560 lines
17 KiB
FortranFixed
560 lines
17 KiB
FortranFixed
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c Energy funtion.
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c ERG is the energy of a loop closed by I,J (new numbering).
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c IP,JP is the other closing base-pair when MODE = 2 or 3.
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c
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c 1/2 Asym. loop correction
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c Extrapolate loops with dG(n)=dG(30)+1.75*ln(n/30)
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c Hairpins of 3 have no terminal stack.
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c
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function erg(mode,i,j,ip,jp)
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include 'rfd.inc'
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dimension e(4)
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integer*2 tlink,tlptr
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logical fce
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100 if (mode.eq.1) then
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c Read energy files
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call ergread
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erg = 0
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return
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endif
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erg = 0
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c Do not allow prohibited bases to pair.
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if (force(i).eq.1.or.force(j).eq.1) then
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erg = infinity
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return
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endif
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if (mode.lt.6) then
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c Add bonus energy to force base-pairs.
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if (force(i).eq.2.or.force(j).eq.2.or.fce(i,j)) then
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erg = erg + eparam(9)
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if (force(i).eq.2.and.force(j).eq.2) erg = erg + eparam(9)
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endif
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endif
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goto (100,200,300,400,500,600,700),mode
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c Nucleotide accesssibility option.
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200 if (force(i).eq.3.or.force(jp).eq.3) then
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erg = infinity
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return
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endif
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c Stacking energy.
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erg = erg + stack(numseq(i),numseq(j),numseq(ip),numseq(jp))
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. + eparam(1)
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return
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300 size1 = ip - i - 1
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size2 = j - jp - 1
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if (size1.eq.0.or.size2.eq.0) then
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c Check for nucleotide accessibility.
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if (size1.eq.0.and.force(i).eq.3) then
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erg = infinity
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return
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endif
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if (size2.eq.0.and.force(jp).eq.3) then
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erg = infinity
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return
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endif
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size = size1+size2
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c Bulge loop.
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if (size.eq.1) then
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erg = erg + stack(numseq(i),numseq(j),numseq(ip),numseq(jp))
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. + bulge(1) + eparam(2)
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else if (size.gt.30) then
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loginc = int(prelog*log((float(size)/30.0)))
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erg = erg + bulge(30) + loginc + eparam(2)
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else
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erg = erg + bulge(size) + eparam(2)
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endif
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return
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else
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size = size1+size2
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lopsid = abs((size1-size2))
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c Interior loop.
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if (size.gt.30) then
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loginc = int(prelog*log((float(size)/30.0)))
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erg = erg + tstk(numseq(i),numseq(j),numseq(i+1),numseq(j-1))
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. + tstk(numseq(jp),numseq(ip),numseq(jp+1),numseq(ip-1))
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. + inter(30) + loginc + eparam(3)
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. + min0(maxpen,(lopsid*poppen(min0(4,size1,size2))))
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else
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erg = erg + tstk(numseq(i),numseq(j),numseq(i+1),numseq(j-1))
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. + tstk(numseq(jp),numseq(ip),numseq(jp+1),numseq(ip-1))
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. + inter(size) + eparam(3)
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. + min0(maxpen,(lopsid*poppen(min0(4,size1,size2))))
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endif
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return
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endif
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400 size = j-i-1
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c Hairpin loop.
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if ((size.eq.3).and.fce(i,j).and.seq(hstnum(i+1)).eq.' ') then
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c Closed excision
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erg = eparam(9)
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return
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endif
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if (size.gt.30) then
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loginc = int(prelog*log((float(size)/30.0)))
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erg = erg + tstk(numseq(i),numseq(j),numseq(i+1),numseq(j-1))
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. + hairpin(30) + loginc + eparam(4)
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else if (size.lt.4) then
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erg=erg+hairpin(size)+eparam(4)
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else
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c
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tlink=0
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if (size.eq.4) then
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key=((numseq(i+4)*8+numseq(i+3))*8+numseq(i+2))*8+numseq(i+1)
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tlptr=1
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do while ((tlptr.le.numoftloops).and.(tloop(tlptr,1).ne.key))
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tlptr=tlptr+1
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enddo
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if (tlptr.le.numoftloops) tlink=tloop(tlptr,2)
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endif
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erg = erg + tstk(numseq(i),numseq(j),numseq(i+1),numseq(j-1))
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. + hairpin(size) + eparam(4) + tlink
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endif
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return
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c Multi-branch loop.
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500 do 501 ii = 1,4
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501 e(ii) = infinity
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if (i.le.n-2) then
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ind1 = (n-1)*i
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ind2 = (n-1)*(i+1)
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else if (i.eq.n-1) then
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ind1 = (n-1)*i
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ind2 = -n
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else
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ind1 = -n
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ind2 = -1
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endif
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do k = i+2,j-3
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c EPARAM(6) is the energy penalty for each single-stranded base
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c in a multi-loop. EPARAM(10) is the energy penalty for each base-pair
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c closing a multi-loop.
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c No dangling ends next to the I,J base-pair.
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e(1) = min0(e(1),wst(ind1+k)+work(k+1,mod(j-1,3)))
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c I+1 dangles on the I,J base-pair.
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e(2) = min0(e(2),dangle(numseq(i),numseq(j),numseq(i+1),1)
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. + wst(ind2+k) + work(k+1,mod(j-1,3)) + eparam(6))
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c J-1 dangles on the I,J base-pair.
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e(3) = min0(e(3),dangle(numseq(i),numseq(j),numseq(j-1),2)
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. + wst(ind1+k) + work(k+1,mod(j-2,3)) + eparam(6))
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c Both I+1 and J-1 dangle on the I,J base-pair.
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e(4) = min0(e(4),dangle(numseq(i),numseq(j),numseq(i+1),1)
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. + dangle(numseq(i),numseq(j),numseq(j-1),2)
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. + wst(ind2+k) + work(k+1,mod(j-2,3)) + 2*eparam(6))
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enddo
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c EPARAM(5) is the energy penalty for closing a multi-loop.
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erg = erg + eparam(5) + eparam(10) + min0(e(1),e(2),e(3),e(4))
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return
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c Dangling base stacking energy. IP dangles over the I,J
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c base-pair. 3' or 5' dangle if JP = 1 or 2 respectively.
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600 erg = erg + dangle(numseq(i),numseq(j),numseq(ip),jp)
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return
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700 if (force(i).eq.3.or.force(jp).eq.3) then
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erg = infinity
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return
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endif
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c Terminal stack or mismatch energy.
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erg = erg + tstk(numseq(i),numseq(j),numseq(ip),numseq(jp))
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return
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end
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subroutine fill
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c This subroutine computes the arrays of optimal energies.
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include 'rfd.inc'
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dimension inc(5,5)
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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
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./
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vmin = infinity
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if (n.le.80) then
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pinc = 5
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elseif (n.le.100) then
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pinc = 2
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else
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pinc = 1
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endif
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pcnt = pinc
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crit = n*n*n/50
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do j = 1,2*n-1
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c How far along is the computation?
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if (n.gt.10) then
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if (j.le.n) then
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if (j**3.ge.pcnt*crit) then
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write (6,1000) pcnt
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pcnt = pcnt + pinc
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endif
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else
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if ((2*n-j)**3.le.(100-pcnt)*crit) then
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write (6,1000) pcnt
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pcnt = pcnt + pinc
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endif
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endif
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endif
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1000 format ('+',5x,i4,'%')
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do i = min0(j,n),max0(1,j-n+1),-1
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vij = infinity
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wij = infinity
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if (j-i.le.loop) goto 300
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c Test for a prohibited base-pair or a pair which cannot form
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c a base-pair.
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if (vst((n-1)*(i-1)+j).eq.1.or.inc(numseq(i),numseq(j)).eq.0)
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. goto 200
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c Compute VIJ, the minimum energy of the fragment from I to J
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c inclusive where I and J base-pair with one another.
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c Perhaps I,J closes a hairpin loop.
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vij = min0(vij,erg(4,i,j,i,j))
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if (j-i-1.ge.loop+2) then
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c Perhaps I,J stacks over I+1,J-1.
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vij = min0(vij,erg(2,i,j,i+1,j-1)+v(i+1,j-1))
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endif
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c Search for a bulge or interior loop.
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if (j-i-1.ge.loop+3) then
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do d = j-i-3,1,-1
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do ip = i+1,j-1-d
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jp = d+ip
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if (j-i-2-d.gt.eparam(7)) goto 100
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if (abs(ip-i+jp-j).le.eparam(8)) then
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if (ip.gt.n) then
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vij = min0(vij,erg(3,i,j,ip,jp)+vst((n-1)*
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. (ip-n-1)+jp-n))
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else
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vij = min0(vij,erg(3,i,j,ip,jp)+vst((n-1)*
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. (ip-1)+jp))
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endif
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endif
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enddo
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enddo
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endif
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100 if (j-i-1.ge.2*loop+4) then
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c Perhaps I,J closes a multi-loop.
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vij=min0(vij,erg(5,i,j,i,j))
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endif
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c Compute WIJ, the minimum energy of a non-empty folding on I to
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c J inclusive. This is the circular folding program and so there
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c are no exterior bases.
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200 wij = min0 ( wij, eparam(10)+vij, v(i+1,j)+eparam(6)+eparam(10)+
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. erg(6,j,i+1,i,2), v(i,j-1)+eparam(6)+eparam(10)+
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. erg(6,j-1,i,j,1), v(i+1,j-1)+2*eparam(6)+eparam(10)+
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. erg(6,j-1,i+1,i,2)+erg(6,j-1,i+1,j,1),
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. w(i+1,j)+eparam(6), w(i,j-1)+eparam(6) )
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if (j-i-1.gt.2*loop+2) then
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index = (n-1)*(i-1)
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c Check for open bifurcation.
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do k = i,j-1
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wij = min0(wij,wst(index+k)+work(k+1,mod(j,3)))
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enddo
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endif
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c Store VIJ and WIJ. They can be regarded as elements V(I,J)
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c and W(I,J) in a two dimensional array. They are actually
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c stored in the one dimensional arrays VST and WST in position
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c (N-1)*(I-1) + J.
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c Columns J,J-1 and J-2 of W are stored again in the WORK array.
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c This is done to reduce virtual memory swaps.
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300 vst((n-1)*(i-1)+j) = vij
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wst((n-1)*(i-1)+j) = wij
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work(i,mod(j,3)) = wij
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if (j.gt.n) then
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c VMIN is the minimum folding energy of the entire sequence.
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c vmin = min0(vmin,vst((n-1)*(i-1)+j)+vst((n-1)*(j-n-1)+i))
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vmin = min(vmin,vst((n-1)*(i-1)+j)+vst((n-1)*(j-n-1)+i))
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endif
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enddo
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if (j.ge.n) then
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do k = j+1,n+1,-1
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c Fill in some WORK array values before beginning work on the
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c next column.
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work(k,mod(j+1,3)) = wst((k-n-1)*(n-1)+j+1-n)
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enddo
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endif
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enddo
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return
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end
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c Used to recall values of V which are actually stored in VST.
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function v(i,j)
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include 'rfd.inc'
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if (i.gt.n) then
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v = vst((n-1)*(i-n-1)+j-n)
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else
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v = vst((n-1)*(i-1)+j)
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endif
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return
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end
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c Used to recall values of W which are actually stored in WST.
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function w(i,j)
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include 'rfd.inc'
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if (i.gt.n) then
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w = wst((n-1)*(i-n-1)+j-n)
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else
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w = wst((n-1)*(i-1)+j)
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endif
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return
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end
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c Computes an optimal structure on the subsequence II to JI where
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c II and JI must base-pair with one another. ERROR = 0 is normal
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c termination.
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c NFORCE is the number of forced base-pairs encountered in the traceback.
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subroutine trace(ii,ji,nforce,error)
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include 'rfd.inc'
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logical fce
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error = 0
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c Zero the appropriate region of BASEPR.
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if (ji.le.n) then
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do k=ii,ji
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basepr(k) = 0
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enddo
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else
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do k=1,ji-n
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basepr(k) = 0
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enddo
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do k = ii,n
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||
|
|
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
|
||
|
|
|