#include <gromacs/utility/smalloc.h>
#include <gromacs/math/do_fit.h>
#include <gromacs/trajectoryanalysis/topologyinformation.h>
+#include "gromacs/topology/topology.h"
+#include "gromacs/topology/index.h"
using namespace gmx;
return crrlts;
}
-void make_correlation_matrix_file(const std::vector< std::vector< std::vector< double > > > correlations, const char* file_name)
-{
- FILE *file;
- file = std::fopen(file_name, "w+");
- std::cout << "writing correlation matrixes: \n";
- for (unsigned int i = 0; i < correlations.size(); i++) {
- std::fprintf(file, "%d\n", i);
- for (unsigned int j = 0; j < correlations[i].size(); j++) {
- for (unsigned int f = 0; f < correlations[i][j].size(); f++) {
- std::fprintf(file, "%.6f ", correlations[i][j][f]); //~16
- }
- std::fprintf(file, "\n");
+template< typename T >
+unsigned int posSrch(std::vector< T > a, T b) {
+ for (unsigned i01 = 0; i01 < a.size(); i01++) {
+ if (a[01] == b) {
+ return i01;
+ break;
}
- std::cout << i << " | ";
}
- std::fclose(file);
- std::cout << "\n";
+ return a.size() + 1;
}
-void make_correlation_pairs_file(std::vector< std::vector< std::vector< double > > > correlations, const char* file_name)
+void make_rout_file(double crl_border, std::vector< int > indx, std::vector< std::string > resNames, std::vector< std::vector< std::vector< std::pair< unsigned int, unsigned int > > > > rout, const char* file_name01)
{
- FILE *file;
- file = std::fopen(file_name, "w+");
- for (unsigned int i = 0; i < correlations.front().size(); i++) {
- for (unsigned int j = 0; j < correlations.front().front().size(); j++) {
- //std::fprintf(file, "correlation between point '%d' and point '%d'\n", i, j);
- std::fprintf(file, "%d %d\n", i, j);
- for (unsigned int k = 0; k < correlations.size(); k++) {
- std::fprintf(file, "%3.4f ", correlations[k][i][j]);
+ FILE *file01;
+ file01 = std::fopen(file_name01, "w+");
+
+ unsigned int f;
+ std::vector< std::tuple< int, int, std::vector< int > > > table;
+
+ for (unsigned int i01 = 0; i01 < rout.size(); i01++) {
+ f = i01;
+ for (unsigned int i02 = i01 + 1; i02 <rout.size(); i02++) {
+ if (rout[i02] == rout[i01]) {
+ f = i02;
+ } else {
+ break;
}
- std::fprintf(file, "\n");
}
- if (i % 10 == 0) {
- std::cout << "correlations in row " << i << " out of " << correlations.front().size() << " completed\n";
+ if (i01 == f) {
+ std::fprintf(file01, "tau = %d | correlations >= %0.2f\n\n", i01, crl_border);
+ } else {
+ std::fprintf(file01, "tau = [%d ; %d] | correlations >= %0.2f\n\n", i01, f, crl_border);
}
- }
- std::fclose(file);
-}
-
-void make_rout_file(double crl_border, std::vector< int > indx, std::vector< std::vector< std::vector< std::pair< unsigned int, unsigned int > > > > rout, const char* file_name)
-{
- FILE *file;
- file = std::fopen(file_name, "w+");
- for (unsigned int i1 = 0; i1 < rout.size(); i1++) {
- std::fprintf(file, "tau = %d | correlations >= %0.2f\n\n", i1, crl_border);
- for (unsigned int i2 = 0; i2 < rout[i1].size(); i2++) {
- for (unsigned int i3 = 0; i3 < rout[i1][i2].size(); i3++) {
- std::fprintf(file, "cgo_arrow (id %3d), (id %3d), radius=0.15\n", indx[rout[i1][i2][i3].first] + 1, indx[rout[i1][i2][i3].second] + 1);
+ for (unsigned int i02 = 0; i02 < rout[i01].size(); i02++) {
+ for (unsigned int i03 = 0; i03 < rout[i01][i02].size(); i03++) {
+ std::fprintf(file01, "cgo_arrow (id %3d), (id %3d), radius=0.15\n", indx[rout[i01][i02][i03].first] + 1, indx[rout[i01][i02][i03].second] + 1);
}
- std::fprintf(file, "\n\n");
+ std::fprintf(file01, "\n");
}
- }
- std::fclose(file);
-}
-
-void make_table_routs(std::vector< RVec > ref, double crl_border, std::vector< int > indx, std::vector< std::vector< std::pair< unsigned int, unsigned int > > > rout, const char* file_name)
-{
- FILE *file;
- file = std::fopen(file_name, "w+");
- std::fprintf(file, "correlations >= %0.2f\n\n", crl_border);
- std::vector< std::tuple< int, int, std::vector< int > > > table;
-
- for (unsigned int i1 = 0; i1 < rout.size(); i1++) {
- for (unsigned int i2 = 0; i2 < rout[i1].size(); i2++) {
- bool flag = true;
- for (unsigned int i3 = 0; i3 < table.size(); i3++) {
- if (std::get<0>(table[i3]) == indx[rout[i1][i2].first] + 1) {
- std::get<1>(table[i3])++;
- std::get<2>(table[i3]).push_back(indx[rout[i1][i2].second] + 1);
- flag = false;
- } else if (std::get<0>(table[i3]) == indx[rout[i1][i2].second] + 1) {
- std::get<1>(table[i3])++;
- std::get<2>(table[i3]).push_back(indx[rout[i1][i2].first] + 1);
- flag = false;
+ table.resize(0);
+ for (unsigned int i02 = 0; i02 < rout[i01].size(); i02++) {
+ for (unsigned int i03 = 0; i03 < rout[i01][i02].size(); i03++) {
+ bool flag = true;
+ for (unsigned int i04 = 0; i04 < table.size(); i04++) {
+ if (std::get<0>(table[i04]) == indx[rout[i01][i02][i03].first] + 1) {
+ std::get<1>(table[i04])++;
+ std::get<2>(table[i04]).push_back(indx[rout[i01][i02][i03].second] + 1);
+ flag = false;
+ } else if (std::get<0>(table[i04]) == indx[rout[i01][i02][i03].second] + 1) {
+ std::get<1>(table[i04])++;
+ std::get<2>(table[i04]).push_back(indx[rout[i01][i02][i03].first] + 1);
+ flag = false;
+ }
+ }
+ if (flag) {
+ std::vector< int > a;
+ a.resize(0);
+ a.push_back(indx[rout[i01][i02][i03].second] + 1);
+ table.push_back(std::make_tuple(indx[rout[i01][i02][i03].first] + 1, 1, a));
+ a.resize(0);
+ a.push_back(indx[rout[i01][i02][i03].first] + 1);
+ table.push_back(std::make_tuple(indx[rout[i01][i02][i03].second] + 1, 1, a));
}
}
- if (flag) {
- std::vector< int > a;
- a.resize(0);
- a.push_back(indx[rout[i1][i2].second] + 1);
- table.push_back(std::make_tuple(indx[rout[i1][i2].first] + 1, 1, a));
- a.resize(0);
- a.push_back(indx[rout[i1][i2].first] + 1);
- table.push_back(std::make_tuple(indx[rout[i1][i2].second] + 1, 1, a));
+ }
+ for (unsigned int i02 = 0; i02 < table.size(); i02++) {
+ std::fprintf(file01, "residue %s connections %d | ", (resNames[posSrch(indx, std::get<0>(table[i02]))]).c_str(), std::get<1>(table[i02]));
+ for (unsigned int i03 = 0; i03 < std::get<2>(table[i03]).size(); i03++) {
+ std::fprintf(file01, "%s ", (resNames[posSrch(indx, std::get<2>(table[i02])[i03])]).c_str());
}
+ std::fprintf(file01, "\n");
}
- }
- for (unsigned int i = 0; i < table.size(); i++) {
- std::fprintf(file, "atomN %d connections %d | ", std::get<0>(table[i]), std::get<1>(table[i]));
- for (unsigned int j = 0; j < std::get<2>(table[i]).size(); j++) {
- std::fprintf(file, "%d ", std::get<2>(table[i])[j]);
- }
- std::fprintf(file, "\n");
- }
- std::fclose(file);
-}
+ /*
+ *
+ *
+ * добавить вывод разницы в плане что +, а что -
+ *
+ *
+ *
+ */
+
-void make_best_corrs_graphics(std::vector< std::vector< std::vector< double > > > correlations,
- std::vector< std::vector< std::pair< unsigned int, unsigned int > > > rout_pairs,
- std::vector< int > indx,
- const char* file_name)
-{
- FILE *file;
- file = std::fopen(file_name, "w+");
- for (unsigned int i = 0; i < rout_pairs.size(); i++) {
- for (unsigned int j = 0; j < rout_pairs[i].size(); j++) {
- std::fprintf(file, "%3d %3d\n", indx[rout_pairs[i][j].first]/* + 1*/, indx[rout_pairs[i][j].second]/* + 1*/);
- for (unsigned int k = 0; k < correlations.size(); k++) {
- std::fprintf(file, "%3.5f ", correlations[k][rout_pairs[i][j].first][rout_pairs[i][j].second]);
- }
- std::fprintf(file, "\n");
- }
}
- std::fclose(file);
+
+ std::fclose(file01);
}
bool mysortfunc (std::vector< int > a, std::vector< int > b) {
std::vector< RVec > reference;
std::vector< int > index;
+ std::vector< std::string > resNms;
+
int frames = 0;
int tau = 0; // selectable
int window = 0;
index.resize(0);
for (ArrayRef< const int >::iterator ai = atomind.begin(); (ai < atomind.end()); ai++) {
index.push_back(*ai);
+ resNms.push_back(*(top.atoms()->resinfo[top.atoms()->atom[*ai].resind].name) + std::to_string((top.atoms()->atom[*ai].resind + 1)));
}
trajectory.resize(0);
-
-
reference.resize(0);
if (top.hasFullTopology()) {
for (unsigned int i = 0; i < index.size(); i++) {
correlation_evaluation(reference, trajectory, k, 1000, (OutPutName + "-DumpData.txt").c_str());
- //make_correlation_matrix_file(crltns, (OutPutName + "-matrix.txt").c_str());
-
- //make_correlation_pairs_file(crltns, (OutPutName + "-matrix-pairs.txt").c_str());
-
- //std::cout << "corelation matrix printed\n";
-
std::cout << "Correlation's evaluation - end\n";
} else if (mode == 1) {
- rout_new.resize(trajectory.size() - window - k);
+ rout_new.resize(trajectory.size() - static_cast< unsigned long>(window) - k);
FILE *file;
file = std::fopen((OutPutName + "-DumpData.txt").c_str(), "r+");
#pragma omp parallel for ordered schedule(dynamic) shared(rout_new) firstprivate(reference, crl_border, eff_rad, m, k)
- for(unsigned int i = 0; i < trajectory.size() - window - k; i++) {
+ for(unsigned long i = 0; i < trajectory.size() - static_cast< unsigned int>(window) - k; i++) {
std::vector< std::vector< std::vector< double > > > crltns;
std::vector< std::vector< std::pair< double, long int > > > graph;
std::vector< std::vector< unsigned int > > sub_graph;
#pragma omp barrier
}
- make_rout_file(static_cast< double >(crl_border), index, rout_new, (OutPutName + "-routs.txt").c_str());
-
-/*
- make_rout_file(static_cast< double >(crl_border), index, rout_new, (OutPutName + "-routs.txt").c_str());
- std::cout << "corelation routs printed\n";
-
- make_best_corrs_graphics(crltns, rout_new, index, (OutPutName + "-routs-graphics.txt").c_str());
- std::cout << "corelation routs' pairs' graphics printed\n";
-
- make_table_routs(reference, static_cast< double >(crl_border), index, rout_new, (OutPutName + "-routs-table.txt").c_str());
+ make_rout_file(static_cast< double >(crl_border), index, resNms, rout_new, (OutPutName + "-routs.txt").c_str());
std::cout << "Finish Analysis - end\n\n";
-*/
-
-
}
void
biod.pnpi.spb.ru / alexxy / gromacs-spacetimecorr.git / blobdiff