Class AsaCalculator

java.lang.Object
org.biojava.nbio.structure.asa.AsaCalculator

public class AsaCalculator extends Object
Class to calculate Accessible Surface Areas based on the rolling ball algorithm by Shrake and Rupley.

The code is adapted from a python implementation at http://boscoh.com/protein/asapy (now source is available at https://github.com/boscoh/asa). Thanks to Bosco K. Ho for a great piece of code and for his fantastic blog.

A few optimizations come from Eisenhaber et al, J Comp Chemistry 1994 (https://onlinelibrary.wiley.com/doi/epdf/10.1002/jcc.540160303)

See Shrake, A., and J. A. Rupley. "Environment and Exposure to Solvent of Protein Atoms. Lysozyme and Insulin." JMB (1973) 79:351-371. Lee, B., and Richards, F.M. "The interpretation of Protein Structures: Estimation of Static Accessibility" JMB (1971) 55:379-400

Author:
Jose Duarte
  • Field Details

    • DEFAULT_N_SPHERE_POINTS

      public static final int DEFAULT_N_SPHERE_POINTS
      The default value for number of sphere points to sample. See this paper for a nice study on the effect of this parameter: https://f1000research.com/articles/5-189/v1
      See Also:
    • DEFAULT_PROBE_SIZE

      public static final double DEFAULT_PROBE_SIZE
      See Also:
    • DEFAULT_NTHREADS

      public static final int DEFAULT_NTHREADS
      See Also:
    • TRIGONAL_CARBON_VDW

      public static final double TRIGONAL_CARBON_VDW
      See Also:
    • TETRAHEDRAL_CARBON_VDW

      public static final double TETRAHEDRAL_CARBON_VDW
      See Also:
    • TRIGONAL_NITROGEN_VDW

      public static final double TRIGONAL_NITROGEN_VDW
      See Also:
    • TETRAHEDRAL_NITROGEN_VDW

      public static final double TETRAHEDRAL_NITROGEN_VDW
      See Also:
    • SULFUR_VDW

      public static final double SULFUR_VDW
      See Also:
    • OXIGEN_VDW

      public static final double OXIGEN_VDW
      See Also:
    • NUC_CARBON_VDW

      public static final double NUC_CARBON_VDW
      See Also:
    • NUC_NITROGEN_VDW

      public static final double NUC_NITROGEN_VDW
      See Also:
    • PHOSPHOROUS_VDW

      public static final double PHOSPHOROUS_VDW
      See Also:
  • Constructor Details

    • AsaCalculator

      public AsaCalculator(Structure structure, double probe, int nSpherePoints, int nThreads, boolean hetAtoms)
      Constructs a new AsaCalculator. Subsequently call calculateAsas() or getGroupAsas() to calculate the ASAs Only non-Hydrogen atoms are considered in the calculation.
      Parameters:
      structure - the structure, all non-H atoms will be used
      probe - the probe size
      nSpherePoints - the number of points to be used in generating the spherical dot-density, the more points the more accurate (and slower) calculation
      nThreads - the number of parallel threads to use for the calculation
      hetAtoms - if true HET residues are considered, if false they aren't, equivalent to NACCESS' -h option
    • AsaCalculator

      public AsaCalculator(Atom[] atoms, double probe, int nSpherePoints, int nThreads)
      Constructs a new AsaCalculator. Subsequently call calculateAsas() or getGroupAsas() to calculate the ASAs.
      Parameters:
      atoms - an array of atoms not containing Hydrogen atoms
      probe - the probe size
      nSpherePoints - the number of points to be used in generating the spherical dot-density, the more points the more accurate (and slower) calculation
      nThreads - the number of parallel threads to use for the calculation
      Throws:
      IllegalArgumentException - if any atom in the array is a Hydrogen atom
    • AsaCalculator

      public AsaCalculator(javax.vecmath.Point3d[] atomCoords, double probe, int nSpherePoints, int nThreads, double radius)
      Constructs a new AsaCalculator. Subsequently call calcSingleAsa(int) to calculate the atom ASAs. The given radius parameter will be taken as the radius for all points given. No ASA calculation per group will be possible with this constructor, so usage of getGroupAsas() will result in a NullPointerException.
      Parameters:
      atomCoords - the coordinates representing the center of atoms
      probe - the probe size
      nSpherePoints - the number of points to be used in generating the spherical dot-density, the more points the more accurate (and slower) calculation
      nThreads - the number of parallel threads to use for the calculation
      radius - the radius that will be assign to all given coordinates
  • Method Details

    • getGroupAsas

      public GroupAsa[] getGroupAsas()
      Calculates ASA for all atoms and return them as a GroupAsa array (one element per residue in structure) containing ASAs per residue and per atom. The sorting of Groups in returned array is as specified by ResidueNumber
      Returns:
    • calculateAsas

      public double[] calculateAsas()
      Calculates the Accessible Surface Areas for the atoms given in constructor and with parameters given. Beware that the parallel implementation is quite memory hungry. It scales well as long as there is enough memory available.
      Returns:
      an array with asa values corresponding to each atom of the input array
    • getRadius

      public static double getRadius(Atom atom)
      Gets the van der Waals radius of the given atom following the values defined by Chothia (1976) J.Mol.Biol.105,1-14 NOTE: the vdw values defined by the paper assume no Hydrogens and thus "inflates" slightly the heavy atoms to account for Hydrogens. Thus this method cannot be used in a structure that contains Hydrogens! If atom is neither part of a nucleotide nor of a standard aminoacid, the default vdw radius for the element is returned. If atom is of unknown type (element) the vdw radius of {@link Element().N} is returned
      Parameters:
      atom -
      Returns: