Package com.actelion.research.chem.io
Class AbstractParser
- java.lang.Object
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- com.actelion.research.chem.io.AbstractParser
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- 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
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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
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Constructor Summary
Constructors Constructor Description AbstractParser()
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Method Summary
All Methods Static Methods Instance Methods Abstract Methods Concrete Methods 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 separatelyvoid
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)
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Method Detail
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loadGroup
public final java.util.List<Molecule3D> loadGroup(java.lang.String fileName) throws java.lang.Exception
- Parameters:
fileName
-- Throws:
java.lang.Exception
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loadGroup
public java.util.List<Molecule3D> loadGroup(java.lang.String fileName, java.io.Reader in) throws java.lang.Exception
- Throws:
java.lang.Exception
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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
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load
public final Molecule3D load(java.io.File file) throws java.lang.Exception
- Parameters:
file
-- Throws:
java.lang.Exception
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load
public final Molecule3D load(java.lang.String fileName) throws java.lang.Exception
- Parameters:
fileName
-- Throws:
java.lang.Exception
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load
public final Molecule3D load(java.lang.String fileName, java.io.Reader in) throws java.lang.Exception
- Parameters:
fileName
-in
-- Throws:
java.lang.Exception
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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
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save
public final void save(Molecule3D mol, java.lang.String fileName) throws java.lang.Exception
- Parameters:
mol
-fileName
-- Throws:
java.lang.Exception
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save
public void save(Molecule3D mol, java.io.Writer writer) throws java.lang.Exception
- Parameters:
mol
-writer
-- Throws:
java.lang.Exception
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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
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convertDataToPrimitiveTypes
public static final void convertDataToPrimitiveTypes(java.util.List<Molecule3D> res)
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writeR
protected static void writeR(java.io.Writer writer, java.lang.String data, int len) throws java.io.IOException
- Throws:
java.io.IOException
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writeL
protected static void writeL(java.io.Writer writer, java.lang.String data, int len) throws java.io.IOException
- Throws:
java.io.IOException
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getErrors
public java.util.List<java.lang.String> getErrors()
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is3D
protected static boolean is3D(Molecule3D m)
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setOptimize3D
public void setOptimize3D(boolean optimize3d)
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isOptimize3D
public boolean isOptimize3D()
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