these tags: NOTE: if you add to this list, be sure to put new entries AT THE BOTTOM, otherwise you will break old pickles.

Enumerator
VERSION
BEGINATOM
ATOM_INDEX
ATOM_NUMBER
ATOM_POS
ATOM_CHARGE
ATOM_NEXPLICIT
ATOM_CHIRALTAG
ATOM_MASS
ATOM_ISAROMATIC
ENDATOM
BEGINBOND
BOND_INDEX
BOND_BEGATOMIDX
BOND_ENDATOMIDX
BOND_TYPE
BOND_DIR
ENDBOND
BEGINPROPS
ENDPROPS
BEGINSSSR
ENDSSSR
ENDMOL
BEGINCONFS
ATOM_MAPNUMBER
BEGINQUERY
QUERY_VALUE
QUERY_ISNEGATED
QUERY_NUMCHILDREN
QUERY_BOOL
QUERY_AND
QUERY_OR
QUERY_XOR
QUERY_EQUALS
QUERY_GREATER
QUERY_GREATEREQUAL
QUERY_LESS
QUERY_LESSEQUAL
QUERY_RANGE
QUERY_SET
QUERY_NULL
QUERY_ATOMRING
QUERY_RECURSIVE
ENDQUERY
ATOM_DUMMYLABEL
BEGIN_ATOM_MONOMER
ATOM_PDB_RESIDUE_SERIALNUMBER
ATOM_PDB_RESIDUE_ALTLOC
ATOM_PDB_RESIDUE_RESIDUENAME
ATOM_PDB_RESIDUE_CHAINID
ATOM_PDB_RESIDUE_INSERTIONCODE
ATOM_PDB_RESIDUE_OCCUPANCY
ATOM_PDB_RESIDUE_TEMPFACTOR
ATOM_PDB_RESIDUE_ISHETEROATOM
ATOM_PDB_RESIDUE_SECONDARYSTRUCTURE
ATOM_PDB_RESIDUE_RESIDUENUMBER
ATOM_PDB_RESIDUE_SEGMENTNUMBER
END_ATOM_MONOMER
BEGINATOMPROPS
BEGINBONDPROPS
BEGINQUERYATOMDATA
BEGINSGROUP
BEGINSTEREOGROUP
BEGINCONFPROPS
BEGINCONFS_DOUBLE
QUERY_TYPELABEL
BEGINSYMMSSSR
BEGINFASTFIND
BEGINFINDOTHERORUNKNOWN
QUERY_PROPERTY
QUERY_PROPERTY_WITH_VALUE
INVALID_TAG

Definition at line 78 of file MolPickler.h.

Member Function Documentation

◆ addCustomPropHandler()

static void RDKit::MolPickler::addCustomPropHandler ( const CustomPropHandler & handler )

static

◆ getCustomPropHandlers()

static const CustomPropHandlerVec & RDKit::MolPickler::getCustomPropHandlers ( )

static

◆ getDefaultPickleProperties()

static unsigned int RDKit::MolPickler::getDefaultPickleProperties ( )

static

◆ molFromPickle() [1/8]

static void RDKit::MolPickler::molFromPickle	(	const std::string &	pickle,
		ROMol &	mol )

inlinestatic

Definition at line 193 of file MolPickler.h.

References molFromPickle().

◆ molFromPickle() [2/8]

static void RDKit::MolPickler::molFromPickle	(	const std::string &	pickle,
		ROMol &	mol,
		unsigned int	propertyFlags )

inlinestatic

Definition at line 185 of file MolPickler.h.

References molFromPickle().

◆ molFromPickle() [3/8]

static void RDKit::MolPickler::molFromPickle	(	const std::string &	pickle,
		ROMol *	mol )

inlinestatic

Definition at line 189 of file MolPickler.h.

References molFromPickle().

◆ molFromPickle() [4/8]

static void RDKit::MolPickler::molFromPickle	(	const std::string &	pickle,
		ROMol *	mol,
		unsigned int	propertyFlags )

static

constructs a molecule from a pickle stored in a string

Referenced by RDKit::CachedMolHolder::getMol(), molFromPickle(), molFromPickle(), molFromPickle(), molFromPickle(), molFromPickle(), and molFromPickle().

◆ molFromPickle() [5/8]

static void RDKit::MolPickler::molFromPickle	(	std::istream &	ss,
		ROMol &	mol )

inlinestatic

Definition at line 209 of file MolPickler.h.

References molFromPickle().

◆ molFromPickle() [6/8]

static void RDKit::MolPickler::molFromPickle	(	std::istream &	ss,
		ROMol &	mol,
		unsigned int	propertyFlags )

inlinestatic

Definition at line 201 of file MolPickler.h.

References molFromPickle().

◆ molFromPickle() [7/8]

static void RDKit::MolPickler::molFromPickle	(	std::istream &	ss,
		ROMol *	mol )

inlinestatic

Definition at line 205 of file MolPickler.h.

References molFromPickle().

◆ molFromPickle() [8/8]

static void RDKit::MolPickler::molFromPickle	(	std::istream &	ss,
		ROMol *	mol,
		unsigned int	propertyFlags )

static

constructs a molecule from a pickle stored in a stream

◆ pickleMol() [1/8]

static void RDKit::MolPickler::pickleMol	(	const ROMol &	mol,
		std::ostream &	ss )

static

◆ pickleMol() [2/8]

static void RDKit::MolPickler::pickleMol	(	const ROMol &	mol,
		std::ostream &	ss,
		unsigned int	propertyFlags )

inlinestatic

Definition at line 167 of file MolPickler.h.

References pickleMol().

◆ pickleMol() [3/8]

static void RDKit::MolPickler::pickleMol	(	const ROMol &	mol,
		std::string &	res )

static

◆ pickleMol() [4/8]

static void RDKit::MolPickler::pickleMol	(	const ROMol &	mol,
		std::string &	res,
		unsigned int	propertyFlags )

inlinestatic

Definition at line 177 of file MolPickler.h.

References pickleMol().

◆ pickleMol() [5/8]

static void RDKit::MolPickler::pickleMol	(	const ROMol *	mol,
		std::ostream &	ss )

static

pickles a molecule and sends the results to stream ss

Referenced by RDKit::CachedMolHolder::addMol(), RDKit::EnumerateLibrary::initFromStream(), pickleMol(), pickleMol(), and RDKit::TautomerQuery::TautomerQueryMatcher.

◆ pickleMol() [6/8]

static void RDKit::MolPickler::pickleMol	(	const ROMol *	mol,
		std::ostream &	ss,
		unsigned int	propertyFlags )

static

◆ pickleMol() [7/8]

static void RDKit::MolPickler::pickleMol	(	const ROMol *	mol,
		std::string &	res )

static

pickles a molecule and adds the results to string res

◆ pickleMol() [8/8]

static void RDKit::MolPickler::pickleMol	(	const ROMol *	mol,
		std::string &	res,
		unsigned int	propertyFlags )

static

◆ setDefaultPickleProperties()

static void RDKit::MolPickler::setDefaultPickleProperties ( unsigned int )

static

Member Data Documentation

◆ endianId

const std::int32_t RDKit::MolPickler::endianId

static

mark the endian-ness of the pickle

Definition at line 72 of file MolPickler.h.

◆ versionMajor

const std::int32_t RDKit::MolPickler::versionMajor

static

mark the pickle major version

Definition at line 69 of file MolPickler.h.

◆ versionMinor

const std::int32_t RDKit::MolPickler::versionMinor

static

mark the pickle minor version

Definition at line 70 of file MolPickler.h.

◆ versionPatch

const std::int32_t RDKit::MolPickler::versionPatch

static

mark the pickle patch version

Definition at line 71 of file MolPickler.h.

The documentation for this class was generated from the following file:

MolPickler.h

Public Types

Static Public Member Functions

Static Public Attributes

Detailed Description

Member Enumeration Documentation

◆ Tags

Member Function Documentation

◆ addCustomPropHandler()

◆ getCustomPropHandlers()

◆ getDefaultPickleProperties()

◆ molFromPickle() [1/8]

◆ molFromPickle() [2/8]

◆ molFromPickle() [3/8]

◆ molFromPickle() [4/8]

◆ molFromPickle() [5/8]

◆ molFromPickle() [6/8]

◆ molFromPickle() [7/8]

◆ molFromPickle() [8/8]

◆ pickleMol() [1/8]

◆ pickleMol() [2/8]

◆ pickleMol() [3/8]

◆ pickleMol() [4/8]

◆ pickleMol() [5/8]

◆ pickleMol() [6/8]

◆ pickleMol() [7/8]

◆ pickleMol() [8/8]

◆ setDefaultPickleProperties()

Member Data Documentation

◆ endianId

◆ versionMajor

◆ versionMinor

◆ versionPatch