org.openscience.cdk.tools

Class HOSECodeGenerator

java.lang.Object

org.openscience.cdk.tools.HOSECodeGenerator

All Implemented Interfaces:

Serializable

public class HOSECodeGenerator
extends Object
implements Serializable

Generates HOSE codes (Bremser, W.. Analytica Chimica Acta. 1978. 103). IMPORTANT: Your molecule must contain implicit or explicit hydrogens for this method to work properly.

Author:

steinbeck

See Also:

Serialized Form

Source code:

master

Belongs to CDK module:

standard

Keywords:

HOSE code, spherical atom search

Created on:

2002-05-10

Field Summary

Fields

Modifier and Type	Field and Description
protected IAtomContainer	atomContainer The molecular structure on which we work
protected String[]	bondSymbols The bond symbols used for bond orders "single", "double", "triple" and "aromatic"
protected String	centerCode
protected StringBuffer	HOSECode The HOSECode string that we assemble
protected int	maxSphere How many spheres are we supposed inspect.
protected List<org.openscience.cdk.tools.HOSECodeGenerator.TreeNode>	nextSphereNodes Container for the node in the next sphere Assembled in a recursive method and then passed to the next recursion to become "sphereNodes".
org.openscience.cdk.tools.HOSECodeGenerator.TreeNode	rootNode
protected int	sphere Counter for the sphere in which we currently work.
protected String[]	sphereDelimiters Delimiters used to separate spheres in the output string.
protected List<org.openscience.cdk.tools.HOSECodeGenerator.TreeNode>	sphereNodes Container for the nodes in a sphere.
protected List<IAtom>	sphereNodesWithAtoms
protected List<org.openscience.cdk.tools.HOSECodeGenerator.TreeNode>[]	spheres Here we store the spheres that we assemble, in order to parse them into a code later.
protected List<IAtom>[]	spheresWithAtoms

Constructor Summary

Constructors

Constructor and Description
HOSECodeGenerator() Constructor for the HOSECodeGenerator.

Method Summary

Modifier and Type	Method and Description
String	getHOSECode(IAtomContainer ac, IAtom root, int noOfSpheres) Produces a HOSE code for Atom root in the IAtomContainer ac.
String	getHOSECode(IAtomContainer ac, IAtom root, int noOfSpheres, boolean ringsize) Produces a HOSE code for Atom root in the IAtomContainer ac.
List<IAtom>	getNodesInSphere(int sphereNumber)
List<IAtom>[]	getSpheres(IAtomContainer ac, IAtom root, int noOfSpheres, boolean ringsize) This method is intended to be used to get the atoms around an atom in spheres.
String	makeBremserCompliant(String code)

Methods inherited from class java.lang.Object

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

Field Detail

sphereNodes

protected List<org.openscience.cdk.tools.HOSECodeGenerator.TreeNode> sphereNodes

Container for the nodes in a sphere.

sphereNodesWithAtoms

protected List<IAtom> sphereNodesWithAtoms

nextSphereNodes

protected List<org.openscience.cdk.tools.HOSECodeGenerator.TreeNode> nextSphereNodes

Container for the node in the next sphere Assembled in a recursive method and then passed to the next recursion to become "sphereNodes".

sphere

protected int sphere

Counter for the sphere in which we currently work.

maxSphere

protected int maxSphere

How many spheres are we supposed inspect.

spheres

protected List<org.openscience.cdk.tools.HOSECodeGenerator.TreeNode>[] spheres

Here we store the spheres that we assemble, in order to parse them into a code later.

spheresWithAtoms

protected List<IAtom>[] spheresWithAtoms

HOSECode

protected StringBuffer HOSECode

The HOSECode string that we assemble

atomContainer

protected IAtomContainer atomContainer

The molecular structure on which we work

sphereDelimiters

protected String[] sphereDelimiters

Delimiters used to separate spheres in the output string. Bremser uses the sequence"(//)" for the first four spheres.

bondSymbols

protected String[] bondSymbols

The bond symbols used for bond orders "single", "double", "triple" and "aromatic"

centerCode

protected String centerCode

rootNode

public org.openscience.cdk.tools.HOSECodeGenerator.TreeNode rootNode

Constructor Detail

HOSECodeGenerator

public HOSECodeGenerator()

Constructor for the HOSECodeGenerator.

Method Detail

getSpheres

public List<IAtom>[] getSpheres(IAtomContainer ac,
                                IAtom root,
                                int noOfSpheres,
                                boolean ringsize)
                         throws CDKException

This method is intended to be used to get the atoms around an atom in spheres. It is not used in this class, but is provided for other classes to use. It also creates the HOSE code in HOSECode as a side-effect.

Parameters:

ac - The IAtomContainer with the molecular skeleton in which the root atom resides.

root - The root atom for which to produce the spheres.

noOfSpheres - The number of spheres to look at.

ringsize - Shall the center code have the ring size in it? Only use if you want to have the hose code later, else say false.

Returns:

An array of List. The list at i-1 contains the atoms at sphere i as TreeNodes.

Throws:

CDKException

getHOSECode

public String getHOSECode(IAtomContainer ac,
                          IAtom root,
                          int noOfSpheres)
                   throws CDKException

Produces a HOSE code for Atom root in the IAtomContainer ac. The HOSE code is produced for the number of spheres given by noOfSpheres. IMPORTANT: if you want aromaticity to be included in the code, you need to run the IAtomContainer ac to the CDKHueckelAromaticityDetector prior to using getHOSECode(). This method only gives proper results if the molecule is fully saturated (if not, the order of the HOSE code might depend on atoms in higher spheres). This method is known to fail for protons sometimes. IMPORTANT: Your molecule must contain implicit or explicit hydrogens for this method to work properly.

Parameters:

ac - The IAtomContainer with the molecular skeleton in which the root atom resides

root - The root atom for which to produce the HOSE code

noOfSpheres - The number of spheres to look at

Returns:

The HOSECode value

Throws:

CDKException - Thrown if something is wrong

getHOSECode

public String getHOSECode(IAtomContainer ac,
                          IAtom root,
                          int noOfSpheres,
                          boolean ringsize)
                   throws CDKException

Produces a HOSE code for Atom root in the IAtomContainer ac. The HOSE code is produced for the number of spheres given by noOfSpheres. IMPORTANT: if you want aromaticity to be included in the code, you need to run the IAtomContainer ac to the CDKHueckelAromaticityDetector prior to using getHOSECode(). This method only gives proper results if the molecule is fully saturated (if not, the order of the HOSE code might depend on atoms in higher spheres). This method is known to fail for protons sometimes. IMPORTANT: Your molecule must contain implicit or explicit hydrogens for this method to work properly.

Parameters:

ac - The IAtomContainer with the molecular skeleton in which the root atom resides

root - The root atom for which to produce the HOSE code

noOfSpheres - The number of spheres to look at

ringsize - The size of the ring(s) it is in is included in center atom code

Returns:

The HOSECode value

Throws:

CDKException - Thrown if something is wrong

makeBremserCompliant

public String makeBremserCompliant(String code)

getNodesInSphere

public List<IAtom> getNodesInSphere(int sphereNumber)