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org.xmlcml.noncml
Class SMILESAtom  

java.lang.Object
  org.xmlcml.noncml.SMILESAtom

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public class SMILESAtom

extends java.lang.Object

parse a SMILES atom [....]. Interprets leading characters of a String as a SMILES atom (used for parsing SMILES. Typical usage:

s = "[13C@H3-2]NOS"
SMILESAtom sa = new SMILESAtom(s);
String rest = s.substring(sa.getLength());
int isotope = sa.getIsotope();
String element = sa.getElementType();
String chiral = sa.getChiral();
int hCount = sa.getHydrogenCount();
int ch = sa.getFormalCharge()

At present SMARTS is not supported

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Field Summary
protected  boolean	aromatic
protected  java.lang.String	chiral
protected  java.lang.String	elementType
protected  int	formalCharge
protected  int	hydrogenCount
protected  int	isotope
protected  int	len
static java.lang.String	UNKNOWN_ELEMENT
static java.lang.String	UNMATCHED_BRACKET
static java.lang.String	UNPARSABLE_ATOM

 

Constructor Summary

SMILESAtom(java.lang.String s)

 

Method Summary
boolean	getAromatic()
java.lang.String	getChiral()
java.lang.String	getElementType()
int	getFormalCharge()
int	getHydrogenCount()
int	getIsotope()
int	getLength()
static void	main(java.lang.String[] args)
java.lang.String	toString()           Convert this Object to a human-readable String.

 

Methods inherited from class java.lang.Object

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

 

Field Detail

UNMATCHED_BRACKET

public static final java.lang.String UNMATCHED_BRACKET

See Also:

Constant Field Values

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UNKNOWN_ELEMENT

public static final java.lang.String UNKNOWN_ELEMENT

See Also:

Constant Field Values

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UNPARSABLE_ATOM

public static final java.lang.String UNPARSABLE_ATOM

See Also:

Constant Field Values

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aromatic

protected boolean aromatic

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len

protected int len

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elementType

protected java.lang.String elementType

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isotope

protected int isotope

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chiral

protected java.lang.String chiral

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hydrogenCount

protected int hydrogenCount

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formalCharge

protected int formalCharge

Constructor Detail

SMILESAtom

public SMILESAtom(java.lang.String s)
           throws org.xmlcml.cml.CMLException

Method Detail

getLength

public int getLength()

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getElementType

public java.lang.String getElementType()

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getIsotope

public int getIsotope()

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getChiral

public java.lang.String getChiral()

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getHydrogenCount

public int getHydrogenCount()

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getFormalCharge

public int getFormalCharge()

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getAromatic

public boolean getAromatic()

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toString

public java.lang.String toString()

Description copied from class: java.lang.Object

Convert this Object to a human-readable String. There are no limits placed on how long this String should be or what it should contain. We suggest you make it as intuitive as possible to be able to place it into System.out.println() 55 and such.

It is typical, but not required, to ensure that this method never completes abruptly with a java.lang.RuntimeException.

This method will be called when performing string concatenation with this object. If the result is null, string concatenation will instead use "null".

The default implementation returns getClass().getName() + "@" + Integer.toHexString(hashCode()).

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main

public static void main(java.lang.String[] args)
                 throws java.lang.Exception

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