Merge "Improved pdb2gmx error message" into release-4-5-patches

diff --git a/src/kernel/gen_ad.c b/src/kernel/gen_ad.c
index 4b6bdb700cbee24adb56846d65ad6bcc444be322..a3234252f95c08574211410e51e6521fe37a383a 100644 (file)
--- a/src/kernel/gen_ad.c
+++ b/src/kernel/gen_ad.c
@@ -452,7 +452,7 @@ static int get_impropers(t_atoms *atoms,t_hackblock hb[],t_param **idih,
        bStop=FALSE;
        for(k=0; (k<4) && !bStop; k++) {
          ai[k] = search_atom(idihs->b[j].a[k],start,
-                             atoms->nr,atoms->atom,atoms->atomname,
+                          atoms,
                              "improper",bAllowMissing);
          if (ai[k] == NO_ATID)
            bStop = TRUE;
@@ -535,10 +535,10 @@ static void gen_excls(t_atoms *atoms, t_excls *excls, t_hackblock hb[],
       
       for(e=0; e<hbexcl->nb; e++) {
        anm = hbexcl->b[e].a[0];
-       i1 = search_atom(anm,astart,atoms->nr,atoms->atom,atoms->atomname,
+       i1 = search_atom(anm,astart,atoms,
                         "exclusion",bAllowMissing);
        anm = hbexcl->b[e].a[1];
-       i2 = search_atom(anm,astart,atoms->nr,atoms->atom,atoms->atomname,
+       i2 = search_atom(anm,astart,atoms,
                         "exclusion",bAllowMissing);
        if (i1!=NO_ATID && i2!=NO_ATID) {
          if (i1 > i2) {

diff --git a/src/kernel/genhydro.c b/src/kernel/genhydro.c
index 94997bfcb9db550475691108241fdd9cfb6545f6..a09693dd03f3e01d3ed3ac0ecfe0e5233b150011 100644 (file)
--- a/src/kernel/genhydro.c
+++ b/src/kernel/genhydro.c
@@ -74,7 +74,7 @@ static atom_id pdbasearch_atom(const char *name,int resind,t_atoms *pdba,
   for(i=0; (i<pdba->nr) && (pdba->atom[i].resind != resind); i++)
     ;
     
-  return search_atom(name,i,pdba->nr,pdba->atom,pdba->atomname,
+  return search_atom(name,i,pdba,
                     searchtype,bAllowMissing);
 }
 

diff --git a/src/kernel/pdb2top.c b/src/kernel/pdb2top.c
index 535c2e53f93e42820949a264e3b162ce10c0510c..98b5d13347601f7353edcff672f91b28219ce2f5 100644 (file)
--- a/src/kernel/pdb2top.c
+++ b/src/kernel/pdb2top.c
@@ -703,20 +703,23 @@ void write_top(FILE *out, char *pr,char *molname,
 }
 
 static atom_id search_res_atom(const char *type,int resind,
-                              int natom,t_atom at[],
-                              char ** const *aname,
+                   t_atoms *atoms,
                               const char *bondtype,gmx_bool bAllowMissing)
 {
   int i;
 
-  for(i=0; (i<natom); i++)
-    if (at[i].resind == resind)
-      return search_atom(type,i,natom,at,aname,bondtype,bAllowMissing);
+  for(i=0; (i<atoms->nr); i++)
+  {
+    if (atoms->atom[i].resind == resind)
+    {
+      return search_atom(type,i,atoms,bondtype,bAllowMissing);
+    }
+  }
   
   return NO_ATID;
 }
 
-static void do_ssbonds(t_params *ps,int natoms,t_atom atom[],char **aname[],
+static void do_ssbonds(t_params *ps,t_atoms *atoms,
                       int nssbonds,t_ssbond *ssbonds,gmx_bool bAllowMissing)
 {
   int     i,ri,rj;
@@ -725,9 +728,9 @@ static void do_ssbonds(t_params *ps,int natoms,t_atom atom[],char **aname[],
   for(i=0; (i<nssbonds); i++) {
     ri = ssbonds[i].res1;
     rj = ssbonds[i].res2;
-    ai = search_res_atom(ssbonds[i].a1,ri,natoms,atom,aname,
+    ai = search_res_atom(ssbonds[i].a1,ri,atoms,
                         "special bond",bAllowMissing);
-    aj = search_res_atom(ssbonds[i].a2,rj,natoms,atom,aname,
+    aj = search_res_atom(ssbonds[i].a2,rj,atoms,
                         "special bond",bAllowMissing);
     if ((ai == NO_ATID) || (aj == NO_ATID))
       gmx_fatal(FARGS,"Trying to make impossible special bond (%s-%s)!",
@@ -743,8 +746,8 @@ static gmx_bool inter_res_bond(const t_rbonded *b)
 }
 
 static void at2bonds(t_params *psb, t_hackblock *hb,
-                     int natoms, t_atom atom[], char **aname[], 
-                     int nres, rvec x[], 
+                     t_atoms *atoms,
+                     rvec x[],
                      real long_bond_dist, real short_bond_dist,
                      gmx_bool bAllowMissing)
 {
@@ -763,16 +766,16 @@ static void at2bonds(t_params *psb, t_hackblock *hb,
 
   fprintf(stderr,"Making bonds...\n");
   i=0;
-  for(resind=0; (resind < nres) && (i<natoms); resind++) {
+  for(resind=0; (resind < atoms->nres) && (i<atoms->nr); resind++) {
     /* add bonds from list of bonded interactions */
     for(j=0; j < hb[resind].rb[ebtsBONDS].nb; j++) {
       /* Unfortunately we can not issue errors or warnings
        * for missing atoms in bonds, as the hydrogens and terminal atoms
        * have not been added yet.
        */
-      ai=search_atom(hb[resind].rb[ebtsBONDS].b[j].AI,i,natoms,atom,aname,
+      ai=search_atom(hb[resind].rb[ebtsBONDS].b[j].AI,i,atoms,
                     ptr,TRUE);
-      aj=search_atom(hb[resind].rb[ebtsBONDS].b[j].AJ,i,natoms,atom,aname,
+      aj=search_atom(hb[resind].rb[ebtsBONDS].b[j].AJ,i,atoms,
                     ptr,TRUE);
       if (ai != NO_ATID && aj != NO_ATID) {
           dist2 = distance2(x[ai],x[aj]);
@@ -790,11 +793,11 @@ static void at2bonds(t_params *psb, t_hackblock *hb,
       }
     }
     /* add bonds from list of hacks (each added atom gets a bond) */
-    while( (i<natoms) && (atom[i].resind == resind) ) {
+    while( (i<atoms->nr) && (atoms->atom[i].resind == resind) ) {
       for(j=0; j < hb[resind].nhack; j++)
        if ( ( hb[resind].hack[j].tp > 0 ||
               hb[resind].hack[j].oname==NULL ) &&
-            strcmp(hb[resind].hack[j].AI,*(aname[i])) == 0 ) {
+            strcmp(hb[resind].hack[j].AI,*(atoms->atomname[i])) == 0 ) {
          switch(hb[resind].hack[j].tp) {
          case 9:          /* COOH terminus */
            add_param(psb,i,i+1,NULL,NULL);     /* C-O  */
@@ -1350,9 +1353,6 @@ static void gen_cmap(t_params *psb, t_restp *restp, t_atoms *atoms, gmx_residuet
 {
     int residx,i,j,k;
     const char *ptr;
-    int natoms = atoms->nr;
-    t_atom *atom = atoms->atom;
-    char ***aname = atoms->atomname;
     t_resinfo *resinfo = atoms->resinfo;
     int nres = atoms->nres;
     gmx_bool bAddCMAP;
@@ -1380,7 +1380,7 @@ static void gen_cmap(t_params *psb, t_restp *restp, t_atoms *atoms, gmx_residuet
             for(k = 0; k < NUM_CMAP_ATOMS && bAddCMAP; k++)
             {
                 cmap_atomid[k] = search_atom(restp[residx].rb[ebtsCMAP].b[j].a[k],
-                                             i,natoms,atom,aname,ptr,TRUE);
+                                             i,atoms,ptr,TRUE);
                 bAddCMAP = bAddCMAP && (cmap_atomid[k] != NO_ATID);
                 if (!bAddCMAP)
                 {
@@ -1389,7 +1389,7 @@ static void gen_cmap(t_params *psb, t_restp *restp, t_atoms *atoms, gmx_residuet
                      * into the atom array. */
                     break;
                 }
-                this_residue_index = atom[cmap_atomid[k]].resind;
+                this_residue_index = atoms->atom[cmap_atomid[k]].resind;
                 if (0 == k)
                 {
                     cmap_chainnum = resinfo[this_residue_index].chainnum;
@@ -1413,7 +1413,7 @@ static void gen_cmap(t_params *psb, t_restp *restp, t_atoms *atoms, gmx_residuet
                
                if(residx<nres-1)
                {
-                       while(atom[i].resind<residx+1)
+                       while(atoms->atom[i].resind<residx+1)
                        {
                                i++;
                        }
@@ -1472,12 +1472,12 @@ void pdb2top(FILE *top_file, char *posre_fn, char *molname,
   
   /* Make bonds */
   at2bonds(&(plist[F_BONDS]), hb, 
-           atoms->nr, atoms->atom, atoms->atomname, atoms->nres, *x, 
+           atoms, *x,
            long_bond_dist, short_bond_dist, bAllowMissing);
   
   /* specbonds: disulphide bonds & heme-his */
   do_ssbonds(&(plist[F_BONDS]),
-            atoms->nr, atoms->atom, atoms->atomname, nssbonds, ssbonds,
+            atoms, nssbonds, ssbonds,
             bAllowMissing);
   
   nmissat = name2type(atoms, &cgnr, atype, restp, rt);

diff --git a/src/kernel/pgutil.c b/src/kernel/pgutil.c
index 7a3e7d86818beb272b4a08cd946016726a58bdb6..e948dea471b19053e92e5ba9d5435c0d2d5ae47a 100644 (file)
--- a/src/kernel/pgutil.c
+++ b/src/kernel/pgutil.c
@@ -45,6 +45,7 @@
 #define BUFSIZE 1024
 static void atom_not_found(int fatal_errno,const char *file,int line,
                           const char *atomname,int resind,
+                           const char *resname,
                           const char *bondtype,gmx_bool bAllowMissing)
 {
     char message_buffer[BUFSIZE];
@@ -53,17 +54,21 @@ static void atom_not_found(int fatal_errno,const char *file,int line,
         if (0 != strcmp(bondtype, "atom"))
         {
             snprintf(message_buffer, 1024,
-                     "Atom %s is used in an interaction of type %s in the topology\n"
-                     "database, but an atom of that name was not found in residue\n"
-                     "number %d.\n",
-                     atomname,bondtype,resind+1);
+                     "Residue %d named %s of a molecule in the input file was mapped\n"
+                     "to an entry in the topology database, but the atom %s used in\n"
+                     "an interaction of type %s in that entry is not found in the\n"
+                     "input file. Perhaps your atom and/or residue naming needs to be\n"
+                     "fixed.\n",
+                     resind+1, resname, atomname, bondtype);
         }
         else
         {
             snprintf(message_buffer, 1024,
-                     "Atom %s is used in the topology database, but an atom of that\n"
-                     "name was not found in residue number %d.\n",
-                     atomname,resind+1);
+                     "Residue %d named %s of a molecule in the input file was mapped\n"
+                     "to an entry in the topology database, but the atom %s used in\n"
+                     "that entry is not found in the input file. Perhaps your atom\n"
+                     "and/or residue naming needs to be fixed.\n",
+                     resind+1, resname, atomname);
         }
         if (bAllowMissing)
         {
@@ -76,12 +81,15 @@ static void atom_not_found(int fatal_errno,const char *file,int line,
     }
 }
        
-atom_id search_atom(const char *type,int start,int natoms,t_atom at[],
-                   char ** const * anm,
+atom_id search_atom(const char *type,int start,
+                    t_atoms *atoms,
                    const char *bondtype,gmx_bool bAllowMissing)
 {
   int     i,resind=-1;
   gmx_bool    bPrevious,bNext;
+  int natoms = atoms->nr;
+  t_atom *at = atoms->atom;
+  char ** const * anm = atoms->atomname;
 
   bPrevious = (strchr(type,'-') != NULL);
   bNext     = (strchr(type,'+') != NULL);
@@ -102,7 +110,9 @@ atom_id search_atom(const char *type,int start,int natoms,t_atom at[],
        return (atom_id) i;
     }
     if (!(bNext && at[start].resind==at[natoms-1].resind))
-      atom_not_found(FARGS,type,at[start].resind,bondtype,bAllowMissing);
+    {
+        atom_not_found(FARGS,type,at[start].resind,*atoms->resinfo[resind].name,bondtype,bAllowMissing);
+    }
   }
   else {
     /* The previous residue */
@@ -113,7 +123,9 @@ atom_id search_atom(const char *type,int start,int natoms,t_atom at[],
       if (gmx_strcasecmp(type,*(anm[i]))==0)
        return (atom_id) i;
     if (start > 0)
-      atom_not_found(FARGS,type,at[start].resind,bondtype,bAllowMissing);
+    {
+        atom_not_found(FARGS,type,at[start].resind,*atoms->resinfo[resind].name,bondtype,bAllowMissing);
+    }
   }
   return NO_ATID;
 }

diff --git a/src/kernel/pgutil.h b/src/kernel/pgutil.h
index b4ac091894b803475b2cecd7e5b82aa8f65967df..040c310f165a2250a55d2524e2966571a247b11a 100644 (file)
--- a/src/kernel/pgutil.h
+++ b/src/kernel/pgutil.h
@@ -39,8 +39,7 @@
 #include "typedefs.h"
 
 extern atom_id search_atom(const char *type,int start,
-                          int natoms,t_atom at[],
-                          char ** const * anm,
+                          t_atoms *atoms,
                           const char *bondtype,gmx_bool bAllowMissing);
 /* Search an atom in array of pointers to strings, starting from start
  * if type starts with '-' then searches backwards from start.