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

#include <MolSupplier.h>

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

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 ()
 
void init ()
 
void reset ()
 
ROMolnext ()
 
bool atEnd ()
 
void moveTo (unsigned int idx)
 
ROMoloperator[] (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)
 
virtual ~ForwardSDMolSupplier ()
 
- Public Member Functions inherited from RDKit::MolSupplier
 MolSupplier ()
 
virtual ~MolSupplier ()
 

Additional Inherited Members

- Protected Member Functions inherited from RDKit::ForwardSDMolSupplier
ROMol_next ()
 
virtual void readMolProps (ROMol *)
 
- Protected Attributes inherited from RDKit::ForwardSDMolSupplier
bool df_end
 
int d_line
 
bool df_sanitize
 
bool df_removeHs
 
bool df_strictParsing
 
- Protected Attributes inherited from RDKit::MolSupplier
std::istream * dp_inStream
 
bool df_owner
 

Detailed Description

Definition at line 108 of file MolSupplier.h.

Constructor & Destructor Documentation

RDKit::SDMolSupplier::SDMolSupplier ( )
inline

Definition at line 122 of file MolSupplier.h.

References RDKit::MolSupplier::init(), and RDKit::MolOps::removeHs().

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 not set, the parser is more lax about correctness of the contents.
RDKit::SDMolSupplier::SDMolSupplier ( std::istream *  inStream,
bool  takeOwnership = true,
bool  sanitize = true,
bool  removeHs = true,
bool  strictParsing = true 
)
explicit
RDKit::SDMolSupplier::~SDMolSupplier ( )
inline

Member Function Documentation

bool RDKit::SDMolSupplier::atEnd ( )
virtual

Reimplemented from RDKit::ForwardSDMolSupplier.

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

returns the text block for a particular item

Parameters
idx- which item to return
void RDKit::SDMolSupplier::init ( )
virtual

Reimplemented from RDKit::ForwardSDMolSupplier.

unsigned int RDKit::SDMolSupplier::length ( )
void RDKit::SDMolSupplier::moveTo ( unsigned int  idx)
ROMol* RDKit::SDMolSupplier::next ( )
virtual

Reimplemented from RDKit::ForwardSDMolSupplier.

ROMol* RDKit::SDMolSupplier::operator[] ( unsigned int  idx)
void RDKit::SDMolSupplier::reset ( )
virtual

Reimplemented from RDKit::ForwardSDMolSupplier.

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