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gde_linux/ZUKER/lin.f

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2006 version init
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 The ends of the sequence cannot be contained in a hairpin, bulge
c or interior loop. By convention, the ends of the sequence are
c put into a special kind of multi-loop. This can be called an
c exterior loop or an open multi-loop.
c
c 1/2 Asym. loop correction
c Extrapolate loops with dG(n)=dG(30)+1.75*ln(n/30)
c
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
c
100 if (mode.eq.1) then
c Read energy files.
call ergread
erg = 0
return
endif
erg = 0
c Do not allow prohibited base 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 accessibility option.
200 if (force(i).eq.3.or.force(jp).eq.3) then
erg = infinity
return
endif
c Molecule is not circular. N is not covalently bonded to N+1.
if (i.eq.n.or.j.eq.n+1) then
erg = infinity
return
endif
c Stacking energy.
erg = erg + stack(numseq(i),numseq(j),numseq(ip),numseq(jp))
. + eparam(1)
return
300 if ((i.le.n.and.ip.gt.n).or.(jp.le.n.and.j.gt.n)) then
c Loop is not allowed to contain the ends of the sequence.
erg = infinity
return
endif
c
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 energy.
if (size.eq.1) then
erg = erg + stack(numseq(i),numseq(j),numseq(ip),numseq(jp))
. + bulge(size) + eparam(2)
elseif (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 if (i.le.n.and.j.gt.n) then
c Hairpin loop must not contain the ends of the sequence.
erg = infinity
return
endif
c
size = j-i-1
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
c
c* Special case for hairpin of 3
c
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 (or multi-) loop closed by I,J.
500 do 501 ii = 1,4
501 e(ii) = infinity
if (i+2.gt.j-3) then
c There are at most 3 bases between I and J. The fragment from
c I to J inclusive contains the origen.
e(1) = 0
if (i.ne.n) e(2) = dangle(numseq(i),numseq(j),numseq(i+1),1)
if (j.ne.n+1) e(3) = dangle(numseq(i),numseq(j),numseq(j-1),2)
if (i.ne.n.and.j.ne.n+1) then
e(4) = dangle(numseq(i),numseq(j),numseq(i+1),1) +
. dangle(numseq(i),numseq(j),numseq(j-1),2)
endif
else if (i.ge.n-1) then
c I is at or next to the end of the sequence.
e(1) = w2(n+1,j-1)
if (i.ne.n) then
e(2) = dangle(numseq(i),numseq(j),numseq(i+1),1) + w2(n+1,j-1)
e(4) = dangle(numseq(i),numseq(j),numseq(i+1),1) +
. dangle(numseq(i),numseq(j),numseq(j-1),2) + w2(n+1,j-2)
endif
e(3) = dangle(numseq(i),numseq(j),numseq(j-1),2) + w2(n+1,j-2)
else if (j.eq.n+1.or.j.eq.n+2) then
c J is at or next to the end of the sequence.
e(1) = wst2((n-1)*i+n)
e(2) = dangle(numseq(i),numseq(j),numseq(i+1),1) +
. wst2((n-1)*(i+1)+n)
if (j.ne.n+1) then
e(3) = dangle(numseq(i),numseq(j),numseq(j-1),2)+wst2((n-1)*i+n)
e(4) = dangle(numseq(i),numseq(j),numseq(i+1),1) +
. dangle(numseq(i),numseq(j),numseq(j-1),2) + wst2((n-1)*(i+1)+n)
endif
else
ind1 = (n-1)*i
ind2 = ind1 + n - 1
do k = i+2,j-3
if (k.eq.n) then
c When K = N, the structure splits into two disconnected
c pieces. This open multi-loop ( exterior loop ) is not given the
c usual EPARAM(5),EPARAM(6) and EPARAM(10) destabilizing energies.
c
ind3 = -n
c No dangling ends next to the I,J base-pair.
c e(1) = min0(e(1),wst2(ind1+k)+wst2(ind3+j-1))
e(1) = min(e(1),wst2(ind1+k)+wst2(ind3+j-1))
c I+1 dangles on the I,J base-pair.
e(2) = min0(e(2),dangle(numseq(i),numseq(j),numseq(i+1),1)
. + wst2(ind2+k) + wst2(ind3+j-1))
c J-1 dangles on the I,J base-pair.
e(3) = min0(e(3),dangle(numseq(i),numseq(j),numseq(j-1),2)
. + wst2(ind1+k) + wst2(ind3+j-2))
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)
. + wst2(ind2+k) + wst2(ind3+j-2))
else
c When K is not N, the ends of the sequence are not in the
c loop. This is a proper multi-loop with an energy of EPARAM(6)
c for each single-stranded base, an energy of EPARAM(10) for
c each closing base-pair, plus and extra energy of EPARAM(5).
c No dangling ends next to the I,J base-pair.
e(1) = min0(e(1),wst1(ind1+k)+work1(k+1,mod(j-1,3))+eparam(5)
. +eparam(10))
c I+1 dangles on the I,J base-pair.
e(2) = min0(e(2),dangle(numseq(i),numseq(j),numseq(i+1),1)
. + wst1(ind2+k) + work1(k+1,mod(j-1,3)) + eparam(5)
. + eparam(6) + eparam(10) )
c J-1 dangles on the I,J base-pair.
e(3) = min0(e(3),dangle(numseq(i),numseq(j),numseq(j-1),2)
. + wst1(ind1+k) + work1(k+1,mod(j-2,3)) + eparam(5)
. + eparam(6) + eparam(10) )
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)
. + wst1(ind2+k) + work1(k+1,mod(j-2,3)) + eparam(5)
. + 2*eparam(6) + eparam(10) )
endif
enddo
endif
erg = erg + min0(e(1),e(2),e(3),e(4))
return
c Dangling base stacking energy. IP dangles over the I,J base-pair.
c 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 function erg
subroutine fill
c This subroutine computes the arrays of optimal energies.
include 'rfd.inc'
dimension inc(5,5),e1(5),e2(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
w1ij = infinity
w2ij = 0
if (j.le.n) then
if (j-i.le.loop) goto 300
else
if (i.eq.n.or.j.eq.n+1) goto 100
endif
c Test for a prohibited base-pair or a pair which cannot form.
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.or.j.gt.n) 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 the best bulge or interior loop closed by I,J.
if (j-i-1.ge.loop+3.or.j.gt.n) 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.or.j.gt.n) then
c Search for the best multi-loop closed by I,J.
vij=min0(vij,erg(5,i,j,i,j))
endif
c Compute W1IJ and W2IJ.
c A multi-loop containing N and 1 (ie. N+1) as single-stranded
c bases is called an exterior loop. W1IJ is the minimum folding
c energy of a non-empty folding on I to J inclusive where an
c exterior loop is given an energy of EPARAM(5) plus EPARAM(6)
c per single-stranded exterior base plus EPARAM(10) per
c double-stranded exterior base-pair in addition to
c possible dangling base energies. W2IJ is similarly
c defined except that the folding can be empty and that an
c exterior loop is given no energy other than possible dangling
c base energies.
200 do ii = 1,5
e1(ii) = infinity
e2(ii) = infinity
enddo
if (i.ne.n) then
c Add single-stranded I to an optimal structure containing
c the base-pair I,J.
e1(1) = v(i+1,j) + eparam(10) + eparam(6) + erg(6,j,i+1,i,2)
e1(4) = w1(i+1,j) + eparam(6)
e2(1) = v(i+1,j) + erg(6,j,i+1,i,2)
e2(4) = w2(i+1,j)
endif
if (j.ne.n+1) then
c Add single-stranded J to an optimal structure containing
c the base-pair I,J.
e1(2) = v(i,j-1) + eparam(10) + eparam(6) + erg(6,j-1,i,j,1)
e1(5) = w1(i,j-1) + eparam(6)
e2(2) = v(i,j-1) + erg(6,j-1,i,j,1)
e2(5) = w2(i,j-1)
endif
if (i.ne.n.and.j.ne.n+1) then
c Add single-stranded I and J to an optimal structure containing
c the base-pair I+1,J-1.
e1(3) = v(i+1,j-1) + eparam(10) + 2*eparam(6) +
. erg(6,j-1,i+1,i,2) + erg(6,j-1,i+1,j,1)
e2(3) = v(i+1,j-1) + erg(6,j-1,i+1,i,2)
. + erg(6,j-1,i+1,j,1)
endif
w1ij = min0(eparam(10)+vij,e1(1),e1(2),e1(3),e1(4),e1(5))
w2ij = min0(vij,w2ij,e2(1),e2(2),e2(3),e2(4),e2(5))
if (j-i-1.gt.2*loop+2.or.j.gt.n) then
index = (n-1)*(i-1)
c Search for an open bifurcation.
do k = i,j-1
if (k.eq.n) then
w1ij = min0(w1ij,wst2(index+k)+work2(k+1))
else
w1ij = min0(w1ij,wst1(index+k)+work1(k+1,mod(j,3)))
w2ij = min0(w2ij,wst2(index+k)+work2(k+1))
endif
enddo
endif
c Store VIJ, W1IJ and W2IJ. They can be regarded as elements
c V(I,J), W1(I,J) and W2(I,J) in two dimensional arrays. They
c are actually stored in one dimensional arrays VST, WST1 and
c WST2 is position (N-1)*(I-1) + J.
c Columns J,J-1 and J-2 of W1 are also stored in the work array,
c WORK1. Column J of W2 is stored again in the work array WORK2.
c This is done to reduce virtual memory swaps.
300 vst((n-1)*(i-1)+j) = vij
wst1((n-1)*(i-1)+j) = w1ij
wst2((n-1)*(i-1)+j) = w2ij
work1(i,mod(j,3)) = w1ij
work2(i) = w2ij
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 on
c the next column.
work1(k,mod(j+1,3)) = wst1((k-n-1)*(n-1)+j+1-n)
work2(k) = wst2((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 W1 which are actually stored in WST1.
function w1(i,j)
include 'rfd.inc'
if (i.gt.n) then
w1 = wst1((n-1)*(i-n-1)+j-n)
else
w1 = wst1((n-1)*(i-1)+j)
endif
return
end
c Used to recall values of W2 which are actually stored in WST2.
function w2(i,j)
include 'rfd.inc'
if (i.gt.n) then
w2 = wst2((n-1)*(i-n-1)+j-n)
else
w2 = wst2((n-1)*(i-1)+j)
endif
return
end
c Computes an optimal structure on the subsequence from II to JI
c where II and JI must base-pair with each other. ERROR = 0
c indicates a normal termination.
c NFORCE is the number of forced base-pairs encountered during the
c traceback.
c Base-pair information is stored in the array BASEPR.
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 II,JI,
c V(II,JI) and 0 on to the stack.
call initst
call push(ii,ji,v(ii,ji),0)
nforce = 0
100 i = j
do while (i.eq.j)
c Pull a fragment ( I to J ) and its expected energy ( E ) from
c the stack. OPENL = 1 indicates that the free bases are part of
c an exterior loop. OPENL = 0 (ie. closed) indicates that the
c free bases are part of a multi-loop.
stz = pull(i,j,e,openl)
if (stz.ne.0) return
enddo
c Do I and J base-pair with one another?
if (e.eq.v(i,j)) goto 300
if (openl.eq.0) then
do while (e.eq.w1(i+1,j)+eparam(6))
c Whittle away from the 5' end.
i = i + 1
e = w1(i,j)
if (i.ge.j) goto 100
enddo
do while (e.eq.w1(i,j-1)+eparam(6))
c Whittle away from the 3' end.
j = j - 1
e = w1(i,j)
if (i.ge.j) goto 100
enddo
if (e.eq.v(i+1,j)+eparam(10)+eparam(6)+erg(6,j,i+1,i,2)) then
c I dangles over I+1,J.
i = i + 1
e = v(i,j)
elseif (e.eq.v(i,j-1)+eparam(10)+eparam(6)+erg(6,j-1,i,j,1)) then
c J dangles over I,J-1.
j = j - 1
e = v(i,j)
elseif (e.eq.v(i+1,j-1) + eparam(10) + 2*eparam(6) +
. erg(6,j-1,i+1,i,2) + erg(6,j-1,i+1,j,1) ) 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)
else
do while (e.eq.w2(i+1,j))
c Whittle away at the 5' end.
i = i + 1
if (i.ge.j) goto 100
enddo
do while (e.eq.w2(i,j-1))
c Whittle away at the 3' end.
j = j - 1
if (i.ge.j) goto 100
enddo
if (e.eq.v(i+1,j)+erg(6,j,i+1,i,2)) then
c I dangles over I+1,J.
i = i + 1
e = v(i,j)
elseif (e.eq.v(i,j-1) + erg(6,j-1,i,j,1)) then
c J dangles over I,J-1.
j = j - 1
e = v(i,j)
elseif (e.eq.v(i+1,j-1)+erg(6,j-1,i+1,i,2)+erg(6,j-1,i+1,j,1))
. then
c Bothe I and J dangle over I+1,J-1.
i = i + 1
j = j - 1
e = v(i,j)
endif
endif
if (e.ne.v(i,j)) then
c Cannot chop away at the ends any more and still the ends do not
c base-pair with one another. Structure MUST bifucate (OPENL).
k = i
200 if (k.eq.j) then
c Structure will not split. Error
ii = hstnum(i)
ji = hstnum(j)
error = 10
return
endif
if (openl.eq.0.and.e.eq.w1(i,k) + w1(k+1,j)) then
c Best structure on I,J splits into best structures on I,K
c and K+1,J. Push these fragments on to the stack. (OPENL = 0)
call push(i,k,w1(i,k),0)
call push(k+1,j,w1(k+1,j),0)
goto 100
else if (openl.eq.1.and.e.eq.w2(i,k) + w2(k+1,j)) then
c Best structure on I,J splits into best structures on I,K
c and K+1,J. Push these fragments on to the stack. (OPENL = 1)
call push(i,k,w2(i,k),1)
call push(k+1,j,w2(k+1,j),1)
goto 100
else
k = k + 1
goto 200
endif
endif
c Base-pair found. All base-pairs are stored in the range 1 <= I < J <= N.
c If I and J form a base-pair, then BASEPR(I) = J and BASEPR(J) = I.
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
openl = 0
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 (i.ne.n.and.j.ne.n+1) then
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
endif
c Perhaps I,J closes a hairpin loop?
if (e.eq.erg(4,i,j,i,j)) goto 100
c E' ( EP in the program ) is E corrcted for possible forced
c base-pairs.
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)
if (i+2.gt.j-3) then
c Tidy up loose ends (trivial).
if (ep.eq.0.or.(i.ne.n.and.ep.eq.erg(6,i,j,i+1,1))) then
goto 100
elseif (j.ne.n+1.and.ep.eq.erg(6,i,j,j-1,2)) then
goto 100
elseif (i.ne.n.and.j.ne.n+1.and.
. ep.eq.erg(6,i,j,i+1,1) + erg(6,i,j,j-1,2)) then
goto 100
else
ii = hstnum(i)
ji = hstnum(j)
error = 12
return
endif
else if (i.ge.n-1) then
c Up to one base hanging on to I.
if (ep.eq.w2(n+1,j-1)) then
call push(n+1,j-1,w2(n+1,j-1),1)
goto 100
elseif (i.ne.n) then
if (ep.eq.erg(6,i,j,i+1,1) + w2(n+1,j-1)) then
call push(n+1,j-1,w2(n+1,j-1),1)
goto 100
else if (ep.eq.erg(6,i,j,i+1,1)+erg(6,i,j,j-1,2) + w2(n+1,j-2))
. then
call push(n+1,j-2,w2(n+1,j-2),1)
goto 100
endif
elseif (ep.eq.erg(6,i,j,j-1,2) + w2(n+1,j-2)) then
call push(n+1,j-2,w2(n+1,j-2),1)
goto 100
else
ii = hstnum(i)
ji = hstnum(j)
error = 12
return
endif
else if (j.eq.n+1.or.j.eq.n+2) then
c Up to one base hanging on to J.
if (ep.eq.w2(i+1,n)) then
call push(i+1,n,w2(i+1,n),1)
goto 100
elseif (ep.eq.erg(6,i,j,i+1,1) + w2(i+2,n)) then
call push(i+2,n,w2(i+2,n),1)
goto 100
elseif (j.ne.n+1) then
if (ep.eq.erg(6,i,j,j-1,2)+w2(i+1,n)) then
call push(i+1,n,w2(i+1,n),1)
goto 100
elseif (ep.eq.erg(6,i,j,i+1,1) + erg(6,i,j,j-1,2) + w2(i+2,n))
. then
call push(i+2,n,w2(i+2,n),1)
goto 100
endif
else
ii = hstnum(i)
ji = hstnum(j)
error = 12
return
endif
else
k = i+2
c Perhaps I,J closes a multi-loop?
400 do while (k.le.j-3)
if (k.ne.n) then
if (ep.eq.w1(i+1,k) + w1(k+1,j-1) + eparam(10) + eparam(5))
. then
c Multi-loop. No dangling ends on I,J.
call push(i+1,k,w1(i+1,k),0)
call push(k+1,j-1,w1(k+1,j-1),0)
goto 100
else if (ep.eq.erg(6,i,j,i+1,1)+w1(i+2,k)+w1(k+1,j-1) +
. eparam(10) + eparam(6) + eparam(5)) then
c Multi-loop. I+1 dangles over the I,J base-pair.
call push(i+2,k,w1(i+2,k),0)
call push(k+1,j-1,w1(k+1,j-1),0)
goto 100
else if (ep.eq.erg(6,i,j,j-1,2)+w1(i+1,k)+w1(k+1,j-2) +
. eparam(10) + eparam(6) + eparam(5)) then
c Multi-loop. J-1 dangles over the I,J base-pair.
call push(i+1,k,w1(i+1,k),0)
call push(k+1,j-2,w1(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)+w1(i+2,k)
. +w1(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,w1(i+2,k),0)
call push(k+1,j-2,w1(k+1,j-2),0)
goto 100
endif
else
if (ep.eq.w2(i+1,k) + w2(k+1,j-1)) then
c Exterior loop. No ends dangling on I,J.
call push(i+1,k,w2(i+1,k),1)
call push(k+1,j-1,w2(k+1,j-1),1)
goto 100
else if (ep.eq.erg(6,i,j,i+1,1)+w2(i+2,k)+w2(k+1,j-1)) then
c Exterior loop. I+1 dangles over the I,J base-pair.
call push(i+2,k,w2(i+2,k),1)
call push(k+1,j-1,w2(k+1,j-1),1)
goto 100
else if (ep.eq.erg(6,i,j,j-1,2)+w2(i+1,k)+w2(k+1,j-2)) then
c Exterior loop. J-1 dangles over the I,J base-pair.
call push(i+1,k,w2(i+1,k),1)
call push(k+1,j-2,w2(k+1,j-2),1)
goto 100
else if (ep.eq.erg(6,i,j,i+1,1)+
. erg(6,i,j,j-1,2)+w2(i+2,k)+w2(k+1,j-2)) then
c Exterior loop. Both I+1 and J-1 dangle over the I,J base-pair.
call push(i+2,k,w2(i+2,k),1)
call push(k+1,j-2,w2(k+1,j-2),1)
goto 100
endif
endif
k = k + 1
enddo
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) (wst1(i),i=1,n*n)
write(30) (wst2(i),i=1,n*n)
write(30) (seq(i),i=nsave(1),nsave(2))
write(30) ((list(i,j),i=1,listsz),j=1,4)
write(30) tloop,numoftloops
write(30) (poppen(i),i=1,4),maxpen,prelog
return
end
c Read results from a SAVE run for a CONTINUATION run.
subroutine getcont
include 'rfd.inc'
read(30,err=10) n,nsave,vmin,listsz,seqlab
read(30,err=10) stack,tstk,dangle,hairpin,bulge,inter,eparam
read(30,err=10) (vst(i),i=1,n*n)
read(30,err=10) (wst1(i),i=1,n*n)
read(30,err=10) (wst2(i),i=1,n*n)
read(30,err=10) (seq(i),i=nsave(1),nsave(2))
read(30,err=10) ((list(i,j),i=1,listsz),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
Reference in a new issue Copy permalink