Merge "Added support for submission to cdash servers." into release-4-6

diff --git a/include/gstat.h b/include/gstat.h
index 574892ec686c4cbb4de4306023760c07301046d7..719fe625125e43794b70da7347e3013086b7c9f0 100644 (file)
--- a/include/gstat.h
+++ b/include/gstat.h
@@ -269,9 +269,9 @@ void low_ana_dih_trans(gmx_bool bTrans, const char *fn_trans,
                              gmx_bool bHisto, const char *fn_histo, int maxchi, 
                              real **dih, int nlist, t_dlist dlist[], 
                               int nframes, int nangles, const char *grpname, 
-                              int xity[], real t0, real dt, gmx_bool bRb, 
+                              int multiplicity[], real t0, real dt, gmx_bool bRb, 
                               real core_frac, const output_env_t oenv); 
-  /* as above but passes dlist so can copy occupancies into it, and xity[] 
+  /* as above but passes dlist so can copy occupancies into it, and multiplicity[] 
    *  (1..nangles, corresp to dih[this][], so can have non-3 multiplicity of
    * rotamers. Also production of xvg output files is conditional 
    * and the fractional width of each rotamer can be set ie for a 3 fold 
@@ -402,12 +402,12 @@ int pr_trans(FILE *fp,int nl,t_dlist dl[],real dt,int Xi);
 void mk_chi_lookup (int **lookup, int maxchi, real **dih, 
                           int nlist, t_dlist dlist[]) ; 
 
-void mk_multiplicity_lookup (int *xity, int maxchi, real **dih, 
+void mk_multiplicity_lookup (int *multiplicity, int maxchi, real **dih, 
                                    int nlist, t_dlist dlist[],int nangle) ; 
 
 void get_chi_product_traj (real **dih,int nframes,int nangles, 
                                  int nlist,int maxchi, t_dlist dlist[], 
-                                  real time[], int **lookup,int *xity,
+                                  real time[], int **lookup,int *multiplicity,
                                   gmx_bool bRb,gmx_bool bNormalize,
                                  real core_frac,gmx_bool bAll,const char *fnall,
                                   const output_env_t oenv); 

diff --git a/src/tools/anadih.c b/src/tools/anadih.c
index 91a67c102c53b13de22d7fcb581ff35edacfea43..c3c32dbaff19ae14d63ec0afab02f1a0563e1cdd 100644 (file)
--- a/src/tools/anadih.c
+++ b/src/tools/anadih.c
@@ -119,28 +119,28 @@ void ana_dih_trans(const char *fn_trans,const char *fn_histo,
   /* just a wrapper; declare extra args, then chuck away at end. */ 
   int maxchi = 0 ; 
   t_dlist *dlist ; 
-  int *xity; 
+  int *multiplicity; 
   int nlist = nangles ; 
   int k ; 
 
   snew(dlist,nlist);  
-  snew(xity,nangles); 
+  snew(multiplicity,nangles); 
   for(k=0; (k<nangles); k++) {
-    xity[k]=3 ; 
+    multiplicity[k]=3 ; 
   }
 
   low_ana_dih_trans(TRUE, fn_trans,TRUE, fn_histo, maxchi, 
                     dih, nlist, dlist, nframes,
-                   nangles, grpname, xity, t0, dt, bRb, 0.5,oenv); 
+                   nangles, grpname, multiplicity, t0, dt, bRb, 0.5,oenv); 
   sfree(dlist); 
-  sfree(xity); 
+  sfree(multiplicity); 
   
 }
 
 void low_ana_dih_trans(gmx_bool bTrans, const char *fn_trans,
                       gmx_bool bHisto, const char *fn_histo, int maxchi, 
                       real **dih, int nlist, t_dlist dlist[], int nframes,
-                      int nangles, const char *grpname, int xity[], 
+                      int nangles, const char *grpname, int multiplicity[], 
                       real t0, real dt, gmx_bool bRb, real core_frac,
                        const output_env_t oenv)
 {
@@ -178,12 +178,12 @@ void low_ana_dih_trans(gmx_bool bTrans, const char *fn_trans,
 #ifdef OLDIE
     mind = maxd = prev = dih[i][0]; 
 #else
-    cur_bin = calc_bin(dih[i][0],xity[i],core_frac);
+    cur_bin = calc_bin(dih[i][0],multiplicity[i],core_frac);
     rot_occ[cur_bin][i]++ ; 
 #endif    
     for (j=1; (j<nframes); j++)
     {
-      new_bin = calc_bin(dih[i][j],xity[i],core_frac);
+      new_bin = calc_bin(dih[i][j],multiplicity[i],core_frac);
       rot_occ[new_bin][i]++ ; 
 #ifndef OLDIE
       if (cur_bin == 0)
@@ -281,11 +281,11 @@ void low_ana_dih_trans(gmx_bool bTrans, const char *fn_trans,
 
 }
 
-void mk_multiplicity_lookup (int *xity, int maxchi, real **dih, 
+void mk_multiplicity_lookup (int *multiplicity, int maxchi, real **dih, 
                             int nlist, t_dlist dlist[],int nangles) 
 {
   /* new by grs - for dihedral j (as in dih[j]) get multiplicity from dlist
-   * and store in xity[j] 
+   * and store in multiplicity[j] 
    */ 
 
   int j, Dih, i ; 
@@ -300,11 +300,11 @@ void mk_multiplicity_lookup (int *xity, int maxchi, real **dih,
          ((Dih == edOmega) && (has_dihedral(edOmega,&(dlist[i])))) ||
          ((Dih  > edOmega) && (dlist[i].atm.Cn[Dih-NONCHI+3] != -1))) {
        /* default - we will correct the rest below */ 
-       xity[j] = 3 ; 
+       multiplicity[j] = 3 ; 
 
        /* make omegas 2fold, though doesn't make much more sense than 3 */ 
        if (Dih == edOmega && (has_dihedral(edOmega,&(dlist[i])))) {
-         xity[j] = 2 ; 
+         multiplicity[j] = 2 ; 
        } 
 
        /* dihedrals to aromatic rings, COO, CONH2 or guanidinium are 2fold*/
@@ -319,7 +319,7 @@ void mk_multiplicity_lookup (int *xity, int maxchi, real **dih,
               ((strstr(name,"GLN") != NULL) && (Dih == edChi3))  ||   
               ((strstr(name,"ASN") != NULL) && (Dih == edChi2))  ||   
               ((strstr(name,"ARG") != NULL) && (Dih == edChi4))  ) {
-           xity[j] = 2; 
+           multiplicity[j] = 2; 
          }
        }
        j++ ; 
@@ -331,7 +331,7 @@ void mk_multiplicity_lookup (int *xity, int maxchi, real **dih,
            j,nangles);
   /* Check for remaining dihedrals */
   for(;(j < nangles); j++)
-    xity[j] = 3;
+    multiplicity[j] = 3;
 
 }
 
@@ -369,7 +369,7 @@ void mk_chi_lookup (int **lookup, int maxchi, real **dih,
 
 void get_chi_product_traj (real **dih,int nframes,int nangles, int nlist,
                           int maxchi, t_dlist dlist[], real time[], 
-                          int **lookup, int *xity,gmx_bool bRb, gmx_bool bNormalize,
+                          int **lookup, int *multiplicity,gmx_bool bRb, gmx_bool bNormalize,
                           real core_frac, gmx_bool bAll, const char *fnall,
                            const output_env_t oenv) 
 {
@@ -407,7 +407,7 @@ void get_chi_product_traj (real **dih,int nframes,int nangles, int nlist,
     for (Xi = 0 ; Xi < maxchi ; Xi ++ ) {
       index = lookup[i][Xi] ; /* chi_(Xi+1) of res i (-1 if off end) */ 
       if ( index >= 0 ) {
-       n = xity[index]; 
+       n = multiplicity[index]; 
        nbin = n*nbin ; 
       }
     }
@@ -423,14 +423,14 @@ void get_chi_product_traj (real **dih,int nframes,int nangles, int nlist,
        bRotZero = TRUE ; 
        bHaveChi = FALSE ; 
       } else {
-       b = calc_bin(dih[index][j],xity[index],core_frac) ; 
+       b = calc_bin(dih[index][j],multiplicity[index],core_frac) ; 
        accum = b - 1 ; 
        if (b == 0 ) 
          bRotZero = TRUE ; 
        for (Xi = 1 ; Xi < maxchi ; Xi ++ ) {
          index = lookup[i][Xi] ; /* chi_(Xi+1) of res i (-1 if off end) */ 
          if ( index >= 0 ) {
-           n = xity[index]; 
+           n = multiplicity[index]; 
            b = calc_bin(dih[index][j],n,core_frac); 
            accum = n * accum + b - 1 ; 
            if (b == 0 ) 

diff --git a/src/tools/gmx_chi.c b/src/tools/gmx_chi.c
index c3971e575ebb4c9928fe16dd1ad0b67f76eef506..94db178b6b71ba096df2def57e8b4baedccd8b13 100644 (file)
--- a/src/tools/gmx_chi.c
+++ b/src/tools/gmx_chi.c
@@ -1133,7 +1133,7 @@ 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,*xity; 
+  int        i,j,**chi_lookup,*multiplicity; 
   
   t_filenm  fnm[] = {
     { efSTX, "-s",  NULL,     ffREAD  },
@@ -1252,8 +1252,8 @@ int gmx_chi(int argc,char *argv[])
    *
    * added multiplicity */ 
 
-  snew(xity,ndih) ;
-  mk_multiplicity_lookup(xity, maxchi, dih, nlist, dlist,ndih); 
+  snew(multiplicity,ndih) ;
+  mk_multiplicity_lookup(multiplicity, maxchi, dih, nlist, dlist,ndih); 
  
   strcpy(grpname, "All residues, "); 
   if(bPhi) 
@@ -1270,7 +1270,7 @@ int gmx_chi(int argc,char *argv[])
 
   low_ana_dih_trans(bDo_ot, opt2fn("-ot",NFILE,fnm),
                    bDo_oh, opt2fn("-oh",NFILE,fnm),maxchi, 
-                   dih, nlist, dlist, nf, nactdih, grpname, xity, 
+                   dih, nlist, dlist, nf, nactdih, grpname, multiplicity, 
                    *time,  dt, FALSE, core_frac,oenv) ; 
 
   /* Order parameters */  
@@ -1303,7 +1303,7 @@ int gmx_chi(int argc,char *argv[])
     mk_chi_lookup(chi_lookup, maxchi, dih, nlist, dlist); 
     
     get_chi_product_traj(dih,nf,nactdih,nlist,
-                        maxchi,dlist,time,chi_lookup,xity,
+                        maxchi,dlist,time,chi_lookup,multiplicity,
                         FALSE,bNormHisto, core_frac,bAll,
                         opt2fn("-cp",NFILE,fnm),oenv); 
 

diff --git a/src/tools/pp2shift.h b/src/tools/pp2shift.h
index 5736ab85916bf9876bde0656d75bb92f70c1afe0..d61b532eb9f752604cc218be5d96f6ed31aca802 100644 (file)
--- a/src/tools/pp2shift.h
+++ b/src/tools/pp2shift.h
@@ -85,7 +85,7 @@ extern void mk_chi_lookup (int **lookup, int maxchi, real **dih,
 
 extern void get_chi_product_traj (real **dih,int nframes,int nangles, 
                           int nlist,int maxchi, t_dlist dlist[], real time[], 
-                          int **lookup,int *xity,gmx_bool bRb,gmx_bool bNormalize,
+                          int **lookup,int *multiplicity,gmx_bool bRb,gmx_bool bNormalize,
                           real core_frac); 
 
 #endif