RDKit::SDMolSupplier Class Reference

#include <MolSupplier.h>

Inheritance diagram for RDKit::SDMolSupplier:

Public Member Functions
	SDMolSupplier ()
	SDMolSupplier (const std::string &fileName, bool sanitize=true, bool removeHs=true, bool strictParsing=true)
	SDMolSupplier (std::istream *inStream, bool takeOwnership=true, bool sanitize=true, bool removeHs=true, bool strictParsing=true)
	~SDMolSupplier () override
void	init () override
void	reset () override
ROMol *	next () override
bool	atEnd () override
void	moveTo (unsigned int idx)
ROMol *	operator[] (unsigned int idx)
std::string	getItemText (unsigned int idx)
	returns the text block for a particular item More...
unsigned int	length ()
void	setData (const std::string &text, bool sanitize=true, bool removeHs=true)
void	setData (const std::string &text, bool sanitize, bool removeHs, bool strictParsing)
void	setStreamIndices (const std::vector< std::streampos > &locs)
Public Member Functions inherited from RDKit::ForwardSDMolSupplier
	ForwardSDMolSupplier ()
	ForwardSDMolSupplier (std::istream *inStream, bool takeOwnership=true, bool sanitize=true, bool removeHs=true, bool strictParsing=false)
	~ForwardSDMolSupplier () override
void	init () override
void	reset () override
ROMol *	next () override
bool	atEnd () override
void	setProcessPropertyLists (bool val)
bool	getProcessPropertyLists () const
bool	getEOFHitOnRead () const
Public Member Functions inherited from RDKit::MolSupplier
	MolSupplier ()
virtual	~MolSupplier ()
virtual void	init ()=0
virtual void	reset ()=0
virtual bool	atEnd ()=0
virtual ROMol *	next ()=0
virtual void	close ()

Additional Inherited Members
Protected Member Functions inherited from RDKit::ForwardSDMolSupplier
virtual void	checkForEnd ()
ROMol *	_next ()
virtual void	readMolProps (ROMol *)
Protected Member Functions inherited from RDKit::MolSupplier
std::istream *	openAndCheckStream (const std::string &filename)
Protected Attributes inherited from RDKit::ForwardSDMolSupplier
bool	df_end = false
int	d_line = 0
bool	df_sanitize = true
bool	df_removeHs = true
bool	df_strictParsing = true
bool	df_processPropertyLists = true
bool	df_eofHitOnRead = false
Protected Attributes inherited from RDKit::MolSupplier
std::istream *	dp_inStream = nullptr
bool	df_owner = false

Detailed Description

Definition at line 158 of file MolSupplier.h.

Constructor & Destructor Documentation

SDMolSupplier() [1/3]

RDKit::SDMolSupplier::SDMolSupplier ( )

inline

Definition at line 172 of file MolSupplier.h.

SDMolSupplier() [2/3]

RDKit::SDMolSupplier::SDMolSupplier ( const std::string &  fileName, bool  sanitize = true, bool  removeHs = true, bool  strictParsing = true  )

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::SDMolSupplier::SDMolSupplier ( std::istream *  inStream, bool  takeOwnership = true, bool  sanitize = true, bool  removeHs = true, bool  strictParsing = true  )

explicit

~SDMolSupplier()

RDKit::SDMolSupplier::~SDMolSupplier ( )

inlineoverride

Definition at line 190 of file MolSupplier.h.

Member Function Documentation

atEnd()

bool RDKit::SDMolSupplier::atEnd ( )

overridevirtual

Reimplemented from RDKit::ForwardSDMolSupplier.

getItemText()

std::string RDKit::SDMolSupplier::getItemText

(

unsigned int

idx

)

returns the text block for a particular item

Parameters

idx	- which item to return

init()

void RDKit::SDMolSupplier::init ( )

overridevirtual

Reimplemented from RDKit::ForwardSDMolSupplier.

length()

unsigned int RDKit::SDMolSupplier::length

(

)

moveTo()

void RDKit::SDMolSupplier::moveTo

(

unsigned int

idx

)

next()

ROMol * RDKit::SDMolSupplier::next ( )

overridevirtual

Reimplemented from RDKit::ForwardSDMolSupplier.

operator[]()

ROMol * RDKit::SDMolSupplier::operator[]

(

unsigned int

idx

)

reset()

void RDKit::SDMolSupplier::reset ( )

overridevirtual

Reimplemented from RDKit::ForwardSDMolSupplier.

setData() [1/2]

void RDKit::SDMolSupplier::setData	(	const std::string &	text,
		bool	sanitize,
		bool	removeHs,
		bool	strictParsing
	)

setData() [2/2]

void RDKit::SDMolSupplier::setData	(	const std::string &	text,
		bool	sanitize = true,
		bool	removeHs = true
	)

setStreamIndices()

void RDKit::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