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joelib.molecule
Class JOEMolVector  

java.lang.Object
  joelib.molecule.JOEMolVector

All Implemented Interfaces:

java.io.Serializable

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public class JOEMolVector

extends java.lang.Object

implements java.io.Serializable

Molecule vector to load single and multiple molecule files.

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Field Summary
(package private)  java.util.Vector	_molvec           java.util.Vector of JOEMol
private static int	DEFAULT_SIZE
private static org.apache.log4j.Category	logger

 

Constructor Summary

JOEMolVector()           Creates an empty molecule vector.

JOEMolVector(java.io.InputStream ifs)           Constructor for the JOEMolVector object

JOEMolVector(java.io.InputStream ifs, int nToRead)           Constructor for the JOEMolVector object

JOEMolVector(java.io.InputStream ifs, joelib.io.IOType in_type, joelib.io.IOType out_type)           Constructor for the JOEMolVector object

JOEMolVector(java.io.InputStream ifs, joelib.io.IOType in_type, joelib.io.IOType out_type, int nToRead)           Constructor for the JOEMolVector object

 

Method Summary
void	addMol(JOEMol mol)           Add molecule to this molecule vector.
void	finalize()           Functions for dealing with groups of molecules.
JOEMol	getMol(int i)           Get a specific molecule from a OEMolVector.
int	getSize()           Gets the size attribute of the JOEMolVector object
java.util.Vector	getVector()
void	read(java.io.InputStream ifs, joelib.io.IOType in_type, joelib.io.IOType out_type, int nToRead)           Read all molecules from a file into a Vector of JOEMol.
java.lang.Object	setMol(int i, JOEMol mol)           Sets the molecule at position i of this molecule vector.
void	write(java.io.OutputStream ofs)           Write a OEMolVector to a file.
void	write(java.io.OutputStream ofs, joelib.io.IOType type)           Write a OEMolVector to a file.

 

Methods inherited from class java.lang.Object

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

 

Field Detail

logger

private static org.apache.log4j.Category logger

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DEFAULT_SIZE

private static final int DEFAULT_SIZE

See Also:

Constant Field Values

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_molvec

java.util.Vector _molvec

java.util.Vector of JOEMol

Constructor Detail

JOEMolVector

public JOEMolVector()

Creates an empty molecule vector.

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JOEMolVector

public JOEMolVector(java.io.InputStream ifs)
             throws java.io.IOException

Constructor for the JOEMolVector object

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JOEMolVector

public JOEMolVector(java.io.InputStream ifs,
                    int nToRead)
             throws java.io.IOException

Constructor for the JOEMolVector object

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JOEMolVector

public JOEMolVector(java.io.InputStream ifs,
                    joelib.io.IOType in_type,
                    joelib.io.IOType out_type)
             throws java.io.IOException

Constructor for the JOEMolVector object

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JOEMolVector

public JOEMolVector(java.io.InputStream ifs,
                    joelib.io.IOType in_type,
                    joelib.io.IOType out_type,
                    int nToRead)
             throws java.io.IOException,
                    joelib.io.MoleculeIOException

Constructor for the JOEMolVector object

Method Detail

setMol

public java.lang.Object setMol(int i,
                               JOEMol mol)

Sets the molecule at position i of this molecule vector.

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getMol

public JOEMol getMol(int i)

Get a specific molecule from a OEMolVector. Index starts at zero.

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getSize

public int getSize()

Gets the size attribute of the JOEMolVector object

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getVector

public java.util.Vector getVector()

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addMol

public void addMol(JOEMol mol)

Add molecule to this molecule vector.

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finalize

public void finalize()

Functions for dealing with groups of molecules. MolVec will read either all molecules from a file or a set of conformers.

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read

public void read(java.io.InputStream ifs,
                 joelib.io.IOType in_type,
                 joelib.io.IOType out_type,
                 int nToRead)
          throws java.io.IOException

Read all molecules from a file into a Vector of JOEMol. Input and output types default to SDF.

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write

public void write(java.io.OutputStream ofs)
           throws java.io.IOException,
                  joelib.io.MoleculeIOException

Write a OEMolVector to a file. Output type defaults to SDF.

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write

public void write(java.io.OutputStream ofs,
                  joelib.io.IOType type)
           throws java.io.IOException,
                  joelib.io.MoleculeIOException

Write a OEMolVector to a file. Output type defaults to SDF.

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Home >> All >> joelib >> [ molecule overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

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