java.lang.Object

org.jmol.smiles.SmilesParser

public class SmilesParser extends Object

Parses a SMILES string or SMARTS pattern to create a SmilesSearch. Currently this parser supports only parts of the SMILES specification.
An example on how to use it:


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

Field Summary

Fields

Modifier and Type

Field

Description

private char

bioType

private boolean

bondDirectionPaired

private int

braceCount

private int

branchLevel

private int

componentCount

private int

componentParenCount

private Map<Integer,SmilesBond>

connections

private int

flags

private Map<String,SmilesMeasure>

htMeasures

private boolean

ignoreStereochemistry

private boolean

isBioSequence

private boolean

isSmarts

private boolean

isTarget
Constructor Summary

Constructors

Constructor

Description

SmilesParser(boolean isSmarts, boolean isTarget)
Method Summary

Modifier and Type

Method

Description

private int

checkBioType(String pattern, int index)

private boolean

checkBrace(SmilesSearch search, char ch, char type)

private int

checkCharge(String pattern, int index, SmilesAtom newAtom)

private boolean

checkLogic(SmilesSearch search, String pattern, SmilesAtom atom, SmilesBond bond, SmilesAtom currentAtom, boolean isAND, boolean isBranchAtom, int[] ret)

private void

checkNested(SmilesSearch search, SmilesAtom atom, int flags)

(package private) static String

cleanPattern(String pattern)

(package private) static String

extractFlags(String pattern, int[] ret)

private void

fixChirality(SmilesSearch search)

(package private) static char

getChar(String pattern, int i)

(package private) static int

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

(package private) static int

getFlags(String pattern)

(package private) static int

getRingNumber(String pattern, int index, char ch, int[] ret)

(package private) static String

getSubPattern(String pattern, int index, char ch)

(package private) SmilesSearch

getSubsearch(SmilesSearch parent, String pattern, int flags)

(package private) static SmilesSearch

newSearch(String pattern, boolean isSmarts, boolean isTarget)

(package private) SmilesSearch

parse(String pattern)

Parses a SMILES String

private SmilesAtom

parseAtom(SmilesSearch search, SmilesAtom atomSet, String pattern, SmilesAtom atom, SmilesBond bond, boolean isBracketed, boolean isAND, boolean isBranchAtom)

Parses an atom definition

private SmilesBond

parseBond(SmilesSearch search, SmilesBond bondSet, String pattern, SmilesBond bond, SmilesAtom currentAtom, boolean isAND, boolean isBranchAtom, int len, int[] ret)

private void

parseConnection(SmilesSearch search, int ringNum, SmilesAtom currentAtom, SmilesBond bond)

Parses a ring definition

private void

parseMeasure(SmilesSearch search, String strMeasure, SmilesAtom currentAtom)

private String

parseNested(SmilesSearch search, String pattern, String prefix)

private void

parseSmiles(SmilesSearch search, String pattern, SmilesAtom currentAtom, boolean isBranchAtom)

Parses a part of a SMILES String

private String

parseVariableLength(String pattern)

private String

parseVariables(String pattern)

variables can be defined, as in select within(SMARTS,'$R1="[CH3, NH2]";$R2="[$([$R1]),OH]"; {a}[$R2]') select within(SMARTS,'$R1="[CH3,NH2]";$R2="[OH]"; {a}[$([$R1]),$([$R2])]') "select aromatic atoms bearing CH3, NH2, or OH"

private void

setBondAtom(SmilesBond bond, SmilesAtom a1, SmilesAtom a2, SmilesSearch search)

set the bond and look for a=a, setting AROMATIC_DOUBLE automatically if found

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 Details
- connections
  
  private Map<Integer,SmilesBond> connections
- htMeasures
  
  private Map<String,SmilesMeasure> htMeasures
- flags
  
  private int flags
- isSmarts
  
  private boolean isSmarts
- isBioSequence
  
  private boolean isBioSequence
- bioType
  
  private char bioType
- braceCount
  
  private int braceCount
- branchLevel
  
  private int branchLevel
- componentCount
  
  private int componentCount
- componentParenCount
  
  private int componentParenCount
- ignoreStereochemistry
  
  private boolean ignoreStereochemistry
- bondDirectionPaired
  
  private boolean bondDirectionPaired
- isTarget
  
  private boolean isTarget
Constructor Details
- SmilesParser
  
  SmilesParser(boolean isSmarts, boolean isTarget)
Method Details
- newSearch
  
  static SmilesSearch newSearch(String pattern, boolean isSmarts, boolean isTarget) throws InvalidSmilesException
  
  Throws:
  
  InvalidSmilesException
- parse
  
  SmilesSearch parse(String pattern) throws InvalidSmilesException
  
  Parses a SMILES String
  
  Parameters:
  
  pattern - SMILES String
  
  Returns:
  
  Molecule corresponding pattern
  
  Throws:
  
  InvalidSmilesException
- parseVariableLength
  
  private String parseVariableLength(String pattern) throws InvalidSmilesException
  
  Throws:
  
  InvalidSmilesException
- getSubsearch
  
  SmilesSearch getSubsearch(SmilesSearch parent, String pattern, int flags) throws InvalidSmilesException
  
  Throws:
  
  InvalidSmilesException
- checkNested
  
  private void checkNested(SmilesSearch search, SmilesAtom atom, int flags) throws InvalidSmilesException
  
  Throws:
  
  InvalidSmilesException
- fixChirality
  
  private void fixChirality(SmilesSearch search) throws InvalidSmilesException
  
  Throws:
  
  InvalidSmilesException
- parseSmiles
  
  private void parseSmiles(SmilesSearch search, String pattern, SmilesAtom currentAtom, boolean isBranchAtom) throws InvalidSmilesException
  
  Parses a part of a SMILES String
  
  Parameters:
  
  search - SmilesSearch being built
  
  pattern - SMILES String
  
  currentAtom - Current atom
  
  isBranchAtom - If we are starting a new branch
  
  Throws:
  
  InvalidSmilesException
- parseConnection
  
  private void parseConnection(SmilesSearch search, int ringNum, SmilesAtom currentAtom, SmilesBond bond) throws InvalidSmilesException
  
  Parses a ring definition
  
  Parameters:
  
  search - Resulting molecule
  
  ringNum -
  
  currentAtom - Current atom
  
  bond -
  
  Throws:
  
  InvalidSmilesException
- setBondAtom
  
  private void setBondAtom(SmilesBond bond, SmilesAtom a1, SmilesAtom a2, SmilesSearch search)
  
  set the bond and look for a=a, setting AROMATIC_DOUBLE automatically if found
  
  Parameters:
  
  bond -
  
  a1 -
  
  a2 -
  
  search -
- getRingNumber
  
  static int getRingNumber(String pattern, int index, char ch, int[] ret) throws InvalidSmilesException
  
  Throws:
  
  InvalidSmilesException
- checkBioType
  
  private int checkBioType(String pattern, int index)
- parseMeasure
  
  private void parseMeasure(SmilesSearch search, String strMeasure, SmilesAtom currentAtom) throws InvalidSmilesException
  
  Throws:
  
  InvalidSmilesException
- checkBrace
  
  private boolean checkBrace(SmilesSearch search, char ch, char type) throws InvalidSmilesException
  
  Throws:
  
  InvalidSmilesException
- parseNested
  
  private String parseNested(SmilesSearch search, String pattern, String prefix) throws InvalidSmilesException
  
  Throws:
  
  InvalidSmilesException
- parseVariables
  
  private String parseVariables(String pattern) throws InvalidSmilesException
  
  variables can be defined, as in select within(SMARTS,'$R1="[CH3, NH2]";$R2="[$([$R1]),OH]"; {a}[$R2]') select within(SMARTS,'$R1="[CH3,NH2]";$R2="[OH]"; {a}[$([$R1]),$([$R2])]') "select aromatic atoms bearing CH3, NH2, or OH"
  
  Parameters:
  
  pattern -
  
  Returns:
  
  substituted pattern
  
  Throws:
  
  InvalidSmilesException
- parseAtom
  
  private SmilesAtom parseAtom(SmilesSearch search, SmilesAtom atomSet, String pattern, SmilesAtom atom, SmilesBond bond, boolean isBracketed, boolean isAND, boolean isBranchAtom) throws InvalidSmilesException
  
  Parses an atom definition
  
  Parameters:
  
  search - current search
  
  atomSet - upper-level SmilesAtom if from checkLogic
  
  pattern - SMILES or SMARTS String
  
  atom - parent atom or null
  
  bond - null or parent bond
  
  isBracketed - true if a bracketed definition [...]
  
  isAND - being called from checkLogic for & or ;
  
  isBranchAtom -
  
  Returns:
  
  New atom
  
  Throws:
  
  InvalidSmilesException
- checkCharge
  
  private int checkCharge(String pattern, int index, SmilesAtom newAtom) throws InvalidSmilesException
  
  Throws:
  
  InvalidSmilesException
- parseBond
  
  private SmilesBond parseBond(SmilesSearch search, SmilesBond bondSet, String pattern, SmilesBond bond, SmilesAtom currentAtom, boolean isAND, boolean isBranchAtom, int len, int[] ret) throws InvalidSmilesException
  
  Throws:
  
  InvalidSmilesException
- checkLogic
  
  private boolean checkLogic(SmilesSearch search, String pattern, SmilesAtom atom, SmilesBond bond, SmilesAtom currentAtom, boolean isAND, boolean isBranchAtom, int[] ret) throws InvalidSmilesException
  
  Parameters:
  
  search -
  
  pattern -
  
  atom -
  
  bond -
  
  currentAtom -
  
  isAND -
  
  isBranchAtom -
  
  ret -
  
  Returns:
  
  true if we are done
  
  Throws:
  
  InvalidSmilesException
- getSubPattern
  
  static String getSubPattern(String pattern, int index, char ch) throws InvalidSmilesException
  
  Throws:
  
  InvalidSmilesException
- getChar
  
  static char getChar(String pattern, int i)
- getDigits
  
  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)
- cleanPattern
  
  static String cleanPattern(String pattern)
  
  Parameters:
  
  pattern -
  
  Returns:
  
  comments and white space removed, also ^^ to '
- extractFlags
  
  static String extractFlags(String pattern, int[] ret) throws InvalidSmilesException
  
  Throws:
  
  InvalidSmilesException
- getFlags
  
  static int getFlags(String pattern) throws InvalidSmilesException
  
  Throws:
  
  InvalidSmilesException

Class SmilesParser

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Details

connections

htMeasures

flags

isSmarts

isBioSequence

bioType

braceCount

branchLevel

componentCount

componentParenCount

ignoreStereochemistry

bondDirectionPaired

isTarget

Constructor Details

SmilesParser

Method Details

newSearch

parse

parseVariableLength

getSubsearch

checkNested

fixChirality

parseSmiles

parseConnection

setBondAtom

getRingNumber

checkBioType

parseMeasure

checkBrace

parseNested

parseVariables

parseAtom

checkCharge

parseBond

checkLogic

getSubPattern

getChar

getDigits

skipTo

cleanPattern

extractFlags

getFlags