| 1 | ! **************************************************************
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| 2 | !
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| 3 | ! This file contains the subroutines: enysol,tessel
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| 4 | !
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| 5 | ! Copyright 2003-2005 Frank Eisenmenger, U.H.E. Hansmann,
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| 6 | ! Shura Hayryan, Chin-Ku
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| 7 | ! Copyright 2007 Frank Eisenmenger, U.H.E. Hansmann,
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| 8 | ! Jan H. Meinke, Sandipan Mohanty
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| 9 | !
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| 10 | ! **************************************************************
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| 11 |
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| 12 |
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| 13 | real*8 function enysol(nmol)
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| 14 |
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| 15 | include 'INCL.H'
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| 16 | include 'mpif.h'
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| 17 |
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| 18 | ! --------------------------------------------------------------
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| 19 | !
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| 20 | ! Double Cubic Lattice algorithm for calculating the
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| 21 | ! solvation energy of proteins using
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| 22 | ! solvent accessible area method.
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| 23 | !
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| 24 | ! if nmol == 0 do solvation energy over all residues.
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| 25 | ! CALLS: nursat
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| 26 | !
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| 27 | ! -------------------------------------------------------------
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| 28 | ! TODO: Check the solvent energy for multiple molecules
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| 29 | double precision startwtime, avr_x, avr_y, avr_z, xmin, ymin, zmin
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| 30 | double precision xmax, ymax, zmax, rmax, diamax, sizex, sizey
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| 31 | double precision sizez, shiftx, shifty, shiftz, boxpp, trad, dx
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| 32 | double precision dy, dz, dd, akrad, dr, xyz, radb, radb2, sdd, sdr
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| 33 | double precision area, volume, eyslsum, endwtime
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| 34 |
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| 35 | integer nmol, nrslow, nrshi, nlow, nup, i, numat, inbox, j, ndx
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| 36 | integer ndy, ndz, nqxy, ncbox, mx, my, mz, nboxj, numbox, jj
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| 37 | integer indsort, iboxmin, iboxmax, ibox, iz, iy, ix, lbn, nsx, nsy
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| 38 | integer nsz, nex, ney, nez, jcnt, jz, jy, jx, jbox, ii, look, ia
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| 39 | integer jbi, nnei, ib, jtk, il, lst, ilk, ik, icount, jres, nursat
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| 40 | integer ierror, nhx, mhx, nbt, mbt
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| 41 |
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| 42 | dimension numbox(mxat),inbox(mxbox+1),indsort(mxat),look(mxat)
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| 43 | dimension xyz(mxinbox,3),radb(mxinbox),radb2(mxinbox)
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| 44 | logical surfc(mxpoint)
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| 45 | integer root
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| 46 |
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| 47 | ! common/ressurf/surfres(mxrs)
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| 48 | real*8 tsurfres(mxrs)
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| 49 | startwtime = MPI_Wtime()
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| 50 | root = 0
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| 51 | enysolct = enysolct + 1
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| 52 | eyslh = 0.0
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| 53 | eyslp = 0.0
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| 54 | if (nmol.eq.0) then
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| 55 | nrslow=irsml1(1)
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| 56 | nrshi=irsml2(ntlml)
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| 57 | else
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| 58 | nrslow = irsml1(nmol)
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| 59 | nrshi = irsml2(nmol)
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| 60 | endif
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| 61 | nlow = iatrs1(nrslow)
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| 62 | nup = iatrs2(nrshi)
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| 63 | do i=nrslow,nrshi
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| 64 | surfres(i) = 0.0d0
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| 65 | end do
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| 66 |
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| 67 | numat= nup - nlow + 1
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| 68 |
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| 69 | do i=1,mxbox+1
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| 70 | inbox(i)=0
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| 71 | end do
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| 72 |
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| 73 | asa=0.0d0
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| 74 | vdvol=0.0d0
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| 75 | eysl=0.0d0
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| 76 |
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| 77 | avr_x=xat(nlow)
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| 78 | avr_y=yat(nlow)
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| 79 | avr_z=zat(nlow)
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| 80 | xmin=xat(nlow)
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| 81 | ymin=yat(nlow)
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| 82 | zmin=zat(nlow)
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| 83 | xmax=xmin
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| 84 | ymax=ymin
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| 85 | zmax=zmin
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| 86 |
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| 87 | rmax=rvdw(nlow)
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| 88 |
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| 89 | do j=nlow+1,nup
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| 90 | if(xat(j).le.xmin) then
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| 91 | xmin=xat(j)
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| 92 | else if(xat(j).ge.xmax) then
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| 93 | xmax=xat(j)
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| 94 | end if
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| 95 | avr_x=avr_x+xat(j)
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| 96 | if(yat(j).le.ymin) then
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| 97 | ymin=yat(j)
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| 98 | else if(yat(j).ge.ymax) then
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| 99 | ymax=yat(j)
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| 100 | end if
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| 101 | avr_y=avr_y+yat(j)
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| 102 | if(zat(j).le.zmin) then
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| 103 | zmin=zat(j)
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| 104 | else if(zat(j).ge.zmax) then
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| 105 | zmax=zat(j)
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| 106 | end if
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| 107 | avr_z=avr_z+zat(j)
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| 108 | if(rvdw(j).ge.rmax) rmax=rvdw(j)
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| 109 | end do
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| 110 |
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| 111 | avr_x=avr_x/dble(numat)
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| 112 | avr_y=avr_y/dble(numat)
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| 113 | avr_z=avr_z/dble(numat)
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| 114 | diamax=2.d0*rmax
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| 115 |
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| 116 | ! The sizes of the big box
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| 117 |
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| 118 | sizex=xmax-xmin
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| 119 | sizey=ymax-ymin
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| 120 | sizez=zmax-zmin
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| 121 |
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| 122 | ! How many maximal diameters in each size ?
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| 123 |
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| 124 | ndx=sizex/diamax + 1
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| 125 | ndy=sizey/diamax + 1
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| 126 | ndz=sizez/diamax + 1
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| 127 |
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| 128 | ! We may need the number of quadratic boxes in (X,Y) plane
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| 129 |
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| 130 | nqxy=ndx*ndy
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| 131 |
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| 132 | ! The number of cubic boxes of the size "diamax"
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| 133 |
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| 134 | ncbox=nqxy*ndz
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| 135 | if(ncbox.ge.mxbox) then
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| 136 | print *,'enysol> bad ncbox',ncbox
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| 137 | stop
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| 138 | end if
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| 139 |
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| 140 | ! Let us shift the borders to home all boxes
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| 141 |
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| 142 | shiftx=(dble(ndx)*diamax-sizex)/2.d0
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| 143 | shifty=(dble(ndy)*diamax-sizey)/2.d0
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| 144 | shiftz=(dble(ndz)*diamax-sizez)/2.d0
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| 145 | xmin=xmin-shiftx
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| 146 | ymin=ymin-shifty
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| 147 | zmin=zmin-shiftz
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| 148 | xmax=xmax+shiftx
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| 149 | ymax=ymax+shifty
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| 150 | zmax=zmax+shiftz
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| 151 |
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| 152 | ! Finding the box of each atom
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| 153 |
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| 154 | do j=nlow,nup
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| 155 | mx=min(int(max((xat(j)-xmin)/diamax,0.0d0)),ndx-1)
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| 156 | my=min(int(max((yat(j)-ymin)/diamax,0.0d0)),ndy-1)
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| 157 | mz=min(int(max((zat(j)-zmin)/diamax,0.0d0)),ndz-1)
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| 158 | nboxj=mx+my*ndx+mz*nqxy+1
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| 159 | numbox(j)=nboxj
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| 160 | if (nboxj.gt.mxbox) then
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| 161 | write (logString, '(a)') 'enysol> bad mxboxe-2'
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| 162 | write (logString, *) 'diagnostics ...'
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| 163 | write (logString, *) 'atom ',j
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| 164 | write (logString, *) 'position ',xat(j),yat(j),zat(j)
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| 165 | write (logString, *) 'box indices ',mx,my,mz
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| 166 | write (logString, *) 'resulting boxindex and limit ',nboxj,
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| 167 | & mxbox
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| 168 |
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| 169 | stop
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| 170 | else
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| 171 | inbox(nboxj)=inbox(nboxj)+1
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| 172 | end if
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| 173 | end do
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| 174 |
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| 175 | ! Summation over the boxes
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| 176 |
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| 177 | do i=1,ncbox
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| 178 | inbox(i+1)=inbox(i+1)+inbox(i)
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| 179 | end do
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| 180 |
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| 181 |
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| 182 | ! Sorting the atoms by the their box numbers
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| 183 |
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| 184 | do i=nlow,nup
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| 185 | j=numbox(i)
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| 186 | jj=inbox(j)
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| 187 | indsort(jj)=i
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| 188 | inbox(j)=jj-1
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| 189 | end do
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| 190 |
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| 191 | ! Getting started
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| 192 | ! We have to loop over ncbox boxes and have no processors available
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| 193 | boxpp = 1.0 * ncbox / no
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| 194 | iboxmin = boxpp * myrank
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| 195 | iboxmax = boxpp * (myrank + 1) - 1
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| 196 | if (myrank.eq.(no - 1)) iboxmax = ncbox
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| 197 | if (myrank.eq.-1) then
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| 198 | write (logString, *) 'enysol> Summary:', enysolct, ncbox,
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| 199 | & boxpp, ndx, ndy, ndz
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| 200 | endif
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| 201 | do ibox = iboxmin + 1, iboxmax + 1
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| 202 | iz = (ibox - 1) / nqxy
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| 203 | iy = (ibox - 1 - iz * nqxy) / ndx
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| 204 | ix = ibox - 1 - iy*ndx - iz*nqxy
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| 205 | ! ibox=ix+iy*ndx+iz*nqxy + 1
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| 206 |
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| 207 | ! Does this box contain atoms ?
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| 208 |
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| 209 | lbn=inbox(ibox+1)-inbox(ibox)
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| 210 |
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| 211 | if(lbn.gt.0) then ! There are some atoms
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| 212 | nsx=max(ix-1,0)
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| 213 | nsy=max(iy-1,0)
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| 214 | nsz=max(iz-1,0)
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| 215 | nex=min(ix+1,ndx-1)
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| 216 | ney=min(iy+1,ndy-1)
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| 217 | nez=min(iz+1,ndz-1)
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| 218 |
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| 219 | ! Atoms in the boxes around
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| 220 |
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| 221 | jcnt=1
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| 222 | do jz=nsz,nez
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| 223 | do jy=nsy,ney
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| 224 | do jx=nsx,nex
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| 225 | jbox=jx+jy*ndx+jz*nqxy+1
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| 226 | do ii=inbox(jbox)+1,inbox(jbox+1)
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| 227 | if(rvdw(indsort(ii)).gt.0.0d0) then
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| 228 | look(jcnt)=indsort(ii)
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| 229 | jcnt=jcnt+1
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| 230 | end if
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| 231 | end do
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| 232 | end do
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| 233 | end do
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| 234 | end do
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| 235 |
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| 236 | do ia=inbox(ibox)+1,inbox(ibox+1)
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| 237 | jbi=indsort(ia)
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| 238 | trad=rvdw(jbi)
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| 239 | if(trad.gt.0.0) then
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| 240 | nnei=0
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| 241 | do ib=1,jcnt-1
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| 242 | jtk=look(ib)
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| 243 | if(jtk.ne.jbi)then
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| 244 | dx=(xat(jbi)-xat(jtk))/trad
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| 245 | dy=(yat(jbi)-yat(jtk))/trad
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| 246 | dz=(zat(jbi)-zat(jtk))/trad
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| 247 | dd=dx*dx+dy*dy+dz*dz
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| 248 | akrad=rvdw(jtk)/trad
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| 249 | dr=1.0d0+akrad
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| 250 | dr=dr*dr
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| 251 | !c if contact
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| 252 | if(dd.le.dr) then
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| 253 | nnei=nnei+1
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| 254 | xyz(nnei,1)=dx
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| 255 | xyz(nnei,2)=dy
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| 256 | xyz(nnei,3)=dz
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| 257 | radb(nnei)=akrad
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| 258 | radb2(nnei)=akrad*akrad
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| 259 | end if
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| 260 | end if
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| 261 | end do
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| 262 | !c
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| 263 | do il=1,npnt
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| 264 | surfc(il)=.false.
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| 265 | end do
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| 266 |
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| 267 | ! Check overlap
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| 268 |
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| 269 | lst=1
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| 270 | do il=1,npnt
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| 271 | sdd = 0.0d0
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| 272 | do ilk=1,3
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| 273 | sdd = sdd +(xyz(lst,ilk)+spoint(il,ilk))**2
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| 274 | end do
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| 275 | if(sdd.gt.radb2(lst)) then
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| 276 | do ik=1,nnei
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| 277 | sdd =0.0d0
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| 278 | do ilk=1,3
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| 279 | sdd = sdd +(xyz(ik,ilk)+spoint(il,ilk))**2
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| 280 | end do
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| 281 | if(sdd.le.radb2(ik)) then
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| 282 | lst=ik
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| 283 | go to 99
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| 284 | end if
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| 285 | end do
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| 286 | 99 continue
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| 287 |
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| 288 | if(ik.gt.nnei)then
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| 289 | surfc(il)=.true.
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| 290 | end if
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| 291 | end if
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| 292 | end do
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| 293 |
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| 294 | icount=0
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| 295 | dx=0.0d0
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| 296 | dy=0.0d0
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| 297 | dz=0.0d0
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| 298 | do il=1,npnt
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| 299 | if(surfc(il)) then
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| 300 | icount=icount+1
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| 301 | dx=dx+spoint(il,1)
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| 302 | dy=dy+spoint(il,2)
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| 303 | dz=dz+spoint(il,3)
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| 304 | end if
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| 305 | end do
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| 306 | sdr=4.d0*pi*trad*trad/dble(npnt)
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| 307 | area = sdr*dble(icount)
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| 308 | volume = sdr/3.0d0*(trad*dble(icount)
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| 309 | & +(xat(jbi)-avr_x)*dx
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| 310 | & +(yat(jbi)-avr_y)*dy
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| 311 | & +(zat(jbi)-avr_z)*dz)
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| 312 |
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| 313 | asa=asa+area
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| 314 | vdvol=vdvol+volume
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| 315 | eysl=eysl+area*sigma(jbi)
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| 316 | ! Separate hydrophilic (h) and hyrdophobic (p) contributions to eysl
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| 317 | if (sigma(jbi).lt.0) then
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| 318 | eyslp = eyslp + area * sigma(jbi)
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| 319 | asap = asap + area
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| 320 | endif
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| 321 | if (sigma(jbi).gt.0) then
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| 322 | eyslh = eyslh + area * sigma(jbi)
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| 323 | asah = asah + area
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| 324 | endif
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| 325 | ! Measure how much a residue is solvent accessible:
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| 326 | jres = nursat(jbi)
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| 327 | surfres(jres) = surfres(jres) + area
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| 328 | end if
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| 329 | end do
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| 330 | end if
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| 331 | ! end do
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| 332 | ! end do
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| 333 | end do
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| 334 | call MPI_ALLREDUCE(eysl, eyslsum, 1, MPI_DOUBLE_PRECISION,
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| 335 | & MPI_SUM,my_mpi_comm, ierror)
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| 336 | write (logString, *) 'enysol>', myrank, eysl, eyslsum
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| 337 | tsurfres = surfres
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| 338 | call MPI_ALLREDUCE(tsurfres, surfres, mxrs, MPI_DOUBLE_PRECISION,
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| 339 | & MPI_SUM,my_mpi_comm, ierror)
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| 340 | eysl = eyslsum
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| 341 |
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| 342 | endwtime = MPI_Wtime()
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| 343 | if (myrank.le.-1) then
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| 344 | write (logString, *) 'enysol>',myrank,enysolct,
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| 345 | & iboxmin + 1, iboxmax + 1,
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| 346 | & endwtime - startwtime, "s"
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| 347 | endif
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| 348 | !
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| 349 | if (isolscl) then
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| 350 | nhx=0
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| 351 | mhx=0
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| 352 | nbt=0
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| 353 | mbt=0
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| 354 | call helix(nhx,mhx,nbt,mbt)
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| 355 | eysl=((nhx+nbt)*eysl)/(irsml2(ntlml)-irsml1(1))
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| 356 | endif
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| 357 |
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| 358 | enysol = eysl
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| 359 |
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| 360 | return
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| 361 | end
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| 362 | ! *********************
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| 363 | subroutine tessel
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| 364 | include 'INCL.H'
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| 365 | integer i
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| 366 |
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| 367 | character lin*80
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| 368 |
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| 369 | ! Skipping comment lines, which begin with '!'
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| 370 |
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| 371 | read(20,'(a)') lin
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| 372 | do while(lin(1:1).eq.'!')
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| 373 | read (20,'(a)') lin
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| 374 | end do
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| 375 |
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| 376 | ! The first non-comment line is the number of the surface points
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| 377 |
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| 378 | read(lin(1:5),'(i5)') npnt
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| 379 | ! write (logString, '(a,i5)') 'the number of points---->',npnt
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| 380 |
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| 381 | ! Read the surface points
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| 382 |
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| 383 | do i=1,npnt
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| 384 | read(20,'(3f20.10)') spoint(i,1),spoint(i,2),spoint(i,3)
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| 385 |
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| 386 | ! write(31,'(3f20.10)') spoint(i,1),spoint(i,2),spoint(i,3)
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| 387 | end do
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| 388 |
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| 389 | return
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| 390 |
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| 391 | end
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| 392 |
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