/**
* 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!
*
* <p>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
*
* @param atom
* @return
*/
public static double getRadius(Atom atom) {
if (atom.getElement() == null) {
System.err.println(
"Warning: unrecognised atom "
+ atom.getName()
+ " with serial "
+ atom.getPDBserial()
+ ", assigning the default vdw radius (Nitrogen vdw radius).");
return Element.N.getVDWRadius();
}
Group res = atom.getGroup();
if (res == null) {
System.err.println(
"Warning: unknown parent residue for atom "
+ atom.getName()
+ " with serial "
+ atom.getPDBserial()
+ ", assigning its default vdw radius");
return atom.getElement().getVDWRadius();
}
String type = res.getType();
if (type.equals(GroupType.AMINOACID)) return getRadiusForAmino(((AminoAcid) res), atom);
if (type.equals(GroupType.NUCLEOTIDE)) return getRadiusForNucl((NucleotideImpl) res, atom);
return atom.getElement().getVDWRadius();
}
/**
* Constructs a new AsaCalculator. Subsequently call {@link #calculateAsas()} or {@link
* #getGroupAsas()} to calculate the ASAs.
*
* @param atoms an array of atoms not containing Hydrogen atoms
* @param probe the probe size
* @param nSpherePoints the number of points to be used in generating the spherical dot-density,
* the more points the more accurate (and slower) calculation
* @param nThreads the number of parallel threads to use for the calculation
* @throws IllegalArgumentException if any atom in the array is a Hydrogen atom
*/
public AsaCalculator(Atom[] atoms, double probe, int nSpherePoints, int nThreads) {
this.atoms = atoms;
this.probe = probe;
this.nThreads = nThreads;
for (Atom atom : atoms) {
if (atom.getElement() == Element.H)
throw new IllegalArgumentException(
"Can't calculate ASA for an array that contains Hydrogen atoms ");
}
// initialising the radii by looking them up through AtomRadii
radii = new double[atoms.length];
for (int i = 0; i < atoms.length; i++) {
radii[i] = getRadius(atoms[i]);
}
// initialising the sphere points to sample
spherePoints = generateSpherePoints(nSpherePoints);
cons = 4.0 * Math.PI / (double) nSpherePoints;
}
/**
* Gets the radius for given nucleotide atom
*
* @param atom
* @return
*/
private static double getRadiusForNucl(NucleotideImpl nuc, Atom atom) {
if (atom.getElement().equals(Element.H)) return Element.H.getVDWRadius();
if (atom.getElement().equals(Element.D)) return Element.D.getVDWRadius();
if (atom.getElement() == Element.C) return NUC_CARBON_VDW;
if (atom.getElement() == Element.N) return NUC_NITROGEN_VDW;
if (atom.getElement() == Element.P) return PHOSPHOROUS_VDW;
if (atom.getElement() == Element.O) return OXIGEN_VDW;
System.err.println(
"Warning: unexpected atom "
+ atom.getName()
+ " for nucleotide "
+ nuc.getPDBName()
+ ", assigning its standard vdw radius");
return atom.getElement().getVDWRadius();
}
private double calcSingleAsa(int i) {
Atom atom_i = atoms[i];
ArrayList<Integer> neighbor_indices = findNeighborIndices(i);
int n_neighbor = neighbor_indices.size();
int j_closest_neighbor = 0;
double radius = probe + radii[i];
int n_accessible_point = 0;
for (Point3d point : spherePoints) {
boolean is_accessible = true;
Point3d test_point =
new Point3d(
point.x * radius + atom_i.getX(),
point.y * radius + atom_i.getY(),
point.z * radius + atom_i.getZ());
int[] cycled_indices = new int[n_neighbor];
int arind = 0;
for (int ind = j_closest_neighbor; ind < n_neighbor; ind++) {
cycled_indices[arind] = ind;
arind++;
}
for (int ind = 0; ind < j_closest_neighbor; ind++) {
cycled_indices[arind] = ind;
arind++;
}
for (int j : cycled_indices) {
Atom atom_j = atoms[neighbor_indices.get(j)];
double r = radii[neighbor_indices.get(j)] + probe;
double diff_sq = test_point.distanceSquared(new Point3d(atom_j.getCoords()));
if (diff_sq < r * r) {
j_closest_neighbor = j;
is_accessible = false;
break;
}
}
if (is_accessible) {
n_accessible_point++;
}
}
return cons * n_accessible_point * radius * radius;
}
/**
* Gets the radius for given amino acid and atom
*
* @param aa
* @param atom
* @return
*/
private static double getRadiusForAmino(AminoAcid amino, Atom atom) {
if (atom.getElement().equals(Element.H)) return Element.H.getVDWRadius();
// some unusual entries (e.g. 1tes) contain Deuterium atoms in standard aminoacids
if (atom.getElement().equals(Element.D)) return Element.D.getVDWRadius();
String atomCode = atom.getName();
char aa = amino.getAminoType();
// here we use the values that Chothia gives in his paper (as NACCESS does)
if (atom.getElement() == Element.O) {
return OXIGEN_VDW;
} else if (atom.getElement() == Element.S) {
return SULFUR_VDW;
} else if (atom.getElement() == Element.N) {
if (atomCode.equals("NZ")) return TETRAHEDRAL_NITROGEN_VDW; // tetrahedral Nitrogen
return TRIGONAL_NITROGEN_VDW; // trigonal Nitrogen
} else if (atom.getElement() == Element.C) { // it must be a carbon
if (atomCode.equals("C")
|| atomCode.equals("CE1")
|| atomCode.equals("CE2")
|| atomCode.equals("CE3")
|| atomCode.equals("CH2")
|| atomCode.equals("CZ")
|| atomCode.equals("CZ2")
|| atomCode.equals("CZ3")) {
return TRIGONAL_CARBON_VDW; // trigonal Carbon
} else if (atomCode.equals("CA")
|| atomCode.equals("CB")
|| atomCode.equals("CE")
|| atomCode.equals("CG1")
|| atomCode.equals("CG2")) {
return TETRAHEDRAL_CARBON_VDW; // tetrahedral Carbon
}
// the rest of the cases (CD, CD1, CD2, CG) depend on amino acid
else {
switch (aa) {
case 'F':
case 'W':
case 'Y':
case 'H':
case 'D':
case 'N':
return TRIGONAL_CARBON_VDW;
case 'P':
case 'K':
case 'R':
case 'M':
case 'I':
case 'L':
return TETRAHEDRAL_CARBON_VDW;
case 'Q':
case 'E':
if (atomCode.equals("CD")) return TRIGONAL_CARBON_VDW;
else if (atomCode.equals("CG")) return TETRAHEDRAL_CARBON_VDW;
default:
System.err.println(
"Warning: unexpected carbon atom "
+ atomCode
+ " for aminoacid "
+ aa
+ ", assigning its standard vdw radius");
return Element.C.getVDWRadius();
}
}
// not any of the expected atoms
} else {
System.err.println(
"Warning: unexpected atom "
+ atomCode
+ " for aminoacid "
+ aa
+ ", assigning its standard vdw radius");
return atom.getElement().getVDWRadius();
}
}