org.openscience.cdk.structgen

Class SingleStructureRandomGenerator

java.lang.Object

org.openscience.cdk.structgen.SingleStructureRandomGenerator

public class SingleStructureRandomGenerator
extends Object

Randomly generates a single, connected, correctly bonded structure for a given molecular formula. To see it working run the graphical test org.openscience.cdk.test.SingleStructureRandomGeneratorTest and add more structures to the panel using the "More" button. In order to use this class, use MFAnalyser to get an AtomContainer from a molecular formula string.

Assign hydrogen counts to each heavy atom. The hydrogens should not be in the atom pool but should be assigned implicitly to the heavy atoms in order to reduce computational cost. Assign this AtomContainer to the SingleStructureRandomGenerator and retrieve a randomly generated, but correctly bonded structure by using the generate() method. You can then repeatedly call the generate() method in order to retrieve further structures.

Agenda:

• add a method for randomly adding hydrogens to the atoms
• add a seed for random generator for reproducability

Author:

steinbeck

Source code:

master

Belongs to CDK module:

structgen

Created on:

2001-09-04

Constructor Summary

Constructors

Constructor and Description
SingleStructureRandomGenerator() Constructor for the SingleStructureRandomGenerator object.
SingleStructureRandomGenerator(long seed) Constructor for the SingleStructureRandomGenerator object.

Method Summary

Modifier and Type	Method and Description
IAtomContainer	generate() Generates a random structure based on the atoms in the given IAtomContainer.
void	setAtomContainer(IAtomContainer ac) Sets the AtomContainer attribute of the SingleStructureRandomGenerator object.

Methods inherited from class java.lang.Object

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

Constructor Detail

SingleStructureRandomGenerator

public SingleStructureRandomGenerator(long seed)
                               throws Exception

Constructor for the SingleStructureRandomGenerator object.

Throws:

Exception

SingleStructureRandomGenerator

public SingleStructureRandomGenerator()
                               throws Exception

Constructor for the SingleStructureRandomGenerator object.

Throws:

Exception

Method Detail

setAtomContainer

public void setAtomContainer(IAtomContainer ac)

Sets the AtomContainer attribute of the SingleStructureRandomGenerator object.

Parameters:

ac - The new AtomContainer value

generate

public IAtomContainer generate()
                        throws CDKException

Generates a random structure based on the atoms in the given IAtomContainer.

Throws:

CDKException