org.biojava.nbio.structure.asa

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.

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 Summary

Fields

Modifier and Type	Field and Description
static int	DEFAULT_N_SPHERE_POINTS The default value for number of sphere points to sample.
static int	DEFAULT_NTHREADS
static double	DEFAULT_PROBE_SIZE
static double	NUC_CARBON_VDW
static double	NUC_NITROGEN_VDW
static double	OXIGEN_VDW
static double	PHOSPHOROUS_VDW
static double	SULFUR_VDW
static double	TETRAHEDRAL_CARBON_VDW
static double	TETRAHEDRAL_NITROGEN_VDW
static double	TRIGONAL_CARBON_VDW
static double	TRIGONAL_NITROGEN_VDW

Constructor Summary

Constructors

Constructor and Description
AsaCalculator(Atom[] atoms, double probe, int nSpherePoints, int nThreads) Constructs a new AsaCalculator.
AsaCalculator(javax.vecmath.Point3d[] atomCoords, double probe, int nSpherePoints, int nThreads, double radius) Constructs a new AsaCalculator.
AsaCalculator(Structure structure, double probe, int nSpherePoints, int nThreads, boolean hetAtoms) Constructs a new AsaCalculator.

Method Summary

Modifier and Type	Method and Description
double[]	calculateAsas() Calculates the Accessible Surface Areas for the atoms given in constructor and with parameters given.
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.
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.

Methods inherited from class java.lang.Object

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

Field Detail

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:

Constant Field Values

DEFAULT_PROBE_SIZE

public static final double DEFAULT_PROBE_SIZE

See Also:

Constant Field Values

DEFAULT_NTHREADS

public static final int DEFAULT_NTHREADS

See Also:

Constant Field Values

TRIGONAL_CARBON_VDW

public static final double TRIGONAL_CARBON_VDW

See Also:

Constant Field Values

TETRAHEDRAL_CARBON_VDW

public static final double TETRAHEDRAL_CARBON_VDW

See Also:

Constant Field Values

TRIGONAL_NITROGEN_VDW

public static final double TRIGONAL_NITROGEN_VDW

See Also:

Constant Field Values

TETRAHEDRAL_NITROGEN_VDW

public static final double TETRAHEDRAL_NITROGEN_VDW

See Also:

Constant Field Values

SULFUR_VDW

public static final double SULFUR_VDW

See Also:

Constant Field Values

OXIGEN_VDW

public static final double OXIGEN_VDW

See Also:

Constant Field Values

NUC_CARBON_VDW

public static final double NUC_CARBON_VDW

See Also:

Constant Field Values

NUC_NITROGEN_VDW

public static final double NUC_NITROGEN_VDW

See Also:

Constant Field Values

PHOSPHOROUS_VDW

public static final double PHOSPHOROUS_VDW

See Also:

Constant Field Values

Constructor Detail

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

See Also:

StructureTools.getAllNonHAtomArray(org.biojava.nbio.structure.Structure, boolean)

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 Detail

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 Element().N is returned

Parameters:

atom -

Returns: