}
}
-void correlation_evaluation(std::vector< std::vector< RVec > > traj, int basic_frame, std::vector< std::vector< std::vector< double > > > &crltns, int tauS, int tauE) {
- #pragma omp parallel shared(crltns)
+void correlation_evaluation(std::vector< std::vector< RVec > > traj, int b_frame, std::vector< std::vector< std::vector< double > > > &crl, int tauS, int tauE) {
+ crl.resize(tauE + 1);
+ for (int i = 0; i < crl.size(); i++) {
+ crl[i].resize(traj.front().size());
+ for (int j = 0; j < crl[i].size(); j++) {
+ crl[i][j].resize(traj.front().size(), 0);
+ }
+ }
+ rvec temp_zero;
+ temp_zero[0] = 0;
+ temp_zero[1] = 0;
+ temp_zero[2] = 0;
+ #pragma omp parallel shared(crl)
{
#pragma omp for schedule(dynamic)
for (int i = tauS; i <= tauE; i += 1) {
- rvec *medx, *medy, temp_zero;
+ real tmp2;
+ rvec *medx, *medy, temp, temp1, temp2;
snew(medx, traj.front().size());
snew(medy, traj.front().size());
- temp_zero[0] = 0;
- temp_zero[1] = 0;
- temp_zero[2] = 0;
for (int i = 0; i < traj.front().size(); i++) {
copy_rvec(temp_zero, medx[i]);
copy_rvec(temp_zero, medy[i]);
}
for (int j = 0; j < traj.size() - i - 1; j++) {
for (int f = 0; f < traj.front().size(); f++) {
- rvec temp;
-
- rvec_sub(traj[basic_frame][f], traj[j][f], temp);
+ rvec_sub(traj[b_frame][f], traj[j][f], temp);
rvec_inc(medx[f], temp);
- rvec_sub(traj[basic_frame][f], traj[j + i][f], temp);
+ rvec_sub(traj[b_frame][f], traj[j + i][f], temp);
rvec_inc(medy[f], temp);
}
}
+
for (int j = 0; j < traj.front().size(); j++) {
- rvec temp;
- real temp2 = traj.size() - 1;
+ tmp2 = 1 / (traj.size() - 1 - i);
+
+ /*temp2 = traj.size() - 1;
temp2 -= i;
- temp2 = 1 / temp2;
+ temp2 = 1 / temp2;*/
copy_rvec(medx[j], temp);
- svmul(temp2, temp, medx[j]);
+ svmul(tmp2, temp, medx[j]);
copy_rvec(medy[j], temp);
- svmul(temp2, temp, medy[j]);
+ svmul(tmp2, temp, medy[j]);
}
std::vector< std::vector< double > > a, b, c;
a.resize(traj.front().size());
for (int j = 0; j < traj.size() - i - 1; j++) {
for (int f1 = 0; f1 < traj.front().size(); f1++) {
for (int f2 = 0; f2 < traj.front().size(); f2++) {
- rvec temp1, temp2;
- rvec_sub(traj[basic_frame][f1], traj[j][f1], temp1);
+
+ rvec_sub(traj[b_frame][f1], traj[j][f1], temp1);
rvec_dec(temp1, medx[f1]);
- rvec_sub(traj[basic_frame][f2], traj[j + i][f2], temp2);
+ rvec_sub(traj[b_frame][f2], traj[j + i][f2], temp2);
rvec_dec(temp2, medy[f2]);
a[f1][f2] += (temp1[0] * temp2[0] + temp1[1] * temp2[1] + temp1[2] * temp2[2]);
}
for (int j = 0; j < traj.front().size(); j++) {
for (int f = 0; f < traj.front().size(); f++) {
- crltns[i][j][f] = a[j][f] / (std::sqrt(b[j][f] * c[j][f]));
+ crl[i][j][f] = a[j][f] / (std::sqrt(b[j][f] * c[j][f]));
}
}
sfree(medx);
sfree(medy);
+ std::cout << i << "\n";
+ }
+ }
+ #pragma omp barrier
+}
+
+void domain_chopping(SelectionList seList, std::vector< int > indx, std::vector< std::vector< int > > &filled_domains, std::vector< RVec > frame) {
+ ConstArrayRef< int > atomInd = seList[0].atomIndices();
+ std::vector< std::vector< int > > init_domains;
+ init_domains.resize(seList.size());
+ for (int i = 0; i < seList.size(); i++) {
+ if (seList.size() != 1 && i == 0) {
+ continue;
+ }
+ atomInd = seList[i].atomIndices();
+ for (ConstArrayRef<int>::iterator ai = atomInd.begin(); (ai < atomInd.end()); ai++) {
+ init_domains[i].push_back(*ai);
+ }
+ }
+ for (int i = 0; i < init_domains.size(); i++) {
+ for (int j = 0; j < init_domains[i].size(); j++) {
+ int k = 0;
+ while (indx[k] != init_domains[i][j]) {
+ k++;
+ }
+ init_domains[i][j] = k;
+ }
+ }
+ for (int i = 0; i < init_domains.size(); i++) {
+ if (init_domains[i].size() >= 2) {
+ filled_domains.push_back(init_domains[i]);
+ for (int k = 0; k < init_domains[i].size(); k++) {
+ for (int j = i + 1; j < init_domains.size(); j++) {
+ for (int x = 0; x < init_domains[j].size(); x++) {
+ if (init_domains[j][x] == init_domains[i][k]) {
+ init_domains[j].erase(init_domains[j].begin() + x);
+ }
+ }
+ }
+ }
+ }
+ }
+ init_domains.resize(0);
+ init_domains = filled_domains;
+ std::vector< bool > flags;
+ flags.resize(indx.size(), true);
+ for (int i = 0; i < init_domains.size(); i++) {
+ for (int j = 0; j < init_domains[i].size(); j++) {
+ flags[init_domains[i][j]] = false;
+ }
+ }
+ int a;
+ rvec temp;
+ for (int i = 0; i < indx.size(); i++) {
+ if (flags[i]) {
+ float dist = 90000001;
+ for (int j = 0; j < init_domains.size(); j++) {
+ for (int k = 0; k < init_domains[j].size(); k++) {
+ rvec_sub(frame[i], frame[init_domains[j][k]], temp);
+ if (norm(temp) <= dist) {
+ dist = norm(temp);
+ a = j;
+ }
+ }
+ }
+ filled_domains[a].push_back(i);
+ flags[i] = false;
+ }
+ }
+}
+
+void graph_calculation(std::vector< std::vector< std::pair< double, int > > > &graph, std::vector< std::vector< int > > &s_graph, std::vector< std::vector< std::pair< int, int > > > &s_graph_rbr,
+ std::vector< std::vector< RVec > > traj, int b_frame,
+ std::vector< std::vector< std::vector< double > > > crl, double crl_b, double e_rad, int tauE) {
+ graph.resize(traj.front().size());
+ for (int i = 0; i < traj.front().size(); i++) {
+ graph[i].resize(traj.front().size(), std::make_pair(0, -1));
+ }
+ rvec temp;
+ for (int i = 1; i <= tauE; i++) {
+ for (int j = 0; j < traj.front().size(); j++) {
+ for (int f = j; f < traj.front().size(); f++) {
+ copy_rvec(traj[b_frame][j], temp);
+ rvec_dec(temp, traj[b_frame][f]);
+ if (std::max(std::abs(crl[i][j][f]), std::abs(crl[i][f][j])) >= crl_b && norm(temp) <= e_rad && std::abs(graph[j][f].first) < std::max(std::abs(crl[i][j][f]), std::abs(crl[i][f][j]))) {
+ if (std::abs(crl[i][j][f]) > std::abs(crl[i][f][j])) {
+ graph[j][f].first = crl[i][j][f];
+ } else {
+ graph[j][f].first = crl[i][f][j];
+ }
+ graph[j][f].second = i;
+ }
+ }
+ }
+ }
+ std::vector< bool > graph_flags;
+ graph_flags.resize(traj.front().size(), true);
+ std::vector< int > a;
+ a.resize(0);
+ std::vector< std::pair< int, int > > b;
+ b.resize(0);
+ std::vector< int > que1, que2, que3;
+ for (int i = 0; i < traj.front().size(); i++) {
+ if (graph_flags[i]) {
+ s_graph.push_back(a);
+ s_graph_rbr.push_back(b);
+ que1.resize(0);
+ que2.resize(0);
+ que3.resize(0);
+ que1.push_back(i);
+ que3.push_back(i);
+ graph_flags[i] = false;
+ while(que1.size() > 0) {
+ que2.clear();
+ for (int k = 0; k < que1.size(); k++) {
+ for (int j = 0; j < traj.front().size(); j++) {
+ if (graph[que1[k]][j].second > -1 && graph_flags[j]) {
+ que2.push_back(j);
+ graph_flags[j] = false;
+ }
+ }
+ }
+ que1 = que2;
+ for (int j = 0; j < que2.size(); j++) {
+ que3.push_back(que2[j]);
+ }
+ }
+ s_graph.back() = que3;
+ for (int j = 0; j < que3.size(); j++) {
+ for (int k = 0; k < traj.front().size(); k++) {
+ if (graph[que3[j]][k].second > -1) {
+ s_graph_rbr.back().push_back(std::make_pair(que3[j], k));
+ }
+ }
+ }
+ //std::cout << s_graph.back().size() << " ";
}
}
-#pragma omp barrier
}
bool myfunction (const std::pair< int, double > i, const std::pair< int, double > j) {
return i.second < j.second;
}
+void graph_back_bone_evaluation(std::vector< std::vector < std::pair< int, int > > > &rout_n, int indxSize,
+ std::vector< std::vector< std::pair< double, int > > > graph, std::vector< std::vector< int > > s_graph, std::vector< std::vector< std::pair< int, int > > > s_graph_rbr) {
+ std::vector< double > key;
+ std::vector< int > path;
+ std::vector< std::pair< int, double > > que;
+ std::vector< std::pair< int, int > > a;
+ int v;
+ for (int i = 0; i < s_graph.size(); i++) {
+ key.resize(0);
+ path.resize(0);
+ que.resize(0);
+ v = 0;
+ if (s_graph[i].size() > 2) {
+ key.resize(indxSize, 2);
+ path.resize(indxSize, -1);
+ key[s_graph[i][0]] = 0;
+ for (int j = 0; j < s_graph[i].size(); j++) {
+ que.push_back(std::make_pair(s_graph[i][j], key[s_graph[i][j]]));
+ }
+ std::sort(que.begin(), que.end(), myfunction);
+ while (!que.empty()) {
+ v = que[0].first;
+ que.erase(que.begin());
+ for (int j = 0; j < s_graph_rbr[i].size(); j++) {
+ int u = -1;
+ if (s_graph_rbr[i][j].first == v) {
+ u = s_graph_rbr[i][j].second;
+ } else if (s_graph_rbr[i][j].second == v) {
+ u = s_graph_rbr[i][j].first;
+ }
+ bool flag = false;
+ int pos = -1;
+ for (int k = 0; k < que.size(); k++) {
+ if (que[k].first == u) {
+ flag = true;
+ pos = k;
+ k = que.size() + 1;
+ }
+ }
+ if (flag && key[u] > 1 - std::abs(graph[v][u].first)) {
+ path[u] = v;
+ key[u] = 1 - std::abs(graph[v][u].first);
+ que[pos].second = key[u];
+ sort(que.begin(), que.end(), myfunction);
+ }
+ }
+ }
+ a.resize(0);
+ rout_n.push_back(a);
+ for (int j = 0; j < indxSize; j++) {
+ if (path[j] != -1) {
+ rout_n.back().push_back(std::make_pair(j, path[j]));
+ }
+ }
+ }
+ }
+}
+
/*! \brief
* \ingroup module_trajectoryanalysis
*/
std::string fnNdx_;
SelectionList sel_;
- std::vector< std::vector< int > > domains;
+
std::vector< std::vector< int > > domains_local;
std::vector< std::vector< RVec > > trajectory;
std::vector< std::vector< RVec > > frankenstein_trajectory;
int frames = 0;
int basic_frame = 0;
int tau = 0;
+ int graph_tau = 0;
double crl_border = 0;
double eff_rad = 1.5;
real **w_rls;
options->addOption(FileNameOption("on").filetype(eftIndex).outputFile()
.store(&fnNdx_).defaultBasename("domains")
.description("Index file from the domains"));
+ // Add option for graph_tau constant
+ options->addOption(gmx::IntegerOption("Gtau")
+ .store(&graph_tau)
+ .description("number of frames for graph to see for time travel"));
// Add option for tau constant
options->addOption(gmx::IntegerOption("tau")
.store(&tau)
Domains::initAfterFirstFrame(const TrajectoryAnalysisSettings &settings,
const t_trxframe &fr)
{
+ //std::vector< std::vector< int > > domains;
ConstArrayRef< int > atomind = sel_[0].atomIndices();
index.resize(0);
for (ConstArrayRef<int>::iterator ai = atomind.begin(); (ai < atomind.end()); ai++) {
for (int i = 0; i < index.size(); i++) {
trajectory.back()[i] = fr.x[index[i]];
}
- domains.resize(sel_.size());
- for (int i = 0; i < sel_.size(); i++) {
- if (sel_.size() != 1 && i == 0) {
- continue;
- }
- atomind = sel_[i].atomIndices();
- for (ConstArrayRef<int>::iterator ai = atomind.begin(); (ai < atomind.end()); ai++) {
- domains[i].push_back(*ai);
- }
- }
- for (int i = 0; i < domains.size(); i++) {
- for (int j = 0; j < domains[i].size(); j++) {
- int k = 0;
- while (index[k] != domains[i][j]) {
- k++;
- }
- domains[i][j] = k;
- }
- }
- for (int i = 0; i < domains.size(); i++) {
- if (domains[i].size() >= 2) {
- domains_local.push_back(domains[i]);
- for (int k = 0; k < domains[i].size(); k++) {
- for (int j = i + 1; j < domains.size(); j++) {
- for (int x = 0; x < domains[j].size(); x++) {
- if (domains[j][x] == domains[i][k]) {
- domains[j].erase(domains[j].begin() + x);
- }
- }
- }
- }
- }
- }
- domains.resize(0);
- domains = domains_local;
- std::vector< bool > flags;
- flags.resize(index.size(), true);
- for (int i = 0; i < domains.size(); i++) {
- for (int j = 0; j < domains[i].size(); j++) {
- flags[domains[i][j]] = false;
- }
- }
- int a;
- rvec temp;
- for (int i = 0; i < index.size(); i++) {
- if (flags[i]) {
- float dist = 90000001;
- for (int j = 0; j < domains.size(); j++) {
- for (int k = 0; k < domains[j].size(); k++) {
- rvec_sub(trajectory.back()[i], trajectory.back()[domains[j][k]], temp);
- if (norm(temp) <= dist) {
- dist = norm(temp);
- a = j;
- }
- }
- }
- domains_local[a].push_back(i);
- flags[i] = false;
- }
- }
+
+ domain_chopping(sel_, index, domains_local, trajectory.back());
+
frankenstein_trajectory.resize(trajectory.size());
frankenstein_trajectory.back() = trajectory.back();
trajectory.resize(trajectory.size() + 1);
- /*snew(w_rls, domains_local.size() + 1);
- for (int i = 0; i < domains_local.size(); i++) {
- snew(w_rls[i], index.size());
- for (int j = 0; j < index.size(); j++) {
- w_rls[i][j] = 0;
- }
- for (int j = 0; j < domains_local[i].size(); j++) {
- w_rls[i][domains_local[i][j]] = 1;
- }
- }
- snew(w_rls[domains_local.size()], index.size());
- for (int i = 0; i < index.size(); i++) {
- w_rls[domains_local.size()][i] = 1;
- }*/
-
w_rls2.resize(domains_local.size() + 1);
for (int i = 0; i < domains_local.size(); i++) {
w_rls2[i].resize(domains_local[i].size());
for (int j = 0; j < domains_local[i].size(); j++) {
frankenstein_trajectory.back()[domains_local[i][j]] = traj[domains_local[i][j]];
}
- /*rvec *basic, *traj;
- snew(basic, index.size());
- for (int k = 0; k < index.size(); k++) {
- copy_rvec(trajectory[basic_frame][k].as_vec(), basic[k]);
- }
- snew(traj, index.size());
- for (int k = 0; k < index.size(); k++) {
- copy_rvec(trajectory.back()[k].as_vec(), traj[k]);
- }
- reset_x(index.size(), NULL, index.size(), NULL, basic, w_rls[i]);
- reset_x(index.size(), NULL, index.size(), NULL, traj, w_rls[i]);
- do_fit(index.size(), w_rls[i], basic, traj);
- for (int j = 0; j < index.size(); j++) {
- if (w_rls[i][j] == 0) {
- copy_rvec(basic[j], traj[j]);
- }
- }
- reset_x(index.size(), NULL, index.size(), NULL, traj, w_rls[domains_local.size()]);
-
- for (int j = 0; j < domains_local[i].size(); j++) {
- frankenstein_trajectory.back()[domains_local[i][j]] = traj[domains_local[i][j]];
- }
- sfree(basic);
- sfree(traj);*/
}
std::cout << "frame № " << frames + 1 <<" analysed\n";
frames++;
if (tau > 0) {
k = tau;
}
- crltns.resize(k + 1);
- for (int i = 0; i < crltns.size(); i++) {
- crltns[i].resize(index.size());
- for (int j = 0; j < crltns[i].size(); j++) {
- crltns[i][j].resize(index.size(), 0);
- }
- }
- std::cout << "Correlation's evaluation - start\n\n";
- #pragma omp parallel shared(crltns)
- {
- #pragma omp for schedule(dynamic)
- for (int i = m; i <= k; i += 1) {
- rvec *medx, *medy, temp_zero;
- snew(medx, index.size());
- snew(medy, index.size());
- temp_zero[0] = 0;
- temp_zero[1] = 0;
- temp_zero[2] = 0;
- for (int i = 0; i < index.size(); i++) {
- copy_rvec(temp_zero, medx[i]);
- copy_rvec(temp_zero, medy[i]);
- }
- for (int j = 0; j < frankenstein_trajectory.size() - i - 1; j++) {
- for (int f = 0; f < index.size(); f++) {
- rvec temp;
- rvec_sub(frankenstein_trajectory[basic_frame][f], frankenstein_trajectory[j][f], temp);
- rvec_inc(medx[f], temp);
+ /*
+ *
+ *
+ *
+ */
- rvec_sub(frankenstein_trajectory[basic_frame][f], frankenstein_trajectory[j + i][f], temp);
- rvec_inc(medy[f], temp);
- }
- }
- for (int j = 0; j < index.size(); j++) {
- rvec temp;
- real temp2 = frankenstein_trajectory.size() - 1;
- temp2 -= i;
- temp2 = 1 / temp2;
-
- copy_rvec(medx[j], temp);
- svmul(temp2, temp, medx[j]);
- copy_rvec(medy[j], temp);
- svmul(temp2, temp, medy[j]);
- }
- std::vector< std::vector< double > > a, b, c;
- a.resize(index.size());
- b.resize(index.size());
- c.resize(index.size());
- for (int j = 0; j < index.size(); j++) {
- a[j].resize(index.size(), 0);
- b[j].resize(index.size(), 0);
- c[j].resize(index.size(), 0);
- }
- for (int j = 0; j < frankenstein_trajectory.size() - i - 1; j++) {
- for (int f1 = 0; f1 < index.size(); f1++) {
- for (int f2 = 0; f2 < index.size(); f2++) {
- rvec temp1, temp2;
- rvec_sub(frankenstein_trajectory[basic_frame][f1], frankenstein_trajectory[j][f1], temp1);
- rvec_dec(temp1, medx[f1]);
+ std::cout << "Correlation's evaluation - start\n\n";
+ correlation_evaluation(frankenstein_trajectory, basic_frame, crltns, m, k);
+ std::cout << "Correlation's evaluation - end\n\n";
- rvec_sub(frankenstein_trajectory[basic_frame][f2], frankenstein_trajectory[j + i][f2], temp2);
- rvec_dec(temp2, medy[f2]);
+ /*
+ *
+ *
+ *
+ */
- a[f1][f2] += (temp1[0] * temp2[0] + temp1[1] * temp2[1] + temp1[2] * temp2[2]);
- b[f1][f2] += (temp1[0] * temp1[0] + temp1[1] * temp1[1] + temp1[2] * temp1[2]);
- c[f1][f2] += (temp2[0] * temp2[0] + temp2[1] * temp2[1] + temp2[2] * temp2[2]);
- }
- }
- }
- for (int j = 0; j < index.size(); j++) {
- for (int f = 0; f < index.size(); f++) {
- crltns[i][j][f] = a[j][f] / (std::sqrt(b[j][f] * c[j][f]));
- }
- }
- sfree(medx);
- sfree(medy);
- }
- }
- #pragma omp barrier
- std::cout << "Correlation's evaluation - end\n\n";
- for (int i1 = 0; i1 < 100; i1++) {
+ //number of corelations in the matrixes
+ /*for (int i1 = 0; i1 < 100; i1++) {
int i5 = 0;
for (int i2 = 1; i2 < crltns.size(); i2++) {
for (int i3 = 0; i3 < crltns[i2].size(); i3++) {
if (i1 % 10 == 0) {
std::cout << "\n" ;
}
- }
+ }*/
+
+ std::cout << "graph evaluation: start\n";
+
std::vector< std::vector< std::pair< double, int > > > graph;
- graph.resize(index.size());
- for (int i = 0; i < index.size(); i++) {
- graph[i].resize(index.size(), std::make_pair(0, -1));
- }
- rvec temp;
- for (int i = 1; i <= k; i++) {
- for (int j = 0; j < index.size(); j++) {
- for (int f = j; f < index.size(); f++) {
- copy_rvec(frankenstein_trajectory[basic_frame][j], temp);
- rvec_dec(temp, frankenstein_trajectory[basic_frame][f]);
- if (std::max(std::abs(crltns[i][j][f]), std::abs(crltns[i][f][j])) >= crl_border && norm(temp) <= eff_rad && std::abs(graph[j][f].first) < std::max(std::abs(crltns[i][j][f]), std::abs(crltns[i][f][j]))) {
- if (std::abs(crltns[i][j][f]) > std::abs(crltns[i][f][j])) {
- graph[j][f].first = crltns[i][j][f];
- } else {
- graph[j][f].first = crltns[i][f][j];
- }
- graph[j][f].second = i;
- }
- }
- }
- }
- std::vector< bool > graph_flags;
- graph_flags.resize(index.size(), true);
std::vector< std::vector< int > > sub_graph;
std::vector< std::vector< std::pair< int, int > > > sub_graph_rbr;
- std::vector< int > a;
- std::vector< std::pair< int, int > > b;
- a.resize(0);
- b.resize(0);
- for (int i = 0; i < index.size(); i++) {
- if (graph_flags[i]) {
- sub_graph.push_back(a);
- sub_graph_rbr.push_back(b);
- std::vector< int > que1, que2, que3;
- que1.resize(0);
- que2.resize(0);
- que3.resize(0);
- que1.push_back(i);
- que3.push_back(i);
- graph_flags[i] = false;
- while(que1.size() > 0) {
- que2.clear();
- for (int k = 0; k < que1.size(); k++) {
- for (int j = 0; j < index.size(); j++) {
- if (graph[que1[k]][j].second > -1 && graph_flags[j]) {
- que2.push_back(j);
- graph_flags[j] = false;
- }
- }
- }
- que1 = que2;
- for (int j = 0; j < que2.size(); j++) {
- que3.push_back(que2[j]);
- }
- }
- sub_graph.back() = que3;
- for (int j = 0; j < que3.size(); j++) {
- for (int k = 0; k < index.size(); k++) {
- if (graph[que3[j]][k].second > -1) {
- sub_graph_rbr.back().push_back(std::make_pair(que3[j], k));
- }
- }
- }
- std::cout << sub_graph.back().size() << " ";
- }
- }
+
+
+ graph_calculation(graph, sub_graph, sub_graph_rbr, frankenstein_trajectory, basic_frame, crltns, crl_border, eff_rad, graph_tau/*k*/);
+
+
std::vector< std::vector < std::pair< int, int > > > rout_new;
- for (int i = 0; i < sub_graph.size(); i++) {
- if (sub_graph[i].size() > 2) {
- std::vector< double > key;
- std::vector< int > path;
- std::vector< std::pair< int, double > > que;
- int v;
- key.resize(index.size(), 2);
- path.resize(index.size(), -1);
- key[sub_graph[i][0]] = 0;
-
- for (int j = 0; j < sub_graph[i].size(); j++) {
- que.push_back(std::make_pair(sub_graph[i][j], key[sub_graph[i][j]]));
- }
- std::sort(que.begin(), que.end(), myfunction);
- while (!que.empty()) {
- v = que[0].first;
- que.erase(que.begin());
- for (int j = 0; j < sub_graph_rbr[i].size(); j++) {
- int u = -1;
- if (sub_graph_rbr[i][j].first == v) {
- u = sub_graph_rbr[i][j].second;
- } else if (sub_graph_rbr[i][j].second == v) {
- u = sub_graph_rbr[i][j].first;
- }
- bool flag = false;
- int pos = -1;
- for (int k = 0; k < que.size(); k++) {
- if (que[k].first == u) {
- flag = true;
- pos = k;
- k = que.size() + 1;
- }
- }
- if (flag && key[u] > 1 - std::abs(graph[v][u].first)) {
- path[u] = v;
- key[u] = 1 - std::abs(graph[v][u].first);
- que[pos].second = key[u];
- sort(que.begin(), que.end(), myfunction);
- }
- }
- }
- std::vector < std::pair< int, int > > a;
- a.resize(0);
- rout_new.push_back(a);
- for (int j = 0; j < index.size(); j++) {
- if (path[j] != -1) {
- rout_new.back().push_back(std::make_pair(j, path[j]));
- }
- }
- }
- }
- make_rout_file2(crl_border, index, rout_new, "Routs_DomainsNFit_2500_0.70_1.txt");
- make_best_corrs_graphics(crltns, rout_new, index, "best_graphics_DomainsNFit_2500_0.70_1.txt");
+
+ std::cout << "graph evaluation: end\n";
+ std::cout << "routs evaluation: start\n";
+
+ graph_back_bone_evaluation(rout_new, index.size(), graph, sub_graph, sub_graph_rbr);
+
+ std::cout << "routs evaluation: end\n";
+
+ make_rout_file2(crl_border, index, rout_new, "Routs_DomainsNFit_5000_0.70_1_t.txt");
+ make_best_corrs_graphics(crltns, rout_new, index, "best_graphics_DomainsNFit_5000_0.70_1_t.txt");
std::cout << "Finish Analysis - end\n\n";
}
biod.pnpi.spb.ru / alexxy / gromacs-testing.git / commitdiff