SmilesFormat Class Reference

Implementation of the SMILES line notation. More...

#include <avogadro/io/smilesformat.h>

Inheritance diagram for SmilesFormat:

Public Member Functions
Operations	supportedOperations () const override
FileFormat *	newInstance () const override
std::string	identifier () const override
	A unique identifier, used to retrieve formats programmatically. CML, XYZ, PDB etc. A runtime warning will be generated if the identifier is not unique.
std::string	name () const override
	The name of the format, should be short such as Chemical Markup Language, XYZ format, Protein Databank etc.
std::string	description () const override
std::string	specificationUrl () const override
std::vector< std::string >	fileExtensions () const override
	Get the file name extension(s) that the format supports reading.
std::vector< std::string >	mimeTypes () const override
	Get the MIME type(s) that the format supports reading.
void	setHydrogenMode (SmilesWriter::HydrogenMode mode)
void	setAtomMaps (bool enable)
void	setAromatic (bool enable)
bool	read (std::istream &inStream, Core::Molecule &molecule) override
	Read the given in stream and load it into molecule.
bool	write (std::ostream &outStream, const Core::Molecule &molecule) override
	Write to the given out stream the contents of molecule.
Public Member Functions inherited from FileFormat
bool	open (const std::string &fileName, Operation mode)
	Open the specified file in Read or Write mode.
Operation	mode ()
	The mode the format is currently operating in.
bool	isMode (Operation isInMode)
	Check if the supplied mode(s) is being used.
void	close ()
	Close any opened file handles.
bool	readMolecule (Core::Molecule &molecule)
	Read in a molecule, if there are no molecules to read molecule will be empty. This can be used to read in one or more molecules from a given file using repeated calls for each molecule.
bool	writeMolecule (const Core::Molecule &molecule)
	Write out a molecule. This can be used to write one or more molecules to a given file using repeated calls for each molecule.
virtual bool	readFile (const std::string &fileName, Core::Molecule &molecule)
	Read the given fileName and load it into molecule.
virtual bool	writeFile (const std::string &fileName, const Core::Molecule &molecule)
	Write to the given fileName the contents of molecule.
bool	readString (const std::string &string, Core::Molecule &molecule)
	Read the given string and load it into molecule.
bool	writeString (std::string &string, const Core::Molecule &molecule)
	Write to the given string the contents of molecule.
std::string	error () const
	Get the error string, contains errors/warnings encountered.
std::string	fileName () const
	Get the file name (if known).
void	setOptions (const std::string &options)
	Set options for the file reader.
std::string	options () const
	Get the file format options, can be used to change file IO.
virtual void	clear ()
virtual std::vector< std::string >	contentPatterns () const
	Get literal strings that identify files in this format by content.

Additional Inherited Members
Public Types inherited from FileFormat
enum	Operation {   None = 0x0 ,   Read = 0x1 ,   Write = 0x2 ,   ReadWrite = Read | Write ,   MultiMolecule = 0x4 ,   Stream = 0x10 ,   String = 0x20 ,   File = 0x40 ,   All = ReadWrite | MultiMolecule | Stream | String | File }
	Flags defining supported operations.
using	Operations = int
Static Public Member Functions inherited from FileFormat
static bool	validateFileName (const std::string &fileName)
	Validates the given file name.
Protected Member Functions inherited from FileFormat
void	appendError (const std::string &errorString, bool newLine=true)
	Append an error to the error string for the format.
bool	boolOption (const std::string &name, bool &value)
	Look up a boolean value in the options() string.
bool	stringOption (const std::string &name, std::string &value)
	Look up a string value in the options() string.
bool	stringArrayOption (const std::string &name, std::vector< std::string > &values)
	Look up an array of strings in the options() string.
long long	maxDecompressedSizeOption ()
	The ceiling on decompressed data for this read, in bytes.
bool	integerOption (const std::string &name, long long &value)
	Look up an integer value in the options() string.

Detailed Description

Writing only. A SMILES string carries no coordinates, so reading one yields a molecule with every atom at the origin; until Avogadro can generate coordinates natively, reading stays with the Open Babel plugin and this format deliberately does not advertise Read.

Behaviour is controlled either through the typed setters below, or – for generic callers that only have a FileFormat – through setOptions() with a JSON object:

{ "hydrogens": "implicit" | "bracket" | "explicit", "atomMaps": false,
  "aromatic": true }

Keys present in the options string override the typed setters. See SmilesWriter for what the values mean. Note that "atomMaps" implies "explicit", and that both default to the interchange-safe values, since this format's output is pasted into other programs and sent to web services.

Member Function Documentation

supportedOperations()

Operations supportedOperations ( ) const

overridevirtual

Returns

Operation flags defining the capabilities of this format.

Implements FileFormat.

newInstance()

FileFormat * newInstance ( ) const

overridevirtual

Create a new instance of the file format class. Ownership passes to the caller.

Implements FileFormat.

identifier()

std::string identifier ( ) const

overridevirtual

Implements FileFormat.

name()

std::string name ( ) const

overridevirtual

Implements FileFormat.

description()

std::string description ( ) const

overridevirtual

A description of the format, along with any relevant help text for users.

Implements FileFormat.

specificationUrl()

std::string specificationUrl ( ) const

overridevirtual

The URL of the format specification if available (relevant web page/wiki otherwise).

Implements FileFormat.

fileExtensions()

std::vector< std::string > fileExtensions ( ) const

overridevirtual

Returns

A vector containing a list of extensions (in lower case).

Implements FileFormat.

mimeTypes()

std::vector< std::string > mimeTypes ( ) const

overridevirtual

Returns

A vector containing a list of MIME type(s) (in lower case).

Implements FileFormat.

setHydrogenMode()

void setHydrogenMode

(

SmilesWriter::HydrogenMode

mode

)

Set how hydrogens are represented. Note that atomMaps() overrides this, see setAtomMaps().

setAtomMaps()

void setAtomMaps

(

bool

enable

)

Emit each atom's index as a Daylight atom map class, so that the string can be correlated back to the molecule it came from.

Classes are written one-based, because Daylight assigns class zero the meaning "unmapped"; a consumer reading the classes back must subtract one to recover the Avogadro atom index.

This implies HydrogenMode::Explicit. A hydrogen folded into a bracket count has nowhere to carry a class, and in Avogadro that hydrogen is a real atom with a real index, so folding it would silently produce a partial mapping.

setAromatic()

void setAromatic

(

bool

enable

)

Write perceived aromatic rings in the lowercase form, so benzene is "c1ccccc1" rather than "C1=CC=CC=C1". Both describe the same molecule; the lowercase form is what most toolkits produce and expect, so it is enabled by default and callers wanting Kekule output must ask for it.

Perception is Core::AromaticityPerceiver; anything it does not recognise is written with its bond orders as stored.

read()

bool read ( std::istream & in, Core::Molecule & molecule )

nodiscardoverridevirtual

Parameters

in	The input file stream.
molecule	The molecule the data will be read into.

Returns

True on success, false on failure.

Implements FileFormat.

write()

bool write ( std::ostream & out, const Core::Molecule & molecule )

nodiscardoverridevirtual

Parameters

out	The output stream to write the data to.
molecule	The contents of this molecule will be written to output.

Returns

True on success, false on failure.

Implements FileFormat.

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

• smilesformat.h