+++ /dev/null
-*************************************************************************
-*************************************************************************
-* This is a subroutine to compare two structures and find the
-* superposition that has the maximum TM-score.
-* Reference: Yang Zhang, Jeffrey Skolnick, Proteins 2004 57:702-10.
-*
-* Explanations:
-* L1--Length of the first structure
-* (x1(i),y1(i),z1(i))--coordinates of i'th residue at the first structure
-* n1(i)--Residue sequence number of i'th residue at the first structure
-* L2--Length of the second structure
-* (x2(i),y2(i),z2(i))--coordinates of i'th residue at the second structure
-* n2(i)--Residue sequence number of i'th residue at the second structure
-* TM--TM-score of the comparison
-* Rcomm--RMSD of two structures in the common aligned residues
-* Lcomm--Length of the common aligned regions
-*
-* Note:
-* 1, Always put native as the second structure, by which TM-score
-* is normalized.
-* 2, The returned (x1(i),y1(i),z1(i)) are the rotated structure after
-* TM-score superposition.
-*************************************************************************
-*************************************************************************
- subroutine TMscore(L1,x1,y1,z1,n1,L2,x2,y2,z2,n2,TM,Rcomm,Lcomm)
- include 'DIMENSIONS'
- PARAMETER(nmax=maxres)
- common/stru/xt(nmax),yt(nmax),zt(nmax),xb(nmax),yb(nmax),zb(nmax)
- common/nres/nresA(nmax),nresB(nmax),nseqA,nseqB
- common/para/d,d0
- common/align/n_ali,iA(nmax),iB(nmax)
- common/nscore/i_ali(nmax),n_cut ![1,n_ali],align residues for the score
- dimension k_ali(nmax),k_ali0(nmax)
- dimension L_ini(100),iq(nmax)
- common/scores/score
- double precision score,score_max
- dimension xa(nmax),ya(nmax),za(nmax)
-
- dimension x1(nmax),y1(nmax),z1(nmax),n1(nmax)
- dimension x2(nmax),y2(nmax),z2(nmax),n2(nmax)
-
-ccc RMSD:
- double precision r_1(3,nmax),r_2(3,nmax),r_3(3,nmax),w(nmax)
- double precision u(3,3),t(3),rms,drms !armsd is real
- data w /nmax*1.0/
-ccc
-
-********* convert input data ****************
- nseqA=L1
- do i=1,nseqA
- xa(i)=x1(i)
- ya(i)=y1(i)
- za(i)=z1(i)
- nresA(i)=n1(i)
- enddo
- nseqB=L2
- do i=1,L2
- xb(i)=x2(i)
- yb(i)=y2(i)
- zb(i)=z2(i)
- nresB(i)=n2(i)
- enddo
-
-******************************************************************
-* pickup the aligned residues:
-******************************************************************
- k=0
- do i=1,nseqA
- do j=1,nseqB
- if(nresA(i).eq.nresB(j))then
- k=k+1
- iA(k)=i
- iB(k)=j
- goto 205
- endif
- enddo
- 205 continue
- enddo
- n_ali=k !number of aligned residues
- Lcomm=n_ali
- if(n_ali.lt.1)then
-c write(*,*)'There is no common residues in the input structures'
- TM=0
- Rcomm=0
- return
- endif
-
-************/////
-* parameters:
-*****************
-*** d0------------->
- d0=1.24*(nseqB-15)**(1.0/3.0)-1.8
- if(d0.lt.0.5)d0=0.5
-*** d0_search ----->
- d0_search=d0
- if(d0_search.gt.8)d0_search=8
- if(d0_search.lt.4.5)d0_search=4.5
-*** iterative parameters ----->
- n_it=20 !maximum number of iterations
- d_output=5 !for output alignment
- n_init_max=6 !maximum number of L_init
- n_init=0
- L_ini_min=4
- if(n_ali.lt.4)L_ini_min=n_ali
- do i=1,n_init_max-1
- n_init=n_init+1
- L_ini(n_init)=n_ali/2**(n_init-1)
- if(L_ini(n_init).le.L_ini_min)then
- L_ini(n_init)=L_ini_min
- goto 402
- endif
- enddo
- n_init=n_init+1
- L_ini(n_init)=L_ini_min
- 402 continue
-
-******************************************************************
-* find the maximum score starting from local structures superposition
-******************************************************************
- score_max=-1 !TM-score
- do 333 i_init=1,n_init
- L_init=L_ini(i_init)
- iL_max=n_ali-L_init+1
- do 300 iL=1,iL_max !on aligned residues, [1,nseqA]
- LL=0
- ka=0
- do i=1,L_init
- k=iL+i-1 ![1,n_ali] common aligned
- r_1(1,i)=xa(iA(k))
- r_1(2,i)=ya(iA(k))
- r_1(3,i)=za(iA(k))
- r_2(1,i)=xb(iB(k))
- r_2(2,i)=yb(iB(k))
- r_2(3,i)=zb(iB(k))
- LL=LL+1
- ka=ka+1
- k_ali(ka)=k
- enddo
- call u3b(w,r_1,r_2,LL,1,rms,u,t,ier) !u rotate r_1 to r_2
- if(i_init.eq.1)then !global superposition
- armsd=dsqrt(rms/LL)
- Rcomm=armsd
- endif
- do j=1,nseqA
- xt(j)=t(1)+u(1,1)*xa(j)+u(1,2)*ya(j)+u(1,3)*za(j)
- yt(j)=t(2)+u(2,1)*xa(j)+u(2,2)*ya(j)+u(2,3)*za(j)
- zt(j)=t(3)+u(3,1)*xa(j)+u(3,2)*ya(j)+u(3,3)*za(j)
- enddo
- d=d0_search-1
- call score_fun !init, get scores, n_cut+i_ali(i) for iteration
- if(score_max.lt.score)then
- score_max=score
- ka0=ka
- do i=1,ka0
- k_ali0(i)=k_ali(i)
- enddo
- endif
-*** iteration for extending ---------------------------------->
- d=d0_search+1
- do 301 it=1,n_it
- LL=0
- ka=0
- do i=1,n_cut
- m=i_ali(i) ![1,n_ali]
- r_1(1,i)=xa(iA(m))
- r_1(2,i)=ya(iA(m))
- r_1(3,i)=za(iA(m))
- r_2(1,i)=xb(iB(m))
- r_2(2,i)=yb(iB(m))
- r_2(3,i)=zb(iB(m))
- ka=ka+1
- k_ali(ka)=m
- LL=LL+1
- enddo
- call u3b(w,r_1,r_2,LL,1,rms,u,t,ier) !u rotate r_1 to r_2
- do j=1,nseqA
- xt(j)=t(1)+u(1,1)*xa(j)+u(1,2)*ya(j)+u(1,3)*za(j)
- yt(j)=t(2)+u(2,1)*xa(j)+u(2,2)*ya(j)+u(2,3)*za(j)
- zt(j)=t(3)+u(3,1)*xa(j)+u(3,2)*ya(j)+u(3,3)*za(j)
- enddo
- call score_fun !get scores, n_cut+i_ali(i) for iteration
- if(score_max.lt.score)then
- score_max=score
- ka0=ka
- do i=1,ka
- k_ali0(i)=k_ali(i)
- enddo
- endif
- if(it.eq.n_it)goto 302
- if(n_cut.eq.ka)then
- neq=0
- do i=1,n_cut
- if(i_ali(i).eq.k_ali(i))neq=neq+1
- enddo
- if(n_cut.eq.neq)goto 302
- endif
- 301 continue !for iteration
- 302 continue
- 300 continue !for shift
- 333 continue !for initial length, L_ali/M
-
-******** return the final rotation ****************
- LL=0
- do i=1,ka0
- m=k_ali0(i) !record of the best alignment
- r_1(1,i)=xa(iA(m))
- r_1(2,i)=ya(iA(m))
- r_1(3,i)=za(iA(m))
- r_2(1,i)=xb(iB(m))
- r_2(2,i)=yb(iB(m))
- r_2(3,i)=zb(iB(m))
- LL=LL+1
- enddo
- call u3b(w,r_1,r_2,LL,1,rms,u,t,ier) !u rotate r_1 to r_2
- do j=1,nseqA
- x1(j)=t(1)+u(1,1)*xa(j)+u(1,2)*ya(j)+u(1,3)*za(j)
- y1(j)=t(2)+u(2,1)*xa(j)+u(2,2)*ya(j)+u(2,3)*za(j)
- z1(j)=t(3)+u(3,1)*xa(j)+u(3,2)*ya(j)+u(3,3)*za(j)
- enddo
- TM=score_max
-
-c^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- return
- END
-
-ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
-c 1, collect those residues with dis<d;
-c 2, calculate score_GDT, score_maxsub, score_TM
-ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
- subroutine score_fun
- include 'DIMENSIONS'
- PARAMETER(nmax=maxres)
-
- common/stru/xa(nmax),ya(nmax),za(nmax),xb(nmax),yb(nmax),zb(nmax)
- common/nres/nresA(nmax),nresB(nmax),nseqA,nseqB
- common/para/d,d0
- common/align/n_ali,iA(nmax),iB(nmax)
- common/nscore/i_ali(nmax),n_cut ![1,n_ali],align residues for the score
- common/scores/score
- double precision score,score_max
-
- d_tmp=d
- 21 n_cut=0 !number of residue-pairs dis<d, for iteration
- score_sum=0 !TMscore
- do k=1,n_ali
- i=iA(k) ![1,nseqA] reoder number of structureA
- j=iB(k) ![1,nseqB]
- dis=sqrt((xa(i)-xb(j))**2+(ya(i)-yb(j))**2+(za(i)-zb(j))**2)
- if(dis.lt.d_tmp)then
- n_cut=n_cut+1
- i_ali(n_cut)=k ![1,n_ali], mark the residue-pairs in dis<d
- endif
- score_sum=score_sum+1/(1+(dis/d0)**2)
- enddo
- if(n_cut.lt.3.and.n_ali.gt.3)then
- d_tmp=d_tmp+.5
- goto 21
- endif
- score=score_sum/float(nseqB) !TM-score
-
- return
- end
-
-cccccccccccccccc Calculate sum of (r_d-r_m)^2 cccccccccccccccccccccccccc
-c w - w(m) is weight for atom pair c m (given)
-c x - x(i,m) are coordinates of atom c m in set x (given)
-c y - y(i,m) are coordinates of atom c m in set y (given)
-c n - n is number of atom pairs (given)
-c mode - 0:calculate rms only (given)
-c 1:calculate rms,u,t (takes longer)
-c rms - sum of w*(ux+t-y)**2 over all atom pairs (result)
-c u - u(i,j) is rotation matrix for best superposition (result)
-c t - t(i) is translation vector for best superposition (result)
-c ier - 0: a unique optimal superposition has been determined(result)
-c -1: superposition is not unique but optimal
-c -2: no result obtained because of negative weights w
-c or all weights equal to zero.
-cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
- subroutine u3b(w, x, y, n, mode, rms, u, t, ier)
- double precision w(*), x(3,*), y(3,*)
- integer n, mode
-
- double precision rms, u(3,3), t(3)
- integer ier
-
- integer i, j, k, l, m1, m
- integer ip(9), ip2312(4)
- double precision r(3,3), xc(3), yc(3), wc
- double precision a(3,3), b(3,3), e(3), rr(6), ss(6)
- double precision e0, d, spur, det, cof, h, g
- double precision cth, sth, sqrth, p, sigma
-
- double precision sqrt3, tol, zero
-
- data sqrt3 / 1.73205080756888d+00 /
- data tol / 1.0d-2 /
- data zero / 0.0d+00 /
- data ip / 1, 2, 4, 2, 3, 5, 4, 5, 6 /
- data ip2312 / 2, 3, 1, 2 /
-
- wc = zero
- rms = zero
- e0 = zero
-
- do i=1, 3
- xc(i) = zero
- yc(i) = zero
- t(i) = zero
- do j=1, 3
- r(i,j) = zero
- u(i,j) = zero
- a(i,j) = zero
- if( i .eq. j ) then
- u(i,j) = 1.0
- a(i,j) = 1.0
- end if
- end do
- end do
-
- ier = -1
- if( n .lt. 1 ) return
- ier = -2
- do m=1, n
- if( w(m) .lt. 0.0 ) return
- wc = wc + w(m)
- do i=1, 3
- xc(i) = xc(i) + w(m)*x(i,m)
- yc(i) = yc(i) + w(m)*y(i,m)
- end do
- end do
- if( wc .le. zero ) return
- do i=1, 3
- xc(i) = xc(i) / wc
- yc(i) = yc(i) / wc
- end do
-
- do m=1, n
- do i=1, 3
- e0=e0+w(m)*((x(i,m)-xc(i))**2+(y(i,m)-yc(i))**2)
- d = w(m) * ( y(i,m) - yc(i) )
- do j=1, 3
- r(i,j) = r(i,j) + d*( x(j,m) - xc(j) )
- end do
- end do
- end do
-
- det = r(1,1) * ( (r(2,2)*r(3,3)) - (r(2,3)*r(3,2)) )
- & - r(1,2) * ( (r(2,1)*r(3,3)) - (r(2,3)*r(3,1)) )
- & + r(1,3) * ( (r(2,1)*r(3,2)) - (r(2,2)*r(3,1)) )
-
- sigma = det
-
- m = 0;
- do j=1, 3
- do i=1, j
- m = m+1
- rr(m) = r(1,i)*r(1,j) + r(2,i)*r(2,j) + r(3,i)*r(3,j)
- end do
- end do
-
- spur = (rr(1)+rr(3)+rr(6)) / 3.0
- cof = (((((rr(3)*rr(6) - rr(5)*rr(5)) + rr(1)*rr(6))
- & - rr(4)*rr(4)) + rr(1)*rr(3)) - rr(2)*rr(2)) / 3.0
- det = det*det
-
- do i=1, 3
- e(i) = spur
- end do
- if( spur .le. zero ) goto 40
- d = spur*spur
- h = d - cof
- g = (spur*cof - det)/2.0 - spur*h
- if( h .le. zero ) then
- if( mode .eq. 0 ) then
- goto 50
- else
- goto 30
- end if
- end if
- sqrth = dsqrt(h)
- d = h*h*h - g*g
- if( d .lt. zero ) d = zero
- d = datan2( dsqrt(d), -g ) / 3.0
- cth = sqrth * dcos(d)
- sth = sqrth*sqrt3*dsin(d)
- e(1) = (spur + cth) + cth
- e(2) = (spur - cth) + sth
- e(3) = (spur - cth) - sth
-
- if( mode .eq. 0 ) then
- goto 50
- end if
-
- do l=1, 3, 2
- d = e(l)
- ss(1) = (d-rr(3)) * (d-rr(6)) - rr(5)*rr(5)
- ss(2) = (d-rr(6)) * rr(2) + rr(4)*rr(5)
- ss(3) = (d-rr(1)) * (d-rr(6)) - rr(4)*rr(4)
- ss(4) = (d-rr(3)) * rr(4) + rr(2)*rr(5)
- ss(5) = (d-rr(1)) * rr(5) + rr(2)*rr(4)
- ss(6) = (d-rr(1)) * (d-rr(3)) - rr(2)*rr(2)
-
- if( dabs(ss(1)) .ge. dabs(ss(3)) ) then
- j=1
- if( dabs(ss(1)) .lt. dabs(ss(6)) ) j = 3
- else if( dabs(ss(3)) .ge. dabs(ss(6)) ) then
- j = 2
- else
- j = 3
- end if
-
- d = zero
- j = 3 * (j - 1)
-
- do i=1, 3
- k = ip(i+j)
- a(i,l) = ss(k)
- d = d + ss(k)*ss(k)
- end do
- if( d .gt. zero ) d = 1.0 / dsqrt(d)
- do i=1, 3
- a(i,l) = a(i,l) * d
- end do
- end do
-
- d = a(1,1)*a(1,3) + a(2,1)*a(2,3) + a(3,1)*a(3,3)
- if ((e(1) - e(2)) .gt. (e(2) - e(3))) then
- m1 = 3
- m = 1
- else
- m1 = 1
- m = 3
- endif
-
- p = zero
- do i=1, 3
- a(i,m1) = a(i,m1) - d*a(i,m)
- p = p + a(i,m1)**2
- end do
- if( p .le. tol ) then
- p = 1.0
- do i=1, 3
- if (p .lt. dabs(a(i,m))) cycle
- p = dabs( a(i,m) )
- j = i
- end do
- k = ip2312(j)
- l = ip2312(j+1)
- p = dsqrt( a(k,m)**2 + a(l,m)**2 )
- if( p .le. tol ) goto 40
- a(j,m1) = zero
- a(k,m1) = -a(l,m)/p
- a(l,m1) = a(k,m)/p
- else
- p = 1.0 / dsqrt(p)
- do i=1, 3
- a(i,m1) = a(i,m1)*p
- end do
- end if
-
- a(1,2) = a(2,3)*a(3,1) - a(2,1)*a(3,3)
- a(2,2) = a(3,3)*a(1,1) - a(3,1)*a(1,3)
- a(3,2) = a(1,3)*a(2,1) - a(1,1)*a(2,3)
-
- 30 do l=1, 2
- d = zero
- do i=1, 3
- b(i,l) = r(i,1)*a(1,l) + r(i,2)*a(2,l) + r(i,3)*a(3,l)
- d = d + b(i,l)**2
- end do
- if( d .gt. zero ) d = 1.0 / dsqrt(d)
- do i=1, 3
- b(i,l) = b(i,l)*d
- end do
- end do
- d = b(1,1)*b(1,2) + b(2,1)*b(2,2) + b(3,1)*b(3,2)
- p = zero
-
- do i=1, 3
- b(i,2) = b(i,2) - d*b(i,1)
- p = p + b(i,2)**2
- end do
- if( p .le. tol ) then
- p = 1.0
- do i=1, 3
- if( p .lt. dabs(b(i,1)) ) cycle
- p = dabs( b(i,1) )
- j = i
- end do
- k = ip2312(j)
- l = ip2312(j+1)
- p = dsqrt( b(k,1)**2 + b(l,1)**2 )
- if( p .le. tol ) goto 40
- b(j,2) = zero
- b(k,2) = -b(l,1)/p
- b(l,2) = b(k,1)/p
- else
- p = 1.0 / dsqrt(p)
- do i=1, 3
- b(i,2) = b(i,2)*p
- end do
- end if
-
- b(1,3) = b(2,1)*b(3,2) - b(2,2)*b(3,1)
- b(2,3) = b(3,1)*b(1,2) - b(3,2)*b(1,1)
- b(3,3) = b(1,1)*b(2,2) - b(1,2)*b(2,1)
-
- do i=1, 3
- do j=1, 3
- u(i,j) = b(i,1)*a(j,1) + b(i,2)*a(j,2) + b(i,3)*a(j,3)
- end do
- end do
-
- 40 do i=1, 3
- t(i) = ((yc(i) - u(i,1)*xc(1)) - u(i,2)*xc(2)) - u(i,3)*xc(3)
- end do
- 50 do i=1, 3
- if( e(i) .lt. zero ) e(i) = zero
- e(i) = dsqrt( e(i) )
- end do
-
- ier = 0
- if( e(2) .le. (e(1) * 1.0d-05) ) ier = -1
-
- d = e(3)
- if( sigma .lt. 0.0 ) then
- d = - d
- if( (e(2) - e(3)) .le. (e(1) * 1.0d-05) ) ier = -1
- end if
- d = (d + e(2)) + e(1)
-
- rms = (e0 - d) - d
- if( rms .lt. 0.0 ) rms = 0.0
-
- return
- end
projects / unres.git / blobdiff