RDKit::v1::SmilesMolSupplier Class Reference

lazy file parser for Smiles tables More...

#include <MolSupplier.v1API.h>

Inheritance diagram for RDKit::v1::SmilesMolSupplier:

Public Types
using	ContainedType = v2::FileParsers::SmilesMolSupplier

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 (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	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 ()
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

lazy file parser for Smiles tables

Definition at line 232 of file MolSupplier.v1API.h.

Member Typedef Documentation

ContainedType

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

Definition at line 245 of file MolSupplier.v1API.h.

Constructor & Destructor Documentation

SmilesMolSupplier() [1/3]

RDKit::v1::SmilesMolSupplier::SmilesMolSupplier ( const std::string & fileName, const std::string & delimiter = " \t", int smilesColumn = 0, int nameColumn = 1, bool titleLine = true, bool sanitize = true )

inlineexplicit

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 separated 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

Definition at line 266 of file MolSupplier.v1API.h.

References RDKit::v2::FileParsers::SmilesMolSupplierParams::delimiter, RDKit::v2::FileParsers::SmilesMolSupplierParams::nameColumn, RDKit::v2::FileParsers::SmilesMolSupplierParams::parseParameters, RDKit::v2::SmilesParse::SmilesParserParams::sanitize, RDKit::v2::FileParsers::SmilesMolSupplierParams::smilesColumn, and RDKit::v2::FileParsers::SmilesMolSupplierParams::titleLine.

SmilesMolSupplier() [2/3]

RDKit::v1::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 )

inlineexplicit

Definition at line 278 of file MolSupplier.v1API.h.

References RDKit::v2::FileParsers::SmilesMolSupplierParams::delimiter, RDKit::v2::FileParsers::SmilesMolSupplierParams::nameColumn, RDKit::v2::FileParsers::SmilesMolSupplierParams::parseParameters, RDKit::v2::SmilesParse::SmilesParserParams::sanitize, RDKit::v2::FileParsers::SmilesMolSupplierParams::smilesColumn, and RDKit::v2::FileParsers::SmilesMolSupplierParams::titleLine.

SmilesMolSupplier() [3/3]

RDKit::v1::SmilesMolSupplier::SmilesMolSupplier ( )

inline

Definition at line 291 of file MolSupplier.v1API.h.

Member Function Documentation

getItemText()

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

inline

returns the text block for a particular item

Parameters

idx	- which item to return

Definition at line 320 of file MolSupplier.v1API.h.

References PRECONDITION.

length()

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

inline

Definition at line 324 of file MolSupplier.v1API.h.

References PRECONDITION.

moveTo()

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

inline

Definition at line 305 of file MolSupplier.v1API.h.

References PRECONDITION.

operator[]()

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

inline

Definition at line 309 of file MolSupplier.v1API.h.

References PRECONDITION.

setData()

void RDKit::v1::SmilesMolSupplier::setData ( const std::string & text, const std::string & delimiter = " ", int smilesColumn = 0, int nameColumn = 1, bool titleLine = true, bool sanitize = true )

inline

Definition at line 293 of file MolSupplier.v1API.h.

References RDKit::v2::FileParsers::SmilesMolSupplierParams::delimiter, RDKit::v2::FileParsers::SmilesMolSupplierParams::nameColumn, RDKit::v2::FileParsers::SmilesMolSupplierParams::parseParameters, PRECONDITION, RDKit::v2::SmilesParse::SmilesParserParams::sanitize, RDKit::v2::FileParsers::SmilesMolSupplierParams::smilesColumn, and RDKit::v2::FileParsers::SmilesMolSupplierParams::titleLine.

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

• MolSupplier.v1API.h