path: root/sci-chemistry/maid/files/fix-warnings.patch

diff -ur glmaid_dist.orig/assignseq.c++ glmaid_dist/assignseq.c++
--- glmaid_dist.orig/assignseq.c++	2005-12-15 08:09:55.000000000 -0800
+++ glmaid_dist/assignseq.c++	2005-12-15 08:36:47.000000000 -0800
@@ -2630,9 +2630,9 @@
    if(ibestden <= 1) // 0.8 or 1.0
        *maxngap = geo.maxngap;
    else if(ibestden ==2) // 1.2
-       *maxngap = 1.5*geo.maxngap;
+       *maxngap = (int) (1.5*geo.maxngap);
    else if (ibestden >2) // 1.4 or 1.6
-       *maxngap = 2.0 *geo.maxngap;   
+       *maxngap = (int) (2.0 *geo.maxngap);   
  }
 #endif
 
diff -ur glmaid_dist.orig/bone.c++ glmaid_dist/bone.c++
--- glmaid_dist.orig/bone.c++	2005-12-15 08:09:55.000000000 -0800
+++ glmaid_dist/bone.c++	2005-12-15 08:31:26.000000000 -0800
@@ -815,7 +815,7 @@
    }
 
 
-   bonemin = bone1.minden*maidfile.denscale;  // lower limit  used to make bone (round down) 
+   bonemin = (int) (bone1.minden*maidfile.denscale);  // lower limit  used to make bone (round down) 
 fprintf(fpout,"bonemin = %d\n",bonemin);
    defineiden(bone1,iden,den1,bonemin); // set point on boundary = REMOVE
    bsort(den1,bone1,sortv,bonemin,sortnum,&maxsize);  // sort density into bins; sort[i] is vector of 1 ..... max
diff -ur glmaid_dist.orig/checkfit.c++ glmaid_dist/checkfit.c++
--- glmaid_dist.orig/checkfit.c++	2005-12-15 08:09:55.000000000 -0800
+++ glmaid_dist/checkfit.c++	2005-12-15 08:22:14.000000000 -0800
@@ -2977,7 +2977,7 @@
    *maxden = -1000.0;
    xtof(den1,pos,fd); /* convert from double word to float sccreen*/
    for(k=0;k<=2;k++)
-       ir[k]=fd[k]+0.5; /*round  to integer*/
+       ir[k]=(int) (fd[k]+0.5); /*round  to integer*/
    for(ii=ir[0]-2;ii<=ir[0]+2;ii++){
      if( (ii>=1)&& (ii<=den1.amax[0]-den1.amin[0]-1) )
         for(jj=ir[1]-2;jj<=ir[1]+2;jj++)
diff -ur glmaid_dist.orig/extend2.c++ glmaid_dist/extend2.c++
--- glmaid_dist.orig/extend2.c++	2005-12-15 08:09:55.000000000 -0800
+++ glmaid_dist/extend2.c++	2005-12-15 08:24:45.000000000 -0800
@@ -363,7 +363,7 @@
    nend[3]=geo.nend[1]+3;
 #if 1  // Works well in most cases
    mrot[0]= 2*nrot;
-   mrot[1]= 1.5*nrot;
+   mrot[1]= (int) (1.5*nrot);
    mrot[2]= nrot;
    mrot[3]= nrot;
 #endif
diff -ur glmaid_dist.orig/extendfit.c++ glmaid_dist/extendfit.c++
--- glmaid_dist.orig/extendfit.c++	2005-12-15 08:09:55.000000000 -0800
+++ glmaid_dist/extendfit.c++	2005-12-15 08:26:43.000000000 -0800
@@ -4024,7 +4024,7 @@
 ext.usenfits = 3;//  I do not think this makes any difference since it reset in other routines -Number of unassigned connected that must be linked to assigne seq. value
    geo.deldist = sqrt( dot(den1.delx,den1.delx) ); // length of den1.delx vector = 1.445 for shad , res = 2.5
    if(geo.deldist < 1.445)
-      geo.gnmax = 7*(1.445/geo.deldist) +1;
+      geo.gnmax = (int) (7*(1.445/geo.deldist) +1);
    else
       geo.gnmax = 7;
    geo.maxugap = 8;  //Maximum gap allowed to connect unassigned fits
diff -ur glmaid_dist.orig/fit.c++ glmaid_dist/fit.c++
--- glmaid_dist.orig/fit.c++	2005-12-15 08:15:43.000000000 -0800
+++ glmaid_dist/fit.c++	2005-12-15 08:36:24.000000000 -0800
@@ -65,7 +65,7 @@
 tordata.torconst=torconstorig;
 tordata2.torconst=torconstorig;   
 tordata.rfor=rfororig; //-BE CAREFUL - MUST BE SURE rfororig defined/geo.maxside = origmaxside;   
-geo.maxside = origmaxside;   
+geo.maxside = (int) origmaxside;   
     if (&client_data) {
         XtRemoveWorkProc (work_id);
     }
diff -ur glmaid_dist.orig/initialize.c++ glmaid_dist/initialize.c++
--- glmaid_dist.orig/initialize.c++	2005-12-15 08:09:55.000000000 -0800
+++ glmaid_dist/initialize.c++	2005-12-15 08:34:02.000000000 -0800
@@ -300,7 +300,7 @@
                            nless=nless+1;
                            dds= -MAXCHAR+1;
                       }
-                      den1.den[i][j][k]=dds;
+                      den1.den[i][j][k]=(signed) dds;
 		     }
 		}
 	}
Files glmaid_dist.orig/initialize.o and glmaid_dist/initialize.o differ
diff -ur glmaid_dist.orig/mapmenu.c++ glmaid_dist/mapmenu.c++
--- glmaid_dist.orig/mapmenu.c++	2005-12-15 08:09:55.000000000 -0800
+++ glmaid_dist/mapmenu.c++	2005-12-15 08:35:53.000000000 -0800
@@ -430,7 +430,7 @@
 {
   int i;
      for(i=0;i<3;i++)
-     map.crange[i] = fcontradius[item_no]/map.delx[i];
+     map.crange[i] = (int) (fcontradius[item_no]/map.delx[i]);
 //printf("map radius = %d\n",map.crange[0]);
 }
 
diff -ur glmaid_dist.orig/math.c++ glmaid_dist/math.c++
--- glmaid_dist.orig/math.c++	2005-12-15 08:09:55.000000000 -0800
+++ glmaid_dist/math.c++	2005-12-15 08:31:55.000000000 -0800
@@ -51,9 +51,9 @@
   z=xx[2]/den1.cvz;
   y=(xx[1]-z*den1.cvy)/den1.singam;
   x=xx[0]-y*den1.cosgam-z*den1.cosbe;
-  ijk[0]=x/den1.delx[0] - den1.amin[0];
-  ijk[1]=y/den1.delx[1] - den1.amin[1];
-  ijk[2]=z/den1.delx[2] - den1.amin[2];
+  ijk[0]=(int) (x/den1.delx[0] - den1.amin[0]);
+  ijk[1]=(int) (y/den1.delx[1] - den1.amin[1]);
+  ijk[2]=(int) (z/den1.delx[2] - den1.amin[2]);
 }
 
 void imcv(struct griddata& den1,int xi[3],float sx[3])  /*convert from  integer xi,xj (grid point)
diff -ur glmaid_dist.orig/menu.c++ glmaid_dist/menu.c++
--- glmaid_dist.orig/menu.c++	2005-12-15 08:09:55.000000000 -0800
+++ glmaid_dist/menu.c++	2005-12-15 08:35:15.000000000 -0800
@@ -321,7 +321,7 @@
 {
    int i;  
    sc.cubecol[0] += 0.01;
-   i= sc.cubecol[0];
+   i= (int) sc.cubecol[0];
    sc.cubecol[0]= sc.cubecol[0]-i;;
    draw_screen(client_data);
     return False; // Runs continually
@@ -987,14 +987,14 @@
     int i;
 
     for(i=0;i<=2;i++) // Use default contour radius
-          den1.crange[i]=sc.contourradius/den1.delx[i];
+          den1.crange[i]=(int) (sc.contourradius/den1.delx[i]);
     den1.contonoff = -1;
     den1.selectcontonoff = -1;
     for(i=0;i<3;i++)
        den1.color[i]=bluev[i];
     den1.conlevel = sc.conlevel*maidfile.denscale;  // Set contourleve to default value
     // Allocate arrays for contour routines
-    den1.ntri = NTRI/(den1.delx[0]*den1.delx[1]*den1.delx[2]); // Scale ntri relative del = 1
+    den1.ntri = (int) (NTRI/(den1.delx[0]*den1.delx[1]*den1.delx[2])); // Scale ntri relative del = 1
 printf("Allocating arrays for contour routines  ntriangles = %d\n",den1.ntri);
     imat2(den1.tri,den1.ntri,9);
 printf("   Done\n");
diff -ur glmaid_dist.orig/pdbtolev.c++ glmaid_dist/pdbtolev.c++
--- glmaid_dist.orig/pdbtolev.c++	2005-12-15 08:09:55.000000000 -0800
+++ glmaid_dist/pdbtolev.c++	2005-12-15 08:27:19.000000000 -0800
@@ -645,7 +645,7 @@
 {
     int i,j,natot,bi;
     float  bsqr;
-    natot=subst[snum].pos[0][0]; /*total # of atoms*/
+    natot=(int) subst[snum].pos[0][0]; /*total # of atoms*/
     bsqr=tsqr(bondlength);
     for(i=1;i<=natot;i++)
        cmat[i][0]=0; /*initally no connections to i*/
diff -ur glmaid_dist.orig/rankside.c++ glmaid_dist/rankside.c++
--- glmaid_dist.orig/rankside.c++	2005-12-15 08:09:55.000000000 -0800
+++ glmaid_dist/rankside.c++	2005-12-15 08:33:32.000000000 -0800
@@ -201,13 +201,13 @@
 #endif
      tbad = fit.ibad[resn][a1] + fit.ibad[resn][a2] +fit.ibad[resn][a3];
      if(tbad==0)
-         return 0+iadd;    
+         return 0+(int) iadd;    
      if(tbad ==1)
-         return 1+iadd;
+         return 1+(int) iadd;
      if(tbad==2)  
-         return 2+iadd;
+         return 2+(int) iadd;
      if(tbad==3)  
-         return 4+iadd;
+         return 4+(int) iadd;
      else if ((fit.ibad[resn][MET]==0)||(fit.ibad[resn][GLU]==0)||(fit.ibad[resn][GLN]==0) )
          return 3;
      else
@@ -245,11 +245,11 @@
         iadd = iadd+1;
 #endif
      if(fit.ibad[resn][a1]==0 ) 
-         return 0+iadd;    
+         return 0+(int) iadd;    
      else if( fit.ibad[resn][a2]==0 )
-         return 1+iadd;
+         return 1+(int) iadd;
      else if( fit.ibad[resn][a3]==0 )
-         return 1+iadd;
+         return 1+(int) iadd;
      else if ((fit.ibad[resn][MET]==0)||(fit.ibad[resn][GLU]==0)||(fit.ibad[resn][GLN]==0) )
          return 3;
      else
@@ -285,11 +285,11 @@
         iadd = iadd+1;
 #endif
      if(fit.ibad[resn][a1]==0 ) 
-         return 0+iadd;    
+         return 0+(int) iadd;    
      else if( fit.ibad[resn][a2]==0 )
-         return 1+iadd;
+         return 1+(int) iadd;
      else if( fit.ibad[resn][a3]==0 )
-         return 1+iadd;
+         return 1+(int) iadd;
      else if ((fit.ibad[resn][MET]==0)||(fit.ibad[resn][GLU]==0)||(fit.ibad[resn][GLN]==0) )
          return 3;
      else
@@ -316,11 +316,11 @@
      if(valden> 1.1*ringden) //change2
         iadd = iadd+1;
      if(fit.ibad[resn][a1]==0 ) 
-         return 0+iadd;    
+         return 0+(int) iadd;    
      else if( fit.ibad[resn][a2]==0 )
-         return 1+iadd;
+         return 1+(int) iadd;
      else if( fit.ibad[resn][a3]==0 )
-         return 1+iadd;
+         return 1+(int) iadd;
      else if ((fit.ibad[resn][MET]==0)||(fit.ibad[resn][GLU]==0)||(fit.ibad[resn][GLN]==0) )
          return 3;
      else
Files glmaid_dist.orig/rankside.o and glmaid_dist/rankside.o differ
diff -ur glmaid_dist.orig/refine.c++ glmaid_dist/refine.c++
--- glmaid_dist.orig/refine.c++	2005-12-15 08:09:55.000000000 -0800
+++ glmaid_dist/refine.c++	2005-12-15 08:26:15.000000000 -0800
@@ -67,8 +67,8 @@
 */
 {
    int ix,rnd;
-   ix = floor(x);
-   rnd = nn*(x-ix) + 0.5;
+   ix = (int) floor(x);
+   rnd = (int) (nn*(x-ix) + 0.5);
    printf("nn = %d x = %5.3f  rnd = %d  Grid point %5.3f\n",nn,x,rnd,ix+(float)rnd/nn);
    return rnd;
 }
@@ -82,8 +82,8 @@
    int k;
 
    for(k=0;k<=2;k++){
-      ivec[k] = floor(fvec[k]);
-      ival[k] = nn*(fvec[k]-ivec[k]) + 0.5;
+      ivec[k] = (int) floor(fvec[k]);
+      ival[k] = (int) (nn*(fvec[k]-ivec[k]) + 0.5);
    }
 }   
 
@@ -115,9 +115,9 @@
    }
    for(k=0;k<=2;k++)
        gzd.dvec[gzd.num][k] =ivec[k];
-   gzd.den[gzd.num] = scalechar* exp(-rad*rad/bfact) +0.5; // mult by 100 and round
+   gzd.den[gzd.num] = (int) (scalechar* exp(-rad*rad/bfact) +0.5); // mult by 100 and round
    for(k=0;k<=2;k++)
-       gzd.forv[gzd.num][k] = 4.0*rad*gzd.den[gzd.num]*diffv[k]/bfact;   
+       gzd.forv[gzd.num][k] = (int) (4.0*rad*gzd.den[gzd.num]*diffv[k]/bfact);   
 }
 
 void assignforce(gzdhead)
@@ -421,7 +421,7 @@
    gzd[0].num = 0; 
    oneatomgrid(den1,geo,ivec0,cenpos,gzd[0],bfact,countfunc);
    printf("totnum = %d\n",gzd[0].num);
-   maxgzd = gzd[0].num = 1.5*gzd[0].num; // increase by 15%
+   maxgzd = gzd[0].num = (int) (1.5*gzd[0].num); // increase by 15%
    allocategzd(gzd[0].num);
    del = 1.0/NDIV;
    for(i=0;i<=NDIV;i++){
diff -ur glmaid_dist.orig/sphere.c++ glmaid_dist/sphere.c++
--- glmaid_dist.orig/sphere.c++	2005-12-15 08:09:55.000000000 -0800
+++ glmaid_dist/sphere.c++	2005-12-15 08:36:06.000000000 -0800
@@ -95,7 +95,7 @@
        fclose(fp);
     } // spherefile opened
     sc.isphere = maidfile.nsphere; // set active sphere to last read
-    sc.drawspheres =1.0;
+    sc.drawspheres =1;
     if (widget = XtNameToWidget (spheremenu,"button_0")) //DEFAULT:  Turn off check box for label on/off button
             XtVaSetValues (widget, XmNset,TRUE, NULL);
 }
diff -ur glmaid_dist.orig/tordyn.c++ glmaid_dist/tordyn.c++
--- glmaid_dist.orig/tordyn.c++	2005-12-15 08:13:32.000000000 -0800
+++ glmaid_dist/tordyn.c++	2005-12-15 08:28:27.000000000 -0800
@@ -337,8 +337,8 @@
     xtof(den1,apos,fd);
 /* New version, interpolates all neighbors*/
     for(k=0;k<=2;k++){
-       ir[k]=fd[k]; /*round down*/
-       irh[k]=fd[k]+0.5; /*round to next 1/2*/
+       ir[k]=(int) fd[k]; /*round down*/
+       irh[k]=(int) (fd[k]+0.5); /*round to next 1/2*/
        if( (ir[k]<1)|| (irh[k]>den1.amax[k]-den1.amin[k]-1) ){
 //         if(verbose>=1)
          if(verbose>=2) // 30nov00 - do not print this line
@@ -683,7 +683,7 @@
    atomden = 0;
    xtof(den1,pos,fd); /* convert from double word to float sccreen*/
    for(kc=0;kc<=2;kc++)
-       ir[kc]=fd[kc]; /*round down to integer*/
+       ir[kc]=(int) fd[kc]; /*round down to integer*/
    for(k=0;k<=2;k++){ // check if pos in density range
       if( (ir[k]<2)|| (ir[k]>den1.amax[k]-den1.amin[k]-2) ){
          if(verbose>=2)
@@ -2898,7 +2898,7 @@
 //printf("oneside = %d geopos6(x) = geo.pos[geo.nend[0]+oneside][6][0] = %5.3f\n",geo.oneside,geo.pos[geo.nend[0]+geo.oneside][6][0]);
    }
    *returnden = bestden;  // return best cterm density
-   *returnbad = bestbad;
+   *returnbad = (int) bestbad;
  }// quitcont <5
  quitrout:;
  geo.fixend = origfixend; // set back to original value
diff -ur glmaid_dist.orig/trace.c++ glmaid_dist/trace.c++
--- glmaid_dist.orig/trace.c++	2005-12-15 08:09:55.000000000 -0800
+++ glmaid_dist/trace.c++	2005-12-15 08:31:07.000000000 -0800
@@ -1079,7 +1079,7 @@
 
    xtoi(den1,pos[resnum][atomnum],ig);
    for(k=0;k<=2;k++)
-     ig[k]=ig[k]+0.5; /*rounds to  nearest grid point*/
+     ig[k]=(int) (ig[k]+0.5); /*rounds to  nearest grid point*/
    for(k=0;k<=2;k++){ // check if pos in density range
       if( (ig[k]<2)|| (ig[k]>den1.amax[k]-den1.amin[k]-2) )
          return 0;
@@ -1099,7 +1099,7 @@
 
    xtof(den1,pos,ijk); /*convert from world co-ord to floating grid i,j,k co-ord*/
    for(k=0;k<=2;k++)
-     ig[k]=ijk[k]+0.5; /*rounds to  nearest grid point*/
+     ig[k]=(int) (ijk[k]+0.5); /*rounds to  nearest grid point*/
    for(k=0;k<=2;k++){ // check if pos in density range
       if( (ig[k]<1)|| (ig[k]>den1.amax[k]-den1.amin[k]-1) ){
          if(verbose>=2)
@@ -1127,7 +1127,7 @@
 
    xtof(den1,pos,ijk); /*convert from world co-ord to floating grid i,j,k co-ord*/
    for(k=0;k<=2;k++)
-     ig[k]=ijk[k]+0.5; /*rounds to  nearest grid point*/
+     ig[k]=(int) (ijk[k]+0.5); /*rounds to  nearest grid point*/
    for(k=0;k<=2;k++){ // check if pos in density range
       if( (ig[k]<1)|| (ig[k]>den1.amax[k]-den1.amin[k]-1) ){
          if(verbose>=2)
@@ -1204,7 +1204,7 @@
 
    xtof(den1,pos,ijk); /*convert from world co-ord to floating grid i,j,k co-ord*/
    for(k=0;k<=2;k++)
-     ig[k]=ijk[k]+0.5; /*rounds to  nearest grid point*/
+     ig[k]=(int) (ijk[k]+0.5); /*rounds to  nearest grid point*/
    for(k=0;k<=2;k++){ // check if pos in density range
       if( ((ig[k]-geo.setrad)<0)|| ((ig[k]+geo.setrad)>den1.griddim[k]-1) ){
          if(verbose>=2)
@@ -2543,7 +2543,7 @@
    atomden = 0;
    xtof(den1,pos,fd); /* convert from double word to float sccreen*/
    for(kc=0;kc<=2;kc++)
-       ir[kc]=fd[kc]; /*round down to integer*/
+       ir[kc]=(int) fd[kc]; /*round down to integer*/
    for(k=0;k<=2;k++){ // check if pos in density range
       if( (ir[k]<1)|| (ir[k]>den1.amax[k]-den1.amin[k]-1) ){
 //if(verbose>=2)
@@ -2569,7 +2569,7 @@
    atomden = 0;
    xtof(den1,pos[inum][itype],fd); /* convert from double word to float sccreen*/
    for(kc=0;kc<=2;kc++)
-       ir[kc]=fd[kc]; /*round down to integer*/
+       ir[kc]=(int) fd[kc]; /*round down to integer*/
    for(k=0;k<=2;k++){ // check if pos in density range
       if( (ir[k]<1)|| (ir[k]>den1.amax[k]-den1.amin[k]-1) ){
         if(verbose>=2)
@@ -3438,7 +3438,7 @@
     dist =distv(pos[1][1],pos[n0+1][1]); // distance from Ca[geo.cafix] to Ca[1]
 dist = dist/2.0;
     thdel = rotdel/dist; // step size of theta rotation
-    mth =1+ thtot/thdel; // max # of theta steps  - round up
+    mth =1+ (int) (thtot/thdel); // max # of theta steps  - round up
     thdel = thtot/mth; // reset th del so that equal steps from 0 to thttot
     maxden = -10000.0;
 for(iaxis=0;iaxis<8;iaxis++){// rotate about origingalca1 caend axis
@@ -3455,7 +3455,7 @@
        }
        else{
          delph = rotdel/(dist*sin(th));//the delta phi angle step
-         mphi = phitot/delph +1; // round up
+         mphi = (int) (phitot/delph) +1; // round up
          delph = phitot/mphi; // make phitot = mphi*delph 
        }
        for(iph = 0;iph<=mphi;iph++){ // the phi step 
@@ -3545,7 +3545,7 @@
     dist =distv(pos[1][1],pos[n0+1][1]); // distance from Ca[geo.cafix] to Ca[1]
 dist = dist/2.0;
     thdel = rotdel/dist; // step size of theta rotation
-    mth =1+ thtot/thdel; // max # of theta steps  - round up
+    mth =1+ (int) (thtot/thdel); // max # of theta steps  - round up
     thdel = thtot/mth; // reset th del so that equal steps from 0 to thttot
     maxden = -10000.0;
 for(iaxis=0;iaxis<8;iaxis++){// rotate about origingalca1 caend axis
@@ -3562,7 +3562,7 @@
        }
        else{
          delph = rotdel/(dist*sin(th));//the delta phi angle step
-         mphi = phitot/delph +1; // round up
+         mphi = (int) (phitot/delph) +1; // round up
          delph = phitot/mphi; // make phitot = mphi*delph 
        }
        for(iph = 0;iph<=mphi;iph++){ // the phi step 
@@ -6905,8 +6905,8 @@
   for(i=0;i<=2;i++)
     avegrid = avegrid+den1.delx[i];
   avegrid = avegrid/3.0;
-  geo.nihel = 0.5 + geo.curdist[1]/(1.414*avegrid); // 0.5 so that rounds to nearest int
-  geo.nisheet = geo.curdist[2]/(1.414*avegrid);
+  geo.nihel = (int) (0.5 + geo.curdist[1]/(1.414*avegrid)); // 0.5 so that rounds to nearest int
+  geo.nisheet = (int) (geo.curdist[2]/(1.414*avegrid));
 printf("\nGRID SIZE:  %5.3f %5.3f %5.3f avegrid = %5.3f  nihel = %d\n", 
       den1.delx[0],den1.delx[1],den1.delx[2],avegrid,geo.nihel);
 
Files glmaid_dist.orig/trace.o and glmaid_dist/trace.o differ