Package org.openscience.cdk.geometry.surface

Class NumericalSurface

  • public class NumericalSurface
extends Object
    A class representing the solvent accessible surface area surface of a molecule.

    This class is based on the Python implementation of the DCLM method ([Eisenhaber, F. et. al.. Journal of Computational Chemistry. 1995. 16]) by Peter McCluskey, which is a non-analytical method to generate a set of points representing the solvent accessible surface area of a molecule.

    The neighbor list is a simplified version of that described in [Eisenhaber, F. et. al.. Journal of Computational Chemistry. 1995. 16] and as a result, the surface areas of the atoms may not be exact (compared to analytical calculations). The tessellation is slightly different from that described by McCluskey and uses recursive subdivision starting from an icosahedral representation.

    The default solvent radius used is 1.4A and setting this to 0 will give the Van der Waals surface. The accuracy can be increased by increasing the tessellation level, though the default of 4 is a good balance between accuracy and speed.

    Author:
    Rajarshi Guha
    This class is affected by these bug(s):
    1846421
    Source code:
    main
    Belongs to CDK module:
    qsarmolecular
    Created on:
    2005-05-08

    • Constructor Detail

      • NumericalSurface

        public NumericalSurface​(IAtomContainer atomContainer)
        Constructor to initialize the surface calculation with default values. This constructor use the Van der Waals radii as defined in org/openscience/cdk/config/data/jmol_atomtypes.txt of the source distribution. Also uses a tesselation level of 4 and solvent radius of 1.4A.
        Parameters:
        atomContainer - The IAtomContainer for which the surface is to be calculated

      • NumericalSurface

        public NumericalSurface​(IAtomContainer atomContainer,
                        double solventRadius,
                        int tesslevel)
        Constructor to initialize the surface calculation with user specified values. This constructor use the Van der Waals radii as defined in org/openscience/cdk/config/data/jmol_atomtypes.txt of the source distribution
        Parameters:
        atomContainer - The IAtomContainer for which the surface is to be calculated
        solventRadius - The radius of a solvent molecule that is used to extend the radius of each atom. Setting to 0 gives the Van der Waals surface
        tesslevel - The number of levels that the subdivision algorithm for tessellation should use

    • Method Detail

      • calculateSurface

        @Deprecated
public void calculateSurface()
        Deprecated.
        Evaluate the surface. This method generates the points on the accessible surface area of each atom as well as calculating the surface area of each atom.

      • getAllSurfacePoints

        public javax.vecmath.Point3d[] getAllSurfacePoints()
        Get an array of all the points on the molecular surface. This returns an array of Point3d objects representing all the points on the molecular surface
        Returns:
        An array of Point3d objects

      • getAtomSurfaceMap

        public Map<IAtom,​List<javax.vecmath.Point3d>> getAtomSurfaceMap()
        Get the map from atom to surface points. If an atom does not appear in the map it is buried. Atoms may share surface points with other atoms.
        Returns:
        surface atoms and associated points on the surface

      • getSurfacePoints

        public javax.vecmath.Point3d[] getSurfacePoints​(int atomIdx)
                                         throws CDKException
        Get an array of the points on the accessible surface of a specific atom.
        Parameters:
        atomIdx - The index of the atom. Ranges from 0 to n-1, where n is the number of atoms in the AtomContainer that the surface was calculated for
        Returns:
        An array of Point3d objects
        Throws:
        CDKException - if the atom index is outside the range of allowable indices

      • getSurfaceArea

        public double getSurfaceArea​(int atomIdx)
                      throws CDKException
        Get the surface area for the specified atom.
        Parameters:
        atomIdx - The index of the atom. Ranges from 0 to n-1, where n is the number of atoms in the AtomContainer that the surface was calculated for
        Returns:
        A double representing the accessible surface area of the atom
        Throws:
        CDKException - if the atom index is outside the range of allowable indices

      • getAllSurfaceAreas

        public double[] getAllSurfaceAreas()
        Get an array containing the accessible surface area for each atom.
        Returns:
        An array of double giving the surface areas of all the atoms

      • getTotalSurfaceArea

        public double getTotalSurfaceArea()
        Get the total surface area for the AtomContainer.
        Returns:
        A double containing the total surface area of the AtomContainer for which the surface was calculated for