errata2.list

mfold

     List of errata and changes in version 2 of suboptimal 
                        folding code.

1. This small bug would give an energy of zero to a hairpin loop of 
size 3 when the closing base pair is forced. This is OK for the 
closed excision case, but not in general.

************ new
LIN.FOR;5
  115         if ((size.eq.3).and.fce(i,j).and.seq(hstnum(i+1)).eq.' ') then
  116   c        Closed excision
****** old
LIN.FOR;4
  115         if ((size.eq.3).and.fce(i,j)) then
  116   c        Closed excision
************

The same change should be made in CIRC.FOR .


2. Jan. 15, 1990.
A knot checking feature has been added to EFN.FOR . Very often, 
phylogenetic or other CT files not produced by the folding program 
can contain knots or conflicting base pairs. The program will now
find and flag these.

************  new
File USR$DISK:[ZUKER.MFOLD]EFN.FOR;24
   61   c     Check for knots
   62   c
   63         do i = 1,n
   64            if (basepr(i).ne.0) then
   65               j = max(i,basepr(i))
   66               ip = min(i,basepr(i))
   67               if (basepr(ip).ne.j.or.basepr(j).ne.ip) then
   68                  write(6,1041) hstnum(ip),hstnum(j)
   69                  stop
   70               endif
   71               do k = ip+1,j-1
   72                  if (basepr(k).ne.0) then
   73                     l = basepr(k)
   74                     if (l.le.ip.or.l.ge.j) then
   75                     write(6,1042) hstnum(ip),hstnum(j),hstnum(k),hstnum(l)
   76                     stop
   77                     endif
   78                  endif
   79               enddo
   80            endif
   81         enddo
   82   1041  format(' Base pair ',i5,'.',i5,39H has 5' or 3' end in 
             .another base pair.)
   83   1042  format(' Base pair ',i5,'.',i5,' conflicts with ',i5,'.',i5)
   84   c
   85   c     Process sequence to find base types.
****** old
File USR$DISK:[ZUKER.MFOLD]EFN.FOR;20
   61   c     Process sequence to find base types.
************
************
File USR$DISK:[ZUKER.MFOLD]EFN.FOR;24
  271               write (6,1010) hstnum(i),hstnum(k),hstnum(kp),hstnum(j)
  272   1010        format(' Knot : ',i5,'.',i5,' conflicts with ',i5,'.',i5)
  273               e = infinity
******
File USR$DISK:[ZUKER.MFOLD]EFN.FOR;20
  247               write (6,*) 'ERROR - KNOT FOUND'
  248               e = infinity
************

3. January 17, 1990.
Lorne Reid (at Allelix) has graciously updated the FIGDOT program so 
that it works with GCG version 6.
************
File USR$DISK:[ZUKER]FIGDOT.FOR;5
    9   *
   10         parameter (nmax=700)
******
File USR$DISK:[ZUKER.MFOLD]FIGDOT.FOR;13
    9   *  1/15/90 - L. Reid, - add pen colour according to value of cell
   10   *  1/15/90 - Change bottom & top of viewport so that it goes 0 -100
   11   *            as per the UWGCG manual  (Rev 6.0 section 13-21)
   12   *  1/17/90 - Zuker changes color option 
   13         parameter (nmax=700)
************
************
File USR$DISK:[ZUKER]FIGDOT.FOR;5
  122         do j=n,1,-1
  123           do i=1,j
  124                   if (m(i,j).ne.0) then
  125   * if we've found a point, see if we can draw a line...
  126                           x=1
  127                           do while (m(i+x,j-x).ne.0)
  128                                   m(i+x,j-x)=0
******
File USR$DISK:[ZUKER.MFOLD]FIGDOT.FOR;13
  125         k = 1
  126         maxm = 1
  127         do while (k.le.maxm)
  128   * put out a pen colour associated with the value
  129            write (15,1024) k
  130            do j=n,1,-1
  131               do i=1,j
  132                   if (k.eq.1.and.m(i,j).gt.maxm) maxm = m(i,j)
  133                   if (m(i,j).eq.k) then
  134   * if we've found a point, see if we can draw a line...
  135                           x=1
  136                           do while (m(i+x,j-x).eq. k)
  137                                   m(i+x,j-x)=0
************
************
File USR$DISK:[ZUKER]FIGDOT.FOR;5
  140           enddo
  141         enddo
******
File USR$DISK:[ZUKER.MFOLD]FIGDOT.FOR;13
  149              enddo
  150            enddo
  151            k = k + 1
  152         enddo
************
************
File USR$DISK:[ZUKER]FIGDOT.FOR;5
  144         do j=n,1,-1
  145           do i=1,j
  146                   if (m(j,i).ne.0) then
  147   * if we've found a point, see if we can draw a line...
  148                           x=1
  149                           do while (m(j-x,i+x).ne.0)
  150                                   m(j-x,i+x)=0
******
File USR$DISK:[ZUKER.MFOLD]FIGDOT.FOR;13
  155         k = 1
  156         maxm = 1
  157         do while (k.le.maxm)
  158   * put out a pen colour associated with the value
  159            write (15,1024) k
  160            do j=n,1,-1
  161              do i=1,j
  162                   if (k.eq.1.and.m(i,j).gt.maxm) maxm = m(j,i)
  163                   if (m(j,i).eq.k) then
  164   * if we've found a point, see if we can draw a line...
  165                           x=1
  166                           do while (m(j-x,i+x) .eq. m(j,i))
  167                                   m(j-x,i+x)=0
************
************
File USR$DISK:[ZUKER]FIGDOT.FOR;5
  162           enddo
  163         enddo
******
File USR$DISK:[ZUKER.MFOLD]FIGDOT.FOR;13
  179              enddo
  180            enddo
  181            k = k + 1
  182         enddo
************
************
File USR$DISK:[ZUKER]FIGDOT.FOR;5
  175   14    format ('.vp 20.455 129.545 100.0 0.0',/,
  176        1        '.wn ',4(f7.2,1x),/,
******
File USR$DISK:[ZUKER.MFOLD]FIGDOT.FOR;13
  194   * Fix up the horizontal axis to run from 0 to 100 rather than reverse
  195   14    format ('.vp 20.455 129.545 0.0 100.0',/,
  196        1        '.wn ',4(f7.2,1x),/,
************
************
File USR$DISK:[ZUKER]FIGDOT.FOR;5
  187   * Point format
******
File USR$DISK:[ZUKER.MFOLD]FIGDOT.FOR;13
  207   1024  format ('.nc ',i1)
  208   * Point format
************

4. Jan. 24, 1990.
Andrew Bettany pointed out a problem with the 'single force' option.
The program gives a 'bonus energy' to each base designated 'double
stranded' that actually is double stranded. However, in a base pair
where both bases are marked 'double stranded', only a single bonus is
given. This is an error and prejudices the program against letting
two such designated bases pair with one another. The fix involves 3 
extra lines of code in LIN.FOR and CIRC.FOR (both changes are 
identical).
************ new
File USR$DISK:[ZUKER.MFOLD]LIN.FOR;7
   37                erg = erg + eparam(9)
   38                if (force(i).eq.2.and.force(j).eq.2) erg = erg + eparam(9)
   39            endif
   40         endif
   41    
******
File USR$DISK:[ZUKER.MFOLD]LIN.FOR;5 old
   37               erg = erg + eparam(9)
   38            endif
   39         endif
   40    
************
************
File USR$DISK:[ZUKER.MFOLD]LIN.FOR;7
  594         if (force(i).eq.2.and.force(j).eq.2) nforce = nforce + 1
  595   c     Perhaps I,J stacks over I+1,J-1?
  596         if (i.ne.n.and.j.ne.n+1) then
  597            if (e.eq.erg(2,i,j,i+1,j-1)
******
File USR$DISK:[ZUKER.MFOLD]LIN.FOR;5
  593   c     Perhaps I,J stacks over I+1,J-1?
  594         if (i.ne.n.and.j.ne.n+1) then
  595            if (e.eq.erg(2,i,j,i+1,j-1)
************
************
File USR$DISK:[ZUKER.MFOLD]LIN.FOR;7
  614         if (force(i).eq.2.and.force(j).eq.2) ep = ep - eparam(9)
  615    
  616         if (i+2.gt.j-3) then
  617   c        Tidy up loose ends (trivial).
******
File USR$DISK:[ZUKER.MFOLD]LIN.FOR;5
  612    
  613         if (i+2.gt.j-3) then
  614   c        Tidy up loose ends (trivial).
************

************  new
File USR$DISK:[ZUKER.MFOLD]CIRC.FOR;6
   31                erg = erg + eparam(9)
   32                if (force(i).eq.2.and.force(j).eq.2) erg = erg + eparam(9)
   33            endif
   34         endif
   35    
****** old
File USR$DISK:[ZUKER.MFOLD]CIRC.FOR;4
   31               erg = erg + eparam(9)
   32            endif
   33         endif
   34    
************
************