Package 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:
Source code:
main
Belongs to CDK module:
standard
Keywords:
HOSE code, spherical atom search
Created on:
2002-05-10

  • Field Details

    • sphereNodes

      protected List<org.openscience.cdk.tools.HOSECodeGenerator.TreeNode> sphereNodes
      Container for the nodes in a sphere.

    • sphere

      protected int sphere
      Counter for the sphere in which we currently work.

    • 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.

    • HOSECode

      protected StringBuffer HOSECode
      The HOSECode string that we assemble

    • atomContainer

      protected IAtomContainer atomContainer
      The molecular structure on which we work

    • bondSymbols

      protected String[] bondSymbols
      The bond symbols used for bond orders "single", "double", "triple" and "aromatic"

    • centerCode

      protected String centerCode

    • LEGACY_MODE

      public static final int LEGACY_MODE
      Ignored parent ordering be considered when sorting spheres (legacy mode) for compatibility with existing ML/AI models.
      See Also:

  • Constructor Details

    • HOSECodeGenerator

      public HOSECodeGenerator(int flags)
      Constructor for the HOSECodeGenerator.

      Important!

      A critical bug was discovered in the implementation (see PR 828) which gave the wrong nesting in "some" cases. Fixing this behaviour invalidates any ML/AI models trained on the incorrect values. If you have a model built with the old algorithm that can not be retrained set legacyMode=true.
      Parameters:
      flags - (default: false)
      See Also:

    • HOSECodeGenerator

      public HOSECodeGenerator()
      Constructor for the HOSECodeGenerator.

      Important!

      A critical bug was discovered in the implementation (see PR 828) which gave the wrong nesting in "some" cases. Fixing this behaviour invalidates any ML/AI models trained on the incorrect values. If you have a model built with the old algorithm that can not be retrained set .
      See Also:

  • Method Details

    • 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)