cleaned and added selectable methods

diff --git a/src/fitng.cpp b/src/fitng.cpp
index 1bf68b8a1f3cca8f0d7b2f8608c31402b36a0968..c317860a03a67a93d2a27dadae399009884b6640 100644 (file)
--- a/src/fitng.cpp
+++ b/src/fitng.cpp
@@ -587,107 +587,3 @@ main(int argc, char *argv[])
 {
     return gmx::TrajectoryAnalysisCommandLineRunner::runAsMain<Fitng>(argc, argv);
 }
-
-
-
-/*    std::vector< std::pair< int, int > > pairs;
-    for (int i = 0; i < index.size(); i++) {
-        pairs.push_back(std::make_pair(i, i));
-    }
-    double dist1 = 0, dist2 = 0;
-    std::vector< real > w_rls;
-    w_rls.resize(index.size(), 1);
-    rvec *traj1, **traj2;
-    snew(traj1, index.size());
-    snew(traj2, trajectory.size());
-    for (int i = 0; i < index.size(); i++) {
-        copy_rvec(trajectory[0][i].as_vec(), traj1[i]);
-    }
-    reset_x(index.size(), NULL, index.size(), NULL, traj1, &w_rls[0]);
-    for (int j = 0; j < trajectory.size(); j++) {
-        snew(traj2[j], index.size());
-        for (int i = 0; i < index.size(); i++) {
-            copy_rvec(trajectory[j][i].as_vec(), traj2[j][i]);
-        }
-    }
-
-    std::chrono::time_point<std::chrono::system_clock> start, end;
-    for (int j = 1; j < trajectory.size(); j++) {
-
-        for (int i = 0; i < index.size(); i++) {
-            dist1 += (    static_cast< double >(trajectory[0][i][0]), static_cast< double >(trajectory[0][i][1]), static_cast< double >(trajectory[0][i][2]),
-                                static_cast< double >(trajectory[j][i][0] + 0), static_cast< double >(trajectory[j][i][1] + 0), static_cast< double >(trajectory[j][i][2] + 0),
-                                static_cast< double >(0), static_cast< double >(0), static_cast< double >(0)    );
-        }
-        std::cout << "\nbasic dist = " << dist1 /* index.size() << "\n";
-
-        //
-        //  My Fit
-        //
-
-        start = std::chrono::system_clock::now();
-        /*ftn:: MyFitNew(trajectory[0], trajectory[j], pairs, FitConst);
-        end = std::chrono::system_clock::now();
-        std::cout << std::chrono::duration_cast<std::chrono::microseconds> (end-start).count() << " ";
-        for (int i = 0; i < index.size(); i++) {
-            dist2 += /*ftn::F (    static_cast< double >(trajectory[0][i][0]), static_cast< double >(trajectory[0][i][1]), static_cast< double >(trajectory[0][i][2]),
-                                static_cast< double >(trajectory[j][i][0] + 0), static_cast< double >(trajectory[j][i][1] + 0), static_cast< double >(trajectory[j][i][2] + 0),
-                                static_cast< double >(0), static_cast< double >(0), static_cast< double >(0));
-        }
-        //std::cout << "my fit dist = " << dist2 /* index.size()<< "\n";
-
-        //
-        //  Old Fit
-        //
-
-        dist2 = 0;
-        //start = std::chrono::system_clock::now();
-        reset_x(index.size(), NULL, index.size(), NULL, traj2[j], &w_rls[0]);
-        do_fit(index.size(), &w_rls[0], traj1, traj2[j]);
-        //end = std::chrono::system_clock::now();
-        //std::cout << std::chrono::duration_cast<std::chrono::microseconds> (end-start).count() << "\n";
-        for (int i = 0; i < index.size(); i++) {
-            dist2 += /*ftn:: F(    static_cast< double >(traj1[i][0]), static_cast< double >(traj1[i][1]), static_cast< double >(traj1[i][2]),
-                                static_cast< double >(traj2[j][i][0] + 0), static_cast< double >(traj2[j][i][1] + 0), static_cast< double >(traj2[j][i][2] + 0),
-                                static_cast< double >(0), static_cast< double >(0), static_cast< double >(0));
-        }
-        std::cout << "old fit dist = " << dist2 / index.size()<< "\n";
-
-        dist1 = 0;
-        dist2 = 0;
-
-    }
-
-    printPDBtraj(OutPutTrjName.c_str(), trajectory);
-
-    int co = 0;
-    freopen ("/home/toluk/Develop/FitSamples/old_fit_result.pdb", "w", stdout);
-    for (int l = 1; l < trajectory.size(); l++) {
-        for (int i = 0; i < index.size(); i++) {
-            //cout << D*i + (float)l * 6;
-            printf("ATOM  %5d  NA   NA %5d    %8.3f%8.3f%8.3f%6.2f%6.2f      %4s%2s  \n", co, co, (traj2[l][i][0] * 10), (traj2[l][i][1] * 10), (traj2[l][i][2] * 10), 1.0, 20.0, "    ", " ");
-            co++;
-        }
-        co = 0;
-        printf("ENDMDL\n");
-    }
-    printf("END\n");
-    freopen ("/home/toluk/Develop/FitSamples/new_fit_result.pdb", "w", stdout);
-    for (int l = 1; l < trajectory.size(); l++) {
-        for (int i = 0; i < index.size(); i++) {
-            //cout << D*i + (float)l * 6;
-            printf("ATOM  %5d  NA   NA %5d    %8.3f%8.3f%8.3f%6.2f%6.2f      %4s%2s  \n", co, co, (trajectory[l][i][0] * 10), (trajectory[l][i][1] * 10), (trajectory[l][i][2] * 10), 1.0, 20.0, "    ", " ");
-            co++;
-        }
-        co = 0;
-        printf("ENDMDL\n");
-    }
-    printf("END\n");
-    fclose(stdout);
-
-    sfree(traj1);
-    for (int i = 0; i < trajectory.size(); i++) {
-        sfree(traj2[i]);
-    }
-    sfree(traj2);
-*/