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path: root/sci-chemistry/maid/files/fix-warnings.patch
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Diffstat (limited to 'sci-chemistry/maid/files/fix-warnings.patch')
-rw-r--r--sci-chemistry/maid/files/fix-warnings.patch419
1 files changed, 419 insertions, 0 deletions
diff --git a/sci-chemistry/maid/files/fix-warnings.patch b/sci-chemistry/maid/files/fix-warnings.patch
new file mode 100644
index 000000000000..b4f48d244a69
--- /dev/null
+++ b/sci-chemistry/maid/files/fix-warnings.patch
@@ -0,0 +1,419 @@
+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