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

lazy file parser for Smiles tables More...

#include <MolSupplier.h>

Inheritance diagram for RDKit::SmilesMolSupplier:
RDKit::MolSupplier

Public Member Functions

 SmilesMolSupplier (const std::string &fileName, const std::string &delimiter=" \t", int smilesColumn=0, int nameColumn=1, bool titleLine=true, bool sanitize=true)
 
 SmilesMolSupplier ()
 
 SmilesMolSupplier (std::istream *inStream, bool takeOwnership=true, const std::string &delimiter=" \t", int smilesColumn=0, int nameColumn=1, bool titleLine=true, bool sanitize=true)
 
 ~SmilesMolSupplier ()
 
void setData (const std::string &text, const std::string &delimiter=" ", int smilesColumn=0, int nameColumn=1, bool titleLine=true, bool sanitize=true)
 
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 ()
 
- Public Member Functions inherited from RDKit::MolSupplier
 MolSupplier ()
 
virtual ~MolSupplier ()
 

Additional Inherited Members

- Protected Attributes inherited from RDKit::MolSupplier
std::istream * dp_inStream
 
bool df_owner
 

Detailed Description

lazy file parser for Smiles tables

Definition at line 181 of file MolSupplier.h.

Constructor & Destructor Documentation

RDKit::SmilesMolSupplier::SmilesMolSupplier ( const std::string &  fileName,
const std::string &  delimiter = " \t",
int  smilesColumn = 0,
int  nameColumn = 1,
bool  titleLine = true,
bool  sanitize = true 
)
explicit
Parameters
fileName- the name of smiles table file
delimiter- delimiting characters between records on a each line NOTE that this is not a string, the tokenizer looks for the individual characters in delimiter, not the full string itself. So the default delimiter: " \t", means " " or "\t".
smilesColumn- column number for the SMILES string (defaults to the first column)
nameColumn- column number for the molecule name (defaults to the second column) If set to -1 we assume that no name is available for the molecule and the name is defaulted to the smiles string
titleLine- if true, the first line is assumed to list the names of properties in order seperated by 'delimiter'. It is also assume that the 'SMILES' column and the 'name' column are not specified here if false - no title line is assumed and the properties are recorded as the "columnX" where "X" is the column number
sanitize- if true sanitize the molecule before returning it
RDKit::SmilesMolSupplier::SmilesMolSupplier ( )
RDKit::SmilesMolSupplier::SmilesMolSupplier ( std::istream *  inStream,
bool  takeOwnership = true,
const std::string &  delimiter = " \t",
int  smilesColumn = 0,
int  nameColumn = 1,
bool  titleLine = true,
bool  sanitize = true 
)
explicit
RDKit::SmilesMolSupplier::~SmilesMolSupplier ( )

Member Function Documentation

bool RDKit::SmilesMolSupplier::atEnd ( )
virtual

Implements RDKit::MolSupplier.

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

returns the text block for a particular item

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

Implements RDKit::MolSupplier.

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

Implements RDKit::MolSupplier.

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

Implements RDKit::MolSupplier.

void RDKit::SmilesMolSupplier::setData ( const std::string &  text,
const std::string &  delimiter = " ",
int  smilesColumn = 0,
int  nameColumn = 1,
bool  titleLine = true,
bool  sanitize = true 
)

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