RDKit::v1::SDMolSupplier Class Reference

#include <MolSupplier.v1API.h>

Inheritance diagram for RDKit::v1::SDMolSupplier:

Public Types
using	ContainedType = v2::FileParsers::SDMolSupplier
Public Types inherited from RDKit::v1::ForwardSDMolSupplier
using	ContainedType = v2::FileParsers::ForwardSDMolSupplier

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)
void	moveTo (unsigned int idx)
ROMol *	operator[] (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, 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::v1::ForwardSDMolSupplier
	ForwardSDMolSupplier ()
	ForwardSDMolSupplier (std::istream *inStream, bool takeOwnership=true, bool sanitize=true, bool removeHs=true, bool strictParsing=false)
	~ForwardSDMolSupplier () override
void	setProcessPropertyLists (bool val)
bool	getProcessPropertyLists () const
bool	getEOFHitOnRead () const
Public Member Functions inherited from RDKit::v1::MolSupplier
	MolSupplier ()
virtual	~MolSupplier ()
void	init ()
void	reset ()
bool	atEnd ()
ROMol *	next ()
virtual void	close ()

Additional Inherited Members
Protected Attributes inherited from RDKit::v1::MolSupplier
std::unique_ptr< v2::FileParsers::MolSupplier >	dp_supplier

Detailed Description

Definition at line 128 of file MolSupplier.v1API.h.

Member Typedef Documentation

ContainedType

using RDKit::v1::SDMolSupplier::ContainedType = v2::FileParsers::SDMolSupplier

Definition at line 142 of file MolSupplier.v1API.h.

Constructor & Destructor Documentation

SDMolSupplier() [1/3]

RDKit::v1::SDMolSupplier::SDMolSupplier ( )

inline

Definition at line 143 of file MolSupplier.v1API.h.

References RDKit::v1::MolSupplier::dp_supplier.

SDMolSupplier() [2/3]

RDKit::v1::SDMolSupplier::SDMolSupplier ( const std::string & fileName, bool sanitize = true, bool removeHs = true, bool strictParsing = true )

inlineexplicit

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.

Definition at line 154 of file MolSupplier.v1API.h.

References RDKit::v1::MolSupplier::dp_supplier, RDKit::v2::FileParsers::MolFileParserParams::removeHs, RDKit::v2::FileParsers::MolFileParserParams::sanitize, and RDKit::v2::FileParsers::MolFileParserParams::strictParsing.

SDMolSupplier() [3/3]

RDKit::v1::SDMolSupplier::SDMolSupplier ( std::istream * inStream, bool takeOwnership = true, bool sanitize = true, bool removeHs = true, bool strictParsing = true )

inlineexplicit

Definition at line 163 of file MolSupplier.v1API.h.

References RDKit::v1::MolSupplier::dp_supplier, RDKit::v2::FileParsers::MolFileParserParams::removeHs, RDKit::v2::FileParsers::MolFileParserParams::sanitize, and RDKit::v2::FileParsers::MolFileParserParams::strictParsing.

Member Function Documentation

getItemText()

std::string RDKit::v1::SDMolSupplier::getItemText ( unsigned int idx )

inline

returns the text block for a particular item

Parameters

idx	- which item to return

Definition at line 188 of file MolSupplier.v1API.h.

References RDKit::v1::MolSupplier::dp_supplier, and PRECONDITION.

length()

unsigned int RDKit::v1::SDMolSupplier::length ( )

inline

Definition at line 192 of file MolSupplier.v1API.h.

References RDKit::v1::MolSupplier::dp_supplier, and PRECONDITION.

moveTo()

void RDKit::v1::SDMolSupplier::moveTo ( unsigned int idx )

inline

Definition at line 174 of file MolSupplier.v1API.h.

References RDKit::v1::MolSupplier::dp_supplier, and PRECONDITION.

operator[]()

ROMol * RDKit::v1::SDMolSupplier::operator[] ( unsigned int idx )

inline

Definition at line 178 of file MolSupplier.v1API.h.

References RDKit::v1::MolSupplier::dp_supplier, and PRECONDITION.

setData() [1/2]

void RDKit::v1::SDMolSupplier::setData ( const std::string & text, bool sanitize, bool removeHs, bool strictParsing )

inline

Definition at line 204 of file MolSupplier.v1API.h.

References RDKit::v1::MolSupplier::dp_supplier, RDKit::v2::FileParsers::MolFileParserParams::removeHs, RDKit::v2::FileParsers::MolFileParserParams::sanitize, and RDKit::v2::FileParsers::MolFileParserParams::strictParsing.

setData() [2/2]

void RDKit::v1::SDMolSupplier::setData ( const std::string & text, bool sanitize = true, bool removeHs = true )

inline

Definition at line 196 of file MolSupplier.v1API.h.

References RDKit::v1::MolSupplier::dp_supplier, PRECONDITION, RDKit::v2::FileParsers::MolFileParserParams::removeHs, and RDKit::v2::FileParsers::MolFileParserParams::sanitize.

setStreamIndices()

void RDKit::v1::SDMolSupplier::setStreamIndices ( const std::vector< std::streampos > & locs )

inline

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.

Definition at line 224 of file MolSupplier.v1API.h.

References RDKit::v1::MolSupplier::dp_supplier, and PRECONDITION.

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

• MolSupplier.v1API.h