Merge branch 'master' into pygromacs

[alexxy/gromacs.git] / src / gromacs / gmxana / gmx_chi.cpp

diff --git a/src/gromacs/gmxana/gmx_chi.c b/src/gromacs/gmxana/gmx_chi.cpp
similarity index 97%
rename from src/gromacs/gmxana/gmx_chi.c
rename to src/gromacs/gmxana/gmx_chi.cpp
index 0b12224e2e98d91dd060b57cd2234bd4f4b744d1..e49878148f5e9b053a639f40e55357640759bd8b 100644 (file)
--- a/src/gromacs/gmxana/gmx_chi.c
+++ b/src/gromacs/gmxana/gmx_chi.cpp
@@ -36,9 +36,11 @@
  */
 #include "gmxpre.h"
 
-#include <math.h>
-#include <stdio.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstring>
+
+#include <algorithm>
 
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/correlationfunctions/autocorr.h"
@@ -130,11 +132,12 @@ static gmx_bool bAllowed(real phi, real psi)
 #define NPP asize(map)
     int                x, y;
 
-#define INDEX(ppp) ((((int) (360+ppp*RAD2DEG)) % 360)/6)
+#define INDEX(ppp) (((static_cast<int> (360+ppp*RAD2DEG)) % 360)/6)
     x = INDEX(phi);
     y = INDEX(psi);
 #undef INDEX
-    return (gmx_bool) map[x][y];
+
+    return (map[x][y] == '1') ? TRUE : FALSE;
 }
 
 atom_id *make_chi_ind(int nl, t_dlist dl[], int *ndih)
@@ -214,7 +217,7 @@ int bin(real chi, int mult)
 {
     mult = 3;
 
-    return (int) (chi*mult/360.0);
+    return static_cast<int>(chi*mult/360.0);
 }
 
 
@@ -311,11 +314,11 @@ static void dump_em_all(int nlist, t_dlist dlist[], int nf, real time[],
     snew(data, nf);
     if (bRAD)
     {
-        strcpy(ystr, "Angle (rad)");
+        std::strcpy(ystr, "Angle (rad)");
     }
     else
     {
-        strcpy(ystr, "Angle (degrees)");
+        std::strcpy(ystr, "Angle (degrees)");
     }
 
     /* Dump em all */
@@ -477,7 +480,7 @@ static void histogramming(FILE *log, int nbin, gmx_residuetype_t *rt,
     real       *normhisto;
     real      **Jc, **Jcsig;
     int     ****his_aa_ss = NULL;
-    int      ***his_aa, **his_aa1, *histmp;
+    int      ***his_aa, *histmp;
     int         i, j, k, m, n, nn, Dih, nres, hindex, angle;
     gmx_bool    bBfac, bOccup;
     char        hisfile[256], hhisfile[256], sshisfile[256], title[256], *ss_str = NULL;
@@ -563,7 +566,7 @@ static void histogramming(FILE *log, int nbin, gmx_residuetype_t *rt,
                     }
                     if (bOccup && ((bfac_max <= 0) || ((bfac_max > 0) && bBfac)))
                     {
-                        hindex = ((dih[j][0]+M_PI)*nbin)/(2*M_PI);
+                        hindex = static_cast<int>(((dih[j][0]+M_PI)*nbin)/(2*M_PI));
                         range_check(hindex, 0, nbin);
 
                         /* Assign dihedral to either of the structure determined
@@ -761,8 +764,8 @@ static void histogramming(FILE *log, int nbin, gmx_residuetype_t *rt,
                         sprintf(title, "\\xc\\f{}\\s%d\\N Distribution for %s",
                                 Dih-NONCHI+1, residue_name);
                 }
-                strcpy(hhisfile, hisfile);
-                strcat(hhisfile, ".xvg");
+                std::strcpy(hhisfile, hisfile);
+                std::strcat(hhisfile, ".xvg");
                 fp = xvgropen(hhisfile, title, "Degrees", "", oenv);
                 if (output_env_get_print_xvgr_codes(oenv))
                 {
@@ -927,12 +930,12 @@ static void do_rama(int nf, int nlist, t_dlist dlist[], real **dih,
                 fprintf(fp, "%10g  %10g\n", phi, psi);
                 if (bViol)
                 {
-                    fprintf(gp, "%d\n", !bAllowed(dih[Phi][j], RAD2DEG*dih[Psi][j]));
+                    fprintf(gp, "%d\n", (bAllowed(dih[Phi][j], RAD2DEG*dih[Psi][j]) == FALSE) );
                 }
                 if (bOm)
                 {
                     omega = RAD2DEG*dih[Om][j];
-                    mat[(int)((phi*NMAT)/360)+NMAT/2][(int)((psi*NMAT)/360)+NMAT/2]
+                    mat[static_cast<int>(((phi*NMAT)/360)+NMAT/2)][static_cast<int>(((psi*NMAT)/360)+NMAT/2)]
                         += omega;
                 }
             }
@@ -951,12 +954,12 @@ static void do_rama(int nf, int nlist, t_dlist dlist[], real **dih,
                     for (k = 0; (k < NMAT); k++)
                     {
                         mat[j][k] /= nf;
-                        lo         = min(mat[j][k], lo);
-                        hi         = max(mat[j][k], hi);
+                        lo         = std::min(mat[j][k], lo);
+                        hi         = std::max(mat[j][k], hi);
                     }
                 }
                 /* Symmetrise */
-                if (fabs(lo) > fabs(hi))
+                if (std::abs(lo) > std::abs(hi))
                 {
                     hi = -lo;
                 }
@@ -1013,7 +1016,6 @@ static void print_transitions(const char *fn, int maxchi, int nlist,
 {
     /* based on order_params below */
     FILE *fp;
-    int   nh[edMax];
     int   i, Dih, Xi;
 
     /*  must correspond with enum in pp2shift.h:38 */
@@ -1035,11 +1037,6 @@ static void print_transitions(const char *fn, int maxchi, int nlist,
                   oenv);
     xvgr_legend(fp, NONCHI+maxchi, (const char**)leg, oenv);
 
-    for (Dih = 0; (Dih < edMax); Dih++)
-    {
-        nh[Dih] = 0;
-    }
-
     fprintf(fp, "%5s ", "#Res.");
     fprintf(fp, "%10s %10s %10s ", leg[edPhi], leg[edPsi], leg[edOmega]);
     for (Xi = 0; Xi < maxchi; Xi++)
@@ -1174,9 +1171,9 @@ static void order_params(FILE *log,
         x0 = y0 = z0 = 1000.0;
         for (i = 0; (i < atoms->nr); i++)
         {
-            x0 = min(x0, x[i][XX]);
-            y0 = min(y0, x[i][YY]);
-            z0 = min(z0, x[i][ZZ]);
+            x0 = std::min(x0, x[i][XX]);
+            y0 = std::min(y0, x[i][YY]);
+            z0 = std::min(z0, x[i][ZZ]);
         }
         x0 *= 10.0; /* nm -> angstrom */
         y0 *= 10.0; /* nm -> angstrom */
@@ -1370,7 +1367,7 @@ int gmx_chi(int argc, char *argv[])
     atom_id            isize, *index;
     int                ndih, nactdih, nf;
     real             **dih, *trans_frac, *aver_angle, *time;
-    int                i, j, **chi_lookup, *multiplicity;
+    int                i, **chi_lookup, *multiplicity;
 
     t_filenm           fnm[] = {
         { efSTX, "-s",  NULL,     ffREAD  },
@@ -1504,23 +1501,23 @@ int gmx_chi(int argc, char *argv[])
     snew(multiplicity, ndih);
     mk_multiplicity_lookup(multiplicity, maxchi, nlist, dlist, ndih);
 
-    strcpy(grpname, "All residues, ");
+    std::strcpy(grpname, "All residues, ");
     if (bPhi)
     {
-        strcat(grpname, "Phi ");
+        std::strcat(grpname, "Phi ");
     }
     if (bPsi)
     {
-        strcat(grpname, "Psi ");
+        std::strcat(grpname, "Psi ");
     }
     if (bOmega)
     {
-        strcat(grpname, "Omega ");
+        std::strcat(grpname, "Omega ");
     }
     if (bChi)
     {
-        strcat(grpname, "Chi 1-");
-        sprintf(grpname + strlen(grpname), "%i", maxchi);
+        std::strcat(grpname, "Chi 1-");
+        sprintf(grpname + std::strlen(grpname), "%i", maxchi);
     }