org.openscience.cdk.smiles

Class SmilesParser

java.lang.Object

org.openscience.cdk.smiles.SmilesParser

public final class SmilesParser
extends Object

Read molecules and reactions from a SMILES (?Authors?, SMILES Tutorial) string. Example usage

 try {
     SmilesParser   sp  = new SmilesParser(SilentChemObjectBuilder.getInstance());
     IAtomContainer m   = sp.parseSmiles("c1ccccc1");
 } catch (InvalidSmilesException e) {
     System.err.println(e.getMessage());
 }
 

Reading Aromatic SMILES

Aromatic SMILES are automatically kekulised producing a structure with assigned bond orders. The aromatic specification on the atoms is maintained from the SMILES even if the structures are not considered aromatic. For example 'c1ccc1' will correctly have two pi bonds assigned but the atoms/bonds will still be flagged as aromatic. Recomputing or clearing the aromaticty will remove these erroneous flags. If a kekulé structure could not be assigned this is considered an error. The most common example is the omission of hydrogens on aromatic nitrogens (aromatic pyrrole is specified as '[nH]1cccc1' not 'n1cccc1'). These structures can not be corrected without modifying their formula. If there are multiple locations a hydrogen could be placed the returned structure would differ depending on the atom input order. If you wish to skip the kekulistation (not recommended) then it can be disabled with kekulise. SMILES can be verified for validity with the DEPICT service. Unsupported Features

The following features are not supported by this parser.

• variable order of bracket atom attributes, '[C-H]', '[CH@]' are considered invalid. The predefined order required by this parser follows the OpenSMILES specification of 'isotope', 'symbol', 'chiral', 'hydrogens', 'charge', 'atom class'
• atom class indication - this information is loaded but not annotated on the structure
• extended tetrahedral stereochemistry (cumulated double bonds)
• trigonal bipyramidal stereochemistry
• octahedral stereochemistry

Atom Class

The atom class is stored as the CDKConstants.ATOM_ATOM_MAPPING property.

 SmilesParser   sp  = new SmilesParser(SilentChemObjectBuilder.getInstance());
 IAtomContainer m   = sp.parseSmiles("c1[cH:5]cccc1");
 Integer        c1  = m.getAtom(1)
                       .getProperty(CDKConstants.ATOM_ATOM_MAPPING); // 5
 Integer        c2  = m.getAtom(2)
                       .getProperty(CDKConstants.ATOM_ATOM_MAPPING); // null

 

Author:

Christoph Steinbeck, Egon Willighagen, John May

Source code:

master

Belongs to CDK module:

smiles

Keywords:

SMILES, parser

Created on:

2002-04-29

Constructor Summary

Constructors

Constructor and Description
SmilesParser(IChemObjectBuilder builder) Create a new SMILES parser which will create IAtomContainers with the specified builder.

Method Summary

Modifier and Type	Method and Description
boolean	isPreservingAromaticity() Deprecated.
void	kekulise(boolean kekulise) Indicated whether structures should be automatically kekulised if they are provided as aromatic.
IReaction	parseReactionSmiles(String smiles) Parse a reaction SMILES.
IAtomContainer	parseSmiles(String smiles) Parses a SMILES string and returns a structure (IAtomContainer).
void	setPreservingAromaticity(boolean preservingAromaticity) Deprecated.
void	setStrict(boolean strict) Sets whether the parser is in strict mode.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SmilesParser

public SmilesParser(IChemObjectBuilder builder)

Create a new SMILES parser which will create IAtomContainers with the specified builder.

Parameters:

builder - used to create the CDK domain objects

Method Detail

setStrict

public void setStrict(boolean strict)

Sets whether the parser is in strict mode. In non-strict mode (default) recoverable issues with SMILES are reported as warnings.

Parameters:

strict - strict mode true/false.

parseReactionSmiles

public IReaction parseReactionSmiles(String smiles)
                              throws InvalidSmilesException

Parse a reaction SMILES.

Parameters:

smiles - The SMILES string to parse

Returns:

An instance of IReaction

Throws:

InvalidSmilesException - if the string cannot be parsed

See Also:

parseSmiles(String)

parseSmiles

public IAtomContainer parseSmiles(String smiles)
                           throws InvalidSmilesException

Parses a SMILES string and returns a structure (IAtomContainer).

Parameters:

smiles - A SMILES string

Returns:

A structure representing the provided SMILES

Throws:

InvalidSmilesException - thrown when the SMILES string is invalid

setPreservingAromaticity

@Deprecated
public void setPreservingAromaticity(boolean preservingAromaticity)

Deprecated.

Makes the Smiles parser set aromaticity as provided in the Smiles itself, without detecting it. Default false. Atoms will not be typed when set to true.

Parameters:

preservingAromaticity - boolean to indicate if aromaticity is to be preserved.

See Also:

kekulise

isPreservingAromaticity

@Deprecated
public boolean isPreservingAromaticity()

Deprecated.

Gets the (default false) setting to preserve aromaticity as provided in the Smiles itself.

Returns:

true or false indicating if aromaticity is preserved.

kekulise

public void kekulise(boolean kekulise)

Indicated whether structures should be automatically kekulised if they are provided as aromatic. Kekulisation is on by default but can be turned off if it is believed the structures can be handled without assigned bond orders (not recommended).

Parameters:

kekulise - should structures be kekulised