{

FILE *fpw,*fpd,*fout;

fpw=fopen(argv[1],"r");

fpd=fopen(argv[2],"r");

char store[100],store2[100];

int cnt=0,cnt2=0,totres_f1,totres_f2,secAt=0;

int start_patch=atoi(argv[3]),end_patch=atoi(argv[4]);

pdb frag1[50000],frag2[50000];

cout<<"Start:"<<start_patch<<" End:"<<end_patch<<endl;

//scanning information from the first fragment

while(fgets(store,100,fpw)!=NULL)

{

sscanf(store,"%s %d %s %s %d %lf %lf %lf",frag1[cnt].atom,&frag1[cnt].atomNo,frag1[cnt].atomtype,//

frag1[cnt].amino,&frag1[cnt].aminoNo,&frag1[cnt].x,&frag1[cnt].y,&frag1[cnt].z);

if(frag1[cnt].aminoNo==end_patch-1)

{

secAt=frag1[cnt].atomNo;

}

cnt++;

}

//scanning information from the second fragment

while(fgets(store2,100,fpd)!=NULL)

{

sscanf(store2,"%s %d %s %s %d %lf %lf %lf",frag2[cnt2].atom,&frag2[cnt2].atomNo,frag2[cnt2].atomtype,//

frag2[cnt2].amino,&frag2[cnt2].aminoNo,&frag2[cnt2].x,&frag2[cnt2].y,&frag2[cnt2].z);

cnt2++;

}

fclose(fpw);

fclose(fpd);

totres_f1=cnt; totres_f2=cnt2;

cout<<"total number of atoms in two fragments "<<totres_f1<<" "<<totres_f2<<endl;

//First part: Calculating values of l,m and n and reference atoms

double l,m,n,a,b,c;

pdb p1,p2,p1d,p2d,ref,refd,temp;

int len=(end_patch-start_patch)+1,i,f1=0,f2=0,f3=0;

for(i=0;i<cnt;i++)//Taking only Backbone atoms for calculations from first fragment

{

if(frag1[i].aminoNo==(start_patch +1) && f1==0)//Reference is first atom of second AA

{

ref=frag1[i];

f1++;

}

if(frag1[i].aminoNo==(start_patch +2) && f2==0)

{

p1=frag1[i];

f2++;

}

if(frag1[i].aminoNo==(start_patch +3) && f3==0)

{

p2=frag1[i];

f3++;

}

}

print_atom(ref);

print_atom(p1);

print_atom(p2);

f1=0;f2=0;f3=0;

for(i=0;i<cnt2;i++)//Taking only backbone atoms for calculations from second fragment

{

if(frag2[i].aminoNo==2 && f1==0)//Reference is first atom of second AA

{

refd=frag2[i];

f1++;

}

if(frag2[i].aminoNo==3 && f2==0)

{

p1d=frag2[i];

f2++;

}

if(frag2[i].aminoNo==4 && f3==0)

{

p2d=frag2[i];

f3++;

}

}

print_atom(refd);

print_atom(p1d);

print_atom(p2d);

//Finding coordinates of p1,p2 wrt ref

pdb r1,r2,r1d,r2d;

r1=p1;r2=p2;r1d=p1d;r2d=p2d;

r1.x=p1.x-ref.x;

r1.y=p1.y-ref.y;

r1.z=p1.z-ref.z;

r2.x=p2.x-ref.x;

r2.y=p2.y-ref.y;

r2.z=p2.z-ref.z;

r1d.x=p1d.x-refd.x;

r1d.y=p1d.y-refd.y;

r1d.z=p1d.z-refd.z;

r2d.x=p2d.x-refd.x;

r2d.y=p2d.y-refd.y;

r2d.z=p2d.z-refd.z;

double dx1,dx2,dy1,dy2,dz1,dz2;

dx1=r1d.x-r1.x;

dx2=r2d.x-r2.x;

dy1=r1d.y-r1.y;

dy2=r2d.y-r2.y;

dz1=r1d.z-r1.z;

dz2=r2d.z-r2.z;

//Finding values of l,m and n

if(dx1==0.0 && dx2==0.0 && dy1==0.0 && dy2==0.0 && dz1==0.0 && dz2==0.0)

{

l=0;

m=0;

n=1;

}

else

{

a=((dy1*dz2)-(dy2*dz1));

b=((dz1*dx2)-(dz2*dx1));

c=((dx1*dy2)-(dx2*dy2));

l=a/(pow(((a*a)+(b*b)+(c*c)),0.5));

m=b/(pow(((a*a)+(b*b)+(c*c)),0.5));

n=c/(pow(((a*a)+(b*b)+(c*c)),0.5));

}

//Finding values of (root 1-x^2) for l,m and n

double ls,ms,ns;

ls=pow((1-l*l),0.5);

ms=pow((1-m*m),0.5);

ns=pow((1-n*n),0.5);

print_atom(r1);

print_atom(r2);

print_atom(r1d);

print_atom(r2d);

//Part two: Finding the rotation angle between the two sets of coordinates

double xf,xfd,yf,yfd,zf,zfd,xs,xsd,ys,ysd,zs,zsd,cosphi,sinphi;

//First rotation about X axis

xf=r1.x;

xfd=r1d.x;

yf=((n*r1.y)-(m*r1.z))/(pow((n*n)+(m*m),0.5));

yfd=((n*r1d.y)-(m*r1d.z))/(pow((n*n)+(m*m),0.5));

zf=((m*r1.y)+(n*r1.z))/(pow((n*n)+(m*m),0.5));

zfd=((m*r1d.y)+(n*r1d.z))/(pow((n*n)+(m*m),0.5));

//Second rotation about Y axis

xs=(ls*xf)-(l*zf);

ys=yf;

zs=(l*xf)+(ls*zf);

xsd=(ls*xfd)-(l*zfd);

ysd=yfd;

zsd=(l*xfd)+(ls*zfd);

//Angle between two fragments when axis of rotation is z axis

cosphi=((xs*xsd)+(ys*ysd))/((xsd*xsd)+(ysd*ysd));

sinphi=((xs*ysd)-(ys*xsd))/((xsd*xsd)+(ysd*ysd));

//Part three: Finding the coordinates of the atoms of the second fragment wrt reference atom

for(i=0;i<cnt2;i++)

{

temp=frag2[i];

frag2[i].x=temp.x-refd.x;

frag2[i].y=temp.y-refd.y;

frag2[i].z=temp.z-refd.z;

}

//Part four: Rotation about reference atom for second fragment

for(i=0;i<cnt2;i++)

{

double c1,c2,c3,ca,cb,x,y,z,xd,yd,zd,xdd,ydd,zdd;

x=frag2[i].x;

y=frag2[i].y;

z=frag2[i].z;

//Applying first rotation

xd=x;

yd=((n*y)-(m*z))/pow((m*m)+(n*n),0.5);

zd=((m*y)+(n*z))/pow((m*m)+(n*n),0.5);

//Applying second rotation

xdd=(ls*xd)-(l*zd);

ydd=yd;

zdd=(l*xd)+(ls*zd);

//Applying third rotation

c1=(xdd*cosphi)+(ydd*sinphi);

c2=(ydd*cosphi)-(xdd*sinphi);

c3=zdd;

//Moving frag2 elements to relative frag1 position

frag2[i].x=((c1*pow((m*m)+(n*n),0.5))-c3)/((m*m)+(n*n)-l);

ca=(c3-(l*frag2[i].x));

cb=(c2*pow((m*m)+(n*n),0.5));

frag2[i].y=((m*ca)+(n*cb))/((m*m)+(n*n));

frag2[i].z=((n*ca)-(m*cb))/((m*m)+(n*n));

}

//Part five: Translation of atoms of second fragment to the first one

for(i=0;i<cnt2;i++)

{

temp=frag2[i];

frag2[i].x=(temp.x)+(ref.x);

frag2[i].y=(temp.y)+(ref.y);

frag2[i].z=(temp.z)+(ref.z);

print_atom(frag2[i]);

}

//Part Six: Merging frag2 with frag1

int op=0;

for(i=0;i<cnt2;i++)

{

if((frag2[i].aminoNo<len))

{

op++;

}

}

//changing residue number of frag 2

for(i=op;i<cnt2;i++)

{

frag2[i].aminoNo=frag2[i].aminoNo+(start_patch-1);

frag2[i].atomNo=secAt+1;

frag1[secAt]=frag2[i];

secAt++;

}

// Calculating new value of Total Residues

totres_f1=secAt;

//writing output of patching

fout=fopen(argv[5],"w");

for(int t=0;t<totres_f1;t++) //fragment 1 contains the updated patched coordinates

{

if(strlen(frag1[t].atom)==4)

fprintf(fout,"ATOM %5d %-4s %3s %4d%12.3lf%8.3lf%8.3lf\n",frag1[t].atomNo,//

frag1[t].atomtype,frag1[t].amino,frag1[t].aminoNo,frag1[t].x,frag1[t].y,frag1[t].z);

else

fprintf(fout,"ATOM %5d %-3s %3s %4d%12.3lf%8.3lf%8.3lf\n",frag1[t].atomNo,//

frag1[t].atomtype,frag1[t].amino,frag1[t].aminoNo,frag1[t].x,frag1[t].y,frag1[t].z);

}

{

cout<<p.atomNo<<" "<<p.aminoNo<<" "<<p.x<<" "<<p.y<<" "<<p.z<<endl;