[bd2278d] | 1 | ! **************************************************************
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| 2 | !
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| 3 | ! This file contains the subroutines: rmsdfun,rmsdopt,fitmol,
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| 4 | ! jacobi,rmsinit
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| 5 | !
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| 6 | ! Copyright 2003-2005 Frank Eisenmenger, U.H.E. Hansmann,
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[32289cd] | 7 | ! Shura Hayryan, Chin-Ku
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[bd2278d] | 8 | ! Copyright 2007 Frank Eisenmenger, U.H.E. Hansmann,
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| 9 | ! Jan H. Meinke, Sandipan Mohanty
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| 10 | !
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| 11 | ! **************************************************************
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[e40e335] | 12 |
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| 13 | real*8 function rmsdfun(nml,ir1,ir2,ixat,xrf,yrf,zrf,isl)
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[bd2278d] | 14 | !
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| 15 | ! --------------------------------------------------------------
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| 16 | ! Wrapping function for calculating rmsd
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| 17 | !
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| 18 | ! LIMITATION: requires call of rmsinit BEFORE calling this function
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| 19 | !
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| 20 | ! CALLS: rmsdopt
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| 21 | !
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| 22 | ! ---------------------------------------------------------------
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| 23 | !
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[e40e335] | 24 | include 'INCL.H'
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| 25 | include 'INCP.H'
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[bd2278d] | 26 | !
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| 27 | ! Input
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[32289cd] | 28 | double precision xrf, yrf, zrf, rm, av1, av2, rssd
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| 29 |
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| 30 | integer nml, ir1, ir2, ixat, isl
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| 31 |
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[e40e335] | 32 | dimension ixat(mxat),xrf(mxatp),yrf(mxatp),zrf(mxatp)
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[bd2278d] | 33 | ! Local
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[e40e335] | 34 | dimension rm(3,3),av1(3),av2(3)
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| 35 | call rmsdopt(nml,ir1,ir2,ixat,xrf,yrf,zrf,isl,rm,av1,av2,rssd)
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| 36 |
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| 37 | rmsdfun = rssd
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| 38 |
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| 39 | return
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| 40 |
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| 41 | end
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| 42 |
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[bd2278d] | 43 | !*******************************************************************
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[e40e335] | 44 | subroutine rmsdopt(nml,ir1,ir2,ixat,xrf,yrf,zrf,isl,
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[bd2278d] | 45 | & rm,av1,av2,rmsd)
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| 46 |
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| 47 | ! ---------------------------------------------------------------
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| 48 | ! PURPOSE: root mean square deviation (rmsd) between current SMMP
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| 49 | ! structure and reference atom coordinates 'x,y,zrf()'
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| 50 | ! for range of SMMP residues [ir1,ir2] in molecule 'nml'
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| 51 | !
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| 52 | ! ixat(i) - points to the atom in ref. coords., which is
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| 53 | ! equivalent to atom i of SMMP structure
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| 54 | ! (=0 if no equivalent in ref. structure exists)
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| 55 | !
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| 56 | ! isl = 0 : select all heavy atoms
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| 57 | ! isl = 1 : backbone atoms n,ca,c
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| 58 | ! isl = 2 : only ca atoms
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| 59 | !
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| 60 | ! CALLS: fitmol [S.K.Kearsley, Acta Cryst. 1989, A45, 208-210]
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| 61 | !
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| 62 | ! NB uncomment last lines in 'fitmol' to return coordinates
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[32289cd] | 63 | ! in 'x2' after fitting the ref. str. onto SMMP structure
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[bd2278d] | 64 | ! ----------------------------------------------------------------
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[e40e335] | 65 |
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| 66 | include 'INCL.H'
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| 67 | include 'INCP.H'
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[32289cd] | 68 |
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| 69 | double precision x1, x2, xrf, yrf, zrf, rm, av1, av2, rmsd
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| 70 |
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| 71 | integer nml, nr, na, n, im, ir, ia, ir1, ir2, ix, ixat, isl
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| 72 |
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[e40e335] | 73 |
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[bd2278d] | 74 | !-------------------------------------------------------- input
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[e40e335] | 75 | dimension ixat(mxat),xrf(mxatp),yrf(mxatp),zrf(mxatp)
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[bd2278d] | 76 | !-------------------------------------------------------- output
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[e40e335] | 77 | dimension rm(3,3),av1(3),av2(3)
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[bd2278d] | 78 | !-------------------------------------------------------- local
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[e40e335] | 79 | dimension x1(3,mxat),x2(3,mxat)
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| 80 | character*4 atnm
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| 81 |
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| 82 |
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| 83 | if (nml.lt.1.or.nml.gt.ntlml) then
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[38d77eb] | 84 | write (logString, *) ' rmsdopt> Sorry, there is no molecule #',
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| 85 | & nml
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[e40e335] | 86 | stop
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| 87 | endif
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| 88 |
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| 89 |
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| 90 | nr=0
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| 91 | na=0
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| 92 | n=0
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| 93 |
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| 94 | do im=1,ntlml
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| 95 | do ir=irsml1(im),irsml2(im)
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| 96 | if (im.eq.nml) nr=nr+1
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| 97 |
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| 98 | do ia=iatrs1(ir),iatrs2(ir)
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| 99 |
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| 100 | na=na+1
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| 101 |
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| 102 | if (im.eq.nml.and.nr.ge.ir1.and.nr.le.ir2) then ! range of res. for 'nml'
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| 103 |
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| 104 | ix=ixat(na)
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| 105 | atnm=nmat(ia)
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| 106 |
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| 107 | if (ix.gt.0.and.atnm(1:1).ne.'h') then
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| 108 |
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| 109 | if ( isl.eq.0
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| 110 |
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[bd2278d] | 111 | & .or.
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[e40e335] | 112 |
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[bd2278d] | 113 | & (isl.eq.1.and.(index(atnm,'n ').gt.0 .or.
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| 114 | & index(atnm,'ca ').gt.0 .or.
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| 115 | & index(atnm,'c ').gt.0 ))
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| 116 | & .or.
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[e40e335] | 117 |
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[bd2278d] | 118 | & (isl.eq.2.and.index(atnm,'ca ').gt.0)
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[e40e335] | 119 |
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[bd2278d] | 120 | & ) then
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[e40e335] | 121 |
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| 122 | n=n+1
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| 123 | x1(1,n)=xat(ia)
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| 124 | x1(2,n)=yat(ia)
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| 125 | x1(3,n)=zat(ia)
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| 126 | x2(1,n)=xrf(ix)
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| 127 | x2(2,n)=yrf(ix)
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| 128 | x2(3,n)=zrf(ix)
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| 129 |
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| 130 | endif ! atom selection
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| 131 | endif ! ix>0 & not 'h'
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| 132 |
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| 133 | endif ! res. range in mol. 'nml'
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| 134 |
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| 135 | enddo ! atoms
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| 136 | enddo ! residues
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| 137 | enddo ! molecules
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| 138 |
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| 139 | if (n.lt.3) then
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[38d77eb] | 140 | write (logString, *) ' rmsdopt> <3 atoms selected !'
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[e40e335] | 141 | stop
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| 142 | endif
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| 143 |
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| 144 | call fitmol(n,x1,x2, rm,av1,av2,rmsd)
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| 145 |
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| 146 | return
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| 147 | end
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[bd2278d] | 148 | ! *********************************************
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[e40e335] | 149 | subroutine fitmol(n,x1,x2, rm,a1,a2,rmsd)
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[bd2278d] | 150 | ! real*8 function fitmol(n,x1,x2)
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| 151 |
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| 152 | ! .......................................................
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| 153 | ! PURPOSE: compute RMSD of n positions in x1(3,) & x2(3,)
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| 154 | ! [S.K.Kearsley Acta Cryst. 1989,A45,208-210]
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| 155 | !
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| 156 | ! CALLS: jacobi
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| 157 | ! .......................................................
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| 158 | !f2py intent(out) rmsd
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[32289cd] | 159 |
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[e40e335] | 160 | include 'INCL.H'
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[bd2278d] | 161 | ! implicit real*8 (a-h,o-z)
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| 162 | ! implicit integer*4 (i-n)
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[32289cd] | 163 |
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[bd2278d] | 164 | ! ------------------------------------------- input/output
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[32289cd] | 165 | double precision dn, a1, a2, x1, x2, q, dm, dp, dxm, dym, dzm, dxp
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| 166 | double precision dyp, dzp, e, v, em, rmsd, rm
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| 167 |
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| 168 | integer n, i, j, ndim4, im
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| 169 |
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[e40e335] | 170 | dimension x1(3,mxat),x2(3,mxat)
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[bd2278d] | 171 | ! -------------------------------------------------- local
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[e40e335] | 172 | dimension e(4),q(4,4),v(4,4),dm(3),dp(3),a1(3),a2(3),rm(3,3)
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| 173 |
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| 174 | dn=dble(n)
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[bd2278d] | 175 | ! ------------------- average of coordinates
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[e40e335] | 176 | do i=1,3
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| 177 | a1(i) = 0.d0
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| 178 | a2(i) = 0.d0
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| 179 | do j=1,n
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| 180 | a1(i) = a1(i) + x1(i,j)
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| 181 | a2(i) = a2(i) + x2(i,j)
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| 182 | enddo
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| 183 | a1(i) = a1(i)/dn
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| 184 | a2(i) = a2(i)/dn
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| 185 | enddo
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[bd2278d] | 186 | ! ------------------------- compile quaternion
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[e40e335] | 187 | do i=1,4
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| 188 | do j=1,4
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| 189 | q(i,j)=0.d0
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| 190 | enddo
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| 191 | enddo
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| 192 |
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| 193 | do i=1,n
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| 194 |
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| 195 | do j=1,3
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| 196 | dm(j) = x1(j,i)-a1(j)
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| 197 | dp(j) = x2(j,i)-a2(j)
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| 198 | enddo
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| 199 |
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| 200 | dxm = dp(1) - dm(1)
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| 201 | dym = dp(2) - dm(2)
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| 202 | dzm = dp(3) - dm(3)
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| 203 | dxp = dp(1) + dm(1)
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| 204 | dyp = dp(2) + dm(2)
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| 205 | dzp = dp(3) + dm(3)
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| 206 |
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| 207 | q(1,1) = q(1,1) + dxm * dxm + dym * dym + dzm * dzm
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| 208 | q(1,2) = q(1,2) + dyp * dzm - dym * dzp
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| 209 | q(1,3) = q(1,3) + dxm * dzp - dxp * dzm
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| 210 | q(1,4) = q(1,4) + dxp * dym - dxm * dyp
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| 211 | q(2,2) = q(2,2) + dyp * dyp + dzp * dzp + dxm * dxm
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| 212 | q(2,3) = q(2,3) + dxm * dym - dxp * dyp
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| 213 | q(2,4) = q(2,4) + dxm * dzm - dxp * dzp
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| 214 | q(3,3) = q(3,3) + dxp * dxp + dzp * dzp + dym * dym
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| 215 | q(3,4) = q(3,4) + dym * dzm - dyp * dzp
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| 216 | q(4,4) = q(4,4) + dxp * dxp + dyp * dyp + dzm * dzm
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| 217 |
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| 218 | enddo
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| 219 |
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| 220 | do i=1,3
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| 221 | do j=i+1,4
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| 222 | q(j,i)=q(i,j)
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| 223 | enddo
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| 224 | enddo
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[bd2278d] | 225 | ! ------------------------------ eigenvalues & -vectors
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[e40e335] | 226 | ndim4=4
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| 227 | call jacobi(q,ndim4,e,v)
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[bd2278d] | 228 | ! --------------------------- lowest eigenvalue
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[e40e335] | 229 | im=1
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| 230 | em=e(1)
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| 231 | do i=2,4
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| 232 | if (e(i).lt.em) then
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| 233 | em=e(i)
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| 234 | im=i
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| 235 | endif
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| 236 | enddo
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| 237 |
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| 238 | rmsd = sqrt(em/dn)
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| 239 |
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[bd2278d] | 240 | ! ================= uncomment following lines to fit molecule 2 onto 1
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[e40e335] | 241 |
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[bd2278d] | 242 | ! ---------------------------------------------------rotation matrix
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[e40e335] | 243 | rm(1,1) = v(1,im)**2+v(2,im)**2-v(3,im)**2-v(4,im)**2
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| 244 | rm(1,2) = 2.d0*( v(2,im)*v(3,im)-v(1,im)*v(4,im) )
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| 245 | rm(1,3) = 2.d0*( v(2,im)*v(4,im)+v(1,im)*v(3,im) )
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| 246 | rm(2,1) = 2.d0*( v(2,im)*v(3,im)+v(1,im)*v(4,im) )
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| 247 | rm(2,2) = v(1,im)**2+v(3,im)**2-v(2,im)**2-v(4,im)**2
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| 248 | rm(2,3) = 2.d0*( v(3,im)*v(4,im)-v(1,im)*v(2,im) )
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| 249 | rm(3,1) = 2.d0*( v(2,im)*v(4,im)-v(1,im)*v(3,im) )
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| 250 | rm(3,2) = 2.d0*( v(3,im)*v(4,im)+v(1,im)*v(2,im) )
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| 251 | rm(3,3) = v(1,im)**2+v(4,im)**2-v(2,im)**2-v(3,im)**2
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| 252 |
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[bd2278d] | 253 | ! do i=1,n
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| 254 | ! do j=1,3
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| 255 | ! dm(j) = x2(j,i) - a2(j)
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| 256 | ! enddo
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| 257 | ! do j=1,3
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| 258 | ! dp(j) = a1(j)
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| 259 | ! do k=1,3
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| 260 | ! dp(j) = dp(j) + rm(j,k) * dm(k)
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| 261 | ! enddo
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| 262 | ! x2(j,i) = dp(j)
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| 263 | ! enddo
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| 264 | ! enddo
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| 265 |
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| 266 | ! fitmol=rmsd
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[e40e335] | 267 |
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| 268 | return
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| 269 | end
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[bd2278d] | 270 | ! ******************************
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[e40e335] | 271 | subroutine jacobi(a,n,d,v)
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| 272 |
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[bd2278d] | 273 | ! ......................................................
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| 274 | ! PURPOSE: for given symmetric matrix 'a(n,n)
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| 275 | ! compute eigenvalues 'd' & eigenvectors 'v(,)'
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| 276 | !
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| 277 | ! [W.H.Press,S.A.Teukolsky,W.T.Vetterling,
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| 278 | ! B.P.Flannery, Numerical Recipes in FORTRAN,
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| 279 | ! Cambridge Univ. Press, 2nd Ed. 1992, 456-462]
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| 280 | !
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| 281 | ! CALLS: none
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| 282 | !
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| 283 | ! ......................................................
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| 284 |
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| 285 | !f2py intent(out) d
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| 286 | !f2py intent(out) v
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[32289cd] | 287 | integer nmax
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| 288 |
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[e40e335] | 289 | parameter (NMAX=500)
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[32289cd] | 290 |
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[e40e335] | 291 | integer n,nrot,i,ip,iq,j
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| 292 |
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[38d77eb] | 293 | character(255) logString
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[e40e335] | 294 | real*8 a(n,n),d(n),v(n,n),
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[bd2278d] | 295 | & c,g,h,s,sm,t,tau,theta,tresh,b(NMAX),z(NMAX),smeps
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[e40e335] | 296 |
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| 297 | smeps=1.0d-6
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| 298 |
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| 299 |
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| 300 | do ip=1,n
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| 301 | b(ip)=a(ip,ip)
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| 302 | d(ip)=b(ip)
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| 303 | z(ip)=0.d0
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| 304 | do iq=1,n
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| 305 | v(ip,iq)=0.d0
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| 306 | enddo
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| 307 | v(ip,ip)=1.d0
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| 308 | enddo
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| 309 |
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| 310 | nrot=0
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| 311 |
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| 312 | do i=1,500
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| 313 |
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| 314 | sm=0.d0
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| 315 |
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| 316 | do ip=1,n-1
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| 317 | do iq=ip+1,n
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| 318 | sm=sm+abs(a(ip,iq))
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| 319 | enddo
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| 320 | enddo
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| 321 |
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| 322 | if (sm.le.smeps) return ! normal end
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| 323 |
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| 324 | if (i.lt.4) then
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| 325 | tresh=0.2d0*sm/n**2
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| 326 | else
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| 327 | tresh=0.d0
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| 328 | endif
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| 329 |
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| 330 | do ip=1,n-1
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| 331 | do iq=ip+1,n
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| 332 |
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| 333 | g=100.d0*abs(a(ip,iq))
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| 334 |
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| 335 | if((i.gt.4).and.(abs(d(ip))+
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| 336 |
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[bd2278d] | 337 | &g.eq.abs(d(ip))).and.(abs(d(iq))+g.eq.abs(d(iq))))then
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[e40e335] | 338 | a(ip,iq)=0.d0
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| 339 |
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| 340 | else if(abs(a(ip,iq)).gt.tresh)then
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| 341 |
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| 342 | h=d(iq)-d(ip)
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| 343 |
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| 344 | if (abs(h)+g.eq.abs(h)) then
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| 345 |
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| 346 | t=a(ip,iq)/h
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| 347 |
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| 348 | else
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| 349 |
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| 350 | theta=0.5d0*h/a(ip,iq)
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| 351 | t=1.d0/(abs(theta)+sqrt(1.d0+theta**2))
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| 352 | if (theta.lt.0.d0) t=-t
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| 353 |
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| 354 | endif
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| 355 |
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| 356 | c=1.d0/sqrt(1.d0+t**2)
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| 357 | s=t*c
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| 358 | tau=s/(1.d0+c)
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| 359 | h=t*a(ip,iq)
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| 360 | z(ip)=z(ip)-h
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| 361 | z(iq)=z(iq)+h
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| 362 | d(ip)=d(ip)-h
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| 363 | d(iq)=d(iq)+h
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| 364 | a(ip,iq)=0.d0
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| 365 |
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| 366 | do j=1,ip-1
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| 367 | g=a(j,ip)
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| 368 | h=a(j,iq)
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| 369 | a(j,ip)=g-s*(h+g*tau)
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| 370 | a(j,iq)=h+s*(g-h*tau)
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| 371 | enddo
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| 372 |
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| 373 | do j=ip+1,iq-1
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| 374 | g=a(ip,j)
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| 375 | h=a(j,iq)
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| 376 | a(ip,j)=g-s*(h+g*tau)
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| 377 | a(j,iq)=h+s*(g-h*tau)
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| 378 | enddo
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| 379 | do j=iq+1,n
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| 380 | g=a(ip,j)
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| 381 | h=a(iq,j)
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| 382 | a(ip,j)=g-s*(h+g*tau)
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| 383 | a(iq,j)=h+s*(g-h*tau)
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| 384 | enddo
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| 385 | do j=1,n
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| 386 | g=v(j,ip)
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| 387 | h=v(j,iq)
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| 388 | v(j,ip)=g-s*(h+g*tau)
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| 389 | v(j,iq)=h+s*(g-h*tau)
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| 390 | enddo
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| 391 | nrot=nrot+1
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| 392 |
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| 393 | endif
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| 394 |
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| 395 | enddo
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| 396 | enddo
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| 397 |
|
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| 398 | do ip=1,n
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| 399 | b(ip)=b(ip)+z(ip)
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| 400 | d(ip)=b(ip)
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| 401 | z(ip)=0.d0
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| 402 | enddo
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| 403 |
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| 404 | enddo
|
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| 405 |
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[38d77eb] | 406 | write (logString, *) ' jacobi> too many iterations'
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[e40e335] | 407 | stop
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| 408 |
|
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| 409 | return
|
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| 410 | end
|
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| 411 |
|
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[bd2278d] | 412 | ! ***********************************************************
|
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[e40e335] | 413 |
|
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| 414 | subroutine rmsinit(nml,string)
|
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[bd2278d] | 415 | !
|
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| 416 | !------------------------------------------------------------------------------
|
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[32289cd] | 417 | ! Reads in pdb-file 'string' into INCP.H and initalizes
|
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[bd2278d] | 418 | ! the files that 'rmdsopt' needs to calculate the rmsd
|
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| 419 | ! of a configuration with the pdb-configuration
|
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| 420 | !
|
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| 421 | ! CALLS: pdbread,atixpdb
|
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| 422 | !
|
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| 423 | ! ----------------------------------------------------------------------------
|
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| 424 | !
|
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[e40e335] | 425 | include 'INCL.H'
|
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| 426 | include 'INCP.H'
|
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| 427 |
|
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[32289cd] | 428 | integer i, nml, ier
|
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| 429 |
|
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[e40e335] | 430 | character string*(*)
|
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[32289cd] | 431 |
|
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[e40e335] | 432 | if(string.eq.'smmp') then
|
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[bd2278d] | 433 | !
|
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| 434 | ! Compare with a smmp-structure
|
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| 435 | !
|
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[e40e335] | 436 | do i=iatrs1(irsml1(nml)),iatrs2(irsml2(nml))
|
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| 437 | if(nmat(i)(1:1).ne.'h') then
|
---|
| 438 | ixatp(i)=i
|
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| 439 | else
|
---|
| 440 | ixatp(i) = 0
|
---|
| 441 | end if
|
---|
| 442 | enddo
|
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[bd2278d] | 443 | !
|
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[e40e335] | 444 | else
|
---|
[bd2278d] | 445 | !
|
---|
| 446 | ! Reference structure is read in from pdb-file
|
---|
| 447 | !
|
---|
[e40e335] | 448 | call pdbread(string,ier)
|
---|
[32289cd] | 449 | if(ier.ne.0) stop
|
---|
[e40e335] | 450 | call atixpdb(nml)
|
---|
[bd2278d] | 451 | !
|
---|
[e40e335] | 452 | end if
|
---|
| 453 | print *,'RMSD initialized with ',string
|
---|
| 454 | return
|
---|
| 455 |
|
---|
| 456 | end
|
---|
| 457 |
|
---|