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java.lang.Objectorg.jmol.smiles.SmilesParser
public class SmilesParser
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
}
Field Summary | |
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private SmilesBond[] |
ringBonds
|
Constructor Summary | |
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SmilesParser()
Constructs a SmilesParser . |
Method Summary | |
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private SmilesAtom |
parseAtom(SmilesMolecule molecule,
java.lang.String smiles,
SmilesAtom currentAtom,
int bondType,
boolean complete)
Parses an atom definition |
private void |
parseRing(SmilesMolecule molecule,
java.lang.String smiles,
SmilesAtom currentAtom,
int bondType)
Parses a ring definition |
private void |
parseSmiles(SmilesMolecule molecule,
java.lang.String smiles,
SmilesAtom currentAtom)
Parses a part of a SMILES String |
SmilesMolecule |
parseSmiles(java.lang.String smiles)
Parses a SMILES String |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
---|
private SmilesBond[] ringBonds
Constructor Detail |
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public SmilesParser()
SmilesParser
.
Method Detail |
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public SmilesMolecule parseSmiles(java.lang.String smiles) throws InvalidSmilesException
smiles
- SMILES String
smiles
InvalidSmilesException
private void parseSmiles(SmilesMolecule molecule, java.lang.String smiles, SmilesAtom currentAtom) throws InvalidSmilesException
molecule
- Resulting moleculesmiles
- SMILES StringcurrentAtom
- Current atom
InvalidSmilesException
private SmilesAtom parseAtom(SmilesMolecule molecule, java.lang.String smiles, SmilesAtom currentAtom, int bondType, boolean complete) throws InvalidSmilesException
molecule
- Resulting moleculesmiles
- SMILES StringcurrentAtom
- Current atombondType
- Bond typecomplete
- Indicates if is a complete definition (between [])
InvalidSmilesException
private void parseRing(SmilesMolecule molecule, java.lang.String smiles, SmilesAtom currentAtom, int bondType) throws InvalidSmilesException
molecule
- Resulting moleculesmiles
- SMILES StringcurrentAtom
- Current atombondType
- Bond type
InvalidSmilesException
|
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