Sort all includes in src/gromacs

[alexxy/gromacs.git] / src / gromacs / gmxpreprocess / pdb2gmx.c

diff --git a/src/gromacs/gmxpreprocess/pdb2gmx.c b/src/gromacs/gmxpreprocess/pdb2gmx.c
index f7207a898c610f5f07f99ca41a60628555cd5d73..ac9f6ec0837524aa9a7b6b5543e086b8ed87bb2f 100644 (file)
--- a/src/gromacs/gmxpreprocess/pdb2gmx.c
+++ b/src/gromacs/gmxpreprocess/pdb2gmx.c
@@ -34,48 +34,46 @@
  * To help us fund GROMACS development, we humbly ask that you cite
  * the research papers on the package. Check out http://www.gromacs.org.
  */
-#include "pdb2gmx.h"
+#include "gmxpre.h"
 
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "pdb2gmx.h"
 
-#include <time.h>
 #include <ctype.h>
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "gromacs/fileio/gmxfio.h"
-#include "smalloc.h"
-#include "copyrite.h"
-#include "string2.h"
-#include "gromacs/fileio/confio.h"
-#include "symtab.h"
-#include "vec.h"
+#include <stdlib.h>
+#include <string.h>
+#include <time.h>
+
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/futil.h"
-#include "gmx_fatal.h"
+#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/pdbio.h"
-#include "toputil.h"
-#include "h_db.h"
-#include "physics.h"
-#include "pgutil.h"
-#include "calch.h"
-#include "resall.h"
-#include "pdb2top.h"
-#include "ter_db.h"
-#include "gromacs/gmxlib/conformation-utilities.h"
-#include "genhydro.h"
-#include "readinp.h"
-#include "atomprop.h"
-#include "index.h"
-#include "fflibutil.h"
-#include "macros.h"
-
 #include "gromacs/fileio/strdb.h"
-
-#include "hizzie.h"
-#include "specbond.h"
-#include "xlate.h"
+#include "gromacs/gmxlib/conformation-utilities.h"
+#include "gromacs/gmxpreprocess/fflibutil.h"
+#include "gromacs/gmxpreprocess/genhydro.h"
+#include "gromacs/gmxpreprocess/h_db.h"
+#include "gromacs/gmxpreprocess/hizzie.h"
+#include "gromacs/gmxpreprocess/pdb2top.h"
+#include "gromacs/gmxpreprocess/pgutil.h"
+#include "gromacs/gmxpreprocess/resall.h"
+#include "gromacs/gmxpreprocess/specbond.h"
+#include "gromacs/gmxpreprocess/ter_db.h"
+#include "gromacs/gmxpreprocess/toputil.h"
+#include "gromacs/gmxpreprocess/xlate.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/readinp.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/atomprop.h"
+#include "gromacs/topology/block.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/topology/residuetypes.h"
+#include "gromacs/topology/symtab.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 typedef struct {
     char gmx[6];
@@ -513,7 +511,7 @@ void write_posres(char *fn, t_atoms *pdba, real fc)
 static int read_pdball(const char *inf, const char *outf, char *title,
                        t_atoms *atoms, rvec **x,
                        int *ePBC, matrix box, gmx_bool bRemoveH,
-                       t_symtab *symtab, gmx_residuetype_t rt, const char *watres,
+                       t_symtab *symtab, gmx_residuetype_t *rt, const char *watres,
                        gmx_atomprop_t aps, gmx_bool bVerbose)
 /* Read a pdb file. (containing proteins) */
 {
@@ -834,7 +832,8 @@ static int remove_duplicate_atoms(t_atoms *pdba, rvec x[], gmx_bool bVerbose)
     return pdba->nr;
 }
 
-void find_nc_ter(t_atoms *pdba, int r0, int r1, int *r_start, int *r_end, gmx_residuetype_t rt)
+void find_nc_ter(t_atoms *pdba, int r0, int r1, int *r_start, int *r_end,
+                 gmx_residuetype_t *rt)
 {
     int         i;
     const char *p_startrestype;
@@ -1230,7 +1229,7 @@ int gmx_pdb2gmx(int argc, char *argv[])
     t_hackblock      *ah;
     t_symtab          symtab;
     gpp_atomtype_t    atype;
-    gmx_residuetype_t rt;
+    gmx_residuetype_t*rt;
     const char       *top_fn;
     char              fn[256], itp_fn[STRLEN], posre_fn[STRLEN], buf_fn[STRLEN];
     char              molname[STRLEN], title[STRLEN], quote[STRLEN];
@@ -1680,7 +1679,7 @@ int gmx_pdb2gmx(int argc, char *argv[])
             chains[i].pdba->atom[j] = pdba_all.atom[pdb_ch[si].start+j];
             snew(chains[i].pdba->atomname[j], 1);
             *chains[i].pdba->atomname[j] =
-                strdup(*pdba_all.atomname[pdb_ch[si].start+j]);
+                gmx_strdup(*pdba_all.atomname[pdb_ch[si].start+j]);
             chains[i].pdba->pdbinfo[j] = pdba_all.pdbinfo[pdb_ch[si].start+j];
             copy_rvec(pdbx[pdb_ch[si].start+j], chains[i].x[j]);
         }
@@ -1697,7 +1696,7 @@ int gmx_pdb2gmx(int argc, char *argv[])
         {
             chains[i].pdba->resinfo[j] = pdba_all.resinfo[k+j];
             snew(chains[i].pdba->resinfo[j].name, 1);
-            *chains[i].pdba->resinfo[j].name = strdup(*pdba_all.resinfo[k+j].name);
+            *chains[i].pdba->resinfo[j].name = gmx_strdup(*pdba_all.resinfo[k+j].name);
             /* make all chain identifiers equal to that of the chain */
             chains[i].pdba->resinfo[j].chainid = pdb_ch[si].chainid;
         }
@@ -1712,7 +1711,7 @@ int gmx_pdb2gmx(int argc, char *argv[])
     printf("There are %d chains and %d blocks of water and "
            "%d residues with %d atoms\n",
            nch-nwaterchain, nwaterchain,
-           pdba_all.resinfo[pdba_all.atom[natom-1].resind].nr, natom);
+           pdba_all.nres, natom);
 
     printf("\n  %5s  %4s %6s\n", "chain", "#res", "#atoms");
     for (i = 0; (i < nch); i++)
@@ -2055,7 +2054,7 @@ int gmx_pdb2gmx(int argc, char *argv[])
 
             nincl++;
             srenew(incls, nincl);
-            incls[nincl-1] = strdup(itp_fn);
+            incls[nincl-1] = gmx_strdup(itp_fn);
             itp_file       = gmx_fio_fopen(itp_fn, "w");
         }
         else
@@ -2066,12 +2065,12 @@ int gmx_pdb2gmx(int argc, char *argv[])
         srenew(mols, nmol+1);
         if (cc->bAllWat)
         {
-            mols[nmol].name = strdup("SOL");
+            mols[nmol].name = gmx_strdup("SOL");
             mols[nmol].nr   = pdba->nres;
         }
         else
         {
-            mols[nmol].name = strdup(molname);
+            mols[nmol].name = gmx_strdup(molname);
             mols[nmol].nr   = 1;
         }
         nmol++;