net.guha.util.cdk
Class Misc

java.lang.Object
  net.guha.util.cdk.Misc

public class Misc
extends java.lang.Object

Miscellaneous utility methods.

Author:

Rajarshi Guha

Field Summary

static java.lang.String

VERSION Version of this library.

Constructor Summary

Misc()

Method Summary

static org.openscience.cdk.interfaces.IMolecule	get2DCoords(org.openscience.cdk.interfaces.IAtomContainer mol) Get a molecule with 2D coordinates.
static org.openscience.cdk.interfaces.IAtomContainer	getNeedle(org.openscience.cdk.interfaces.IAtomContainer target, java.lang.String pattern) Get the substructure of a target structure based on a SMARTS pattern.
static org.openscience.cdk.interfaces.IAtomContainer[]	loadMolecules(java.lang.String[] filenames) Loads one or more files into IAtomContainer objects.
static void	writeMolecules(org.openscience.cdk.interfaces.IAtomContainer[] molecules, java.lang.String prefix, int writeProps) Write molecules to individual files.
static void	writeMoleculesInOneFile(org.openscience.cdk.interfaces.IAtomContainer[] molecules, java.lang.String filename, int writeProps) Write multiple molecules to a single SD file.

Methods inherited from class java.lang.Object

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

Field Detail

VERSION

public static final java.lang.String VERSION

Version of this library.

See Also:

Constant Field Values

Constructor Detail

Misc

public Misc()

Method Detail

writeMoleculesInOneFile

public static void writeMoleculesInOneFile(org.openscience.cdk.interfaces.IAtomContainer[] molecules,
                                           java.lang.String filename,
                                           int writeProps)
                                    throws java.lang.Exception

Write multiple molecules to a single SD file.

Parameters:

molecules - An array of molecules

filename - The filename to write to

writeProps - If true, properties will be added as SD tags

Throws:

java.lang.Exception - if there is an error during writing

writeMolecules

public static void writeMolecules(org.openscience.cdk.interfaces.IAtomContainer[] molecules,
                                  java.lang.String prefix,
                                  int writeProps)
                           throws java.lang.Exception

Write molecules to individual files.

Parameters:

molecules - An array of molecules

prefix - The prefix for the individual files. By default this will be mol

writeProps - If true properties will be written as SD tags

Throws:

java.lang.Exception - if there is an error during writing

loadMolecules

public static org.openscience.cdk.interfaces.IAtomContainer[] loadMolecules(java.lang.String[] filenames)
                                                                     throws org.openscience.cdk.exception.CDKException

Loads one or more files into IAtomContainer objects.

This method does not need knowledge of the format since it is autodetected.

NOTE It does not perform aromaticity detection

Parameters:

filenames - An array of String's containing the filenames of the structures we want to load

Returns:

An array of AtoContainer's

Throws:

org.openscience.cdk.exception.CDKException - if there is an error when reading a file

get2DCoords

public static org.openscience.cdk.interfaces.IMolecule get2DCoords(org.openscience.cdk.interfaces.IAtomContainer mol)
                                                            throws java.lang.Exception

Get a molecule with 2D coordinates.

Parameters:

mol - the input molecule

Returns:

a new molecule with 2D coordinates

Throws:

java.lang.Exception - if there was an error generating coordinates

getNeedle

public static org.openscience.cdk.interfaces.IAtomContainer getNeedle(org.openscience.cdk.interfaces.IAtomContainer target,
                                                                      java.lang.String pattern)
                                                               throws org.openscience.cdk.exception.CDKException

Get the substructure of a target structure based on a SMARTS pattern.

Parameters:

target - The target molecule

pattern - The SMARTS pattern for the substructure. The string can be a plain SMARTS or a Base64 encoded string

Returns:

A fragment representing the fragmentif present, null otherwise

Throws:

org.openscience.cdk.exception.CDKException - if there is an error during SMARTS parsing or matching