Merge branch 'master' into pygromacs

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

diff --git a/src/gromacs/gmxana/gmx_make_ndx.c b/src/gromacs/gmxana/gmx_make_ndx.cpp
similarity index 95%
rename from src/gromacs/gmxana/gmx_make_ndx.c
rename to src/gromacs/gmxana/gmx_make_ndx.cpp
index 55dc3ab47b4027dda9599d1634b2d3994fb9d124..4bd93584a5fe6de862d502c299639301e7c90a00 100644 (file)
--- a/src/gromacs/gmxana/gmx_make_ndx.c
+++ b/src/gromacs/gmxana/gmx_make_ndx.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -36,11 +36,14 @@
  */
 #include "gmxpre.h"
 
-#include <ctype.h>
-#include <string.h>
+#include <cctype>
+#include <cstring>
+
+#include <algorithm>
 
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
+#include "gromacs/gmxana/gmx_ana.h"
 #include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/vec.h"
@@ -149,7 +152,7 @@ static gmx_bool is_name_char(char c)
      */
     const char *spec = " !&|";
 
-    return (c != '\0' && strchr(spec, c) == NULL);
+    return (c != '\0' && std::strchr(spec, c) == NULL);
 }
 
 static int parse_names(char **string, int *n_names, char **names)
@@ -209,22 +212,22 @@ static gmx_bool parse_int_char(char **string, int *nr, char *c)
 
     *c = ' ';
 
-    if (isdigit((*string)[0]))
+    if (std::isdigit((*string)[0]))
     {
         *nr = (*string)[0]-'0';
         (*string)++;
-        while (isdigit((*string)[0]))
+        while (std::isdigit((*string)[0]))
         {
             *nr = (*nr)*10+(*string)[0]-'0';
             (*string)++;
         }
-        if (isalpha((*string)[0]))
+        if (std::isalpha((*string)[0]))
         {
             *c = (*string)[0];
             (*string)++;
         }
         /* Check if there is at most one non-digit character */
-        if (!isalnum((*string)[0]))
+        if (!std::isalnum((*string)[0]))
         {
             bRet = TRUE;
         }
@@ -278,7 +281,7 @@ static gmx_bool parse_string(char **string, int *nr, int ngrps, char **grpname)
         c = (*string)[0];
         (*string)++;
         s  = gmx_strdup((*string));
-        sp = strchr(s, c);
+        sp = std::strchr(s, c);
         if (sp != NULL)
         {
             (*string) += sp-s + 1;
@@ -325,7 +328,7 @@ static int select_atomnumbers(char **string, t_atoms *atoms, atom_id n1,
             {
                 sprintf(buf, "a_%d-%d", n1, up);
             }
-            strcpy(gname, buf);
+            std::strcpy(gname, buf);
         }
     }
     else
@@ -339,7 +342,7 @@ static int select_atomnumbers(char **string, t_atoms *atoms, atom_id n1,
                 index[*nr] = i-1;
                 (*nr)++;
                 sprintf(buf, "_%d", i);
-                strcat(gname, buf);
+                std::strcat(gname, buf);
             }
             else
             {
@@ -399,7 +402,7 @@ static int select_residuenumbers(char **string, t_atoms *atoms,
         {
             sprintf(buf, "r_%d-%d", n1, up);
         }
-        strcpy(gname, buf);
+        std::strcpy(gname, buf);
     }
     else
     {
@@ -418,7 +421,7 @@ static int select_residuenumbers(char **string, t_atoms *atoms,
                 }
             }
             sprintf(buf, "_%d", j);
-            strcat(gname, buf);
+            std::strcat(gname, buf);
         }
         while (parse_int_char(string, &j, &c));
     }
@@ -474,7 +477,7 @@ static int select_residueindices(char **string, t_atoms *atoms,
         {
             sprintf(buf, "r_%d-%d", n1, up);
         }
-        strcpy(gname, buf);
+        std::strcpy(gname, buf);
     }
     else
     {
@@ -493,7 +496,7 @@ static int select_residueindices(char **string, t_atoms *atoms,
                 }
             }
             sprintf(buf, "_%d", j);
-            strcat(gname, buf);
+            std::strcat(gname, buf);
         }
         while (parse_int_char(string, &j, &c));
     }
@@ -559,7 +562,7 @@ static gmx_bool comp_name(char *name, char *search)
                 break;
             default:
                 /* Compare a single character */
-                if (( bCase && strncmp(name, search, 1)) ||
+                if (( bCase && std::strncmp(name, search, 1)) ||
                     (!bCase && gmx_strncasecmp(name, search, 1)))
                 {
                     return FALSE;
@@ -698,11 +701,11 @@ static void make_gname(int n, char **names, char *gname)
 {
     int i;
 
-    strcpy(gname, names[0]);
+    std::strcpy(gname, names[0]);
     for (i = 1; i < n; i++)
     {
-        strcat(gname, "_");
-        strcat(gname, names[i]);
+        std::strcat(gname, "_");
+        std::strcat(gname, names[i]);
     }
 }
 
@@ -817,7 +820,7 @@ static int split_chain(t_atoms *atoms, rvec *x,
 
     while (ca_start < natoms)
     {
-        while ((ca_start < natoms) && strcmp(*atoms->atomname[ca_start], "CA"))
+        while ((ca_start < natoms) && std::strcmp(*atoms->atomname[ca_start], "CA"))
         {
             ca_start++;
         }
@@ -841,7 +844,7 @@ static int split_chain(t_atoms *atoms, rvec *x,
                 {
                     i++;
                 }
-                while ((i < natoms) && strcmp(*atoms->atomname[i], "CA"));
+                while ((i < natoms) && std::strcmp(*atoms->atomname[i], "CA"));
                 if (i < natoms)
                 {
                     rvec_sub(x[ca_end], x[i], vec);
@@ -973,7 +976,7 @@ static gmx_bool parse_entry(char **string, int natoms, t_atoms *atoms,
         if ((sel_nr1 >= 0) && (sel_nr1 < block->nr))
         {
             copy_group(sel_nr1, block, nr, index);
-            strcpy(gname, (*gn)[sel_nr1]);
+            std::strcpy(gname, (*gn)[sel_nr1]);
             printf("Copied index group %d '%s'\n", sel_nr1, (*gn)[sel_nr1]);
             bRet = TRUE;
         }
@@ -1015,7 +1018,7 @@ static gmx_bool parse_entry(char **string, int natoms, t_atoms *atoms,
             }
         }
     }
-    else if (strncmp(*string, "res", 3) == 0)
+    else if (std::strncmp(*string, "res", 3) == 0)
     {
         (*string) += 3;
         if (check_have_atoms(atoms, ostring) &&
@@ -1027,7 +1030,7 @@ static gmx_bool parse_entry(char **string, int natoms, t_atoms *atoms,
             sprintf(gname, "atom_%s", (*gn)[sel_nr1]);
         }
     }
-    else if (strncmp(*string, "ri", 2) == 0)
+    else if (std::strncmp(*string, "ri", 2) == 0)
     {
         (*string) += 2;
         if (check_have_atoms(atoms, ostring) &&
@@ -1052,7 +1055,7 @@ static gmx_bool parse_entry(char **string, int natoms, t_atoms *atoms,
             }
         }
     }
-    else if (strncmp(*string, "chain", 5) == 0)
+    else if (std::strncmp(*string, "chain", 5) == 0)
     {
         (*string) += 5;
         if (check_have_atoms(atoms, ostring) &&
@@ -1062,7 +1065,7 @@ static gmx_bool parse_entry(char **string, int natoms, t_atoms *atoms,
             sprintf(gname, "ch%s", names[0]);
             for (i = 1; i < n_names; i++)
             {
-                strcat(gname, names[i]);
+                std::strcat(gname, names[i]);
             }
         }
     }
@@ -1095,7 +1098,7 @@ static gmx_bool parse_entry(char **string, int natoms, t_atoms *atoms,
         }
         sfree(index1);
 
-        for (i = strlen(gname)+1; i > 0; i--)
+        for (i = std::strlen(gname)+1; i > 0; i--)
         {
             gname[i] = gname[i-1];
         }
@@ -1119,8 +1122,8 @@ static void list_residues(t_atoms *atoms)
         resind = atoms->atom[i].resind;
         if ((resind != prev_resind) || (i == atoms->nr-1))
         {
-            if ((bDiff = strcmp(*atoms->resinfo[resind].name,
-                                *atoms->resinfo[start].name)) ||
+            if ((bDiff = std::strcmp(*atoms->resinfo[resind].name,
+                                     *atoms->resinfo[start].name)) ||
                 (i == atoms->nr-1))
             {
                 if (bDiff)
@@ -1221,7 +1224,7 @@ static void edit_index(int natoms, t_atoms *atoms, rvec *x, t_blocka *block, cha
         {
             gmx_fatal(FARGS, "Error reading user input");
         }
-        inp_string[strlen(inp_string)-1] = 0;
+        inp_string[std::strlen(inp_string)-1] = 0;
         printf("\n");
         string = inp_string;
         while (string[0] == ' ')
@@ -1279,7 +1282,7 @@ static void edit_index(int natoms, t_atoms *atoms, rvec *x, t_blocka *block, cha
                 getchar();
             }
         }
-        else if (strncmp(string, "del", 3) == 0)
+        else if (std::strncmp(string, "del", 3) == 0)
         {
             string += 3;
             if (parse_int(&string, &sel_nr))
@@ -1311,7 +1314,7 @@ static void edit_index(int natoms, t_atoms *atoms, rvec *x, t_blocka *block, cha
                 }
             }
         }
-        else if (strncmp(string, "keep", 4) == 0)
+        else if (std::strncmp(string, "keep", 4) == 0)
         {
             string += 4;
             if (parse_int(&string, &sel_nr))
@@ -1320,7 +1323,7 @@ static void edit_index(int natoms, t_atoms *atoms, rvec *x, t_blocka *block, cha
                 remove_group(0, sel_nr-1, block, gn);
             }
         }
-        else if (strncmp(string, "name", 4) == 0)
+        else if (std::strncmp(string, "name", 4) == 0)
         {
             string += 4;
             if (parse_int(&string, &sel_nr))
@@ -1333,7 +1336,7 @@ static void edit_index(int natoms, t_atoms *atoms, rvec *x, t_blocka *block, cha
                 }
             }
         }
-        else if (strncmp(string, "case", 4) == 0)
+        else if (std::strncmp(string, "case", 4) == 0)
         {
             bCase = !bCase;
             printf("Switched to case %s\n", bCase ? "sensitive" : "insensitive");
@@ -1350,7 +1353,7 @@ static void edit_index(int natoms, t_atoms *atoms, rvec *x, t_blocka *block, cha
                 list_residues(atoms);
             }
         }
-        else if (strncmp(string, "splitch", 7) == 0)
+        else if (std::strncmp(string, "splitch", 7) == 0)
         {
             string += 7;
             if (check_have_atoms(atoms, ostring) &&
@@ -1360,7 +1363,7 @@ static void edit_index(int natoms, t_atoms *atoms, rvec *x, t_blocka *block, cha
                 split_chain(atoms, x, sel_nr, block, gn);
             }
         }
-        else if (strncmp(string, "splitres", 8) == 0)
+        else if (std::strncmp(string, "splitres", 8) == 0)
         {
             string += 8;
             if (check_have_atoms(atoms, ostring) &&
@@ -1370,7 +1373,7 @@ static void edit_index(int natoms, t_atoms *atoms, rvec *x, t_blocka *block, cha
                 split_group(atoms, sel_nr, block, gn, FALSE);
             }
         }
-        else if (strncmp(string, "splitat", 7) == 0)
+        else if (std::strncmp(string, "splitat", 7) == 0)
         {
             string += 7;
             if (check_have_atoms(atoms, ostring) &&
@@ -1386,7 +1389,6 @@ static void edit_index(int natoms, t_atoms *atoms, rvec *x, t_blocka *block, cha
         }
         else if (string[0] != 'q')
         {
-            nr1 = -1;
             nr2 = -1;
             if (parse_entry(&string, natoms, atoms, block, gn, &nr, index, gname))
             {
@@ -1416,7 +1418,7 @@ static void edit_index(int natoms, t_atoms *atoms, rvec *x, t_blocka *block, cha
                         {
                             index1[i] = index[i];
                         }
-                        strcpy(gname1, gname);
+                        std::strcpy(gname1, gname);
                         if (parse_entry(&string, natoms, atoms, block, gn, &nr2, index2, gname2))
                         {
                             if (bOr)
@@ -1469,7 +1471,7 @@ static int block2natoms(t_blocka *block)
     natoms = 0;
     for (i = 0; i < block->nra; i++)
     {
-        natoms = max(natoms, block->a[i]);
+        natoms = std::max(natoms, block->a[i]);
     }
     natoms++;