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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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 | #ifndef PR_GRID_H
#define PR_GRID_H
#include <MoleculeGrid.h>
#include <Atom.h>
#include <vector>
class ProbGrid : public MoleculeGrid {
public:
ProbGrid(const Surface &surface, const float inDelta, const float maxRadius);
template<class MoleculeT>
void markProbs(const MoleculeT &M);
float getProb(const Vector3 &point) const;
private:
std::vector< float > probs;
};
class VolumeGrid : public MoleculeGrid {
public:
VolumeGrid(const Surface &surface, const float inDelta, const float maxRadius);
void computeVolumes(const float radius, const float maxRadius);
void getVolumeFuncAndNormal(const Vector3 ¢er, float &volFunc, Vector3& volNormal) const;
float getVolumeFunc(const Vector3 ¢er) const;
const Vector3& getVolumeNormal(const Vector3 ¢er) const;
private:
std::vector< Vector3 > volumeNormals;
std::vector< float > volumeFunctions;
};
class ResidueGrid : public MoleculeGrid {
public:
ResidueGrid(const Surface &surface, const float inDelta, const float maxRadius);
template<class MoleculeT>
void markResidues(const MoleculeT &M);
int getResidueEntry(const Vector3 &point) const;
void printGrid(std::ofstream& file) const;
protected:
std::vector< int > residues;
};
class AtomsGrid : public MoleculeGrid {
public:
AtomsGrid(const Surface &surface, const float inDelta, const float maxRadius);
template<class MoleculeT>
void markAtoms(const MoleculeT &M, float radius);
const std::vector<unsigned int>& getAtoms(const Vector3 &point) const;
unsigned int getAtomsNumber(const Vector3 &point) const;
private:
std::vector<std::vector<unsigned int > > atoms;
};
// stores closest atom number for every grid point
class AtomGrid : public MoleculeGrid {
public:
AtomGrid(const Surface &surface, const float inDelta, const float maxRadius):
MoleculeGrid(surface, inDelta, maxRadius), atoms_(maxEntry) {}
template<class MoleculeT>
void markAtoms(const MoleculeT &mol, std::vector<float>& radii);
// get volume corresponding to each atom
template<class MoleculeT>
void getVolume(const MoleculeT &mol, std::vector<float>& volume);
unsigned int getAtom(const Vector3 &point) const;
private:
std::vector<unsigned int> atoms_;
};
class AtomTypeGrid : public MoleculeGrid {
public:
AtomTypeGrid(const Surface &surface, const float inDelta, const float maxRadius);
template<class MoleculeT>
void markAtomTypes(const MoleculeT &M);
unsigned int getAtomType(const Vector3 &point) const {
int index = getIndexForPoint(point);
if(!isValidIndex(index))
return 0;
return atomTypes[index];
}
private:
std::vector<unsigned int > atomTypes;
};
class SurfacePointGrid : public MoleculeGrid {
public:
SurfacePointGrid(const Surface &surface, const float inDelta, const float maxRadius);
void computeDistAndPointers(const Surface &surface, bool precise = false);
const SurfacePoint* getSpPointer(const Vector3& point) const {
int index = getIndexForPoint(point);
if (!isValidIndex(index))
return NULL;
return spPointers[index];
}
bool getDistAndSpPointer(const Vector3& point, float& distance, SurfacePoint* spPoint) const {
int index = getIndexForPoint(point);
if (!isValidIndex(index))
return false;
distance=grid[index];
spPoint = (SurfacePoint *)spPointers[index];
return true;
}
float getExactDist2(const Vector3& point) const {
int index = getIndexForPoint(point);
if(!isValidIndex(index) || spPointers[index]==NULL)
return MAX_FLOAT*MAX_FLOAT;
return point.dist2(spPointers[index]->position());
}
float getExactDist(const Vector3& point) const {
int index = getIndexForPoint(point);
if(!isValidIndex(index))
return MAX_FLOAT;
if(spPointers[index]==NULL)
return grid[index];
if(grid[index] < 0)
return -(point.dist(spPointers[index]->position()));
else
return point.dist(spPointers[index]->position());
}
protected:
// sets distance func. falue for index to be the distance from p.
// and p to be the closest point
bool setDistAndPointer(int index, const SurfacePoint* p) {
float d = getPointForIndex(index).dist(p->position());
if (d >= grid[index]) return false;
grid[index] = d;
spPointers[index] = p;
return true;
}
private:
std::vector<const SurfacePoint*> spPointers;
};
template<class MoleculeT>
void ProbGrid::markProbs(const MoleculeT &M) {
std::vector<float> weights;
weights.insert(weights.end(), maxEntry, 0.0);
for(typename MoleculeT::const_iterator it=M.begin(); it!=M.end(); it++) {
float atomRadius = it->getAtomRadius();
float radius = atomRadius*2; //may be +1 is enough
int centerIndex = getIndexForPoint(it->position());
if (!isValidIndex(centerIndex)) {
std::cerr << "Error: Point out of grid" << std::endl;
exit(1);
}
int intRadius = getIntGridRadius(radius);
int radius2 = intRadius*intRadius;
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 = centerIndex + i + xGridNum * j + xyGridNum * k;
if(isValidIndex(index) && grid[index] <= 0) {
Vector3 point = getPointForIndex(index);
float dist = point.dist(it->position());
if(dist == 0.0) {
probs[index]=it->getSteadyProb();
continue; }
float weight = atomRadius/dist;
if(weight <= weights[index])
continue;
weights[index]=weight;
probs[index]=it->getSteadyProb();
}
}
}
}
}
weights.clear();
}
template<class MoleculeT>
void ResidueGrid::markResidues(const MoleculeT &M) {
std::vector<float> weights;
weights.insert(weights.end(), maxEntry, 0.0);
for(typename MoleculeT::const_iterator it=M.begin(); it!=M.end(); it++) {
float atomRadius = it->getRadius();
float radius = atomRadius*2; //may be +1 is enough
int centerIndex = getIndexForPoint(it->position());
if (!isValidIndex(centerIndex)) {
std::cerr << "Error: Point out of grid" << std::endl;
exit(1);
}
int intRadius = getIntGridRadius(radius);
int radius2 = intRadius*intRadius;
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 = centerIndex + i + xGridNum * j + xyGridNum * k;
if(isValidIndex(index) && grid[index] <= 0) {
Vector3 point = getPointForIndex(index);
float dist = point.dist(it->position());
if(dist == 0.0) {
if(it->isBackbone())
residues[index] = M.residueEntry(it->chainId(), it->residueSequenceID()) * -1;
else
residues[index] = M.residueEntry(it->chainId(), it->residueSequenceID());
continue;
}
float weight = atomRadius/dist;
if(weight <= weights[index])
continue;
weights[index] = weight;
if(it->isBackbone())
residues[index] = M.residueEntry(it->chainId(), it->residueSequenceID()) * -1;
else
residues[index] = M.residueEntry(it->chainId(), it->residueSequenceID());
}
}
}
}
}
weights.clear();
}
template<class MoleculeT>
void AtomsGrid::markAtoms(const MoleculeT &M, float radius) {
int atomIndex=0;
int intRadius = getIntGridRadius(radius);
int radius2 = intRadius*intRadius;
for(typename MoleculeT::const_iterator it=M.begin(); it!=M.end(); it++, atomIndex++) {
int centerIndex = getIndexForPoint(it->position());
if (!isValidIndex(centerIndex)) {
std::cerr << "Error: Point out of grid" << std::endl;
exit(1);
}
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 = centerIndex + i + xGridNum * j + xyGridNum * k;
if(isValidIndex(index)) {
atoms[index].push_back(atomIndex);
}
}
}
}
}
}
template<class MoleculeT>
void AtomGrid::markAtoms(const MoleculeT &mol, std::vector<float>& radii) {
std::vector<float> weights;
weights.insert(weights.end(), maxEntry, 0.0);
int atomIndex=0;
for(typename MoleculeT::const_iterator it=mol.begin(); it!=mol.end(); it++, atomIndex++) {
int centerIndex = getIndexForPoint(it->position());
if (!isValidIndex(centerIndex)) {
std::cerr << "Error: Point out of grid" << std::endl;
exit(1);
}
float atomRadius = radii[atomIndex];
float radius = atomRadius*2; //may be +1 is enough
int intRadius = getIntGridRadius(radius);
int radius2 = intRadius*intRadius;
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 = centerIndex + i + xGridNum * j + xyGridNum * k;
if(isValidIndex(index)) {
Vector3 point = getPointForIndex(index);
float dist = point.dist(it->position());
if(dist == 0.0) {
atoms_[index] = atomIndex;
continue;
}
float weight = radius/dist;
if(weight <= weights[index]) continue;
weights[index] = weight;
atoms_[index] = atomIndex;
}
}
}
}
}
weights.clear();
}
template<class MoleculeT>
void AtomGrid::getVolume(const MoleculeT &mol, std::vector<float>& volume) {
std::vector<int> fullCube(mol.size(), 0), halfCube(mol.size(), 0);
for(int i=0; i< (int)grid.size();i++) {
if(grid[i] < 0)
fullCube[atoms_[i]]++;
if(grid[i] == 0)
halfCube[atoms_[i]]++;
}
float cubeVolume = delta*delta*delta;
float halfVolume = cubeVolume/2;
volume.resize(mol.size(), 0.0);
for(unsigned int i=0; i<mol.size(); i++) {
volume[i] = cubeVolume * fullCube[i] + halfVolume * halfCube[i];
}
}
template<class MoleculeT>
void AtomTypeGrid::markAtomTypes(const MoleculeT &M) {
std::vector<float> weights;
weights.insert(weights.end(), maxEntry, 0.0);
int atomIndex=0;
for(typename MoleculeT::const_iterator it=M.begin(); it!=M.end(); it++, atomIndex++) {
float atomRadius = it->getRadius();
float radius = atomRadius*2; //may be +1 is enough
int centerIndex = getIndexForPoint(it->position());
if (!isValidIndex(centerIndex)) {
std::cerr << "Error: Point out of grid" << std::endl;
exit(1);
}
int intRadius = getIntGridRadius(radius);
int radius2 = intRadius*intRadius;
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 = centerIndex + i + xGridNum * j + xyGridNum * k;
if(isValidIndex(index)) {
Vector3 point = getPointForIndex(index);
float dist = point.dist(it->position());
if(dist == 0.0) {
atomTypes[index] = it->getChemType();
continue;
}
float weight = atomRadius/dist;
if(weight <= weights[index])
continue;
weights[index] = weight;
atomTypes[index] = it->getChemType();
}
}
}
}
}
weights.clear();
}
#endif
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