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39 #include <gromacs/trajectoryanalysis.h>
40 #include <gromacs/math/do_fit.h>
41 #include <gromacs/utility/smalloc.h>
42 #include "gromacs/selection/selection.h"
43 #include "gromacs/selection/selectionoption.h"
47 struct kernel_maxima {
50 std::vector< RVec > krnl;
53 long double Fx (long double x0, long double y0, long double z0, long double p1, long double p2, long double p3, std::vector< RVec > x) {
55 for (int i = 0; i < x.size(); i++) {
57 sqrt ( pow (p2 * (x[i][2] - z0) - p3 * (x[i][1] - y0), 2) +
58 pow (p3 * (x[i][0] - x0) - p1 * (x[i][2] - z0), 2) +
59 pow (p1 * (x[i][1] - y0) - p2 * (x[i][0] - x0), 2)) /
60 sqrt (p1 * p1 + p2 * p2 + p3 * p3);
65 long double fx0 (long double x0, long double y0, long double z0, long double p1, long double p2, long double p3, std::vector< RVec > x) {
67 for (int i = 0; i < x.size(); i++) {
69 (2 * p2 * (p2 * (x0 - x[i][0]) - p1 * (y0 - x[i][1])) + 2 * p3 * (p3 * (x0 - x[i][0]) - p1 * (z0 - x[i][2]))) /
70 (2 * sqrt ( pow (p2 * (x0 - x[i][0]) - p1 * (y0 - x[i][1]), 2) +
71 pow (p3 * (x0 - x[i][0]) - p1 * (z0 - x[i][2]), 2) +
72 pow (p3 * (y0 - x[i][1]) - p2 * (z0 - x[i][2]), 2)) *
73 sqrt (p1 * p1 + p2 * p2 + p3 * p3));
78 long double fy0 (long double x0, long double y0, long double z0, long double p1, long double p2, long double p3, std::vector< RVec > x) {
80 for (int i = 0; i < x.size(); i++) {
82 -(2 * p1 * (p2 * (x0 - x[i][0]) - p1 * (y0 - x[i][1])) - 2 * p3 * (p3 * (y0 - x[i][1]) - p2 * (z0 - x[i][2]))) /
83 (2 * sqrt ( pow (p2 * (x0 - x[i][0]) - p1 * (y0 - x[i][1]), 2) +
84 pow (p3 * (x0 - x[i][0]) - p1 * (z0 - x[i][2]), 2) +
85 pow (p3 * (y0 - x[i][1]) - p2 * (z0 - x[i][2]), 2)) *
86 sqrt (p1 * p1 + p2 * p2 + p3 * p3));
91 long double fz0 (long double x0, long double y0, long double z0, long double p1, long double p2, long double p3, std::vector< RVec > x) {
93 for (int i = 0; i < x.size(); i++) {
95 -(2 * p1 * (p3 * (x0 - x[i][0]) - p1 * (z0 - x[i][2])) + 2 * p2 * (p3 * (y0 - x[i][1]) - p2 * (z0 - x[i][2]))) /
96 (2 * sqrt ( pow (p2 * (x0 - x[i][0]) - p1 * (y0 - x[i][1]), 2) +
97 pow (p3 * (x0 - x[i][0]) - p1 * (z0 - x[i][2]), 2) +
98 pow (p3 * (y0 - x[i][1]) - p2 * (z0 - x[i][2]), 2)) *
99 sqrt (p1 * p1 + p2 * p2 + p3 * p3));
104 long double fp1 (long double x0, long double y0, long double z0, long double p1, long double p2, long double p3, std::vector< RVec > x) {
106 for (int i = 0; i < x.size(); i++) {
108 -(2 * (p2 * (x0 - x[i][0]) - p1 * (y0 - x[i][1])) * (y0 - x[i][1]) + 2 * (p3 * (x0 - x[i][0]) - p1 * (z0 - x[i][2])) * (z0 - x[i][2])) /
109 (2 * sqrt ( pow (p2 * (x0 - x[i][0]) - p1 * (y0 - x[i][1]), 2) +
110 pow (p3 * (x0 - x[i][0]) - p1 * (z0 - x[i][2]), 2) +
111 pow (p3 * (y0 - x[i][1]) - p2 * (z0 - x[i][2]), 2)) *
112 sqrt (p1 * p1 + p2 * p2 + p3 * p3)) -
113 (p1 * sqrt ( pow (p2 * (x0 - x[i][0]) - p1 * (y0 - x[i][1]), 2) +
114 pow (p3 * (x0 - x[i][0]) - p1 * (z0 - x[i][2]), 2) +
115 pow (p3 * (y0 - x[i][1]) - p2 * (z0 - x[i][2]), 2))) /
116 pow (p1 * p1 + p2 * p2 + p3 * p3, 1.5);
121 long double fp2 (long double x0, long double y0, long double z0, long double p1, long double p2, long double p3, std::vector< RVec > x) {
123 for (int i = 0; i < x.size(); i++) {
125 (2 * (p2 * (x0 - x[i][0]) - p1 * (y0 - x[i][1])) * (x0 - x[i][0]) - 2 * (p3 * (y0 - x[i][1]) - p2 * (z0 - x[i][2])) * (z0 - x[i][2])) /
126 (2 * sqrt ( pow (p2 * (x0 - x[i][0]) - p1 * (y0 - x[i][1]), 2) +
127 pow (p3 * (x0 - x[i][0]) - p1 * (z0 - x[i][2]), 2) +
128 pow (p3 * (y0 - x[i][1]) - p2 * (z0 - x[i][2]), 2)) *
129 sqrt (p1 * p1 + p2 * p2 + p3 * p3)) -
130 (p2 * sqrt ( pow (p2 * (x0 - x[i][0]) - p1 * (y0 - x[i][1]), 2) +
131 pow (p3 * (x0 - x[i][0]) - p1 * (z0 - x[i][2]), 2) +
132 pow (p3 * (y0 - x[i][1]) - p2 * (z0 - x[i][2]), 2))) /
133 pow (p1 * p1 + p2 * p2 + p3 * p3, 1.5);
138 long double fp3 (long double x0, long double y0, long double z0, long double p1, long double p2, long double p3, std::vector< RVec > x) {
140 for (int i = 0; i < x.size(); i++) {
142 (2 * (p3 * (x0 - x[i][0]) - p1 * (z0 - x[i][2])) * (x0 - x[i][0]) + 2 * (p3 * (y0 - x[i][1]) - p2 * (z0 - x[i][2])) * (y0 - x[i][1])) /
143 (2 * sqrt ( pow (p2 * (x0 - x[i][0]) - p1 * (y0 - x[i][1]), 2) +
144 pow (p3 * (x0 - x[i][0]) - p1 * (z0 - x[i][2]), 2) +
145 pow (p3 * (y0 - x[i][1]) - p2 * (z0 - x[i][2]), 2)) *
146 sqrt (p1 * p1 + p2 * p2 + p3 * p3)) -
147 (p3 * sqrt ( pow (p2 * (x0 - x[i][0]) - p1 * (y0 - x[i][1]), 2) +
148 pow (p3 * (x0 - x[i][0]) - p1 * (z0 - x[i][2]), 2) +
149 pow (p3 * (y0 - x[i][1]) - p2 * (z0 - x[i][2]), 2))) /
150 pow (p1 * p1 + p2 * p2 + p3 * p3, 1.5);
155 void linear_kernel_search (long double &x0, long double &y0, long double &z0, long double &p1, long double &p2, long double &p3, std::vector< RVec > x, long double epsi) {
156 long double FX = 0, FX0 = 0, FY0 = 0, FZ0 = 0, FP1 = 0, FP2 = 0, FP3 = 0;
157 long double L1, L2, L3, L4, L5, L6;
160 FX = Fx(x0, y0, z0, p1, p2, p3, x);
161 FX0 = fx0(x0, y0, z0, p1, p2, p3, x);
162 FY0 = fy0(x0, y0, z0, p1, p2, p3, x);
163 FZ0 = fz0(x0, y0, z0, p1, p2, p3, x);
164 FP1 = fp1(x0, y0, z0, p1, p2, p3, x);
165 FP2 = fp2(x0, y0, z0, p1, p2, p3, x);
166 FP3 = fp3(x0, y0, z0, p1, p2, p3, x);
169 while (Fx(x0 - L1 * FX0, y0, z0, p1, p2, p3, x) - FX > 0) {
171 if (x0 - L1 * FX0 < epsi) {
175 std::cout << FX - Fx(x0 - L1 * FX0, y0, z0, p1, p2, p3, x) << " ";
177 while (Fx(x0, y0 - L2 * FY0, z0, p1, p2, p3, x) - FX > 0) {
179 if (y0 - L2 * FY0 < epsi) {
183 std::cout << FX - Fx(x0, y0 - L2 * FY0, z0, p1, p2, p3, x) << " ";
185 while (Fx(x0, y0, z0 - L3 * FZ0, p1, p2, p3, x) - FX > 0) {
187 if (z0 - L3 * FZ0 < epsi) {
191 std::cout << FX - Fx(x0, y0, z0 - L3 * FZ0, p1, p2, p3, x) << " ";
193 while (Fx(x0, y0, z0, p1 - L4 * FP1, p2, p3, x) - FX > 0) {
195 if (p1 - L4 * FP1 < epsi) {
199 std::cout << FX - Fx(x0, y0, z0, p1 - L4 * FP1, p2, p3, x) << " ";
201 while (Fx(x0, y0, z0, p1, p2 - L5 * FP2, p3, x) - FX > 0) {
203 if (p2 - L5 * FP2 < epsi) {
207 std::cout << FX - Fx(x0, y0, z0, p1, p2 - L5 * FP2, p3, x) << " ";
209 while (Fx(x0, y0, z0, p1, p2, p3 - L6 * FP3, x) - FX > 0) {
211 if (p3 - L6 * FP3 < epsi) {
215 std::cout << FX - Fx(x0, y0, z0, p1, p2, p3 - L6 * FP3, x) << " ";
216 std::cout << FX - Fx(x0 - L1 * FX0, y0 - L2 * FY0, z0 - L3 * FZ0, p1 - L4 * FP1, p2 - L5 * FP2, p3 - L6 * FP3, x) << "\n";
217 if (FX - Fx(x0 - L1 * FX0, y0 - L2 * FY0, z0 - L3 * FZ0, p1 - L4 * FP1, p2 - L5 * FP2, p3 - L6 * FP3, x) > epsi) {
230 //std::cout << count << "\n";
233 RVec kernel_pro (double x0, double y0, double z0, double p1, double p2, double p3, RVec x) {
234 double lambda = (p1 * (x[0] - x0) + p2 * (x[1] - y0) + p3 * (x[2] - z0)) / (p1 * p1 + p2 * p2 + p3 * p3);
236 pro[0] = x0 + p1 * lambda;
237 pro[1] = y0 + p2 * lambda;
238 pro[2] = z0 + p3 * lambda;
242 double left_right_turn (RVec a, RVec b, RVec c) {
243 return a[0] * b[1] * c[2] + a[1] * b[2] * c[0] + b[0] * c[1] * a[2] -
244 (a[2] * b[1] * c[0] + a[0] * b[2] * c[1] + a[1] * b[0] * c[2]);
248 * Template class to serve as a basis for user analysis tools.
250 class Spirals : public TrajectoryAnalysisModule
255 virtual void initOptions(IOptionsContainer *options,
256 TrajectoryAnalysisSettings *settings);
257 virtual void initAnalysis(const TrajectoryAnalysisSettings &settings,
258 const TopologyInformation &top);
260 virtual void analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
261 TrajectoryAnalysisModuleData *pdata);
263 virtual void finishAnalysis(int nframes);
264 virtual void writeOutput();
273 AnalysisNeighborhood nb_;
276 AnalysisDataAverageModulePointer avem_;
280 double epsi = 0.00001;
282 std::vector< std::vector< RVec > > monomers;
283 std::vector< kernel_maxima > kernel;
284 std::vector< std::vector< std::vector< int > > > circles;
290 registerAnalysisDataset(&data_, "avedist");
294 Spirals::initOptions(IOptionsContainer *options,
295 TrajectoryAnalysisSettings *settings)
297 static const char *const desc[] = {
298 "Analysis tool for finding molecular core."
301 // Add the descriptive text (program help text) to the options
302 settings->setHelpText(desc);
303 // Add option for output file name
304 options->addOption(FileNameOption("on").filetype(eftIndex).outputFile()
305 .store(&fnNdx_).defaultBasename("rcore")
306 .description("Index file from the rcore"));
307 // Add option for selection list
308 options->addOption(SelectionOption("select").storeVector(&sel_)
309 .required().dynamicMask().multiValue()
310 .description("Position to calculate distances for"));
313 // -s '/home/toluk/Develop/samples/reca_rd/reca_rd.mono.tpr' -f '/home/toluk/Develop/samples/reca_rd/reca_rd.mono.xtc' -n '/home/toluk/Develop/samples/reca_rd/test.ndx' -on '/home/toluk/Develop/samples/reca_rd/core.ndx'
316 Spirals::initAnalysis(const TrajectoryAnalysisSettings &settings,
317 const TopologyInformation & /*top*/)
325 Spirals::analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
326 TrajectoryAnalysisModuleData *pdata)
328 const SelectionList &sel = pdata->parallelSelections(sel_);
329 std::vector< RVec > temp;
330 temp.resize(sel_.size());
331 for (int i = 0; i < sel.size(); i++) {
332 copy_rvec(sel[i].position(0).x(), temp[i]);
335 monomers.resize(monomers.size() + 1);
336 for (int i = 0; i < sel.size(); i++) {
337 monomers.back().push_back(temp[i]);
350 for (int i = 0; i < sel.size(); i++) {
351 rvec_inc(temp[i], mid);
353 mid[0] /= sel.size();
354 mid[1] /= sel.size();
355 mid[2] /= sel.size();
356 rvec_sub(temp.back(), temp.front(), arrow);
358 long double t1, t2, t3, t4, t5, t6;
366 //linear_kernel_search(mid[0], mid[1], mid[2], arrow[0], arrow[1], arrow[2], temp, epsi); //изменить формат функции для изменения значений переменных
367 linear_kernel_search(t1, t2, t3, t4, t5, t6, temp, epsi);
369 //std::cout << t1 << " " << t2 << " " << t3 << " " << t4 << " " << t5 << " " << t6 << "\n";
378 kernel.resize(kernel.size() + 1);
379 kernel.back().x = mid;
380 kernel.back().p = arrow;
381 for (int i = 0; i < sel.size(); i++) {
382 kernel.back().krnl.push_back(kernel_pro(mid[0], mid[1], mid[2], arrow[0], arrow[1], arrow[2], temp[i]));
385 /*circles.resize(circles.size() + 1);
387 int prev_sign = -9999, change = 0;
389 rvec_sub(temp[0], kernel.back().krnl.front(), a);
390 rvec_sub(kernel.back().krnl.front(), kernel.back().krnl.back(), b);
391 for (int i = 1; i < sel.size(); i++) {
392 rvec_sub(temp[i], kernel.back().krnl[i], c);
393 if (std::signbit(left_right_turn(a, b, c)) != prev_sign) {
395 prev_sign == std::signbit(left_right_turn(a, b, c));
398 if (circles.back().size() == 0) {
399 circles.back().resize(1);
401 circles.back().back().push_back(i);
403 circles.back().resize(circles.back().size() + 1);
404 circles.back().back().push_back(i);
413 Spirals::finishAnalysis(int /*nframes*/)
419 file = std::fopen("linear_kernel.txt", "w+");
420 for (int i = 0; i < kernel.size(); i++) {
421 for (int j = 0; j < monomers[i].size(); j++) {
422 std::fprintf(file, "%3.2f %3.2f %3.2f\n", monomers[i][j][0], monomers[i][j][1], monomers[i][j][2]);
424 for (int j = 0; j < kernel[i].krnl.size(); j++) {
425 std::fprintf(file, "%3.2f %3.2f %3.2f\n", kernel[i].krnl[j][0], kernel[i].krnl[j][1], kernel[i].krnl[j][2]);
427 std::fprintf(file, "\n");
435 file = std::fopen("spiral_dist.txt", "w+");
436 for (int i = 0; i < spiral_dist.size(); i++) {
437 for (int j = 0; j < spiral_dist[i].size(); j++) {
438 std::fprintf(file, "%3.2Lf\n", spiral_dist[i][j]);
440 std::fprintf(file, "\n");
446 Spirals::writeOutput()
452 * The main function for the analysis template.
455 main(int argc, char *argv[])
457 return gmx::TrajectoryAnalysisCommandLineRunner::runAsMain<Spirals>(argc, argv);