#include <MolSupplier.h>

Inheritance diagram for RDKit::v2::FileParsers::SDMolSupplier:

Public Types
using	iterator = RandomAccessSupplierIter<SDMolSupplier>
using	reverse_iterator = std::reverse_iterator<iterator>
Public Types inherited from RDKit::v2::FileParsers::ForwardSDMolSupplier
using	iterator = ForwardSupplierIter<ForwardSDMolSupplier>

Public Member Functions
	SDMolSupplier ()
	SDMolSupplier (const std::string &fileName, const MolFileParserParams &params=MolFileParserParams())
	SDMolSupplier (std::istream *inStream, bool takeOwnership=true, const MolFileParserParams &params=MolFileParserParams())
	~SDMolSupplier () override
void	init () override
void	reset () override
std::unique_ptr< RWMol >	next () override
bool	atEnd () override
void	moveTo (unsigned int idx)
std::unique_ptr< RWMol >	operator[] (unsigned int idx)
std::shared_ptr< RWMol >	getShared (unsigned int idx)
	!
std::string	getItemText (unsigned int idx)
	returns the text block for a particular item
unsigned int	length ()
void	setData (const std::string &text)
void	setData (const std::string &text, const MolFileParserParams &params)
void	setStreamIndices (const std::vector< std::streampos > &locs)
iterator	begin ()
iterator	end ()
reverse_iterator	rbegin ()
reverse_iterator	rend ()
void	setCaching (bool val)
bool	getCaching () const
Public Member Functions inherited from RDKit::v2::FileParsers::ForwardSDMolSupplier
	ForwardSDMolSupplier ()
	ForwardSDMolSupplier (std::istream *inStream, bool takeOwnership=true, const MolFileParserParams &params=MolFileParserParams())
	~ForwardSDMolSupplier () override
std::shared_ptr< RWMol >	nextShared ()
void	setProcessPropertyLists (bool val)
bool	getProcessPropertyLists () const
bool	getEOFHitOnRead () const
iterator	begin ()
iterator	end ()
Public Member Functions inherited from RDKit::v2::FileParsers::MolSupplier
	MolSupplier ()
virtual	~MolSupplier ()
virtual void	close ()

Additional Inherited Members
Protected Member Functions inherited from RDKit::v2::FileParsers::ForwardSDMolSupplier
std::unique_ptr< RWMol >	_next ()
virtual void	readMolProps (ROMol &)
Protected Member Functions inherited from RDKit::v2::FileParsers::MolSupplier
std::istream *	openAndCheckStream (const std::string &filename)
Protected Attributes inherited from RDKit::v2::FileParsers::ForwardSDMolSupplier
bool	df_end = false
int	d_line = 0
MolFileParserParams	d_params
bool	df_processPropertyLists = true
bool	df_eofHitOnRead = false
Protected Attributes inherited from RDKit::v2::FileParsers::MolSupplier
std::istream *	dp_inStream = nullptr
bool	df_owner = false

Detailed Description

Definition at line 356 of file MolSupplier.h.

Member Typedef Documentation

◆ iterator

using RDKit::v2::FileParsers::SDMolSupplier::iterator = RandomAccessSupplierIter<SDMolSupplier>

Definition at line 367 of file MolSupplier.h.

◆ reverse_iterator

using RDKit::v2::FileParsers::SDMolSupplier::reverse_iterator = std::reverse_iterator<iterator>

Definition at line 368 of file MolSupplier.h.

Constructor & Destructor Documentation

◆ SDMolSupplier() [1/3]

RDKit::v2::FileParsers::SDMolSupplier::SDMolSupplier ( )

inline

Definition at line 370 of file MolSupplier.h.

References init().

◆ SDMolSupplier() [2/3]

RDKit::v2::FileParsers::SDMolSupplier::SDMolSupplier	(	const std::string &	fileName,
		const MolFileParserParams &	params = MolFileParserParams() )

explicit

Parameters

fileName	- the name of the SD file
sanitize	- if true sanitize the molecule before returning it
removeHs	- if true remove Hs from the molecule before returning it (triggers sanitization)
strictParsing	- if set to false, the parser is more lax about correctness of the contents.

◆ SDMolSupplier() [3/3]

RDKit::v2::FileParsers::SDMolSupplier::SDMolSupplier	(	std::istream *	inStream,
		bool	takeOwnership = true,
		const MolFileParserParams &	params = MolFileParserParams() )

explicit

◆ ~SDMolSupplier()

RDKit::v2::FileParsers::SDMolSupplier::~SDMolSupplier ( )

inlineoverride

Definition at line 389 of file MolSupplier.h.

References RDKit::v2::FileParsers::MolSupplier::close().

Member Function Documentation

◆ atEnd()

bool RDKit::v2::FileParsers::SDMolSupplier::atEnd ( )

overridevirtual

Reimplemented from RDKit::v2::FileParsers::ForwardSDMolSupplier.

◆ begin()

iterator RDKit::v2::FileParsers::SDMolSupplier::begin ( )

inline

Definition at line 421 of file MolSupplier.h.

Referenced by rend().

◆ end()

iterator RDKit::v2::FileParsers::SDMolSupplier::end ( )

inline

Definition at line 422 of file MolSupplier.h.

References length().

Referenced by rbegin().

◆ getCaching()

bool RDKit::v2::FileParsers::SDMolSupplier::getCaching ( ) const

inline

Definition at line 427 of file MolSupplier.h.

◆ getItemText()

std::string RDKit::v2::FileParsers::SDMolSupplier::getItemText ( unsigned int idx )

returns the text block for a particular item

Parameters

idx	- which item to return

◆ getShared()

std::shared_ptr< RWMol > RDKit::v2::FileParsers::SDMolSupplier::getShared ( unsigned int idx )

!

returns a shared pointer to the molecule at the given index.

◆ init()

void RDKit::v2::FileParsers::SDMolSupplier::init ( )

overridevirtual

Reimplemented from RDKit::v2::FileParsers::ForwardSDMolSupplier.

Referenced by SDMolSupplier().

◆ length()

unsigned int RDKit::v2::FileParsers::SDMolSupplier::length ( )

Referenced by end().

◆ moveTo()

void RDKit::v2::FileParsers::SDMolSupplier::moveTo ( unsigned int idx )

◆ next()

std::unique_ptr< RWMol > RDKit::v2::FileParsers::SDMolSupplier::next ( )

overridevirtual

Reimplemented from RDKit::v2::FileParsers::ForwardSDMolSupplier.

◆ operator[]()

std::unique_ptr< RWMol > RDKit::v2::FileParsers::SDMolSupplier::operator[] ( unsigned int idx )

◆ rbegin()

reverse_iterator RDKit::v2::FileParsers::SDMolSupplier::rbegin ( )

inline

Definition at line 423 of file MolSupplier.h.

References end().

◆ rend()

reverse_iterator RDKit::v2::FileParsers::SDMolSupplier::rend ( )

inline

Definition at line 424 of file MolSupplier.h.

References begin().

◆ reset()

void RDKit::v2::FileParsers::SDMolSupplier::reset ( )

overridevirtual

Reimplemented from RDKit::v2::FileParsers::ForwardSDMolSupplier.

◆ setCaching()

void RDKit::v2::FileParsers::SDMolSupplier::setCaching ( bool val )

inline

Definition at line 426 of file MolSupplier.h.

◆ setData() [1/2]

void RDKit::v2::FileParsers::SDMolSupplier::setData ( const std::string & text )

◆ setData() [2/2]

void RDKit::v2::FileParsers::SDMolSupplier::setData	(	const std::string &	text,
		const MolFileParserParams &	params )

◆ setStreamIndices()

void RDKit::v2::FileParsers::SDMolSupplier::setStreamIndices ( const std::vector< std::streampos > & locs )

Resets our internal state and sets the indices of molecules in the stream. The client should be very careful about calling this method, as it's trivial to end up with a completely useless supplier.

Parameters

locs	- the vector of stream positions.

Note that this can be used not only to make reading selected molecules from a large SD file much faster, but it can also allow subsetting an SD file or rearranging the order of the molecules.

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

MolSupplier.h

Public Types

Public Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ iterator

◆ reverse_iterator

Constructor & Destructor Documentation

◆ SDMolSupplier() [1/3]

◆ SDMolSupplier() [2/3]

◆ SDMolSupplier() [3/3]

◆ ~SDMolSupplier()

Member Function Documentation

◆ atEnd()

◆ begin()

◆ end()

◆ getCaching()

◆ getItemText()

◆ getShared()

◆ init()

◆ length()

◆ moveTo()

◆ next()

◆ operator[]()

◆ rbegin()

◆ rend()

◆ reset()

◆ setCaching()

◆ setData() [1/2]

◆ setData() [2/2]

◆ setStreamIndices()