Package com.actelion.research.chem.io

Class AbstractParser

java.lang.Object

com.actelion.research.chem.io.AbstractParser

Direct Known Subclasses:

Mol2FileParser

public abstract class AbstractParser
extends java.lang.Object

A parser is used to load and save molecules from the filesystem. The save procedure is optional

Author:

freyssj

Field Summary

Fields

Modifier and Type	Field	Description
protected java.util.List<java.lang.String>	errors
protected static java.lang.String	NEWLINE
protected boolean	optimize3D

Constructor Summary

Constructors

Constructor	Description
AbstractParser()

Method Summary

Modifier and Type	Method	Description
static void	convertDataToPrimitiveTypes(java.util.List<Molecule3D> res)
java.util.List<java.lang.String>	getErrors()
protected static boolean	is3D(Molecule3D m)
boolean	isOptimize3D()
Molecule3D	load(java.io.File file)
Molecule3D	load(java.lang.String fileName)
Molecule3D	load(java.lang.String fileName, java.io.Reader in)
java.util.List<Molecule3D>	loadGroup(java.lang.String fileName)
java.util.List<Molecule3D>	loadGroup(java.lang.String fileName, java.io.Reader in)
abstract java.util.List<Molecule3D>	loadGroup(java.lang.String fileName, java.io.Reader in, int from, int to)
void	save(Molecule3D mol, java.io.Writer writer)
void	save(Molecule3D mol, java.lang.String fileName)
void	save(java.util.List<Molecule3D> mols, java.io.Writer writer)	If not subclassed, save the files separately
void	save(java.util.List<Molecule3D> mol, java.lang.String fileName)
void	setOptimize3D(boolean optimize3d)
protected static void	writeL(java.io.Writer writer, java.lang.String data, int len)
protected static void	writeR(java.io.Writer writer, java.lang.String data, int len)

Methods inherited from class java.lang.Object

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

Field Detail

NEWLINE

protected static final java.lang.String NEWLINE

errors

protected java.util.List<java.lang.String> errors

optimize3D

protected boolean optimize3D

Constructor Detail

AbstractParser

public AbstractParser()

Method Detail

loadGroup

public final java.util.List<Molecule3D> loadGroup(java.lang.String fileName)
                                           throws java.lang.Exception

Parameters:

fileName -

Throws:

java.lang.Exception

loadGroup

public java.util.List<Molecule3D> loadGroup(java.lang.String fileName,
                                            java.io.Reader in)
                                     throws java.lang.Exception

Throws:

java.lang.Exception

loadGroup

public abstract java.util.List<Molecule3D> loadGroup(java.lang.String fileName,
                                                     java.io.Reader in,
                                                     int from,
                                                     int to)
                                              throws java.lang.Exception

Throws:

java.lang.Exception

load

public final Molecule3D load(java.io.File file)
                      throws java.lang.Exception

Parameters:

file -

Throws:

java.lang.Exception

load

public final Molecule3D load(java.lang.String fileName)
                      throws java.lang.Exception

Parameters:

fileName -

Throws:

java.lang.Exception

load

public final Molecule3D load(java.lang.String fileName,
                             java.io.Reader in)
                      throws java.lang.Exception

Parameters:

fileName -

in -

Throws:

java.lang.Exception

save

public final void save(java.util.List<Molecule3D> mol,
                       java.lang.String fileName)
                throws java.lang.Exception

Parameters:

mol -

fileName -

Throws:

java.lang.Exception

save

public final void save(Molecule3D mol,
                       java.lang.String fileName)
                throws java.lang.Exception

Parameters:

mol -

fileName -

Throws:

java.lang.Exception

save

public void save(Molecule3D mol,
                 java.io.Writer writer)
          throws java.lang.Exception

Parameters:

mol -

writer -

Throws:

java.lang.Exception

save

public void save(java.util.List<Molecule3D> mols,
                 java.io.Writer writer)
          throws java.lang.Exception

If not subclassed, save the files separately

Parameters:

mols -

writer -

Throws:

java.lang.Exception

convertDataToPrimitiveTypes

public static final void convertDataToPrimitiveTypes(java.util.List<Molecule3D> res)

writeR

protected static void writeR(java.io.Writer writer,
                             java.lang.String data,
                             int len)
                      throws java.io.IOException

Throws:

java.io.IOException

writeL

protected static void writeL(java.io.Writer writer,
                             java.lang.String data,
                             int len)
                      throws java.io.IOException

Throws:

java.io.IOException

getErrors

public java.util.List<java.lang.String> getErrors()

is3D

protected static boolean is3D(Molecule3D m)

setOptimize3D

public void setOptimize3D(boolean optimize3d)

isOptimize3D

public boolean isOptimize3D()