File size: 2,793 Bytes
8efb4bd | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 | #include "SASurface.h"
SASurface::SASurface(ChemMolecule& molecule, float probeRadius, float d) :
molecule_(molecule), probeRadius_(probeRadius), density_(d), molIntersection_(&molecule_, probeRadius_)
{}
unsigned int SASurface::buildCapsSurface(Surface& surface) {
surface.reserve(int(molecule_.size() * density_)); //CHECK!!!
for(unsigned int i=0; i<molecule_.size(); i++) {
// create dot sphere for an atom
const float atomRadius = molecule_[i].getRadius();
DotSphere dotSphere(atomRadius, density_);
float pointArea = (4 * pi * atomRadius * atomRadius)/dotSphere.size();
for(DotSphere::iterator it=dotSphere.begin(); it!=dotSphere.end(); it++) {
// the sphere dots are around (0,0,0) so we have to move them
Vector3 dotCoord = *it + molecule_(i);
Vector3 normal = *it/(*it).norm();
Vector3 probeCenter = dotCoord + normal*probeRadius_;
if(!molIntersection_.isIntersecting(probeCenter, i)) {
surface.push_back(SurfacePoint(dotCoord, normal, pointArea, i , -1 , -1));
}
}
}
return surface.size();
}
float SASurface::computeASAForAtoms() {
float ASA = 0;
for(unsigned int i=0; i<molecule_.size(); i++) {
const float atomRadius = molecule_[i].getRadius();
// create dot sphere for an atom
DotSphere dotSphere(atomRadius, density_);
float pointArea = (4 * pi * atomRadius * atomRadius)/dotSphere.size();
float atomASA = 0;
for(DotSphere::iterator it=dotSphere.begin(); it!=dotSphere.end(); it++) {
// the sphere dots are around (0,0,0) so we have to move them
Vector3 dotCoord = *it + molecule_(i);
Vector3 normal = *it/(*it).norm();
Vector3 probeCenter = dotCoord + normal*probeRadius_;
if(!molIntersection_.isIntersecting(probeCenter, i)) {
atomASA += pointArea;
}
}
molecule_[i].setASA(atomASA);
ASA += atomASA;
}
return ASA;
}
// unsigned int SASurface::buildBeltsSurface(Surface& surface) {
// surface.reserve(int(molecule.size() * density)); //CHECK!!!
// for(unsigned int i=0; i<molecule.size(); i++) {
// for(unsigned int j=i+1; j<molecule.size(); j++) {
// if(molIntersection.isNeighbours(i, j)) {
// Torus torus(molecule(i), molecule(j), molecule[i].getRadius(), molecule[j].getRadius(), probeRadius, density);
// const Vector3& center = torus.getCenter();
// for(Torus::iterator it=torus.begin(); it!=torus.end(); it++) {
// Vector3 normal = (*it-center)/(*it-center).norm();
// Vector3 probeCenter = *it + normal*probeRadius;
// if(!molIntersection.isIntersecting(probeCenter, i, j)) {
// surface.push_back(SurfacePoint(*it, normal, 1.0 , i , j , -1));
// }
// }
// }
// }
// }
// return surface.size();
// }
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