RDKit
Open-source cheminformatics and machine learning.
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RDKit::v2::FileParsers::SDMolSupplier Class Reference

#include <MolSupplier.h>

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

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< RWMolnext () override
 
bool atEnd () override
 
void moveTo (unsigned int idx)
 
std::unique_ptr< RWMoloperator[] (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)
 
- Public Member Functions inherited from RDKit::v2::FileParsers::ForwardSDMolSupplier
 ForwardSDMolSupplier ()
 
 ForwardSDMolSupplier (std::istream *inStream, bool takeOwnership=true, const MolFileParserParams &params=MolFileParserParams())
 
 ~ForwardSDMolSupplier () override
 
void setProcessPropertyLists (bool val)
 
bool getProcessPropertyLists () const
 
bool getEOFHitOnRead () const
 
- 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 159 of file MolSupplier.h.

Constructor & Destructor Documentation

◆ SDMolSupplier() [1/3]

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

Definition at line 173 of file MolSupplier.h.

◆ 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 192 of file MolSupplier.h.

Member Function Documentation

◆ atEnd()

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

◆ 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

Referenced by RDKit::v1::SDMolSupplier::getItemText().

◆ init()

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

◆ length()

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

◆ moveTo()

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

◆ next()

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

◆ operator[]()

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

◆ reset()

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

◆ 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.

Referenced by RDKit::v1::SDMolSupplier::setStreamIndices().


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