Moved first batch of analysis tool source to C++

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

diff --git a/src/gromacs/gmxana/gmx_do_dssp.c b/src/gromacs/gmxana/gmx_do_dssp.cpp
similarity index 94%
rename from src/gromacs/gmxana/gmx_do_dssp.c
rename to src/gromacs/gmxana/gmx_do_dssp.cpp
index cc33e1764130faae364939cabea2206a0680a2b5..2abed999d596c3444257341c8e80e2eb7f9d76fc 100644 (file)
--- a/src/gromacs/gmxana/gmx_do_dssp.c
+++ b/src/gromacs/gmxana/gmx_do_dssp.cpp
@@ -36,7 +36,10 @@
  */
 #include "gmxpre.h"
 
-#include <stdlib.h>
+#include <cstdlib>
+#include <cstring>
+
+#include <algorithm>
 
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
@@ -45,6 +48,7 @@
 #include "gromacs/fileio/strdb.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
 #include "gromacs/gmxana/gstat.h"
 #include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/typedefs.h"
@@ -81,7 +85,7 @@ static int strip_dssp(char *dsspfile, int nres,
     {
         fgets2(buf, STRLEN, tapeout);
     }
-    while (strstr(buf, "KAPPA") == NULL);
+    while (std::strstr(buf, "KAPPA") == NULL);
     if (bFirst)
     {
         /* Since we also have empty lines in the dssp output (temp) file,
@@ -170,7 +174,7 @@ static int strip_dssp(char *dsspfile, int nres,
     for (i = 0; i < nr; i++)
     {
         c.c1                  = ssbuf[i];
-        mat->matrix[frame][i] = max(0, searchcmap(mat->nmap, mat->map, c));
+        mat->matrix[frame][i] = std::max(static_cast<t_matelmt>(0), searchcmap(mat->nmap, mat->map, c));
     }
     frame++;
     mat->nx = frame;
@@ -217,15 +221,15 @@ static void check_oo(t_atoms *atoms)
 
     for (i = 0; (i < atoms->nr); i++)
     {
-        if (strcmp(*(atoms->atomname[i]), "OXT") == 0)
+        if (std::strcmp(*(atoms->atomname[i]), "OXT") == 0)
         {
             *atoms->atomname[i] = OOO;
         }
-        else if (strcmp(*(atoms->atomname[i]), "O1") == 0)
+        else if (std::strcmp(*(atoms->atomname[i]), "O1") == 0)
         {
             *atoms->atomname[i] = OOO;
         }
-        else if (strcmp(*(atoms->atomname[i]), "OC1") == 0)
+        else if (std::strcmp(*(atoms->atomname[i]), "OC1") == 0)
         {
             *atoms->atomname[i] = OOO;
         }
@@ -324,12 +328,12 @@ void write_sas_mat(const char *fn, real **accr, int nframe, int nres, t_matrix *
         {
             for (j = 0; j < nres; j++)
             {
-                lo = min(lo, accr[i][j]);
-                hi = max(hi, accr[i][j]);
+                lo = std::min(lo, accr[i][j]);
+                hi = std::max(hi, accr[i][j]);
             }
         }
         fp   = gmx_ffopen(fn, "w");
-        nlev = hi-lo+1;
+        nlev = static_cast<int>(hi-lo+1);
         write_xpm(fp, 0, "Solvent Accessible Surface", "Surface (A^2)",
                   "Time", "Residue Index", nframe, nres,
                   mat->axis_x, mat->axis_y, accr, lo, hi, rlo, rhi, &nlev);
@@ -362,7 +366,7 @@ void analyse_ss(const char *outfile, t_matrix *mat, const char *ss_string,
     {
         fprintf(fp, "@ subtitle \"Structure = ");
     }
-    for (s = 0; s < strlen(ss_string); s++)
+    for (s = 0; s < std::strlen(ss_string); s++)
     {
         if (s > 0)
         {
@@ -387,7 +391,7 @@ void analyse_ss(const char *outfile, t_matrix *mat, const char *ss_string,
     for (f = 0; f < mat->nx; f++)
     {
         ss_count = 0;
-        for (s = 0; s < (size_t)mat->nmap; s++)
+        for (s = 0; s < static_cast<size_t>(mat->nmap); s++)
         {
             count[s] = 0;
         }
@@ -396,16 +400,16 @@ void analyse_ss(const char *outfile, t_matrix *mat, const char *ss_string,
             count[mat->matrix[f][r]]++;
             total[mat->matrix[f][r]]++;
         }
-        for (s = 0; s < (size_t)mat->nmap; s++)
+        for (s = 0; s < static_cast<size_t>(mat->nmap); s++)
         {
-            if (strchr(ss_string, map[s].code.c1))
+            if (std::strchr(ss_string, map[s].code.c1))
             {
                 ss_count    += count[s];
                 total_count += count[s];
             }
         }
         fprintf(fp, "%8g %5d", mat->axis_x[f], ss_count);
-        for (s = 0; s < (size_t)mat->nmap; s++)
+        for (s = 0; s < static_cast<size_t>(mat->nmap); s++)
         {
             fprintf(fp, " %5d", count[s]);
         }
@@ -413,17 +417,17 @@ void analyse_ss(const char *outfile, t_matrix *mat, const char *ss_string,
     }
     /* now print column totals */
     fprintf(fp, "%-8s %5d", "# Totals", total_count);
-    for (s = 0; s < (size_t)mat->nmap; s++)
+    for (s = 0; s < static_cast<size_t>(mat->nmap); s++)
     {
         fprintf(fp, " %5d", total[s]);
     }
     fprintf(fp, "\n");
 
     /* now print percentages */
-    fprintf(fp, "%-8s %5.2f", "# SS %", total_count / (real) (mat->nx * mat->ny));
-    for (s = 0; s < (size_t)mat->nmap; s++)
+    fprintf(fp, "%-8s %5.2f", "# SS %", total_count / static_cast<real>(mat->nx * mat->ny));
+    for (s = 0; s < static_cast<size_t>(mat->nmap); s++)
     {
-        fprintf(fp, " %5.2f", total[s] / (real) (mat->nx * mat->ny));
+        fprintf(fp, " %5.2f", total[s] / static_cast<real>(mat->nx * mat->ny));
     }
     fprintf(fp, "\n");
 
@@ -552,7 +556,7 @@ int gmx_do_dssp(int argc, char *argv[])
     }
     fprintf(stderr, "There are %d residues in your selected group\n", nres);
 
-    strcpy(pdbfile, "ddXXXXXX");
+    std::strcpy(pdbfile, "ddXXXXXX");
     gmx_tmpnam(pdbfile);
     if ((tmpf = fopen(pdbfile, "w")) == NULL)
     {
@@ -568,7 +572,7 @@ int gmx_do_dssp(int argc, char *argv[])
         fclose(tmpf);
     }
 
-    strcpy(tmpfile, "ddXXXXXX");
+    std::strcpy(tmpfile, "ddXXXXXX");
     gmx_tmpnam(tmpfile);
     if ((tmpf = fopen(tmpfile, "w")) == NULL)
     {
@@ -720,7 +724,7 @@ int gmx_do_dssp(int argc, char *argv[])
 
         for (i = 0; i < atoms->nres; i++)
         {
-            av_area[i] = (average_area[i] / (real)nframe);
+            av_area[i] = (average_area[i] / static_cast<real>(nframe));
         }
 
         norm_acc(atoms, nres, av_area, norm_av_area);