org.jmol.smiles

Class SmilesParser

java.lang.Object

org.jmol.smiles.SmilesParser

public class SmilesParser
extends Object

Parses a SMILES String to create a SmilesMolecule. The SMILES specification has been found at the SMILES Home Page. An other explanation can be found in the Daylight Theory Manual.
Currently this parser supports only parts of the SMILES specification.
An example on how to use it:

 try {
   SmilesParser sp = new SmilesParser();
   SmilesMolecule sm = sp.parseSmiles("CC(C)C(=O)O");
   // Use the resulting molecule 
 } catch (InvalidSmilesException e) {
   // Exception management
 }
 

See Also:

SMILES Home Page

Field Summary

Fields

Modifier and Type	Field and Description
private char	bioType
private int	braceCount
private int	branchLevel
private int	flags
(package private) Map<String,SmilesMeasure>	htMeasures
private boolean	isBioSequence
private boolean	isSmarts
private Map<Integer,SmilesBond>	ringBonds

Constructor Summary

Constructors

Constructor and Description
SmilesParser(boolean isSmarts)

Method Summary

Modifier and Type	Method and Description
private int	checkBioType(String pattern, int index)
private boolean	checkBrace(SmilesSearch molecule, char ch, char type)
private int	checkCharge(String pattern, int index, SmilesAtom newAtom)
private int	checkChirality(String pattern, int index, SmilesAtom newAtom)
private boolean	checkLogic(SmilesSearch molecule, String pattern, SmilesAtom atom, SmilesBond bond, SmilesAtom currentAtom, boolean isPrimitive, boolean isBranchAtom)
private void	checkNested(SmilesSearch molecule, SmilesAtom atom, int flags)
(package private) static String	cleanPattern(String pattern)
private void	fixChirality(SmilesSearch molecule)
private static char	getChar(String pattern, int i)
private static int	getDigits(String pattern, int index, int[] ret)
static SmilesSearch	getMolecule(String pattern, boolean isSmarts)
(package private) static String	getRingPointer(int i)
(package private) SmilesSearch	getSearch(SmilesSearch parent, String pattern, int flags)
private static String	getSubPattern(String pattern, int index, char ch)
(package private) SmilesSearch	parse(String pattern) Parses a SMILES String
private SmilesAtom	parseAtom(SmilesSearch molecule, SmilesAtom atomSet, String pattern, SmilesAtom currentAtom, SmilesBond bond, boolean isBracketed, boolean isPrimitive, boolean isBranchAtom) Parses an atom definition
private SmilesBond	parseBond(SmilesSearch molecule, SmilesBond bondSet, String pattern, SmilesBond bond, SmilesAtom currentAtom, boolean isPrimitive, boolean isBranchAtom)
private void	parseMeasure(SmilesSearch molecule, String strMeasure, SmilesAtom currentAtom)
private String	parseNested(SmilesSearch molecule, String pattern, String prefix)
private void	parseRing(SmilesSearch molecule, int ringNum, SmilesAtom currentAtom, SmilesBond bond) Parses a ring definition
private void	parseSmiles(SmilesSearch molecule, String pattern, SmilesAtom currentAtom, boolean isBranchAtom) Parses a part of a SMILES String
private String	parseVariableLength(String pattern)
private String	parseVariables(String pattern)
(package private) void	reset()
private static int	skipTo(String pattern, int index, char ch0)

Methods inherited from class java.lang.Object

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

Field Detail

isSmarts

private boolean isSmarts

isBioSequence

private boolean isBioSequence

bioType

private char bioType

ringBonds

private Map<Integer,SmilesBond> ringBonds

braceCount

private int braceCount

branchLevel

private int branchLevel

flags

private int flags

htMeasures

Map<String,SmilesMeasure> htMeasures

Constructor Detail

SmilesParser

SmilesParser(boolean isSmarts)

Method Detail

getMolecule

public static SmilesSearch getMolecule(String pattern,
                                       boolean isSmarts)
                                throws InvalidSmilesException

Throws:

InvalidSmilesException

reset

void reset()

parse

SmilesSearch parse(String pattern)
            throws InvalidSmilesException

Parses a SMILES String

Parameters:

pattern - SMILES String

Returns:

Molecule corresponding to pattern

Throws:

InvalidSmilesException

parseVariableLength

private String parseVariableLength(String pattern)
                            throws InvalidSmilesException

Throws:

InvalidSmilesException

getSearch

SmilesSearch getSearch(SmilesSearch parent,
                       String pattern,
                       int flags)
                throws InvalidSmilesException

Throws:

InvalidSmilesException

checkNested

private void checkNested(SmilesSearch molecule,
                         SmilesAtom atom,
                         int flags)
                  throws InvalidSmilesException

Throws:

InvalidSmilesException

fixChirality

private void fixChirality(SmilesSearch molecule)
                   throws InvalidSmilesException

Throws:

InvalidSmilesException

parseSmiles

private void parseSmiles(SmilesSearch molecule,
                         String pattern,
                         SmilesAtom currentAtom,
                         boolean isBranchAtom)
                  throws InvalidSmilesException

Parses a part of a SMILES String

Parameters:

molecule - Resulting molecule

pattern - SMILES String

currentAtom - Current atom

isBranchAtom - If we are starting a new branch

Throws:

InvalidSmilesException

checkBioType

private int checkBioType(String pattern,
                         int index)

parseMeasure

private void parseMeasure(SmilesSearch molecule,
                          String strMeasure,
                          SmilesAtom currentAtom)
                   throws InvalidSmilesException

Throws:

InvalidSmilesException

checkBrace

private boolean checkBrace(SmilesSearch molecule,
                           char ch,
                           char type)
                    throws InvalidSmilesException

Throws:

InvalidSmilesException

parseNested

private String parseNested(SmilesSearch molecule,
                           String pattern,
                           String prefix)
                    throws InvalidSmilesException

Throws:

InvalidSmilesException

parseVariables

private String parseVariables(String pattern)
                       throws InvalidSmilesException

Throws:

InvalidSmilesException

parseAtom

private SmilesAtom parseAtom(SmilesSearch molecule,
                             SmilesAtom atomSet,
                             String pattern,
                             SmilesAtom currentAtom,
                             SmilesBond bond,
                             boolean isBracketed,
                             boolean isPrimitive,
                             boolean isBranchAtom)
                      throws InvalidSmilesException

Parses an atom definition

Parameters:

molecule - Resulting molecule

atomSet -

pattern - SMILES String

currentAtom - Current atom

bond -

isBracketed - Indicates if is a isBracketed definition (between [])

isPrimitive -

isBranchAtom -

Returns:

New atom

Throws:

InvalidSmilesException

parseRing

private void parseRing(SmilesSearch molecule,
                       int ringNum,
                       SmilesAtom currentAtom,
                       SmilesBond bond)
                throws InvalidSmilesException

Parses a ring definition

Parameters:

molecule - Resulting molecule

ringNum -

currentAtom - Current atom

bond -

Throws:

InvalidSmilesException

checkCharge

private int checkCharge(String pattern,
                        int index,
                        SmilesAtom newAtom)
                 throws InvalidSmilesException

Throws:

InvalidSmilesException

checkChirality

private int checkChirality(String pattern,
                           int index,
                           SmilesAtom newAtom)
                    throws InvalidSmilesException

Throws:

InvalidSmilesException

parseBond

private SmilesBond parseBond(SmilesSearch molecule,
                             SmilesBond bondSet,
                             String pattern,
                             SmilesBond bond,
                             SmilesAtom currentAtom,
                             boolean isPrimitive,
                             boolean isBranchAtom)
                      throws InvalidSmilesException

Throws:

InvalidSmilesException

checkLogic

private boolean checkLogic(SmilesSearch molecule,
                           String pattern,
                           SmilesAtom atom,
                           SmilesBond bond,
                           SmilesAtom currentAtom,
                           boolean isPrimitive,
                           boolean isBranchAtom)
                    throws InvalidSmilesException

Throws:

InvalidSmilesException

getSubPattern

private static String getSubPattern(String pattern,
                                    int index,
                                    char ch)
                             throws InvalidSmilesException

Throws:

InvalidSmilesException

getChar

private static char getChar(String pattern,
                            int i)

getDigits

private static int getDigits(String pattern,
                             int index,
                             int[] ret)

Parameters:

pattern -

index -

ret -

Returns:

pointer to the character AFTER the digits

skipTo

private static int skipTo(String pattern,
                          int index,
                          char ch0)

getRingPointer

static String getRingPointer(int i)

cleanPattern

static String cleanPattern(String pattern)

Parameters:

pattern -

Returns:

comments and white space removed, also ^^ to '