gde_linux/ZUKER/circ.f

560 lines
17 KiB
FortranFixed
Raw Normal View History

2022-03-08 04:43:05 +08:00
c Energy funtion.
c ERG is the energy of a loop closed by I,J (new numbering).
c IP,JP is the other closing base-pair when MODE = 2 or 3.
c
c 1/2 Asym. loop correction
c Extrapolate loops with dG(n)=dG(30)+1.75*ln(n/30)
c Hairpins of 3 have no terminal stack.
c
function erg(mode,i,j,ip,jp)
include 'rfd.inc'
dimension e(4)
integer*2 tlink,tlptr
logical fce
100 if (mode.eq.1) then
c Read energy files
call ergread
erg = 0
return
endif
erg = 0
c Do not allow prohibited bases to pair.
if (force(i).eq.1.or.force(j).eq.1) then
erg = infinity
return
endif
if (mode.lt.6) then
c Add bonus energy to force base-pairs.
if (force(i).eq.2.or.force(j).eq.2.or.fce(i,j)) then
erg = erg + eparam(9)
if (force(i).eq.2.and.force(j).eq.2) erg = erg + eparam(9)
endif
endif
goto (100,200,300,400,500,600,700),mode
c Nucleotide accesssibility option.
200 if (force(i).eq.3.or.force(jp).eq.3) then
erg = infinity
return
endif
c Stacking energy.
erg = erg + stack(numseq(i),numseq(j),numseq(ip),numseq(jp))
. + eparam(1)
return
300 size1 = ip - i - 1
size2 = j - jp - 1
if (size1.eq.0.or.size2.eq.0) then
c Check for nucleotide accessibility.
if (size1.eq.0.and.force(i).eq.3) then
erg = infinity
return
endif
if (size2.eq.0.and.force(jp).eq.3) then
erg = infinity
return
endif
size = size1+size2
c Bulge loop.
if (size.eq.1) then
erg = erg + stack(numseq(i),numseq(j),numseq(ip),numseq(jp))
. + bulge(1) + eparam(2)
else if (size.gt.30) then
loginc = int(prelog*log((float(size)/30.0)))
erg = erg + bulge(30) + loginc + eparam(2)
else
erg = erg + bulge(size) + eparam(2)
endif
return
else
size = size1+size2
lopsid = abs((size1-size2))
c Interior loop.
if (size.gt.30) then
loginc = int(prelog*log((float(size)/30.0)))
erg = erg + tstk(numseq(i),numseq(j),numseq(i+1),numseq(j-1))
. + tstk(numseq(jp),numseq(ip),numseq(jp+1),numseq(ip-1))
. + inter(30) + loginc + eparam(3)
. + min0(maxpen,(lopsid*poppen(min0(4,size1,size2))))
else
erg = erg + tstk(numseq(i),numseq(j),numseq(i+1),numseq(j-1))
. + tstk(numseq(jp),numseq(ip),numseq(jp+1),numseq(ip-1))
. + inter(size) + eparam(3)
. + min0(maxpen,(lopsid*poppen(min0(4,size1,size2))))
endif
return
endif
400 size = j-i-1
c Hairpin loop.
if ((size.eq.3).and.fce(i,j).and.seq(hstnum(i+1)).eq.' ') then
c Closed excision
erg = eparam(9)
return
endif
if (size.gt.30) then
loginc = int(prelog*log((float(size)/30.0)))
erg = erg + tstk(numseq(i),numseq(j),numseq(i+1),numseq(j-1))
. + hairpin(30) + loginc + eparam(4)
else if (size.lt.4) then
erg=erg+hairpin(size)+eparam(4)
else
c
tlink=0
if (size.eq.4) then
key=((numseq(i+4)*8+numseq(i+3))*8+numseq(i+2))*8+numseq(i+1)
tlptr=1
do while ((tlptr.le.numoftloops).and.(tloop(tlptr,1).ne.key))
tlptr=tlptr+1
enddo
if (tlptr.le.numoftloops) tlink=tloop(tlptr,2)
endif
erg = erg + tstk(numseq(i),numseq(j),numseq(i+1),numseq(j-1))
. + hairpin(size) + eparam(4) + tlink
endif
return
c Multi-branch loop.
500 do 501 ii = 1,4
501 e(ii) = infinity
if (i.le.n-2) then
ind1 = (n-1)*i
ind2 = (n-1)*(i+1)
else if (i.eq.n-1) then
ind1 = (n-1)*i
ind2 = -n
else
ind1 = -n
ind2 = -1
endif
do k = i+2,j-3
c EPARAM(6) is the energy penalty for each single-stranded base
c in a multi-loop. EPARAM(10) is the energy penalty for each base-pair
c closing a multi-loop.
c No dangling ends next to the I,J base-pair.
e(1) = min0(e(1),wst(ind1+k)+work(k+1,mod(j-1,3)))
c I+1 dangles on the I,J base-pair.
e(2) = min0(e(2),dangle(numseq(i),numseq(j),numseq(i+1),1)
. + wst(ind2+k) + work(k+1,mod(j-1,3)) + eparam(6))
c J-1 dangles on the I,J base-pair.
e(3) = min0(e(3),dangle(numseq(i),numseq(j),numseq(j-1),2)
. + wst(ind1+k) + work(k+1,mod(j-2,3)) + eparam(6))
c Both I+1 and J-1 dangle on the I,J base-pair.
e(4) = min0(e(4),dangle(numseq(i),numseq(j),numseq(i+1),1)
. + dangle(numseq(i),numseq(j),numseq(j-1),2)
. + wst(ind2+k) + work(k+1,mod(j-2,3)) + 2*eparam(6))
enddo
c EPARAM(5) is the energy penalty for closing a multi-loop.
erg = erg + eparam(5) + eparam(10) + min0(e(1),e(2),e(3),e(4))
return
c Dangling base stacking energy. IP dangles over the I,J
c base-pair. 3' or 5' dangle if JP = 1 or 2 respectively.
600 erg = erg + dangle(numseq(i),numseq(j),numseq(ip),jp)
return
700 if (force(i).eq.3.or.force(jp).eq.3) then
erg = infinity
return
endif
c Terminal stack or mismatch energy.
erg = erg + tstk(numseq(i),numseq(j),numseq(ip),numseq(jp))
return
end
subroutine fill
c This subroutine computes the arrays of optimal energies.
include 'rfd.inc'
dimension inc(5,5)
data loop/3/,inc/0,0,0,1,0,0,0,1,0,0,0,1,0,1,0,1,0,1,0,0,0,0,0,0,0
./
vmin = infinity
if (n.le.80) then
pinc = 5
elseif (n.le.100) then
pinc = 2
else
pinc = 1
endif
pcnt = pinc
crit = n*n*n/50
do j = 1,2*n-1
c How far along is the computation?
if (n.gt.10) then
if (j.le.n) then
if (j**3.ge.pcnt*crit) then
write (6,1000) pcnt
pcnt = pcnt + pinc
endif
else
if ((2*n-j)**3.le.(100-pcnt)*crit) then
write (6,1000) pcnt
pcnt = pcnt + pinc
endif
endif
endif
1000 format ('+',5x,i4,'%')
do i = min0(j,n),max0(1,j-n+1),-1
vij = infinity
wij = infinity
if (j-i.le.loop) goto 300
c Test for a prohibited base-pair or a pair which cannot form
c a base-pair.
if (vst((n-1)*(i-1)+j).eq.1.or.inc(numseq(i),numseq(j)).eq.0)
. goto 200
c Compute VIJ, the minimum energy of the fragment from I to J
c inclusive where I and J base-pair with one another.
c Perhaps I,J closes a hairpin loop.
vij = min0(vij,erg(4,i,j,i,j))
if (j-i-1.ge.loop+2) then
c Perhaps I,J stacks over I+1,J-1.
vij = min0(vij,erg(2,i,j,i+1,j-1)+v(i+1,j-1))
endif
c Search for a bulge or interior loop.
if (j-i-1.ge.loop+3) then
do d = j-i-3,1,-1
do ip = i+1,j-1-d
jp = d+ip
if (j-i-2-d.gt.eparam(7)) goto 100
if (abs(ip-i+jp-j).le.eparam(8)) then
if (ip.gt.n) then
vij = min0(vij,erg(3,i,j,ip,jp)+vst((n-1)*
. (ip-n-1)+jp-n))
else
vij = min0(vij,erg(3,i,j,ip,jp)+vst((n-1)*
. (ip-1)+jp))
endif
endif
enddo
enddo
endif
100 if (j-i-1.ge.2*loop+4) then
c Perhaps I,J closes a multi-loop.
vij=min0(vij,erg(5,i,j,i,j))
endif
c Compute WIJ, the minimum energy of a non-empty folding on I to
c J inclusive. This is the circular folding program and so there
c are no exterior bases.
200 wij = min0 ( wij, eparam(10)+vij, v(i+1,j)+eparam(6)+eparam(10)+
. erg(6,j,i+1,i,2), v(i,j-1)+eparam(6)+eparam(10)+
. erg(6,j-1,i,j,1), v(i+1,j-1)+2*eparam(6)+eparam(10)+
. erg(6,j-1,i+1,i,2)+erg(6,j-1,i+1,j,1),
. w(i+1,j)+eparam(6), w(i,j-1)+eparam(6) )
if (j-i-1.gt.2*loop+2) then
index = (n-1)*(i-1)
c Check for open bifurcation.
do k = i,j-1
wij = min0(wij,wst(index+k)+work(k+1,mod(j,3)))
enddo
endif
c Store VIJ and WIJ. They can be regarded as elements V(I,J)
c and W(I,J) in a two dimensional array. They are actually
c stored in the one dimensional arrays VST and WST in position
c (N-1)*(I-1) + J.
c Columns J,J-1 and J-2 of W are stored again in the WORK array.
c This is done to reduce virtual memory swaps.
300 vst((n-1)*(i-1)+j) = vij
wst((n-1)*(i-1)+j) = wij
work(i,mod(j,3)) = wij
if (j.gt.n) then
c VMIN is the minimum folding energy of the entire sequence.
c vmin = min0(vmin,vst((n-1)*(i-1)+j)+vst((n-1)*(j-n-1)+i))
vmin = min(vmin,vst((n-1)*(i-1)+j)+vst((n-1)*(j-n-1)+i))
endif
enddo
if (j.ge.n) then
do k = j+1,n+1,-1
c Fill in some WORK array values before beginning work on the
c next column.
work(k,mod(j+1,3)) = wst((k-n-1)*(n-1)+j+1-n)
enddo
endif
enddo
return
end
c Used to recall values of V which are actually stored in VST.
function v(i,j)
include 'rfd.inc'
if (i.gt.n) then
v = vst((n-1)*(i-n-1)+j-n)
else
v = vst((n-1)*(i-1)+j)
endif
return
end
c Used to recall values of W which are actually stored in WST.
function w(i,j)
include 'rfd.inc'
if (i.gt.n) then
w = wst((n-1)*(i-n-1)+j-n)
else
w = wst((n-1)*(i-1)+j)
endif
return
end
c Computes an optimal structure on the subsequence II to JI where
c II and JI must base-pair with one another. ERROR = 0 is normal
c termination.
c NFORCE is the number of forced base-pairs encountered in the traceback.
subroutine trace(ii,ji,nforce,error)
include 'rfd.inc'
logical fce
error = 0
c Zero the appropriate region of BASEPR.
if (ji.le.n) then
do k=ii,ji
basepr(k) = 0
enddo
else
do k=1,ji-n
basepr(k) = 0
enddo
do k = ii,n
basepr(k) = 0
enddo
endif
c Initialize the stack of outstanding base-pairs and push
c II, JI and V(II,JI) on to the stack. The fourth stack position
c is unused in this subroutine.
call initst
call push(ii,ji,v(ii,ji),0)
nforce = 0
c Pull a fragment and its expected energy from the stack.
c End if there are no fragments left.
100 stz = pull(i,j,e,xx)
if (stz.ne.0) return
c Do I and J base-pair with one another?
if (e.eq.v(i,j)) goto 300
tst = w(i+1,j) + eparam(6)
do while (e.eq.tst)
c Whittle away from the 5' end.
i = i + 1
if (i.ge.j) goto 100
e = w(i,j)
tst = w(i+1,j) + eparam(6)
enddo
tst = w(i,j-1) + eparam(6)
do while (e.eq.tst)
c Whittle away from the 3' end.
j = j - 1
if (i.ge.j) goto 100
e = w(i,j)
tst = w(i,j-1) + eparam(6)
enddo
tst1 = v(i+1,j) + eparam(6) + eparam(10) +
. dangle(numseq(j),numseq(i+1),numseq(i),2)
tst2 = v(i,j-1) + eparam(6) + eparam(10) +
. dangle(numseq(j-1),numseq(i),numseq(j),1)
tst3 = v(i+1,j-1) + 2*eparam(6) + eparam(10) +
. dangle(numseq(j-1),numseq(i+1),numseq(i),2)
. + dangle(numseq(j-1),numseq(i+1),numseq(j),1)
if (e.eq.tst1) then
c I dangles over I+1,J.
i = i + 1
e = v(i,j)
else if (e.eq.tst2) then
c J dangles over I,J-1.
j = j - 1
e = v(i,j)
else if (e.eq.tst3) then
c Both I and J dangle over I+1,J-1.
i = i + 1
j = j - 1
e = v(i,j)
endif
c Check for stem closing a multi-loop.
if (e.eq.v(i,j)+eparam(10)) e = v(i,j)
if (e.ne.v(i,j)) then
c Cannot chop away at ends any more and still the ends do not
c base-pair with one another. Structure MUST bifurcate (OPEN).
k = i+1
200 if (k.eq.j) then
c Structure will not split. Error
ii = hstnum(i)
ji = hstnum(j)
error = 10
return
endif
if (e.eq.w(i,k) + w(k+1,j)) then
c Best structure on I,J splits into best structures on I,K and
c K+1,J. Push these fragments on to the stack.
call push(i,k,w(i,k),0)
call push(k+1,j,w(k+1,j),0)
goto 100
else
k = k + 1
goto 200
endif
endif
c Base-pair found. Base-pairs are stored in the range 1 <= I < J <= N.
300 if (j.le.n) then
basepr(i) = j
basepr(j) = i
else if (i.gt.n) then
basepr(i-n) = j-n
basepr(j-n) = i-n
i = i - n
j = j - n
else
basepr(j-n) = i
basepr(i) = j-n
endif
c Check if this is a forced base-pair.
if (force(i).eq.2.or.force(j).eq.2.or.fce(i,j))
. nforce = nforce + 1
if (force(i).eq.2.and.force(j).eq.2) nforce = nforce + 1
c Perhaps I,J stacks over I+1,J-1?
if (e.eq.erg(2,i,j,i+1,j-1)
. + v(i+1,j-1)) then
i = i + 1
j = j - 1
e = v(i,j)
goto 300
endif
c Perhaps I,J closes a hairpin loop?
if (e.eq.erg(4,i,j,i,j)) goto 100
c Define E' ( EP in the program ) to be E corrected by a
c possible bonus energy for forced base-pairing.
c
ep = e
if (force(i).eq.2.or.force(j).eq.2.or.fce(i,j))
. ep = ep - eparam(9)
if (force(i).eq.2.and.force(j).eq.2) ep = ep - eparam(9)
k = i+2
c Perhaps I,J closes a multi-loop?
400 if (k.ge.j-3) goto 500
if (ep.eq.w(i+1,k) + w(k+1,j-1) + eparam(10) + eparam(5)) then
c Multi-loop. No dangling ends on I,J.
call push(i+1,k,w(i+1,k),0)
call push(k+1,j-1,w(k+1,j-1),0)
goto 100
else if (ep.eq.erg(6,i,j,i+1,1)+w(i+2,k)+w(k+1,j-1)+eparam(10)+
. eparam(6)+eparam(5)) then
c Multi-loop. I+1 dangles over I,J base-pair.
call push(i+2,k,w(i+2,k),0)
call push(k+1,j-1,w(k+1,j-1),0)
goto 100
else if (ep.eq.erg(6,i,j,j-1,2)+w(i+1,k)+w(k+1,j-2)+eparam(10)+
. eparam(6)+eparam(5)) then
c Multi-loop. J-1 dangles over I,J base-pair.
call push(i+1,k,w(i+1,k),0)
call push(k+1,j-2,w(k+1,j-2),0)
goto 100
else if (ep.eq.erg(6,i,j,i+1,1)+erg(6,i,j,j-1,2)+w(i+2,k)
. +w(k+1,j-2)+ eparam(10)+2*eparam(6)+eparam(5)) then
c Multi-loop. Both I+1 and J-1 dangle over the I,J base-pair.
call push(i+2,k,w(i+2,k),0)
call push(k+1,j-2,w(k+1,j-2),0)
goto 100
else
k = k + 1
goto 400
endif
c None of the above work. I,J MUST close a bulge or interior loop.
500 do d = j-i-3,1,-1
do ip = i+1,j-1-d
jp = d+ip
if (j-i-2-d.gt.eparam(7)) then
c Error, bulge or interior loop not found.
ii = hstnum(i)
ji = hstnum(j)
error = 11
return
endif
if (abs(ip-i+jp-j).le.eparam(8)) then
if (e.eq.erg(3,i,j,ip,jp)+v(ip,jp)) then
i = ip
j = jp
e = v(i,j)
goto 300
endif
endif
enddo
enddo
c Error, bulge or interior loop not found.
ii = hstnum(i)
ji = hstnum(j)
error = 11
return
end
c Store results of a SAVE run for a CONTINUATION run.
subroutine putcont
include 'rfd.inc'
write(30) n,nsave,vmin,listsz,seqlab
write(30) stack,tstk,dangle,hairpin,bulge,inter,eparam
write(30) (vst(i),i=1,n*n)
write(30) (wst(i),i=1,n*n)
write(30) (seq(i),i=nsave(1),nsave(2))
write(30) ((list(i,j),i=1,100),j=1,4)
write(30) tloop,numoftloops
write(30) (poppen(i),i=1,4),maxpen,prelog
return
end
c Read results of a SAVE run for a CONTINUATION run.
subroutine getcont
include 'rfd.inc'
read(30,end=10) n,nsave,vmin,listsz,seqlab
read(30,end=10) stack,tstk,dangle,hairpin,bulge,inter,eparam
read(30,end=10) (vst(i),i=1,n*n)
read(30,end=10) (wst(i),i=1,n*n)
read(30,end=10) (seq(i),i=nsave(1),nsave(2))
read(30,end=10) ((list(i,j),i=1,100),j=1,4)
read(30,err=10) tloop,numoftloops
read(30,err=10) (poppen(i),i=1,4),maxpen,prelog
goto 11
10 call errmsg(40,0,0)
11 return
end