c
c
c     ###################################################
c     ##  COPYRIGHT (C)  1992  by  Jay William Ponder  ##
c     ##              All Rights Reserved              ##
c     ###################################################
c
c     ##############################################################
c     ##                                                          ##
c     ##  subroutine embed  --  structures via distance geometry  ##
c     ##                                                          ##
c     ##############################################################
c
c
c     "embed" is a distance geometry routine patterned after the
c     ideas of Gordon Crippen, Irwin Kuntz and Tim Havel; it takes
c     as input a set of upper and lower bounds on the interpoint
c     distances, chirality restraints and torsional restraints,
c     and attempts to generate a set of coordinates that satisfy
c     the input bounds and restraints
c
c     literature references:
c
c     G. M. Crippen and T. F. Havel, "Distance Geometry and Molecular
c     Conformation", Research Studies Press, Letchworth U.K., 1988,
c     John Wiley and Sons, U.S. distributor
c
c     T. F. Havel, "An Evaluation of Computational Strategies for
c     Use in the Determination of Protein Structure from Distance
c     Constraints obtained by Nuclear Magnetic Resonance", Progress
c     in Biophysics and Molecular Biology, 56, 43-78 (1991)
c
c
      subroutine embed
      implicit none
      include 'sizes.i'
      include 'atoms.i'
      include 'disgeo.i'
      include 'files.i'
      include 'inform.i'
      include 'iounit.i'
      include 'minima.i'
      include 'refer.i'
      integer maxeigen
      parameter (maxeigen=5)
      integer i,j,nstep,lext
      integer igeo,freeunit
      integer maxneg,nneg
      integer maxinner,ninner
      integer maxouter,nouter
      real*8 fctval,grdmin,secs
      real*8 dt,temp_start,temp_stop
      real*8 rg,rmsorig,rmsflip,mass
      real*8 bounds,contact,local,chiral,torsion
      real*8 bnderr,vdwerr,locerr,chirer,torser
      real*8 derivs(3,maxgeo),matrix(maxgeo,maxgeo)
      real*8 evl(maxeigen),evc(maxgeo,maxeigen)
      real*8 v(maxvar),a(maxvar)
      character*7 errtyp,ext
      character*60 title,geofile
      logical done,valid,exist,info
c
c
c     initialize any chirality restraints, then smooth the
c     bounds via triangle and inverse triangle inequalities;
c     currently these functions are performed by "distgeom"
c
c     call chirin
c     if (verbose .and. n.le.130) then
c        title = 'Input Distance Bounds :'
c        call grafic (n,maxgeo,bnd,title)
c     end if
c     call geodesic
c     if (verbose .and. n.le.130) then
c        title = 'Triangle Smoothed Bounds :'
c        call grafic (n,maxgeo,bnd,title)
c     end if
c
c     generate a distance matrix between the upper and
c     lower bounds, then convert to a metric matrix
c
      maxinner = 3
      maxouter = 3
      maxneg = 2
      nouter = 0
      valid = .false.
      dowhile (.not. valid)
         ninner = 0
         done = .false.
         dowhile (.not. done)
            ninner = ninner + 1
            call dstmat (matrix)
            call metric (matrix,nneg)
            if (nneg.le.maxneg .or. ninner.eq.maxinner)  done = .true.
            compact = 0.0d0
         end do
         if (verbose .and. nneg.gt.maxneg) then
            write (iout,10)  nneg
   10       format (/,' EMBED  --  Warning, Using Metric Matrix',
     &                  ' with',i4,' Negative Distances')
         end if
c
c     find the principle components of metric matrix, then
c     generate the trial Cartesian coordinates
c
         nouter = nouter + 1
         call eigen (evl,evc,matrix,valid)
         call coords (evl,evc)
         if (nouter.eq.maxouter .and. .not.valid) then
            valid = .true.
            if (verbose) then
               write (iout,20)
   20          format (/,' EMBED  --  Warning, Using Poor Initial',
     &                    ' Coordinates')
            end if
         end if
      end do
c
c     compute an index of compaction from the embedded structure
c
      call chksize
c
c     use majorization to improve the approximate coordinates
c
      do i = 1, n
         matrix(i,i) = 0.0d0
         do j = i+1, n
            matrix(j,i) = matrix(i,j)
         end do
      end do
      call majorize (matrix)
c
c     superimpose embedded structure or enantiomer on reference
c
      info = verbose
      verbose = .false.
      call impose (nref,xref,yref,zref,n,x,y,z,rmsorig)
      if (use_invert) then
         do i = 1, n
            x(i) = -x(i)
         end do
         call impose (nref,xref,yref,zref,n,x,y,z,rmsflip)
         if (rmsorig .lt. rmsflip) then
            do i = 1, n
               x(i) = -x(i)
            end do
            call impose (nref,xref,yref,zref,n,x,y,z,rmsorig)
         end if
         write (iout,30)  rmsorig,rmsflip
   30    format (/,' RMS Superposition for Original and',
     &              ' Enantiomer : ',2f12.4)
      end if
      verbose = info
c
c     write out the embedded unrefined atomic coordinate set
c
      if (debug) then
         i = 0
         exist = .true.
         dowhile (exist)
            i = i + 1
            lext = 3
            call numeral (i,ext,lext)
            geofile = filename(1:leng)//'-embed'//'.'//ext(1:lext)
            inquire (file=geofile,exist=exist)
         end do
         igeo = freeunit ()
         open (unit=igeo,file=geofile,status='new')
         call prtxyz (igeo)
         close (unit=igeo)
      end if
c
c     square the bounds for use during structure refinement
c
      do i = 1, n
         do j = 1, n
            bnd(j,i) = bnd(j,i)**2
         end do
      end do
c
c     minimize the error function via simulated annealing
c
      if (verbose)  call setime
      if (use_anneal) then
         iprint = 0
         if (verbose)  iprint = 10
         grdmin = 1.0d0
         mass = 10000.0d0
         do i = 1, 3*n
            v(i) = 0.0d0
            a(i) = 0.0d0
         end do
         errtyp = 'FINAL'
         call refine (errtyp,fctval,grdmin)
         nstep = 1000
         dt = 0.04d0
         temp_start = 200.0d0
         temp_stop = 200.0d0
         call explore (errtyp,nstep,dt,mass,temp_start,temp_stop,v,a)
         nstep = 10000
         dt = 0.2d0
         temp_start = 200.0d0
         temp_stop = 0.0d0
         call explore (errtyp,nstep,dt,mass,temp_start,temp_stop,v,a)
         grdmin = 0.01d0
         call refine (errtyp,fctval,grdmin)
c
c     minimize the error function via nonlinear optimization
c
      else
         iprint = 0
         if (verbose)  iprint = 10
         grdmin = 0.01d0
         errtyp = 'INITIAL'
         call refine (errtyp,fctval,grdmin)
         errtyp = 'MIDDLE'
         call refine (errtyp,fctval,grdmin)
         errtyp = 'FINAL'
         call refine (errtyp,fctval,grdmin)
      end if
      if (verbose) then
         call getime (secs)
         write (iout,40)  secs
   40    format (/,' Time Required for Refinement :',10x,f12.2,
     &              ' seconds')
      end if
c
c     print the final error function and its components
c
      bounds = bnderr (derivs)
      contact = vdwerr (derivs)
      local = locerr (derivs)
      chiral = chirer (derivs)
      torsion = torser (derivs)
      write (iout,50)  fctval,bounds,contact,local,chiral,torsion
   50 format (/,' Results of Distance Geometry Protocol :',
     &        //,' Final Error Function Value :',10x,f16.4,
     &        //,' Distance Restraint Error :',12x,f16.4,
     &        /,' Hard Sphere Contact Error :',11x,f16.4,
     &        /,' Local Geometry Error :',16x,f16.4,
     &        /,' Chirality-Planarity Error :',11x,f16.4,
     &        /,' Torsional Restraint Error :',11x,f16.4)
c
c     take the root of the currently squared distance bounds
c
      do i = 1, n
         do j = 1, n
            bnd(j,i) = sqrt(bnd(j,i))
         end do
      end do
c
c     print the final rms deviations and radius of gyration
c
      title = 'after Refinement :'
      call rmserror (title)
      call gyrate (rg)
      write (iout,60)  rg
   60 format (/,' Radius of Gyration after Refinement :',6x,f16.4)
      if (verbose .and. n.le.130) then
         call dmdump (matrix)
      end if
      return
      end
c
c
c     ###############################################################
c     ##                                                           ##
c     ##  subroutine chirin  --  initializes chirality restraints  ##
c     ##                                                           ##
c     ###############################################################
c
c
c     "chirin" determines the target value for each chirality
c     and planarity restraint as the signed volume of the
c     parallelpiped spanned by vectors from a common atom to
c     each of three other atoms
c
c
      subroutine chirin
      implicit none
      include 'sizes.i'
      include 'atoms.i'
      include 'disgeo.i'
      include 'inform.i'
      include 'iounit.i'
      integer i,j,ia,ib,ic,id
      real*8 xad,yad,zad
      real*8 xbd,ybd,zbd
      real*8 xcd,ycd,zcd
      real*8 c1,c2,c3
c
c
c     compute the signed volume of each parallelpiped;
c     if the defining atoms almost lie in a plane, then
c     set the signed volume to exactly zero
c
      do i = 1, nchir
         ia = ichir(1,i)
         ib = ichir(2,i)
         ic = ichir(3,i)
         id = ichir(4,i)
         xad = x(ia) - x(id)
         yad = y(ia) - y(id)
         zad = z(ia) - z(id)
         xbd = x(ib) - x(id)
         ybd = y(ib) - y(id)
         zbd = z(ib) - z(id)
         xcd = x(ic) - x(id)
         ycd = y(ic) - y(id)
         zcd = z(ic) - z(id)
         c1 = ybd*zcd - zbd*ycd
         c2 = ycd*zad - zcd*yad
         c3 = yad*zbd - zad*ybd
         vchir(i) = xad*c1 + xbd*c2 + xcd*c3
         if (abs(vchir(i)) .lt. 1.0d0)  vchir(i) = 0.0d0
      end do
c
c     print out the results for each restraint
c
      if (verbose) then
         if (nchir .ne. 0) then
            write (iout,10)
   10       format (/,' Chirality and Planarity Constraints :')
            write (iout,20)
   20       format (/,18x,'Atom Numbers',12x,'Signed Volume',/)
         end if
         do i = 1, nchir
            write (iout,30)  i,(ichir(j,i),j=1,4),vchir(i)
   30       format (i6,5x,4i6,5x,f12.4)
         end do
      end if
      return
      end
c
c
c     ##############################################################
c     ##                                                          ##
c     ##  subroutine triangle  --  triangle inequality smoothing  ##
c     ##                                                          ##
c     ##############################################################
c
c
c     "triangle" smooths the upper and lower distance bounds via
c     the triangle inequality using a full-matrix variant of the
c     Floyd-Warshall shortest path algorithm; this routine is
c     usually much slower than the sparse matrix shortest path
c     methods in "geodesic" and "trifix", and should be used only
c     for comparison with answers generated by those routines
c
c     literature reference:
c
c     A. W. M. Dress and T. F. Havel, "Shortest-Path Problems and
c     Molecular Conformation", Discrete Applied Mathematics, 19,
c     129-144 (1988)
c
c
      subroutine triangle
      implicit none
      include 'sizes.i'
      include 'atoms.i'
      include 'disgeo.i'
      include 'iounit.i'
      integer i,j,k
      integer ik1,ik2
      integer jk1,jk2
      real*8 eps
      real*8 lij,lik,ljk
      real*8 uij,uik,ujk
c
c
c     use full-matrix algorithm to smooth upper and lower bounds
c
      eps = 1.0d-10
      do k = 1, n
         do i = 1, n-1
            ik1 = min(i,k)
            ik2 = max(i,k)
            lik = bnd(ik2,ik1)
            uik = bnd(ik1,ik2)
            do j = i+1, n
               lij = bnd(j,i)
               uij = bnd(i,j)
               jk1 = min(j,k)
               jk2 = max(j,k)
               ljk = bnd(jk2,jk1)
               ujk = bnd(jk1,jk2)
               lij = max(lij,lik-ujk,ljk-uik)
               uij = min(uij,uik+ujk)
               if (lij-uij .gt. eps) then
                  write (iout,10)
   10             format (/,' TRIANGLE  --  Inconsistent Bounds;',
     &                       ' Geometrically Impossible')
                  write (iout,20)  i,j,lij,uij
   20             format (/,' Error at :',6x,2i6,3x,2f9.4)
                  write (iout,30)  i,k,lik,uik,j,k,ljk,ujk
   30             format (/,' Traced to :',5x,2i6,3x,2f9.4,
     &                    /,17x,2i6,3x,2f9.4)
                  call fatal
               end if
               if (lij-bnd(j,i) .gt. eps) then
                  write (iout,40)  i,j,bnd(j,i),lij
   40             format (' TRIANGLE  --  Altered Lower Bound at',
     &                       2x,2i6,3x,f9.4,' -->',f9.4)
               end if
               if (bnd(i,j)-uij .gt. eps) then
                  write (iout,50)  i,j,bnd(i,j),uij
   50             format (' TRIANGLE  --  Altered Upper Bound at',
     &                       2x,2i6,3x,f9.4,' -->',f9.4)
               end if
               bnd(j,i) = lij
               bnd(i,j) = uij
            end do
         end do
      end do
      return
      end
c
c
c     #################################################################
c     ##                                                             ##
c     ##  subroutine geodesic  --  sparse matrix triangle smoothing  ##
c     ##                                                             ##
c     #################################################################
c
c
c     "geodesic" smooths the upper and lower distance bounds via
c     the triangle inequality using a sparse matrix version of a
c     shortest path algorithm
c
c     literature reference:
c
c     G. M. Crippen and T. F. Havel, "Distance Geometry and Molecular
c     Conformation", Research Studies Press, Letchworth U.K., 1988,
c     John Wiley and Sons, U.S. distributor, see section 6-2
c
c
      subroutine geodesic
      implicit none
      include 'sizes.i'
      include 'atoms.i'
      include 'disgeo.i'
      include 'restrn.i'
      integer maxlist
      parameter (maxlist=2*maxfix)
      integer i,j,k,nlist
      integer start(maxatm),stop(maxatm)
      integer list(maxlist),key(maxlist)
      real*8 upper(maxatm),lower(maxatm)
c
c
c     build an indexed list of atoms in distance restraints
c
      do i = 1, n
         start(i) = 0
         stop(i) = -1
      end do
      nlist = 2 * ndfix
      do i = 1, ndfix
         list(i) = idfix(1,i)
         list(i+ndfix) = idfix(2,i)
      end do
      call sort3 (nlist,list,key)
      j = -1
      do i = 1, nlist
         k = list(i)
         if (k .ne. j) then
            start(k) = i
            j = k
         end if
      end do
      j = -1
      do i = nlist, 1, -1
         k = list(i)
         if (k .ne. j) then
            stop(k) = i
            j = k
         end if
      end do
      do i = 1, nlist
         k = key(i)
         if (k .le. ndfix) then
            list(i) = idfix(2,k)
         else
            list(i) = idfix(1,k-ndfix)
         end if
      end do
c
c     triangle smooth bounds via sparse shortest path method
c
      do i = 1, n
         call minpath (i,upper,lower,start,stop,list)
         do j = i+1, n
            bnd(i,j) = upper(j)
            bnd(j,i) = max(lower(j),bnd(j,i))
         end do
      end do
      return
      end
c
c
c     ################################################################
c     ##                                                            ##
c     ##  subroutine minpath  --  triangle smoothed bounds to atom  ##
c     ##                                                            ##
c     ################################################################
c
c
c     "minpath" is a routine for finding the triangle smoothed upper
c     and lower bounds of each atom to a specified root atom using a
c     sparse variant of the Bellman-Ford shortest path algorithm
c
c     literature reference:
c
c     D. P. Bertsekas, "A Simple and Fast Label Correcting Algorithm
c     for Shortest Paths", Networks, 23, 703-709 (1993)
c
c
      subroutine minpath (root,upper,lower,start,stop,list)
      implicit none
      include 'sizes.i'
      include 'atoms.i'
      include 'couple.i'
      include 'disgeo.i'
      integer maxlist
      parameter (maxlist=2*maxfix)
      integer i,j,k,root
      integer narc,iarc(maxatm)
      integer head,tail,queue(maxatm)
      integer start(maxatm),stop(maxatm)
      integer list(maxlist)
      real*8 big,upper(maxatm)
      real*8 small,lower(maxatm)
      logical enter,queued(maxatm)
c
c
c     initialize candidate atom queue and the path lengths
c
      do i = 1, n
         queued(i) = .false.
         upper(i) = 1000000.0d0
         lower(i) = 0.0d0
      end do
c
c     put the root atom into the queue of candidate atoms
c
      head = root
      tail = root
      queue(root) = 0
      queued(root) = .true.
      upper(root) = 0.0d0
c
c     get the next candidate atom from head of queue
c
      dowhile (head .ne. 0)
         j = head
         queued(j) = .false.
         head = queue(head)
c
c     make a list of arcs to the current candidate atom
c
         narc = 0
         do i = 1, n12(j)
            k = i12(i,j)
            if (k .ne. root) then
               narc = narc + 1
               iarc(narc) = k
            end if
         end do
         do i = 1, n13(j)
            k = i13(i,j)
            if (k .ne. root) then
               narc = narc + 1
               iarc(narc) = k
            end if
         end do
         do i = 1, n14(j)
            k = i14(i,j)
            if (k .ne. root) then
               narc = narc + 1
               iarc(narc) = k
            end if
         end do
         do i = start(j), stop(j)
            k = list(i)
            if (k .ne. root) then
               narc = narc + 1
               iarc(narc) = k
            end if
         end do
c
c     check each arc for alteration of the path length bounds
c
         do i = 1, narc
            k = iarc(i)
            if (k .lt. j) then
               big = upper(j) + bnd(k,j)
               small = max(bnd(j,k)-upper(j),lower(j)-bnd(k,j))
            else
               big = upper(j) + bnd(j,k)
               small = max(bnd(k,j)-upper(j),lower(j)-bnd(j,k))
            end if
            enter = .false.
            if (upper(k) .gt. big) then
               upper(k) = big
               if (.not. queued(k))  enter = .true.
            end if
            if (lower(k) .lt. small) then
               lower(k) = small
               if (.not. queued(k))  enter = .true.
            end if
c
c     enter a new candidate atom at the tail of the queue
c
            if (enter) then
               queued(k) = .true.
               if (head .eq. 0) then
                  head = k
                  tail = k
                  queue(k) = 0
               else
                  queue(tail) = k
                  queue(k) = 0
                  tail = k
               end if
            end if
         end do
      end do
      return
      end
c
c
c     ################################################################
c     ##                                                            ##
c     ##  subroutine trifix  --  update triangle inequality bounds  ##
c     ##                                                            ##
c     ################################################################
c
c
c     "trifix" rebuilds both the upper and lower distance bound
c     matrices following tightening of one or both of the bounds
c     between a specified pair of atoms, "p" and "q", using a
c     modification of Murchland's shortest path update algorithm
c
c     literature references:
c
c     P. A. Steenbrink, "Optimization of Transport Networks", John
c     Wiley and Sons, Bristol, 1974; see section 7.7
c
c     R. Dionne, "Etude et Extension d'un Algorithme de Murchland",
c     Infor, 16, 132-146 (1978)
c
c
      subroutine trifix (p,q)
      implicit none
      include 'sizes.i'
      include 'atoms.i'
      include 'disgeo.i'
      include 'inform.i'
      include 'iounit.i'
      integer i,k,p,q,ip,iq,np,nq
      integer pt(maxgeo),qt(maxgeo)
      real*8 eps,ipmin,ipmax,iqmin,iqmax
      real*8 pmin(maxgeo),pmax(maxgeo)
      real*8 qmin(maxgeo),qmax(maxgeo)
      logical pun(maxgeo),qun(maxgeo)
c
c
c     initialize the set of nodes that may have changed bounds
c
      eps = 1.0d-10
      np = 0
      nq = 0
      do i = 1, n
         pun(i) = .true.
         qun(i) = .true.
      end do
c
c     store the upper and lower bounds to "p" and "q"
c
      do i = 1, p
         pmin(i) = bnd(p,i)
         pmax(i) = bnd(i,p)
      end do
      do i = p+1, n
         pmin(i) = bnd(i,p)
         pmax(i) = bnd(p,i)
      end do
      do i = 1, q
         qmin(i) = bnd(q,i)
         qmax(i) = bnd(i,q)
      end do
      do i = q+1, n
         qmin(i) = bnd(i,q)
         qmax(i) = bnd(q,i)
      end do
c
c     check for changes in the upper bounds to "p" and "q"
c
      do i = 1, n
         ipmax = qmax(p) + qmax(i)
         if (pmax(i) .gt. ipmax+eps) then
            np = np + 1
            pt(np) = i
            pmax(i) = ipmax
            pun(i) = .false.
         end if
         iqmax = pmax(q) + pmax(i)
         if (qmax(i) .gt. iqmax+eps) then
            nq = nq + 1
            qt(nq) = i
            qmax(i) = iqmax
            qun(i) = .false.
         end if
      end do
c
c     for node pairs whose bounds to "p" and "q" have changed,
c     make any needed changes to upper bound of the pair
c
      do ip = 1, np
         i = pt(ip)
         ipmax = pmax(i)
         do iq = 1, nq
            k = qt(iq)
            if (i .lt. k) then
               bnd(i,k) = min(bnd(i,k),ipmax+pmax(k))
            else
               bnd(k,i) = min(bnd(k,i),ipmax+pmax(k))
            end if
         end do
      end do
c
c     check for changes in the lower bounds to "p" and "q"
c
      do i = 1, n
         ipmin = max(qmin(p)-qmax(i),qmin(i)-qmax(p))
         if (pmin(i) .lt. ipmin-eps) then
            if (pun(i)) then
               np = np + 1
               pt(np) = i
            end if
            pmin(i) = ipmin
         end if
         iqmin = max(pmin(q)-pmax(i),pmin(i)-pmax(q))
         if (qmin(i) .lt. iqmin-eps) then
            if (qun(i)) then
               nq = nq + 1
               qt(nq) = i
            end if
            qmin(i) = iqmin
         end if
      end do
c
c     for node pairs whose bounds to "p" and "q" have changed,
c     make any needed changes to lower bound of the pair
c
      do ip = 1, np
         i = pt(ip)
         ipmin = pmin(i)
         ipmax = pmax(i)
         do iq = 1, nq
            k = qt(iq)
            if (i .lt. k) then
               bnd(k,i) = max(bnd(k,i),ipmin-pmax(k),pmin(k)-ipmax)
            else
               bnd(i,k) = max(bnd(i,k),ipmin-pmax(k),pmin(k)-ipmax)
            end if
         end do
      end do
c
c     update the upper and lower bounds to "p" and "q"
c
      do i = 1, p
         bnd(p,i) = pmin(i)
         bnd(i,p) = pmax(i)
      end do
      do i = p+1, n
         bnd(i,p) = pmin(i)
         bnd(p,i) = pmax(i)
      end do
      do i = 1, q
         bnd(q,i) = qmin(i)
         bnd(i,q) = qmax(i)
      end do
      do i = q+1, n
         bnd(i,q) = qmin(i)
         bnd(q,i) = qmax(i)
      end do
c
c     output the atoms updated and amount of work required
c
      if (debug) then
         write (iout,10)  p,q,np*nq
   10    format (' TRIFIX  --  Bounds Update for Atoms',2i6,
     &              ' with',i8,' Searches')
      end if
      return
      end
c
c
c     ################################################################
c     ##                                                            ##
c     ##  subroutine grafic  --  schematic graphical matrix output  ##
c     ##                                                            ##
c     ################################################################
c
c
c     "grafic" outputs the upper & lower triangles and diagonal
c     of a square matrix in a schematic form for visual inspection
c
c
      subroutine grafic (n,np,a,title)
      implicit none
      include 'iounit.i'
      integer i,j,k,m,n,np
      integer maxj,nrow,ndash
      integer minrow,maxrow
      real*8 a(np,np),big
      real*8 amin,dmin,bmin
      real*8 amax,dmax,bmax
      real*8 v,rcl,scl,tcl
      real*8 ca,cb,cc,cd
      real*8 cw,cx,cy,cz
      character*1 ta,tb,tc,td,te
      character*1 dash,digit(0:9)
      character*1 symbol(130)
      character*60 title
      data ta,tb,tc,td,te  / ' ','.','+','X','#' /
      data dash   / '-' /
      data digit  / '0','1','2','3','4','5','6','7','8','9' /
c
c
c     set bounds of length of print row and write the header
c
      minrow = 54
      maxrow = 130
      ndash = min(max(n,minrow),maxrow)
      write (iout,10)  (dash,i=1,ndash)
   10 format (/,1x,130a1)
      write (iout,20)  title
   20 format (/,1x,a60)
c
c     find the maximum and minimum elements of the matrix
c
      big = 1.0d6
      dmax = -big
      dmin = big
      amax = -big
      amin = big
      bmax = -big
      bmin = big
      do i = 1, n
         if (a(i,i) .gt. dmax)  dmax = a(i,i)
         if (a(i,i) .lt. dmin)  dmin = a(i,i)
         do j = 1, i-1
            if (a(j,i) .gt. amax)  amax = a(j,i)
            if (a(j,i) .lt. amin)  amin = a(j,i)
            if (a(i,j) .gt. bmax)  bmax = a(i,j)
            if (a(i,j) .lt. bmin)  bmin = a(i,j)
         end do
      end do
      write (iout,30)  amin,amax,dmin,dmax,bmin,bmax
   30 format (/,' Range of Above Diag Elements : ',f13.4,' to',f13.4,
     &        /,' Range of Diagonal Elements :   ',f13.4,' to',f13.4,
     &        /,' Range of Below Diag Elements : ',f13.4,' to',f13.4)
c
c     now, print out the graphical representation
c
      write (iout,40)
   40 format (/,' Symbol Magnitude Ordering :',14x,
     &          '# > X > + > . > '' ''',/)
      rcl = (bmax-bmin) / 5.0d0
      scl = (amax-amin) / 5.0d0
      tcl = (dmax-dmin) / 9.0d0
      if (rcl .eq. 0.0d0)  rcl = 1.0d0
      if (scl .eq. 0.0d0)  scl = 1.0d0
      if (tcl .eq. 0.0d0)  tcl = 1.0d0
      ca = amin + scl
      cb = ca + scl
      cc = cb + scl
      cd = cc + scl
      cw = bmin + rcl
      cx = cw + rcl
      cy = cx + rcl
      cz = cy + rcl
      do j = 1, n, maxrow
         maxj = j + maxrow - 1
         if (maxj .gt. n)  maxj = n
         nrow = maxj - j + 1
         do i = 1, n
            do k = j, maxj
               m = k - j + 1
               if (k .lt. i) then
                  v = abs(a(i,k))
                  if (v .le. cw) then
                     symbol(m) = ta
                  else if (v .le. cx) then
                     symbol(m) = tb
                  else if (v .le. cy) then
                     symbol(m) = tc
                  else if (v .le. cz) then
                     symbol(m) = td
                  else
                     symbol(m) = te
                  end if
               else if (k .eq. i) then
                  symbol(m) = digit(nint((a(i,i)-dmin)/tcl))
               else if (k .gt. i) then
                  v = abs(a(i,k))
                  if (v .le. ca) then
                     symbol(m) = ta
                  else if (v .le. cb) then
                     symbol(m) = tb
                  else if (v .le. cc) then
                     symbol(m) = tc
                  else if (v .le. cd) then
                     symbol(m) = td
                  else
                     symbol(m) = te
                  end if
               end if
            end do
            write (iout,50)  (symbol(k),k=1,nrow)
   50       format (1x,130a1)
         end do
         write (iout,60)  (dash,i=1,ndash)
   60    format (/,1x,130a1)
         if (maxj .lt. n) then
            write (iout,70)
   70       format ()
         end if
      end do
      return
      end
c
c
c     ################################################################
c     ##                                                            ##
c     ##  subroutine dstmat  --  choose values for distance matrix  ##
c     ##                                                            ##
c     ################################################################
c
c
c     "dstmat" selects a distance matrix containing values between
c     the previously smoothed upper and lower bounds; the distance
c     values are chosen as uniform random fractions, in a triangle
c     correlated fashion, or via various metrization algorithms
c
c
      subroutine dstmat (dmx)
      implicit none
      include 'sizes.i'
      include 'atoms.i'
      include 'disgeo.i'
      include 'inform.i'
      include 'iounit.i'
      include 'keys.i'
      include 'restrn.i'
      integer maxpair
      parameter (maxpair=maxgeo*(maxgeo-1)/2)
      integer i,j,k,m,index,next
      integer npart,nmetrize,npair
      integer mik,mjk,nik,njk
      integer list(maxpair)
      real*8 random,normal
      real*8 fraction,fracdist
      real*8 corr,dmean,dwidth
      real*8 denom,swap,delta
      real*8 eps,gap,secs
      real*8 value(maxpair)
      real*8 dmx(maxgeo,maxgeo)
      character*8 method
      character*20 keyword
      character*80 record,string
      logical initial
      save initial,method,npart,dmean
      data initial  / .true. /
c
c
c     initialize the method for distance element selection
c
      if (initial) then
         initial = .false.
         method = 'PAIRWISE'
         npart = 0
         dmean = 0.0d0
c
c     search each line of the keyword file for options
c
         do i = 1, nkey
            next = 1
            record = keyline(i)
            call gettext (record,keyword,next)
            call upcase (keyword)
            if (keyword(1:15) .eq. 'TRIAL-DISTANCE ') then
               call gettext (record,method,next)
               call lowcase (method)
               call getnumb (record,npart,next)
            else if (keyword(1:19) .eq. 'TRIAL-DISTRIBUTION ') then
               string = record(next:80)
               read (string,*,err=10,end=10)  dmean
   10          continue
            end if
         end do
c
c     set the number of atoms to use in partial metrization
c
         if (method .eq. 'HAVEL') then
            if (npart.le.0 .or. npart.ge.n-1)  npart = n
         else if (method .eq. 'PARTIAL') then
            if (npart.le.0 .or. npart.ge.n-1)  npart = 4
         else if (method .eq. 'PAIRWISE') then
            if (npart.le.0 .or. npart.ge.100)  npart = 100
         end if
c
c     set the initial distribution for selection of trial distances
c
         if (method.eq.'RANDOM' .or. method.eq.'PARTIAL'
     &             .or. method.eq.'PAIRWISE') then
            compact = 0.0d0
c           if (dmean .eq. 0.0d0)  dmean = 2.35d0 / log(pathmax)
            if (dmean .eq. 0.0d0)  dmean = 1.65d0 / (pathmax)**0.25d0
c           if (dmean .eq. 0.0d0)  dmean = 1.30d0 / (pathmax)**0.20d0
         end if
      end if
c
c     write out the final choice for distance matrix generation
c
      if (verbose) then
         call setime
         if (method .eq. 'CLASSIC') then
            write (iout,20)
   20       format (/,' Distance Matrix via Uniform Random',
     &                 ' Fractions without Metrization :')
         else if (method .eq. 'RANDOM') then
            write (iout,30)
   30       format (/,' Distance Matrix Generated via Normal',
     &                 ' Fractions without Metrization :')
         else if (method .eq. 'TRICOR') then
            write (iout,40)
   40       format (/,' Distance Matrix Generated via Triangle',
     &                 ' Correlated Fractions :')
         else if (method.eq.'HAVEL' .and. npart.lt.n) then
            write (iout,50)  npart
   50       format (/,' Distance Matrix Generated via',i4,'-Atom',
     &                 ' Partial Metrization :')
         else if (method .eq. 'HAVEL') then
            write (iout,60)
   60       format (/,' Distance Matrix Generated via Randomized',
     &                 ' Atom-Based Metrization :')
         else if (method .eq. 'PARTIAL') then
            write (iout,70)  npart
   70       format (/,' Distance Matrix Generated via',i4,'-Atom',
     &                 ' Partial Metrization :')
         else if (method.eq.'PAIRWISE' .and. npart.lt.100) then
            write (iout,80)  npart
   80       format (/,' Distance Matrix Generated via',i3,'%',
     &                 ' Random Pairwise Metrization :')
         else
            write (iout,90)
   90       format (/,' Distance Matrix Generated via Randomized',
     &                 ' Pairwise Metrization :')
         end if
      end if
c
c     adjust the distribution for selection of trial distances
c
      if (method.eq.'RANDOM' .or. method.eq.'PARTIAL'
     &          .or. method.eq.'PAIRWISE') then
         dmean = dmean - 0.02d0*sign(sqrt(abs(compact)),compact)
         dwidth = 0.15d0
         if (verbose) then
            write (iout,100)  dmean,dwidth
  100       format (/,' Trial Distance Normal Distribution :',
     &                 10x,f5.2,' +/-',f5.2)
         end if
      else
         write (iout,110)
  110    format (/,' Trial Distances selected at Random from',
     &              ' Uniform Distribution')
      end if
c
c     uniform or normally distributed distances without metrization
c
      if (method.eq.'CLASSIC' .or. method.eq.'RANDOM') then
         do i = 1, n
            dmx(i,i) = 0.0d0
         end do
         do i = 1, n-1
            do j = i+1, n
               if (method .eq. 'CLASSIC') then
                  fraction = random ()
               else
                  fraction = fracdist (dmean,dwidth)
               end if
               delta = bnd(i,j) - bnd(j,i)
               dmx(j,i) = bnd(j,i) + delta*fraction
               dmx(i,j) = dmx(j,i)
            end do
         end do
c
c     Crippen's triangle correlated distance selection
c
      else if (method .eq. 'TRICOR') then
         do i = 1, n
            dmx(i,i) = 0.0d0
         end do
         do i = 1, n-1
            do j = i+1, n
               dmx(j,i) = random ()
               dmx(i,j) = dmx(j,i)
            end do
         end do
         do i = 1, n-1
            do j = i+1, n
               denom = 0.0d0
               dmx(i,j) = 0.0d0
               do k = 1, n
                  if (k .ne. i) then
                     mik = max(i,k)
                     mjk = max(j,k)
                     nik = min(i,k)
                     njk = min(j,k)
                     if (k .eq. j) then
                        dmx(i,j) = dmx(i,j) + dmx(j,i)
                        denom = denom + 1.0d0
                     else if (bnd(njk,mjk) .le. 0.2d0*bnd(nik,mik)) then
                        if (i .gt. k)  corr = 0.9d0 * dmx(i,k)
                        if (k .gt. i)  corr = 0.9d0 * dmx(k,i)
                        dmx(i,j) = dmx(i,j) + corr
                        denom = denom + 0.9d0
                     else if (bnd(nik,mik) .le. 0.2d0*bnd(njk,mjk)) then
                        if (j .gt. k)  corr = 0.9d0 * dmx(j,k)
                        if (k .gt. j)  corr = 0.9d0 * dmx(k,j)
                        dmx(i,j) = dmx(i,j) + corr
                        denom = denom + 0.9d0
                     else if (bnd(mik,nik) .ge. 0.9d0*bnd(njk,mjk)) then
                        if (j .gt. k)  corr = 0.5d0 * (1.0d0-dmx(j,k))
                        if (k .gt. j)  corr = 0.5d0 * (1.0d0-dmx(k,j))
                        dmx(i,j) = dmx(i,j) + corr
                        denom = denom + 0.5d0
                     else if (bnd(mjk,njk) .ge. 0.9d0*bnd(nik,mik)) then
                        if (i .gt. k)  corr = 0.5d0 * (1.0d0-dmx(i,k))
                        if (k .gt. i)  corr = 0.5d0 * (1.0d0-dmx(k,i))
                        dmx(i,j) = dmx(i,j) + corr
                        denom = denom + 0.5d0
                     end if
                  end if
               end do
               dmx(i,j) = dmx(i,j) / denom
            end do
         end do
         do i = 1, n-1
            do j = i+1, n
               delta = bnd(i,j) - bnd(j,i)
               dmx(i,j) = bnd(j,i) + delta*dmx(i,j)
               dmx(j,i) = dmx(i,j)
            end do
         end do
c
c     Havel/XPLOR atom-based metrization over choice of distribution
c
      else if (method.eq.'HAVEL' .or. method.eq.'PARTIAL') then
         do i = 1, n
            do j = 1, n
               dmx(j,i) = bnd(j,i)
            end do
         end do
         do i = 1, n
            value(i) = random ()
         end do
         call sort2 (n,value,list)
         gap = 0.0d0
         do i = 1, n-1
            k = list(i)
            do j = i+1, n
               m = list(j)
               if (method .eq. 'HAVEL') then
                  fraction = random ()
               else
                  fraction = fracdist (dmean,dwidth)
               end if
               delta = abs(bnd(k,m) - bnd(m,k))
               if (k .lt. m) then
                  bnd(k,m) = bnd(m,k) + delta*fraction
                  bnd(m,k) = bnd(k,m)
               else
                  bnd(k,m) = bnd(k,m) + delta*fraction
                  bnd(m,k) = bnd(k,m)
               end if
               if (i .le. npart)  call trifix (k,m)
               if (i .gt. npart)  gap = gap + delta
            end do
         end do
         do i = 1, n
            do j = 1, n
               swap = dmx(j,i)
               dmx(j,i) = bnd(j,i)
               bnd(j,i) = swap
            end do
         end do
         if (verbose .and. npart.lt.n-1) then
            write (iout,120)  gap/dble((n-npart)*(n-npart-1)/2)
  120       format (/,' Average Bound Gap after Partial Metrization :',
     &                 3x,f12.4)
         end if
c
c     use partial randomized pairwise distance-based metrization
c
      else if (method.eq.'PAIRWISE' .and. npart.le.10) then
         npair = n*(n-1) / 2
         nmetrize = nint(0.01d0*dble(npart)*dble(npair))
         do i = 1, n
            do j = 1, n
               dmx(j,i) = bnd(j,i)
            end do
         end do
         do i = 1, nmetrize
  130       continue
            k = int(dble(n)*random()) + 1
            m = int(dble(n)*random()) + 1
            if (bnd(k,m) .eq. bnd(m,k))  goto 130
            if (k .gt. m) then
               swap = k
               k = m
               m = swap
            end if
            fraction = fracdist (dmean,dwidth)
            delta = bnd(k,m) - bnd(m,k)
            bnd(k,m) = bnd(m,k) + delta*fraction
            bnd(m,k) = bnd(k,m)
            call trifix (k,m)
         end do
         gap = 0.0d0
         do i = 1, n-1
            do j = i, n
               delta = bnd(i,j) - bnd(j,i)
               if (delta .ne. 0.0d0) then
                  gap = gap + delta
                  fraction = dmean + dwidth*normal()
                  fraction = max(0.0d0,min(1.0d0,fraction))
                  bnd(i,j) = bnd(j,i) + delta*fraction
                  bnd(j,i) = bnd(i,j)
               end if
            end do
         end do
         do i = 1, n
            do j = 1, n
               swap = dmx(j,i)
               dmx(j,i) = bnd(j,i)
               bnd(j,i) = swap
            end do
         end do
         if (verbose .and. nmetrize.lt.npair) then
            write (iout,140)  gap/dble(npair-nmetrize)
  140       format (/,' Average Bound Gap after Partial Metrization :',
     &                 3x,f12.4)
         end if
c
c     use randomized pairwise distance-based metrization
c
      else if (method .eq. 'PAIRWISE') then
         npair = n*(n-1) / 2
         nmetrize = nint(0.01d0*dble(npart)*dble(npair))
         do i = 1, n
            do j = 1, n
               dmx(j,i) = bnd(j,i)
            end do
         end do
         do i = 1, npair
            value(i) = random ()
         end do
         call sort2 (npair,value,list)
         eps = 1.0d-10
         gap = 0.0d0
         do i = 1, npair
            index = list(i)
            k = int(0.5d0 * (dble(2*n+1)
     &                 - sqrt(dble(4*n*(n-1)-8*index+9))) + eps)
            m = n*(1-k) + k*(k+1)/2 + index
            fraction = fracdist (dmean,dwidth)
            delta = bnd(k,m) - bnd(m,k)
            bnd(k,m) = bnd(m,k) + delta*fraction
            bnd(m,k) = bnd(k,m)
            if (i .le. nmetrize)  call trifix (k,m)
            if (i .gt. nmetrize)  gap = gap + delta
         end do
         do i = 1, n
            do j = 1, n
               swap = dmx(j,i)
               dmx(j,i) = bnd(j,i)
               bnd(j,i) = swap
            end do
         end do
         if (verbose .and. nmetrize.lt.npair) then
            write (iout,150)  gap/dble(npair-nmetrize)
  150       format (/,' Average Bound Gap after Partial Metrization :',
     &                 3x,f12.4)
         end if
      end if
c
c     get the time required for distance matrix generation
c
      if (verbose) then
         call getime (secs)
         write (iout,160)  secs
  160    format (/,' Time Required for Distance Matrix :',5x,f12.2,
     &              ' seconds')
      end if
      return
      end
c
c
c     #############################################################
c     ##                                                         ##
c     ##  function fracdist  --  random fraction distance value  ##
c     ##                                                         ##
c     #############################################################
c
c
c     "fracdist" computes a random fractional distance in the
c     range [0,1] based on a skewed Gaussian distribution with
c     the input mean and standard deviation
c
c
      function fracdist (dmean,dwidth)
      implicit none
      real*8 dmean,dwidth
      real*8 fracdist,normal
c
c
c     compute a random fractional distance between 0 and 1
c
      fracdist = normal ()
      if (fracdist .ge. 0.0d0) then
         if (1.0d0-dmean .ge. 3.0d0*dwidth) then
            fracdist = dmean + fracdist*dwidth
         else
            fracdist = dmean + fracdist*(1.0d0-dmean)/3.0d0
         end if
      else
         if (dmean .ge. 3.0d0*dwidth) then
            fracdist = dmean + fracdist*dwidth
         else
            fracdist = dmean + fracdist*dmean/3.0d0
         end if
      end if
      fracdist = max(0.0d0,min(1.0d0,fracdist))
      return
      end
c
c
c     ###############################################################
c     ##                                                           ##
c     ##  subroutine metric  --  computation of the metric matrix  ##
c     ##                                                           ##
c     ###############################################################
c
c
c     "metric" takes as input the trial distance matrix and computes
c     the metric matrix of all possible dot products between the atomic
c     vectors and the center of mass using the law of cosines and the
c     following formula for the distances to the center of mass:
c
c        dcm(i)**2 = (1/n) * sum(j=1,n)(dist(i,j)**2)
c                          - (1/n**2) * sum(j<k)(dist(j,k)**2)
c
c     upon output, the metric matrix is stored in the lower triangle
c     plus diagonal of the input trial distance matrix, the upper
c     triangle of the input matrix is unchanged
c
c     literature reference:
c
c     G. M. Crippen and T. F. Havel, "Stable Calculation of Coordinates
c     from Distance Information", Acta Cryst., A34, 282-284 (1978)
c
c
      subroutine metric (gmx,nneg)
      implicit none
      include 'sizes.i'
      include 'atoms.i'
      include 'disgeo.i'
      include 'inform.i'
      include 'iounit.i'
      integer i,j,nneg
      real*8 total,sum,rg
      real*8 dsq(maxgeo),dcm(maxgeo)
      real*8 gmx(maxgeo,maxgeo)
c
c
c     square and sum trial distances to get radius of gyration
c
      total = 0.0d0
      do i = 1, n
         do j = i, n
            gmx(j,i) = gmx(j,i)**2
            total = total + gmx(j,i)
         end do
      end do
      total = total / dble(n**2)
      rg = sqrt(total)
      if (verbose) then
         write (iout,10)  rg
   10    format (/,' Radius of Gyration before Embedding :',7x,f16.4)
      end if
c
c     sum squared distances from each atom; the center
c     of mass is derived using the formula shown above
c
      nneg = 0
      do i = 1, n
         sum = 0.0d0
         do j = 1, i-1
            sum = sum + gmx(i,j)
         end do
         do j = i, n
            sum = sum + gmx(j,i)
         end do
         dsq(i) = sum/dble(n) - total
         dcm(i) = sqrt(abs(dsq(i)))
         if (dsq(i) .lt. 0.0d0) then
            nneg = nneg + 1
            dcm(i) = -dcm(i)
         end if
      end do
      if (verbose .and. n.le.130) then
         write (iout,20)
   20    format (/,' Atomic Distances to the Center of Mass :',/)
         write (iout,30)  (dcm(i),i=1,n)
   30    format (6f13.4)
      end if
c
c     calculate the metric matrix using the law of cosines, and
c     place into the lower triangle of the input distance matrix
c
      do i = 1, n
         do j = i, n
            gmx(j,i) = 0.5d0 * (dsq(i)+dsq(j)-gmx(j,i))
         end do
      end do
      return
      end
c
c
c     ##################################################################
c     ##                                                              ##
c     ##  subroutine eigen  --  largest eigenvalues of metric metrix  ##
c     ##                                                              ##
c     ##################################################################
c
c
c     "eigen" uses the power method to compute the largest eigenvalues
c     and eigenvectors of the metric matrix, "valid" is set true if the
c     first three eigenvalues are positive
c
c
      subroutine eigen (evl,evc,gmx,valid)
      implicit none
      include 'sizes.i'
      include 'atoms.i'
      include 'inform.i'
      include 'iounit.i'
      integer maxeigen
      parameter (maxeigen=5)
      integer i,j,neigen
      real*8 evl(maxeigen)
      real*8 evc(maxgeo,maxeigen)
      real*8 gmx(maxgeo,maxgeo)
      real*8 secs,work(maxgeo)
      logical valid
c
c
c     initialize number of eigenvalues and convergence criteria
c
      if (verbose)  call setime
      neigen = 3
c
c     compute the largest few eigenvalues via the power method
c
      call power (n,maxgeo,neigen,gmx,evl,evc,work)
c
c     check to see if the first three eigenvalues are positive
c
      valid = .true.
      do i = 1, 3
         if (evl(i) .lt. 0.0d0)  valid = .false.
      end do
c
c     print out the eigenvalues and their eigenvectors
c
      if (verbose) then
         write (iout,10)
   10    format (/,' Eigenvalues from Metric Matrix :',/)
         write (iout,20)  (evl(i),i=1,neigen)
   20    format (5f15.4)
      end if
      if (debug) then
         write (iout,30)
   30    format (/,' Eigenvectors from Metric Matrix :',/)
         do i = 1, n
            write (iout,40)  (evc(i,j),j=1,neigen)
   40       format (5f15.4)
         end do
      end if
c
c     get the time required for partial matrix diagonalization
c
      if (verbose) then
         call getime (secs)
         write (iout,50)  secs
   50    format (/,' Time Required for Eigenvalues :',9x,f12.2,
     &              ' seconds')
      end if
      return
      end
c
c
c     ##################################################################
c     ##                                                              ##
c     ##  subroutine coords  --  converts eigenvalues to coordinates  ##
c     ##                                                              ##
c     ##################################################################
c
c
c     "coords" converts the three principal eigenvalues/vectors from
c     the metric matrix into atomic coordinates, and calls a routine
c     to compute the rms deviation from the bounds
c
c
      subroutine coords (evl,evc)
      implicit none
      include 'sizes.i'
      include 'atoms.i'
      include 'disgeo.i'
      include 'inform.i'
      include 'iounit.i'
      integer maxeigen
      parameter (maxeigen=5)
      integer i,j,neigen
      real*8 rg,evl(maxeigen)
      real*8 evc(maxgeo,maxeigen)
      character*60 title
c
c
c     compute coordinates from the largest eigenvalues and vectors
c
      neigen = 3
      do j = 1, neigen
         evl(j) = sqrt(abs(evl(j)))
      end do
      do j = 1, neigen
         do i = 1, n
            evc(i,j) = evl(j) * evc(i,j)
         end do
      end do
c
c     transfer the final coordinates back to atomic vectors
c
      do i = 1, n
         x(i) = evc(i,1)
         y(i) = evc(i,2)
         z(i) = evc(i,3)
      end do
c
c     find the rms bounds deviations and radius of gyration
c
      if (verbose) then
         title = 'after Embedding :'
         call rmserror (title)
         call gyrate (rg)
         write (iout,10)  rg
   10    format (/,' Radius of Gyration after Embedding :',8x,f16.4)
      end if
      return
      end
c
c
c     ################################################################
c     ##                                                            ##
c     ##  subroutine chksize  --  estimate compaction or expansion  ##
c     ##                                                            ##
c     ################################################################
c
c
c     "chksize" computes a measure of overall global structural
c     expansion or compaction from the number of excess upper
c     or lower bounds matrix violations
c
c
      subroutine chksize
      implicit none
      include 'sizes.i'
      include 'atoms.i'
      include 'couple.i'
      include 'disgeo.i'
      include 'inform.i'
      include 'iounit.i'
      integer i,k,npair,nskip
      integer nlarge,nsmall
      integer skip(maxatm)
      real*8 xi,yi,zi
      real*8 dstsq,bupsq,blosq
c
c
c     zero out the list of atoms locally connected to each atom
c
      nskip = 0
      do i = 1, n
         skip(i) = 0
      end do
c
c     initialize counters, total pair number, and cutoff distance
c
      nlarge = 0
      nsmall = 0
      npair = n*(n-1) / 2
c
c     count the number of excess upper or lower bound violations
c
      do i = 1, n-1
         xi = x(i)
         yi = y(i)
         zi = z(i)
         do k = 1, n12(i)
            skip(i12(k,i)) = i
         end do
         do k = 1, n13(i)
            skip(i13(k,i)) = i
         end do
         do k = 1, n14(i)
            skip(i14(k,i)) = i
         end do
         do k = i+1, n
            if (skip(k) .eq. i) then
               nskip = nskip + 1
            else
               dstsq = (x(k)-xi)**2 + (y(k)-yi)**2 + (z(k)-zi)**2
               bupsq = bnd(i,k)**2
               blosq = bnd(k,i)**2
               if (dstsq .gt. bupsq) then
                  nlarge = nlarge + 1
               else if (blosq .gt. dstsq) then
                  nsmall = nsmall + 1
               end if
            end if
         end do
      end do
c
c     set the value for the overall index of compaction
c
      compact = 100.0d0 * dble(nlarge-nsmall)/dble(npair-nskip)
      if (verbose) then
         write (iout,10)  compact
   10    format (/,' Index of Structure Expansion/Compaction :',
     &              7x,f12.4)
      end if
      return
      end
c
c
c     ###############################################################
c     ##                                                           ##
c     ##  subroutine majorize  --  Guttman transform majorization  ##
c     ##                                                           ##
c     ###############################################################
c
c
c     "majorize" refines the projected coordinates by attempting to
c     minimize the least square residual between the trial distance
c     matrix and the distances computed from the coordinates
c
c     literature reference:
c
c     T. F. Havel, "An Evaluation of Computational Strategies for
c     Use in the Determination of Protein Structure from Distance
c     Constraints obtained by Nuclear Magnetic Resonance", Progress
c     in Biophysics and Molecular Biology, 56, 43-78 (1991)
c
c
      subroutine majorize (dmx)
      implicit none
      include 'sizes.i'
      include 'atoms.i'
      include 'inform.i'
      include 'iounit.i'
      integer i,k,iter,niter,period
      real*8 pairs,dn1,dn2,rg,secs
      real*8 target,dist,error
      real*8 rmserr,average
      real*8 xi,yi,zi,b(maxatm)
      real*8 dmx(maxgeo,maxgeo)
      real*8 xx(maxatm),yy(maxatm),zz(maxatm)
      character*60 title
c
c
c     set number of iterations and some other needed values
c
      if (verbose)  call setime
      niter = 20
      period = 5
      pairs = dble(n*(n-1)/2)
      dn1 = dble(n-1)
      dn2 = dble(n*n)
c
c     find the average and rms error from trial distances
c
      iter = 0
      rmserr = 0.0d0
      average = 0.0d0
      do i = 1, n-1
         xi = x(i)
         yi = y(i)
         zi = z(i)
         do k = i+1, n
            target = dmx(k,i)
            dist = sqrt((x(k)-xi)**2+(y(k)-yi)**2+(z(k)-zi)**2)
            error = dist - target
            rmserr = rmserr + error**2
            average = average + error/target
         end do
      end do
      rmserr = sqrt(rmserr/pairs)
      average = 100.0d0 * average / pairs
c
c     write a header with the initial error values
c
      if (verbose) then
         write (iout,10)
   10    format (/,' Majorization to Trial Distances using',
     &              ' Constant Weights :',
     &           //,4x,'Iteration',6x,'RMS Error',5x,'Ave % Error',/)
         write (iout,20)  iter,rmserr,average
   20    format (5x,i5,2f16.4)
      end if
c
c     initialize the transformed coordinates for each atom
c
      do iter = 1, niter
         do i = 1, n
            xi = x(i)
            yi = y(i)
            zi = z(i)
            b(i) = 0.0d0
            xx(i) = 0.0d0
            yy(i) = 0.0d0
            zz(i) = 0.0d0
c
c     form a single row of the B matrix assuming unity weights
c
            do k = 1, i-1
               dist = sqrt((x(k)-xi)**2+(y(k)-yi)**2+(z(k)-zi)**2)
               b(k) = -dmx(k,i) / dist
               b(i) = b(i) - b(k)
            end do
            do k = i+1, n
               dist = sqrt((x(k)-xi)**2+(y(k)-yi)**2+(z(k)-zi)**2)
               b(k) = -dmx(k,i) / dist
               b(i) = b(i) - b(k)
            end do
c
c     multiply the row of the B matrix by the atomic coordinates
c
            do k = 1, n
               xx(i) = xx(i) + b(k)*x(k)
               yy(i) = yy(i) + b(k)*y(k)
               zz(i) = zz(i) + b(k)*z(k)
            end do
         end do
c
c     move the intermediate values into the coordinate arrays
c
         do i = 1, n
            x(i) = xx(i)
            y(i) = yy(i)
            z(i) = zz(i)
         end do
c
c     multiply the inverse weight matrix S+ by the coordinates
c
         do i = 1, n
            xx(i) = (dn1/dn2) * x(i)
            yy(i) = (dn1/dn2) * y(i)
            zz(i) = (dn1/dn2) * z(i)
            do k = 1, i-1
               xx(i) = xx(i) - x(k)/dn2
               yy(i) = yy(i) - y(k)/dn2
               zz(i) = zz(i) - z(k)/dn2
            end do
            do k = i+1, n
               xx(i) = xx(i) - x(k)/dn2
               yy(i) = yy(i) - y(k)/dn2
               zz(i) = zz(i) - z(k)/dn2
            end do
         end do
c
c     copy the new coordinates into their permanent arrays
c
         do i = 1, n
            x(i) = xx(i)
            y(i) = yy(i)
            z(i) = zz(i)
         end do
c
c     find the average and rms error from trial distances
c
         rmserr = 0.0d0
         average = 0.0d0
         do i = 1, n-1
            xi = x(i)
            yi = y(i)
            zi = z(i)
            do k = i+1, n
               target = dmx(k,i)
               dist = sqrt((x(k)-xi)**2+(y(k)-yi)**2+(z(k)-zi)**2)
               error = dist - target
               rmserr = rmserr + error**2
               average = average + error/target
            end do
         end do
         rmserr = sqrt(rmserr/pairs)
         average = 100.0d0 * average / pairs
         if (verbose .and. mod(iter,period).eq.0) then
            write (iout,30)  iter,rmserr,average
   30       format (5x,i5,2f16.4)
         end if
      end do
c
c     find the rms bounds deviations and radius of gyration
c
      if (verbose) then
         title = 'after Majorization :'
         call rmserror (title)
         call gyrate (rg)
         write (iout,40)  rg
   40    format (/,' Radius of Gyration after Majorization :',5x,f16.4)
c
c     get the time required for the majorization procedure
c
         call getime (secs)
         write (iout,50)  secs
   50    format (/,' Time Required for Majorization :',8x,f12.2,
     &              ' seconds')
      end if
      end
c
c
c     ################################################################
c     ##                                                            ##
c     ##  subroutine refine  --  minimization of initial embedding  ##
c     ##                                                            ##
c     ################################################################
c
c
c     "refine" performs minimization of the atomic coordinates
c     of an initial crude embedded distance geometry structure versus
c     the bound, chirality, planarity and torsional error functions
c
c
      subroutine refine (mode,fctval,grdmin)
      implicit none
      include 'sizes.i'
      include 'atoms.i'
      include 'disgeo.i'
      include 'inform.i'
      include 'iounit.i'
      include 'minima.i'
      include 'output.i'
      integer i,nvar
      real*8 initer,miderr,toterr
      real*8 fctval,grdmin,xx(maxvar)
      character*7 mode
      external initer,miderr,toterr
      external optsave
c
c
c     translate the atomic coordinates to optimization variables
c
      nvar = 0
      do i = 1, n
         nvar = nvar + 1
         xx(nvar) = x(i)
         nvar = nvar + 1
         xx(nvar) = y(i)
         nvar = nvar + 1
         xx(nvar) = z(i)
      end do
c
c     set values of parameters needed for optimization
c
      coordtype = 'NONE'
      cyclesave = .true.
c     grdmin = 0.01d0
      maxiter = 2 * nvar
      iwrite = 0
c     iprint = 0
c     if (verbose)  iprint = 10
c
c     minimize initially only on the local geometry and torsions,
c     then on local geometry and chirality, torsions, and finally
c     minimize on all distance bounds, chirality and torsions
c
      if (mode .eq. 'INITIAL') then
         call lmqn (nvar,xx,fctval,grdmin,initer,optsave)
      else if (mode .eq. 'MIDDLE') then
         call lmqn (nvar,xx,fctval,grdmin,miderr,optsave)
      else if (mode .eq. 'FINAL') then
         call lmqn (nvar,xx,fctval,grdmin,toterr,optsave)
      end if
c
c     translate optimization variables back to coordinates
c
      nvar = 0
      do i = 1, n
         nvar = nvar + 1
         x(i) = xx(nvar)
         nvar = nvar + 1
         y(i) = xx(nvar)
         nvar = nvar + 1
         z(i) = xx(nvar)
      end do
      return
      end
c
c
c     ##############################################################
c     ##                                                          ##
c     ##  subroutine explore  --  simulated annealing refinement  ##
c     ##                                                          ##
c     ##############################################################
c
c
c     "explore" uses simulated annealing on an initial crude
c     embedded distance geoemtry structure to refine versus the
c     bound, chirality, planarity and torsional error functions
c
c
      subroutine explore (mode,nstep,dt,mass,temp_start,temp_stop,v,a)
      implicit none
      include 'sizes.i'
      include 'atoms.i'
      include 'inform.i'
      include 'iounit.i'
      include 'math.i'
      include 'units.i'
      integer i,istep,nstep,nvar,period
      real*8 error,total,prior,change
      real*8 dt,dt2,dt_2,dt2_2
      real*8 xbig,xrms,mass,kinetic
      real*8 temp_start,temp_stop
      real*8 tau_start,tau_stop
      real*8 ratio,sigmoid,scale
      real*8 target,temp,tautemp
      real*8 initer,miderr,toterr
      real*8 xx(maxvar),xmove(maxvar)
      real*8 g(maxvar),v(maxvar),a(maxvar)
      character*7 mode
c
c
c     set values of the basic simulated annealing parameters
c
c     nstep = 5000
c     dt = 0.1d0
c     temp_start = 200.0d0
c     temp_stop = 0.0d0
c     mass = 1000.0d0
c
c     translate the atomic coordinates to annealing variables
c
      nvar = 0
      do i = 1, n
         nvar = nvar + 1
         xx(nvar) = x(i)
         nvar = nvar + 1
         xx(nvar) = y(i)
         nvar = nvar + 1
         xx(nvar) = z(i)
      end do
c
c     initialize the velocities, accelerations and other parameters
c
      dt2 = dt * dt
      dt_2 = dt / 2.0d0
      dt2_2 = dt2 / 2.0d0
      period = 100
      tau_start = 100.0d0 * dt
      tau_stop = 10.0d0 * dt
      tautemp = tau_start
c
c     print a header for the simulated annealing protocol
c
      write (iout,10)
   10 format (/,' Molecular Dynamics Simulated Annealing Refinement :')
      write (iout,20)  nstep,dt,log(mass)/logten,temp_start,temp_stop
   20 format (/,' Steps:',i6,3x,'Time/Step:',f6.3,' ps',3x,
     &           'LogMass:',f5.2,3x,'Temp:',f6.1,' to',f6.1)
c
c     get the total error and temperature at start of dynamics
c
      if (mode .eq. 'INITIAL') then
         error = initer (xx,g)
      else if (mode .eq. 'MIDDLE') then
         error = miderr (xx,g)
      else if (mode .eq. 'FINAL') then
         error = toterr (xx,g)
      end if
      kinetic = 0.0d0
      do i = 1, nvar
         kinetic = kinetic + mass*v(i)**2
      end do
      kinetic = 0.5d0 * kinetic / convert
      temp = 2.0d0 * kinetic / (dble(nvar) * gasconst)
      total = error + kinetic
      prior = total
      if (verbose) then
         write (iout,30)
   30    format (/,' MD Step    E Total   E Potential   E Kinetic',
     &              '     Temp    MaxMove   RMS Move',/)
         write (iout,40)  0,total,error,kinetic,temp
   40    format (i6,2f13.4,f12.4,f11.2)
      end if
c
c     find new positions and half-step velocities via Verlet
c
      do istep = 1, nstep
         xbig = 0.0d0
         xrms = 0.0d0
         do i = 1, nvar
            xmove(i) = v(i)*dt + a(i)*dt2_2
            xx(i) = xx(i) + xmove(i)
            v(i) = v(i) + a(i)*dt_2
            if (abs(xmove(i)) .gt. xbig)  xbig = abs(xmove(i))
            xrms = xrms + xmove(i)**2
         end do
         xrms = sqrt(xrms/dble(nvar))
c
c     get the error function value and gradient
c
         if (mode .eq. 'INITIAL') then
            error = initer (xx,g)
         else if (mode .eq. 'MIDDLE') then
            error = miderr (xx,g)
         else if (mode .eq. 'FINAL') then
            error = toterr (xx,g)
         end if
c
c     use Newton's second law to get the next accelerations;
c     find the full-step velocities using the Verlet recursion
c
         do i = 1, nvar
            a(i) = -convert * g(i) / mass
            v(i) = v(i) + a(i)*dt_2
         end do
c
c     find the total kinetic energy and system temperature
c
         kinetic = 0.0d0
         do i = 1, nvar
            kinetic = kinetic + mass*v(i)**2
         end do
         kinetic = 0.5d0 * kinetic / convert
         temp = 2.0d0 * kinetic / (dble(nvar) * gasconst)
         if (temp .eq. 0.0d0)  temp = 0.1d0
c
c     set target temperature and coupling via a sigmoidal cooling
c
         ratio = dble(istep) / dble(nstep)
         ratio = sigmoid (3.5d0,ratio)
         target = temp_start*(1.0d0-ratio) + temp_stop*ratio
         tautemp = tau_start*(1.0d0-ratio) + tau_stop*ratio
c
c     couple to external temperature bath via velocity scaling
c
         scale = sqrt(1.0d0 + (dt/tautemp)*(target/temp-1.0d0))
         do i = 1, nvar
            v(i) = scale * v(i)
         end do
c
c     write results for the current annealing step
c
         total = error + kinetic
         if (verbose .and. mod(istep,period).eq.0) then
            write (iout,50)  istep,total,error,kinetic,temp,xbig,xrms
   50       format (i6,2f13.4,f12.4,f11.2,2f10.4)
         end if
c
c     check the energy change for instability in the dynamics
c
         change = total - prior
         if (change .gt. dble(n)) then
            do i = 1, nvar
               xx(i) = xx(i) - xmove(i)
            end do
            if (verbose .and. mod(istep,period).ne.0) then
               write (iout,60)  istep,total,error,kinetic,temp,xbig,xrms
   60          format (i6,2f13.4,f12.4,f11.2,2f10.4)
            end if
            write (iout,70)
   70       format (/,' EXPLORE  --  Simulated Annealing Unstable;',
     &                 ' Switching to Minimization')
            goto 80
         end if
      end do
c
c     translate annealing variables back to coordinates
c
   80 continue
      nvar = 0
      do i = 1, n
         nvar = nvar + 1
         x(i) = xx(nvar)
         nvar = nvar + 1
         y(i) = xx(nvar)
         nvar = nvar + 1
         z(i) = xx(nvar)
      end do
      return
      end
c
c
c     ##############################################################
c     ##                                                          ##
c     ##  subroutine rmserror  --  rms bound and restraint error  ##
c     ##                                                          ##
c     ##############################################################
c
c
c     "rmserror" computes the maximum absolute deviation and the
c     rms deviation from the distance bounds, and the number and
c     rms value of the distance restraint violations
c
c
      subroutine rmserror (title)
      implicit none
      include 'sizes.i'
      include 'atoms.i'
      include 'disgeo.i'
      include 'iounit.i'
      include 'restrn.i'
      integer i,j,k,npair
      integer nhierr,nloerr
      integer ihi,jhi,ilo,jlo
      integer leng,trimtext
      real*8 rms,himax,lomax
      real*8 dist,hierr,loerr
      character*60 title
c
c
c     search all atom pairs for maximal bounds deviations
c
      npair = n*(n-1) / 2
      nloerr = 0
      nhierr = 0
      ilo = 0
      jlo = 0
      ihi = 0
      jhi = 0
      rms = 0.0d0
      lomax = 0.0d0
      himax = 0.0d0
      do i = 1, n-1
         do j = i+1, n
            dist = (x(i)-x(j))**2 + (y(i)-y(j))**2 + (z(i)-z(j))**2
            dist = sqrt(dist)
            hierr = dist - bnd(i,j)
            if (hierr .gt. 0.0d0) then
               nhierr = nhierr + 1
               rms = rms + hierr**2
               if (hierr .gt. himax) then
                  himax = hierr
                  ihi = i
                  jhi = j
               end if
            end if
            loerr = bnd(j,i) - dist
            if (loerr .gt. 0.0d0) then
               nloerr = nloerr + 1
               rms = rms + loerr**2
               if (loerr .gt. lomax) then
                  lomax = loerr
                  ilo = i
                  jlo = j
               end if
            end if
         end do
      end do
      rms = sqrt(rms/dble(n*(n-1)/2))
c
c     print the maximal and rms bound deviations
c
      leng = trimtext(title)
      write (iout,10)  title(1:leng)
   10 format (/,' Fit to Bounds ',a)
      write (iout,20)  nhierr,npair,nloerr,npair,himax,
     &                 ihi,jhi,lomax,ilo,jlo,rms
   20 format (/,' Num Upper Bound Violations :',4x,i11,'  of ',i12,
     &        /,' Num Lower Bound Violations :',4x,i11,'  of ',i12,
     &        /,' Max Upper Bound Violation :',4x,f12.4,'  at ',2i6,
     &        /,' Max Lower Bound Violation :',4x,f12.4,'  at ',2i6,
     &        /,' RMS Deviation from Bounds :',4x,f12.4)
c
c     search the list of distance restraints for violations
c
      if (ndfix .gt. 0) then
         nloerr = 0
         nhierr = 0
         ilo = 0
         jlo = 0
         ihi = 0
         jhi = 0
         rms = 0.0d0
         himax = 0.0d0
         lomax = 0.0d0
         do k = 1, ndfix
            i = idfix(1,k)
            j = idfix(2,k)
            dist = (x(i)-x(j))**2 + (y(i)-y(j))**2 + (z(i)-z(j))**2
            dist = sqrt(dist)
            if (dist .lt. dfix(1,k)) then
               nloerr = nloerr + 1
               loerr = dfix(1,k) - dist
               rms = rms + (dist-dfix(1,k))**2
               if (loerr .gt. lomax) then
                  lomax = loerr
                  ilo = i
                  jlo = j
               end if
            else if (dist .gt. dfix(2,k)) then
               nhierr = nhierr + 1
               hierr = dist - dfix(2,k)
               rms = rms + hierr**2
               if (hierr .gt. himax) then
                  himax = hierr
                  ihi = i
                  jhi = j
               end if
            end if
         end do
         rms = sqrt(rms/dble(ndfix))
c
c     print total number and rms value of restraint violations
c
         write (iout,30)  nhierr,ndfix,nloerr,ndfix,himax,
     &                    ihi,jhi,lomax,ilo,jlo,rms
   30    format (/,' Num Upper Restraint Violations :',i11,'  of ',i12,
     &           /,' Num Lower Restraint Violations :',i11,'  of ',i12,
     &           /,' Max Upper Restraint Violation :',f12.4,'  at ',2i6,
     &           /,' Max Lower Restraint Violation :',f12.4,'  at ',2i6,
     &           /,' RMS Restraint Dist Violation : ',f12.4)
      end if
      return
      end
c
c
c     ##############################################################
c     ##                                                          ##
c     ##  subroutine dmdump  --  final distance and error matrix  ##
c     ##                                                          ##
c     ##############################################################
c
c
c     "dmdump" puts the distance matrix of the final structure
c     into the upper half of a matrix, the distance of each atom
c     to the centroid on the diagonal, and the individual terms
c     of the bounds errors into the lower half of the matrix
c
c
      subroutine dmdump (dmd)
      implicit none
      include 'sizes.i'
      include 'atoms.i'
      include 'disgeo.i'
      include 'iounit.i'
      integer i,j
      real*8 sum,dist,dist2,rgsq
      real*8 dmd(maxgeo,maxgeo)
      character*60 title
c
c
c     store the final distance matrix and bound violations
c
      do i = 1, n
         dmd(i,i) = 0.0d0
      end do
      sum = 0.0d0
      do i = 1, n-1
         do j = i+1, n
            dist2 = (x(i)-x(j))**2 + (y(i)-y(j))**2 + (z(i)-z(j))**2
            sum = sum + dist2
            dmd(i,i) = dmd(i,i) + dist2
            dmd(j,j) = dmd(j,j) + dist2
            dist = sqrt(dist2)
            dmd(i,j) = dist
            if (dist .gt. bnd(i,j)) then
               dmd(j,i) = dist - bnd(i,j)
            else if (dist .lt. bnd(j,i)) then
               dmd(j,i) = bnd(j,i) - dist
            else
               dmd(j,i) = 0.0d0
            end if
         end do
      end do
c
c     put the distance to the centroid on the diagonal
c
      rgsq = sum / dble(n**2)
      do i = 1, n
         dmd(i,i) = sqrt(dmd(i,i)/dble(n) - rgsq)
      end do
c
c     write out the interatomic distance and error matrices
c
      title = 'Final Dist Matrix Above; DCM on Diag; Error Below :'
      call grafic (n,maxgeo,dmd,title)
      return
      end
c
c
c     ################################################################
c     ##                                                            ##
c     ##  function initer  --  initial error function and gradient  ##
c     ##                                                            ##
c     ################################################################
c
c
c     "initer" is the initial error function and derivatives for
c     a distance geometry embedding; it includes components from
c     the local geometry and torsional restraint errors
c
c
      function initer (xx,g)
      implicit none
      include 'sizes.i'
      include 'atoms.i'
      integer i,j,nvar
      real*8 initer,local,torsion
      real*8 locerr,torser
      real*8 xx(maxvar),g(maxvar)
      real*8 derivs(3,maxgeo)
      external locerr,torser
c
c
c     translate optimization parameters to atomic coordinates
c
      nvar = 0
      do i = 1, n
         nvar = nvar + 1
         x(i) = xx(nvar)
         nvar = nvar + 1
         y(i) = xx(nvar)
         nvar = nvar + 1
         z(i) = xx(nvar)
      end do
c
c     zero out the values of the atomic gradient components
c
      do i = 1, n
         do j = 1, 3
            derivs(j,i) = 0.0d0
         end do
      end do
c
c     compute the local goemetry and the torsional
c     components of the error function and its gradient
c
      local = locerr (derivs)
      torsion = torser (derivs)
      initer = local + torsion
c
c     store the atomic gradients as the optimization gradient
c
      nvar = 0
      do i = 1, n
         nvar = nvar + 1
         g(nvar) = derivs(1,i)
         nvar = nvar + 1
         g(nvar) = derivs(2,i)
         nvar = nvar + 1
         g(nvar) = derivs(3,i)
      end do
      return
      end
c
c
c     ###############################################################
c     ##                                                           ##
c     ##  function miderr  --  second error function and gradient  ##
c     ##                                                           ##
c     ###############################################################
c
c
c     "miderr" is the secondary error function and derivatives
c     for a distance geometry embedding; it includes components
c     from the distance bounds, local geometry, chirality and
c     torsional restraint errors
c
c
      function miderr (xx,g)
      implicit none
      include 'sizes.i'
      include 'atoms.i'
      integer i,j,nvar
      real*8 miderr,bounds,local
      real*8 chiral,torsion
      real*8 bnderr,locerr
      real*8 chirer,torser
      real*8 xx(maxvar),g(maxvar)
      real*8 derivs(3,maxgeo)
c
c
c     translate optimization parameters to atomic coordinates
c
      nvar = 0
      do i = 1, n
         nvar = nvar + 1
         x(i) = xx(nvar)
         nvar = nvar + 1
         y(i) = xx(nvar)
         nvar = nvar + 1
         z(i) = xx(nvar)
      end do
c
c     zero out the values of the atomic gradient components
c
      do i = 1, n
         do j = 1, 3
            derivs(j,i) = 0.0d0
         end do
      end do
c
c     compute the local geometry, chirality and torsional
c     components of the error function and its gradient
c
      bounds = bnderr (derivs)
      local = locerr (derivs)
      chiral = chirer (derivs)
      torsion = torser (derivs)
      miderr = bounds + local + chiral + torsion
c
c     store the atomic gradients as the optimization gradient
c
      nvar = 0
      do i = 1, n
         nvar = nvar + 1
         g(nvar) = derivs(1,i)
         nvar = nvar + 1
         g(nvar) = derivs(2,i)
         nvar = nvar + 1
         g(nvar) = derivs(3,i)
      end do
      return
      end
c
c
c     ##############################################################
c     ##                                                          ##
c     ##  function toterr  --  total error function and gradient  ##
c     ##                                                          ##
c     ##############################################################
c
c
c     "toterr" is the error function and derivatives for a distance
c     geometry embedding; it includes components from the distance
c     bounds, hard sphere contacts, local geometry, chirality and
c     torsional restraint errors
c
c
      function toterr (xx,g)
      implicit none
      include 'sizes.i'
      include 'atoms.i'
      integer i,j,nvar
      real*8 toterr,bounds,contact
      real*8 local,chiral,torsion
      real*8 bnderr,vdwerr,locerr
      real*8 chirer,torser
      real*8 xx(maxvar),g(maxvar)
      real*8 derivs(3,maxgeo)
      external bnderr,vdwerr,chirer,torser
c
c
c     translate optimization parameters to atomic coordinates
c
      nvar = 0
      do i = 1, n
         nvar = nvar + 1
         x(i) = xx(nvar)
         nvar = nvar + 1
         y(i) = xx(nvar)
         nvar = nvar + 1
         z(i) = xx(nvar)
      end do
c
c     zero out the values of the atomic gradient components
c
      do i = 1, n
         do j = 1, 3
            derivs(j,i) = 0.0d0
         end do
      end do
c
c     compute the distance bound, vdw, chirality and torsional
c     components of the error function and its gradient
c
      bounds = bnderr (derivs)
      contact = vdwerr (derivs)
      local = locerr (derivs)
      chiral = chirer (derivs)
      torsion = torser (derivs)
      toterr = bounds + contact + local + chiral + torsion
c
c     store the atomic gradients as the optimization gradient
c
      nvar = 0
      do i = 1, n
         nvar = nvar + 1
         g(nvar) = derivs(1,i)
         nvar = nvar + 1
         g(nvar) = derivs(2,i)
         nvar = nvar + 1
         g(nvar) = derivs(3,i)
      end do
      return
      end
c
c
c     ################################################################
c     ##                                                            ##
c     ##  function bnderr  --  computes total distance bound error  ##
c     ##                                                            ##
c     ################################################################
c
c
c     "bnderr" is the distance bound error function and derivatives;
c     this version implements the original and Havel's normalized
c     lower bound penalty, the normalized version is preferred when
c     lower bounds are small (as with NMR NOE restraints), the
c     original penalty is needed if large lower bounds are present
c
c
      function bnderr (derivs)
      implicit none
      include 'sizes.i'
      include 'atoms.i'
      include 'restrn.i'
      integer i,j,k
      real*8 bnderr,error,cutsq
      real*8 scale,chain,term
      real*8 gap,buffer,weight
      real*8 dx,dy,dz,gx,gy,gz
      real*8 dstsq,bupsq,blosq
      real*8 derivs(3,maxgeo)
c
c
c     zero out the distance bounds error function
c
      bnderr = 0.0d0
      scale = 10.0d0
      cutsq = 40.0d0
c
c     calculate the pairwise distances between atoms
c
      do k = 1, ndfix
         i = idfix(1,k)
         j = idfix(2,k)
         dx = x(i) - x(j)
         dy = y(i) - y(j)
         dz = z(i) - z(j)
c
c     calculate squared actual distance and bound distances;
c     use of a small "buffer" cleans up the final error count
c
         dstsq = dx*dx + dy*dy + dz*dz
         gap = dfix(2,k) - dfix(1,k)
         buffer = 0.05d0 * min(1.0d0,gap)
         blosq = (dfix(1,k) + buffer)**2
         bupsq = (dfix(2,k) - buffer)**2
c
c     error and derivatives for upper bound violation
c
         if (dstsq .gt. bupsq) then
            weight = scale * dfix(3,k)
            term = (dstsq-bupsq) / bupsq
            chain = 4.0d0 * weight * term / bupsq
            error = weight * term**2
            gx = dx * chain
            gy = dy * chain
            gz = dz * chain
            bnderr = bnderr + error
            derivs(1,i) = derivs(1,i) + gx
            derivs(2,i) = derivs(2,i) + gy
            derivs(3,i) = derivs(3,i) + gz
            derivs(1,j) = derivs(1,j) - gx
            derivs(2,j) = derivs(2,j) - gy
            derivs(3,j) = derivs(3,j) - gz
c
c     error and derivatives for lower bound violation
c
         else if (dstsq .lt. blosq) then
            weight = scale * dfix(3,k)
            if (blosq .gt. cutsq) then
               term = (blosq-dstsq) / dstsq
               chain = -4.0d0 * weight * term * (blosq/dstsq**2)
            else
               term = (blosq-dstsq) / (blosq+dstsq)
               chain = -8.0d0 * weight * term * (blosq/(blosq+dstsq)**2)
            end if
            error = weight * term**2
            gx = dx * chain
            gy = dy * chain
            gz = dz * chain
            bnderr = bnderr + error
            derivs(1,i) = derivs(1,i) + gx
            derivs(2,i) = derivs(2,i) + gy
            derivs(3,i) = derivs(3,i) + gz
            derivs(1,j) = derivs(1,j) - gx
            derivs(2,j) = derivs(2,j) - gy
            derivs(3,j) = derivs(3,j) - gz
         end if
      end do
      return
      end
c
c
c     ###############################################################
c     ##                                                           ##
c     ##  function vdwerr  --  computes van der Waals bound error  ##
c     ##                                                           ##
c     ###############################################################
c
c
c     "vdwerr" is the hard sphere van der Waals bound error function
c     and derivatives that penalizes close nonbonded contacts,
c     pairwise neighbors are generated via the method of lights
c
c
      function vdwerr (derivs)
      implicit none
      include 'sizes.i'
      include 'atoms.i'
      include 'couple.i'
      include 'disgeo.i'
      include 'light.i'
      include 'shunt.i'
      integer i,j,k,kgy,kgz
      integer skip(maxgeo)
      integer map(maxlight)
      real*8 vdwerr,error
      real*8 scale,chain,term
      real*8 xi,yi,zi
      real*8 dx,dy,dz,gx,gy,gz
      real*8 dstsq,blosq
      real*8 radi,radsq
      real*8 derivs(3,maxgeo)
      real*8 xsort(maxlight)
      real*8 ysort(maxlight)
      real*8 zsort(maxlight)
c
c
c     zero out the distance van der Waals error function
c
      vdwerr = 0.0d0
      scale = 1.0d0
c
c     set maximum value of vdw radii sum for a pair of atoms
c
      off = vdwmax
c
c     transfer coordinates and zero out atoms to be skipped
c
      do i = 1, n
         xsort(i) = x(i)
         ysort(i) = y(i)
         zsort(i) = z(i)
         skip(i) = 0
      end do
c
c     use the method of lights to generate neighbors
c
      call lights (n,map,xsort,ysort,zsort)
c
c     now, loop over all atoms computing the interactions
c
      do i = 1, n
         radi = vdwrad(i)
         xi = xsort(rgx(i))
         yi = ysort(rgy(i))
         zi = zsort(rgz(i))
         do j = 1, n12(i)
            skip(i12(j,i)) = i
         end do
         do j = 1, n13(i)
            skip(i13(j,i)) = i
         end do
         do j = 1, n14(i)
            skip(i14(j,i)) = i
         end do
         do j = kbx(i)+1, kex(i)
            k = locx(j)
            if (skip(k) .eq. i)  goto 10
            kgy = rgy(k)
            if (kgy.lt.kby(i) .or. kgy.gt.key(i))  goto 10
            kgz = rgz(k)
            if (kgz.lt.kbz(i) .or. kgz.gt.kez(i))  goto 10
c
c     calculate squared distances and bounds
c
            dx = xi - xsort(j)
            dy = yi - ysort(kgy)
            dz = zi - zsort(kgz)
            dstsq = dx*dx + dy*dy + dz*dz
            radsq = (radi + vdwrad(k))**2
            blosq = min(bnd(k,i),bnd(i,k),radsq)
c
c     error and derivatives for lower bound violation
c
            if (dstsq .lt. blosq) then
               term = (blosq-dstsq) / (blosq+dstsq)
               chain = -8.0d0 * scale * term * (blosq/(blosq+dstsq)**2)
               error = scale * term**2
               gx = dx * chain
               gy = dy * chain
               gz = dz * chain
               vdwerr = vdwerr + error
               derivs(1,i) = derivs(1,i) + gx
               derivs(2,i) = derivs(2,i) + gy
               derivs(3,i) = derivs(3,i) + gz
               derivs(1,k) = derivs(1,k) - gx
               derivs(2,k) = derivs(2,k) - gy
               derivs(3,k) = derivs(3,k) - gz
            end if
   10       continue
         end do
      end do
      return
      end
c
c
c     ################################################################
c     ##                                                            ##
c     ##  function locerr  --  computes local geometry error value  ##
c     ##                                                            ##
c     ################################################################
c
c
c     "locerr" is the local geometry error function and derivatives
c     including the 1-2, 1-3 and 1-4 distance bound restraints
c
c
      function locerr (derivs)
      implicit none
      include 'sizes.i'
      include 'angle.i'
      include 'atoms.i'
      include 'bond.i'
      include 'disgeo.i'
      include 'tors.i'
      integer i,ia,ib,ic,id
      real*8 locerr,error
      real*8 scale,chain,term
      real*8 dx,dy,dz,gx,gy,gz
      real*8 dstsq,bupsq,blosq
      real*8 derivs(3,maxgeo)
c
c
c     zero out the local geometry error function
c
      locerr = 0.0d0
      scale = 10.0d0
c
c     calculate the bounds error for bond length distances
c
      do i = 1, nbond
         ia = min(ibnd(1,i),ibnd(2,i))
         ib = max(ibnd(1,i),ibnd(2,i))
         dx = x(ia) - x(ib)
         dy = y(ia) - y(ib)
         dz = z(ia) - z(ib)
         dstsq = dx*dx + dy*dy + dz*dz
         bupsq = bnd(ia,ib)
         blosq = bnd(ib,ia)
         if (dstsq .gt. bupsq) then
            term = (dstsq-bupsq) / bupsq
            chain = 4.0d0 * scale * term / bupsq
            error = scale * term**2
            gx = dx * chain
            gy = dy * chain
            gz = dz * chain
            locerr = locerr + error
            derivs(1,ia) = derivs(1,ia) + gx
            derivs(2,ia) = derivs(2,ia) + gy
            derivs(3,ia) = derivs(3,ia) + gz
            derivs(1,ib) = derivs(1,ib) - gx
            derivs(2,ib) = derivs(2,ib) - gy
            derivs(3,ib) = derivs(3,ib) - gz
         else if (dstsq .lt. blosq) then
            term = (blosq-dstsq) / (blosq+dstsq)
            chain = -8.0d0 * scale * term * (blosq/(blosq+dstsq)**2)
            error = scale * term**2
            gx = dx * chain
            gy = dy * chain
            gz = dz * chain
            locerr = locerr + error
            derivs(1,ia) = derivs(1,ia) + gx
            derivs(2,ia) = derivs(2,ia) + gy
            derivs(3,ia) = derivs(3,ia) + gz
            derivs(1,ib) = derivs(1,ib) - gx
            derivs(2,ib) = derivs(2,ib) - gy
            derivs(3,ib) = derivs(3,ib) - gz
         end if
      end do
c
c     calculate the bounds error for the bond angle distances
c
      do i = 1, nangle
         ia = min(iang(1,i),iang(3,i))
         ic = max(iang(1,i),iang(3,i))
         dx = x(ia) - x(ic)
         dy = y(ia) - y(ic)
         dz = z(ia) - z(ic)
         dstsq = dx*dx + dy*dy + dz*dz
         bupsq = bnd(ia,ic)
         blosq = bnd(ic,ia)
         if (dstsq .gt. bupsq) then
            term = (dstsq-bupsq) / bupsq
            chain = 4.0d0 * scale * term / bupsq
            error = scale * term**2
            gx = dx * chain
            gy = dy * chain
            gz = dz * chain
            locerr = locerr + error
            derivs(1,ia) = derivs(1,ia) + gx
            derivs(2,ia) = derivs(2,ia) + gy
            derivs(3,ia) = derivs(3,ia) + gz
            derivs(1,ic) = derivs(1,ic) - gx
            derivs(2,ic) = derivs(2,ic) - gy
            derivs(3,ic) = derivs(3,ic) - gz
         else if (dstsq .lt. blosq) then
            term = (blosq-dstsq) / (blosq+dstsq)
            chain = -8.0d0 * scale * term * (blosq/(blosq+dstsq)**2)
            error = scale * term**2
            gx = dx * chain
            gy = dy * chain
            gz = dz * chain
            locerr = locerr + error
            derivs(1,ia) = derivs(1,ia) + gx
            derivs(2,ia) = derivs(2,ia) + gy
            derivs(3,ia) = derivs(3,ia) + gz
            derivs(1,ic) = derivs(1,ic) - gx
            derivs(2,ic) = derivs(2,ic) - gy
            derivs(3,ic) = derivs(3,ic) - gz
         end if
      end do
c
c     calculate the bounds error for the torsion angle distances
c
      do i = 1, ntors
         ia = min(itors(1,i),itors(4,i))
         id = max(itors(1,i),itors(4,i))
         dx = x(ia) - x(id)
         dy = y(ia) - y(id)
         dz = z(ia) - z(id)
         dstsq = dx*dx + dy*dy + dz*dz
         bupsq = bnd(ia,id)
         blosq = bnd(id,ia)
         if (dstsq .gt. bupsq) then
            term = (dstsq-bupsq) / bupsq
            chain = 4.0d0 * scale * term / bupsq
            error = scale * term**2
            gx = dx * chain
            gy = dy * chain
            gz = dz * chain
            locerr = locerr + error
            derivs(1,ia) = derivs(1,ia) + gx
            derivs(2,ia) = derivs(2,ia) + gy
            derivs(3,ia) = derivs(3,ia) + gz
            derivs(1,id) = derivs(1,id) - gx
            derivs(2,id) = derivs(2,id) - gy
            derivs(3,id) = derivs(3,id) - gz
         else if (dstsq .lt. blosq) then
            term = (blosq-dstsq) / (blosq+dstsq)
            chain = -8.0d0 * scale * term * (blosq/(blosq+dstsq)**2)
            error = scale * term**2
            gx = dx * chain
            gy = dy * chain
            gz = dz * chain
            locerr = locerr + error
            derivs(1,ia) = derivs(1,ia) + gx
            derivs(2,ia) = derivs(2,ia) + gy
            derivs(3,ia) = derivs(3,ia) + gz
            derivs(1,id) = derivs(1,id) - gx
            derivs(2,id) = derivs(2,id) - gy
            derivs(3,id) = derivs(3,id) - gz
         end if
      end do
      return
      end
c
c
c     ##############################################################
c     ##                                                          ##
c     ##  function chirer  --  computes chirality error function  ##
c     ##                                                          ##
c     ##############################################################
c
c
c     "chirer" computes the chirality error and its derivatives
c     with respect to atomic Cartesian coordinates as a sum the
c     squares of deviations of chiral volumes from target values
c
c
      function chirer (derivs)
      implicit none
      include 'sizes.i'
      include 'atoms.i'
      include 'disgeo.i'
      integer i,ia,ib,ic,id
      real*8 chirer,error,scale
      real*8 vol,dv,dedv
      real*8 xad,yad,zad
      real*8 xbd,ybd,zbd
      real*8 xcd,ycd,zcd
      real*8 c1,c2,c3
      real*8 dedxia,dedyia,dedzia
      real*8 dedxib,dedyib,dedzib
      real*8 dedxic,dedyic,dedzic
      real*8 dedxid,dedyid,dedzid
      real*8 derivs(3,maxgeo)
c
c
c     zero the chirality restraint error function
c
      chirer = 0.0d0
      scale = 0.1d0
c
c     find signed volume value and compute chirality error
c
      do i = 1, nchir
         ia = ichir(1,i)
         ib = ichir(2,i)
         ic = ichir(3,i)
         id = ichir(4,i)
         xad = x(ia) - x(id)
         yad = y(ia) - y(id)
         zad = z(ia) - z(id)
         xbd = x(ib) - x(id)
         ybd = y(ib) - y(id)
         zbd = z(ib) - z(id)
         xcd = x(ic) - x(id)
         ycd = y(ic) - y(id)
         zcd = z(ic) - z(id)
         c1 = ybd*zcd - zbd*ycd
         c2 = ycd*zad - zcd*yad
         c3 = yad*zbd - zad*ybd
         vol = xad*c1 + xbd*c2 + xcd*c3
         dv = vol - vchir(i)
         error = scale * dv**2
         dedv = 2.0d0 * scale * dv
c
c     chain rule terms for first derivative components
c
         dedxia = dedv * (ybd*zcd - zbd*ycd)
         dedyia = dedv * (zbd*xcd - xbd*zcd)
         dedzia = dedv * (xbd*ycd - ybd*xcd)
         dedxib = dedv * (zad*ycd - yad*zcd)
         dedyib = dedv * (xad*zcd - zad*xcd)
         dedzib = dedv * (yad*xcd - xad*ycd)
         dedxic = dedv * (yad*zbd - zad*ybd)
         dedyic = dedv * (zad*xbd - xad*zbd)
         dedzic = dedv * (xad*ybd - yad*xbd)
         dedxid = -dedxia - dedxib - dedxic
         dedyid = -dedyia - dedyib - dedyic
         dedzid = -dedzia - dedzib - dedzic
c
c     increment the chirality restraint error and derivatives
c
         chirer = chirer + error
         derivs(1,ia) = derivs(1,ia) + dedxia
         derivs(2,ia) = derivs(2,ia) + dedyia
         derivs(3,ia) = derivs(3,ia) + dedzia
         derivs(1,ib) = derivs(1,ib) + dedxib
         derivs(2,ib) = derivs(2,ib) + dedyib
         derivs(3,ib) = derivs(3,ib) + dedzib
         derivs(1,ic) = derivs(1,ic) + dedxic
         derivs(2,ic) = derivs(2,ic) + dedyic
         derivs(3,ic) = derivs(3,ic) + dedzic
         derivs(1,id) = derivs(1,id) + dedxid
         derivs(2,id) = derivs(2,id) + dedyid
         derivs(3,id) = derivs(3,id) + dedzid
      end do
      return
      end
c
c
c     ##############################################################
c     ##                                                          ##
c     ##  function torser  --  computes torsional error function  ##
c     ##                                                          ##
c     ##############################################################
c
c
c     "torser" computes the torsional error function and its first
c     derivatives with respect to the atomic Cartesian coordinates
c     based on the deviation of specified torsional angles from
c     desired values, the contained bond angles are also restrained
c     to avoid a numerical instability
c
c
      function torser (derivs)
      implicit none
      include 'sizes.i'
      include 'atoms.i'
      include 'couple.i'
      include 'disgeo.i'
      include 'math.i'
      include 'refer.i'
      include 'restrn.i'
      integer i,j,k,ia,ib,ic,id
      real*8 torser,derivs(3,maxgeo)
      real*8 error,dt,deddt,dedphi
      real*8 angle,target,scale
      real*8 xia,yia,zia,xib,yib,zib
      real*8 xic,yic,zic,xid,yid,zid
      real*8 xria,yria,zria,xrib,yrib,zrib
      real*8 xric,yric,zric,xrid,yrid,zrid
      real*8 rba,rcb,rdc,dot,cosine,sine
      real*8 rrba,rrcb,rrdc,rrca,rrdb
      real*8 bndfac,angfac
      real*8 xp,yp,zp,rp
      real*8 terma,termb,termc,termd
      real*8 angmax,angmin,cosmax,cosmin
      real*8 bamax,bamin,cbmax,cbmin,dcmax,dcmin
      real*8 camax,camin,dbmax,dbmin
      real*8 xba,yba,zba,xcb,ycb,zcb,xdc,ydc,zdc
      real*8 xca,yca,zca,xdb,ydb,zdb
      real*8 xt,yt,zt,rt2,xu,yu,zu,ru2
      real*8 xtu,ytu,ztu,rtru
      real*8 tf1,tf2,tf3,t1,t2
      real*8 dedxt,dedyt,dedzt
      real*8 dedxu,dedyu,dedzu
      real*8 dedxia,dedyia,dedzia
      real*8 dedxib,dedyib,dedzib
      real*8 dedxic,dedyic,dedzic
      real*8 dedxid,dedyid,dedzid
      logical bonded
c
c
c     zero the torsional restraint error function
c
      torser = 0.0d0
      scale = 0.01d0
c
c     compute error value and derivs for torsional restraints
c
      do i = 1, ntfix
         ia = itfix(1,i)
         ib = itfix(2,i)
         ic = itfix(3,i)
         id = itfix(4,i)
         xia = x(ia)
         yia = y(ia)
         zia = z(ia)
         xib = x(ib)
         yib = y(ib)
         zib = z(ib)
         xic = x(ic)
         yic = y(ic)
         zic = z(ic)
         xid = x(id)
         yid = y(id)
         zid = z(id)
         xba = xib - xia
         yba = yib - yia
         zba = zib - zia
         xcb = xic - xib
         ycb = yic - yib
         zcb = zic - zib
         xdc = xid - xic
         ydc = yid - yic
         zdc = zid - zic
c
c     find the actual distances between the four atoms
c
         rba = sqrt(xba*xba + yba*yba + zba*zba)
         rcb = sqrt(xcb*xcb + ycb*ycb + zcb*zcb)
         rdc = sqrt(xdc*xdc + ydc*ydc + zdc*zdc)
c
c     see if the torsion involves four directly bonded atoms
c
         k = 0
         do j = 1, n12(ia)
            if (i12(j,ia) .eq. ib)  k = k + 1
         end do
         do j = 1, n12(ib)
            if (i12(j,ib) .eq. ic)  k = k + 1
         end do
         do j = 1, n12(ic)
            if (i12(j,ic) .eq. id)  k = k + 1
         end do
         if (k .eq. 3) then
            bonded = .true.
         else
            bonded = .false.
         end if
c
c     get maximum and minimum distances from distance matrix
c
         if (bonded) then
            bamax = sqrt(bnd(min(ib,ia),max(ib,ia)))
            bamin = sqrt(bnd(max(ib,ia),min(ib,ia)))
            cbmax = sqrt(bnd(min(ic,ib),max(ic,ib)))
            cbmin = sqrt(bnd(max(ic,ib),min(ic,ib)))
            dcmax = sqrt(bnd(min(id,ic),max(id,ic)))
            dcmin = sqrt(bnd(max(id,ic),min(id,ic)))
            camax = sqrt(bnd(min(ic,ia),max(ic,ia)))
            camin = sqrt(bnd(max(ic,ia),min(ic,ia)))
            dbmax = sqrt(bnd(min(id,ib),max(id,ib)))
            dbmin = sqrt(bnd(max(id,ib),min(id,ib)))
c
c     get maximum and minimum distances from input structure
c
         else
            xria = xref(ia)
            yria = yref(ia)
            zria = zref(ia)
            xrib = xref(ib)
            yrib = yref(ib)
            zrib = zref(ib)
            xric = xref(ic)
            yric = yref(ic)
            zric = zref(ic)
            xrid = xref(id)
            yrid = yref(id)
            zrid = zref(id)
            rrba = sqrt((xrib-xria)**2+(yrib-yria)**2+(zrib-zria)**2)
            rrcb = sqrt((xric-xrib)**2+(yric-yrib)**2+(zric-zrib)**2)
            rrdc = sqrt((xrid-xric)**2+(yrid-yric)**2+(zrid-zric)**2)
            rrca = sqrt((xric-xria)**2+(yric-yria)**2+(zric-zria)**2)
            rrdb = sqrt((xrid-xrib)**2+(yrid-yrib)**2+(zrid-zrib)**2)
            bndfac = 0.05d0
            angfac = 0.05d0
            bamax = (1.0d0 + bndfac) * rrba
            bamin = (1.0d0 - bndfac) * rrba
            cbmax = (1.0d0 + bndfac) * rrcb
            cbmin = (1.0d0 - bndfac) * rrcb
            dcmax = (1.0d0 + bndfac) * rrdc
            dcmin = (1.0d0 - bndfac) * rrdc
            camax = (1.0d0 + angfac) * rrca
            camin = (1.0d0 - angfac) * rrca
            dbmax = (1.0d0 + angfac) * rrdb
            dbmin = (1.0d0 - angfac) * rrdb
         end if
c
c     compute the ia-ib-ic bond angle and any error
c
         dot = xba*xcb + yba*ycb + zba*zcb
         cosine = -dot / (rba*rcb)
         cosine = min(1.0d0,max(-1.0d0,cosine))
         angle = radian * acos(cosine)
         cosmax = (bamin**2+cbmin**2-camax**2) / (2.0d0*bamin*cbmin)
         cosmax = min(1.0d0,max(-1.0d0,cosmax))
         angmax = radian * acos(cosmax)
         cosmin = (bamax**2+cbmax**2-camin**2) / (2.0d0*bamax*cbmax)
         cosmin = min(1.0d0,max(-1.0d0,cosmin))
         angmin = radian * acos(cosmin)
         if (angle .gt. angmax) then
            dt = angle - angmax
         else if (angle .lt. angmin) then
            dt = angle - angmin
         else
            dt = 0.0d0
         end if
         error = scale * dt**2
         deddt = 2.0d0 * radian * scale * dt
c
c     compute derivative components for this interaction
c
         xp = zcb*yba - ycb*zba
         yp = xcb*zba - zcb*xba
         zp = ycb*xba - xcb*yba
         rp = sqrt(xp*xp + yp*yp + zp*zp)
         if (rp .ne. 0.0d0) then
            terma = -deddt / (rba*rba*rp)
            termc = deddt / (rcb*rcb*rp)
            dedxia = terma * (zba*yp-yba*zp)
            dedyia = terma * (xba*zp-zba*xp)
            dedzia = terma * (yba*xp-xba*yp)
            dedxic = termc * (ycb*zp-zcb*yp)
            dedyic = termc * (zcb*xp-xcb*zp)
            dedzic = termc * (xcb*yp-ycb*xp)
            dedxib = -dedxia - dedxic
            dedyib = -dedyia - dedyic
            dedzib = -dedzia - dedzic
c
c     increment the bond angle restraint error and derivatives
c
            torser = torser + error
            derivs(1,ia) = derivs(1,ia) + dedxia
            derivs(2,ia) = derivs(2,ia) + dedyia
            derivs(3,ia) = derivs(3,ia) + dedzia
            derivs(1,ib) = derivs(1,ib) + dedxib
            derivs(2,ib) = derivs(2,ib) + dedyib
            derivs(3,ib) = derivs(3,ib) + dedzib
            derivs(1,ic) = derivs(1,ic) + dedxic
            derivs(2,ic) = derivs(2,ic) + dedyic
            derivs(3,ic) = derivs(3,ic) + dedzic
         end if
c
c     compute the ib-ic-id bond angle and any error
c
         dot = xdc*xcb + ydc*ycb + zdc*zcb
         cosine = -dot / (rdc*rcb)
         cosine = min(1.0d0,max(-1.0d0,cosine))
         angle = radian * acos(cosine)
         cosmax = (dcmin**2+cbmin**2-dbmax**2) / (2.0d0*dcmin*cbmin)
         cosmax = min(1.0d0,max(-1.0d0,cosmax))
         angmax = radian * acos(cosmax)
         cosmin = (dcmax**2+cbmax**2-dbmin**2) / (2.0d0*dcmax*cbmax)
         cosmax = min(1.0d0,max(-1.0d0,cosmin))
         angmin = radian * acos(cosmin)
         if (angle .gt. angmax) then
            dt = angle - angmax
         else if (angle .lt. angmin) then
            dt = angle - angmin
         else
            dt = 0.0d0
         end if
         error = scale * dt**2
         deddt = 2.0d0 * radian * scale * dt
c
c     compute derivative components for this interaction
c
         xp = zdc*ycb - ydc*zcb
         yp = xdc*zcb - zdc*xcb
         zp = ydc*xcb - xdc*ycb
         rp = sqrt(xp*xp + yp*yp + zp*zp)
         if (rp .ne. 0.0d0) then
            termb = -deddt / (rcb*rcb*rp)
            termd = deddt / (rdc*rdc*rp)
            dedxib = termb * (zcb*yp-ycb*zp)
            dedyib = termb * (xcb*zp-zcb*xp)
            dedzib = termb * (ycb*xp-xcb*yp)
            dedxid = termd * (ydc*zp-zdc*yp)
            dedyid = termd * (zdc*xp-xdc*zp)
            dedzid = termd * (xdc*yp-ydc*xp)
            dedxic = -dedxib - dedxid
            dedyic = -dedyib - dedyid
            dedzic = -dedzib - dedzid
c
c     increment the bond angle restraint error and derivatives
c
            torser = torser + error
            derivs(1,ib) = derivs(1,ib) + dedxib
            derivs(2,ib) = derivs(2,ib) + dedyib
            derivs(3,ib) = derivs(3,ib) + dedzib
            derivs(1,ic) = derivs(1,ic) + dedxic
            derivs(2,ic) = derivs(2,ic) + dedyic
            derivs(3,ic) = derivs(3,ic) + dedzic
            derivs(1,id) = derivs(1,id) + dedxid
            derivs(2,id) = derivs(2,id) + dedyid
            derivs(3,id) = derivs(3,id) + dedzid
         end if
c
c     compute the value of the ia-ib-ic-id torsional angle
c
         xt = yba*zcb - ycb*zba
         yt = zba*xcb - zcb*xba
         zt = xba*ycb - xcb*yba
         xu = ycb*zdc - ydc*zcb
         yu = zcb*xdc - zdc*xcb
         zu = xcb*ydc - xdc*ycb
         xtu = yt*zu - yu*zt
         ytu = zt*xu - zu*xt
         ztu = xt*yu - xu*yt
         rt2 = xt*xt + yt*yt + zt*zt
         ru2 = xu*xu + yu*yu + zu*zu
         rtru = sqrt(rt2 * ru2)
         if (rtru .ne. 0.0d0) then
            rcb = sqrt(xcb*xcb + ycb*ycb + zcb*zcb)
            cosine = (xt*xu + yt*yu + zt*zu) / rtru
            sine = (xcb*xtu + ycb*ytu + zcb*ztu) / (rcb*rtru)
            cosine = min(1.0d0,max(-1.0d0,cosine))
            angle = radian * acos(cosine)
            if (sine .lt. 0.0d0)  angle = -angle
c
c     calculate the torsional restraint error for this angle
c
            tf1 = tfix(1,i)
            tf2 = tfix(2,i)
            tf3 = tfix(3,i)
            if (angle.gt.tf1 .and. angle.lt.tf2) then
               target = angle
            else if (angle.gt.tf1 .and. tf1.gt.tf2) then
               target = angle
            else if (angle.lt.tf2 .and. tf1.gt.tf2) then
               target = angle
            else
               t1 = angle - tf1
               t2 = angle - tf2
               if (t1 .gt. 180.0d0) then
                  t1 = t1 - 360.0d0
               else if (t1 .lt. -180.0d0) then
                  t1 = t1 + 360.0d0
               end if
               if (t2 .gt. 180.0d0) then
                  t2 = t2 - 360.0d0
               else if (t2 .lt. -180.0d0) then
                  t2 = t2 + 360.0d0
               end if
               if (abs(t1) .lt. abs(t2)) then
                  target = tf1
               else
                  target = tf2
               end if
            end if
            dt = angle - target
            if (dt .gt. 180.0d0) then
               dt = dt - 360.0d0
            else if (dt .lt. -180.0d0) then
               dt = dt + 360.0d0
            end if
            error = scale * tf3 * dt**2
            dedphi = 2.0d0 * radian * scale * tf3 * dt
c
c     chain rule terms for first derivative components
c
            xca = xic - xia
            yca = yic - yia
            zca = zic - zia
            xdb = xid - xib
            ydb = yid - yib
            zdb = zid - zib
            dedxt = dedphi * (yt*zcb - ycb*zt) / (rt2*rcb)
            dedyt = dedphi * (zt*xcb - zcb*xt) / (rt2*rcb)
            dedzt = dedphi * (xt*ycb - xcb*yt) / (rt2*rcb)
            dedxu = -dedphi * (yu*zcb - ycb*zu) / (ru2*rcb)
            dedyu = -dedphi * (zu*xcb - zcb*xu) / (ru2*rcb)
            dedzu = -dedphi * (xu*ycb - xcb*yu) / (ru2*rcb)
c
c     compute first derivative components for torsion angle
c
            dedxia = zcb*dedyt - ycb*dedzt
            dedyia = xcb*dedzt - zcb*dedxt
            dedzia = ycb*dedxt - xcb*dedyt
            dedxib = yca*dedzt - zca*dedyt + zdc*dedyu - ydc*dedzu
            dedyib = zca*dedxt - xca*dedzt + xdc*dedzu - zdc*dedxu
            dedzib = xca*dedyt - yca*dedxt + ydc*dedxu - xdc*dedyu
            dedxic = zba*dedyt - yba*dedzt + ydb*dedzu - zdb*dedyu
            dedyic = xba*dedzt - zba*dedxt + zdb*dedxu - xdb*dedzu
            dedzic = yba*dedxt - xba*dedyt + xdb*dedyu - ydb*dedxu
            dedxid = zcb*dedyu - ycb*dedzu
            dedyid = xcb*dedzu - zcb*dedxu
            dedzid = ycb*dedxu - xcb*dedyu
c
c     increment the torsional restraint error and derivatives
c
            torser = torser + error
            derivs(1,ia) = derivs(1,ia) + dedxia
            derivs(2,ia) = derivs(2,ia) + dedyia
            derivs(3,ia) = derivs(3,ia) + dedzia
            derivs(1,ib) = derivs(1,ib) + dedxib
            derivs(2,ib) = derivs(2,ib) + dedyib
            derivs(3,ib) = derivs(3,ib) + dedzib
            derivs(1,ic) = derivs(1,ic) + dedxic
            derivs(2,ic) = derivs(2,ic) + dedyic
            derivs(3,ic) = derivs(3,ic) + dedzic
            derivs(1,id) = derivs(1,id) + dedxid
            derivs(2,id) = derivs(2,id) + dedyid
            derivs(3,id) = derivs(3,id) + dedzid
         end if
      end do
      return
      end
