com.chemaxon.calculations.io

Class MoleculeIo

java.lang.Object

com.chemaxon.calculations.io.MoleculeIo

@PublicAPI
 @Beta
public final class MoleculeIo
extends Object

Utility class with Molecule IO related functions.

Please note that this class is marked with @Beta annotation, so it can be subject of incompatible changes or removal in later releases.

Method Summary

Modifier and Type	Method and Description
static Function<Molecule,String>	molExporterToSmilesFunction() Convert a Molecule to SMILES.
static Function<String,Molecule>	molImporterFromSourceFunction() Import a String source into a Molecule.
static Molecule	molImporterImport(String source) Import Molecule from source String.
static CloseableIterator<Molecule>	molImporterIterateMolecules(InputStream is) A Closeable Iterator view of a MolImporter.
static SmilesMemoizingMoleculeIterator	molImporterMemoizingIterator(CloseableIterator<Molecule> base, Consumer<Exception> errorHandler) Create a SmilesMemoizingMoleculeIterator over a CloseableIterator of Molecules.

Methods inherited from class java.lang.Object

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

Method Detail

molExporterToSmilesFunction

public static Function<Molecule,String> molExporterToSmilesFunction()

Convert a Molecule to SMILES. Delegate MolExporter.exportToFormat(chemaxon.struc.Molecule, java.lang.String) with options smiles:n to preserve name. Please note that the current implementation contains limitations of the representable structures. For example only a set of atoms (see 3.4.2 Aromaticity from http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html) can be part of an aromatic ring.

The implementation throws IllegalArgumentException when SMILES conversion failed.

Returns:

Converter Function

molImporterFromSourceFunction

public static Function<String,Molecule> molImporterFromSourceFunction()

Import a String source into a Molecule.

Returns:

Importer Function

molImporterImport

public static Molecule molImporterImport(String source)

Import Molecule from source String.

Parameters:

source - Source

Returns:

Imported Molecule

Throws:

IllegalArgumentException - when MolImporter.importMol(java.lang.String) failed

molImporterIterateMolecules

public static CloseableIterator<Molecule> molImporterIterateMolecules(InputStream is)
                                                               throws IOException

A Closeable Iterator view of a MolImporter.

Parameters:

is - Delegated to MolImporter.MolImporter(java.io.InputStream)

Returns:

Iterator

Throws:

IOException - propagated from MolImporter.MolImporter(java.io.InputStream)

molImporterMemoizingIterator

public static SmilesMemoizingMoleculeIterator molImporterMemoizingIterator(CloseableIterator<Molecule> base,
                                                                           Consumer<Exception> errorHandler)

Create a SmilesMemoizingMoleculeIterator over a CloseableIterator of Molecules.

Parameters:

base - Base CloseableIterator

errorHandler - Error handler to pass to SmilesMemoizingMoleculeIterator#SmilesMemoizingMoleculeIterator(com.chemaxon.calculations.io.CloseableIterator, com.google.common.base.Function, com.chemaxon.calculations.io.Sink) Errors are expected during the execution of SMILES conversion of iterated structures for memoization

Returns:

Constructed instance