File size: 7,203 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 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 | #include "prGrid.h"
ProbGrid::ProbGrid(const Surface &surface, const float inDelta, const float maxRadius):
MoleculeGrid(surface, inDelta, maxRadius)
{
probs.insert(probs.end(), maxEntry, 0.0);
}
float ProbGrid::getProb(const Vector3& point) const
{
int index = getIndexForPoint(point);
if (!isValidIndex(index))
return MAX_FLOAT;
return probs[index];
}
ResidueGrid::ResidueGrid(const Surface &surface, const float inDelta, const float maxRadius):
MoleculeGrid(surface, inDelta, maxRadius)
{
residues.insert(residues.end(), maxEntry, (int)0);
}
int ResidueGrid::getResidueEntry(const Vector3& point) const {
int index = getIndexForPoint(point);
if(!isValidIndex(index))
return 0;
return residues[index];
}
void ResidueGrid::printGrid(std::ofstream& file) const {
for(int i=0; i< (int)residues.size();i++) {
if(residues[i] < 0) {
Vector3 point = getPointForIndex(i);
Atom atom(point, 'A', i, residues[i], "PRB", 'X');
file << atom << std::endl;
}
}
}
// const std::vector<unsigned int>& AtomGrid::getAtoms(const Vector3 &point) const {
// const static std::vector<unsigned int> emptyVec;
// int index = getIndexForPoint(point);
// if(isValidIndex(index))
// return atoms[index];
// return emptyVec;
// }
// unsigned int AtomGrid::getAtomsNumber(const Vector3 &point) const {
// int index = getIndexForPoint(point);
// if(!isValidIndex(index))
// return 0;
// return atoms[index].size();
// }
AtomTypeGrid::AtomTypeGrid(const Surface &surface, const float inDelta, const float maxRadius):
MoleculeGrid(surface, inDelta, maxRadius), atomTypes(maxEntry) {}
SurfacePointGrid::SurfacePointGrid(const Surface &surface, const float inDelta, const float maxRadius):
MoleculeGrid(surface, inDelta, maxRadius)
{
spPointers.insert(spPointers.end(), maxEntry, (SurfacePoint*)NULL);
}
void SurfacePointGrid::computeDistAndPointers(const Surface &surface, bool precise) {
std::vector<long> layer1, layer2, *curr = &layer1, *next = &layer2, *tmp;
std::vector<const SurfacePoint*> sps1, sps2, *currSps = &sps1, *nextSps = &sps2, *tmpSps;
std::vector<int> gridLayer;
gridLayer.insert(gridLayer.end(),maxEntry,-1);
layer1.reserve(surface.size()*10);
layer2.reserve(surface.size()*10);
sps1.reserve(surface.size()*10);
sps2.reserve(surface.size()*10);
// mark zero in Grid for each surface point and insert indexes of voxels for first layer
int index;
for (Surface::const_iterator it = surface.begin(); it!= surface.end(); ++it) {
index = getIndexForPoint(it->position());
if (gridLayer[index] != 0) {
if (precise) sps1.push_back(&(*it));
layer1.push_back(index);
grid[index] = 0.0;
spPointers[index] = &(*it);
gridLayer[index] = 0;
}
}
// work on every layer to be computed
const SurfacePoint* p = NULL;
for (int layer = 0; layer < maxGridRadius; layer++) {
std::cerr << " In Layer " << layer << " out of " << maxGridRadius << " curr->size() " << curr->size() << std::endl;
// update voxels with current layer distance and insert indices for next layer
for (unsigned int i = 0; i < curr->size(); i++) {
int index = (*curr)[i];
for (int j = 0; j < 26; j++) {
int nIndex = index + neigbor[j];
if (isValidIndex(nIndex)) {
if (precise) {
p = (*currSps)[i];
if (setDistAndPointer(nIndex, p)) {
if (gridLayer[nIndex] < layer + 1) {
next->push_back(nIndex);
nextSps->push_back(p);
gridLayer[nIndex] = layer + 1;
}
}
} else {
float dist = grid[index] + neigborDist[j];
if ( dist <= 0 ) {
std::cerr << " dist = grid[index] + neigborDist[j] grid[nIndex] " << dist << " " << grid[index] << " " << neigborDist[j] << " j " << j << " nIndex " << nIndex << " grid[nIndex] " << grid[nIndex] << std::endl;
}
if (grid[nIndex] > dist) {
grid[nIndex] = dist;
spPointers[nIndex] = spPointers[index];
if (gridLayer[nIndex] < layer + 1) {
next->push_back(nIndex);
gridLayer[nIndex] = layer + 1;
}
}
}
}
}
}
curr->clear();
tmp = curr; curr = next; next = tmp;
if (precise) {
currSps->clear();
tmpSps = currSps; currSps = nextSps; nextSps = tmpSps;
}
}
}
VolumeGrid::VolumeGrid(const Surface &surface, const float inDelta, const float maxRadius):
MoleculeGrid(surface, inDelta, maxRadius)
{
volumeNormals.insert(volumeNormals.end(), maxEntry, Vector3());
volumeFunctions.insert(volumeFunctions.end(), maxEntry, 0);
}
void VolumeGrid::getVolumeFuncAndNormal(const Vector3 ¢er, float &volFunc, Vector3& volNormal) const {
int centerIndex = getIndexForPoint(center);
if (!isValidIndex(centerIndex)) {
std::cerr << "Error: Point out of grid" << std::endl;
exit(1);
}
volFunc = volumeFunctions[centerIndex];
volNormal = volumeNormals[centerIndex];
}
float VolumeGrid::getVolumeFunc(const Vector3 ¢er) const {
int centerIndex = getIndexForPoint(center);
if (!isValidIndex(centerIndex)) {
std::cerr << "Error: Point out of grid" << std::endl;
exit(1);
}
return volumeFunctions[centerIndex];
}
const Vector3& VolumeGrid::getVolumeNormal(const Vector3 ¢er) const {
int centerIndex = getIndexForPoint(center);
if (!isValidIndex(centerIndex)) {
std::cerr << "Error: Point out of grid" << std::endl;
exit(1);
}
return volumeNormals[centerIndex];
}
void VolumeGrid::computeVolumes(const float radius, const float maxRadius) {
for(unsigned int gridIndex=0; gridIndex < grid.size(); gridIndex++) {
if(fabs(grid[gridIndex]) <= maxRadius) {
float r = (radius > 1+fabs(grid[gridIndex])? radius : 1+fabs(grid[gridIndex]));
int intRadius = getIntGridRadius(r);
int radius2 = intRadius*intRadius;
int outsideNum = 0;
int insideNum = 0;
int xOut(0), yOut(0), zOut(0);
int i_bound,j_bound,k_bound;
i_bound = intRadius;
for (int i = -i_bound; i <= i_bound; i++ ) {
j_bound = (int)sqrt(radius2 - i*i);
for (int j = -j_bound; j <= j_bound; j++) {
k_bound = (int)sqrt(radius2 - i*i - j*j);
for (int k = -k_bound; k <= k_bound; k++) {
int index = gridIndex + i + xGridNum * j + xyGridNum * k;
if(isValidIndex(index) && grid[index] <= 0.0) {
insideNum++;
} else {
outsideNum++;
xOut+=i;
yOut+=j;
zOut+=k;
}
}
}
}
volumeFunctions[gridIndex] = ((float)insideNum) / (insideNum + outsideNum);
volumeNormals[gridIndex] = Vector3((float)xOut, (float)yOut, (float)zOut);
if(volumeNormals[gridIndex].norm() == 0) {
std::cerr << "Error in calculateVolumeNormFunc " << std::endl;
}
volumeNormals[gridIndex] = volumeNormals[gridIndex]/volumeNormals[gridIndex].norm();
}
}
}
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