| 1 | ! **************************************************************
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| 2 | !
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| 3 | ! This file contains the subroutines: bldmol, fnd3ba,eyring,
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| 4 | ! setsys,setgbl
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| 5 | !
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| 6 | ! Copyright 2003-2005 Frank Eisenmenger, U.H.E. Hansmann,
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| 7 | ! Shura Hayryan, Chin-Ku
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| 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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| 12 |
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| 13 | subroutine bldmol(nml)
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| 14 |
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| 15 | ! .................................................
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| 16 | ! PURPOSE: calculate coordinates for molecule 'nml'
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| 17 | !
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| 18 | ! OUTPUT: xat,yat,zat,xbaat,ybaat,zbaat,xtoat,ytoat,
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| 19 | ! ztoat (via 'eyring')
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| 20 | !
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| 21 | ! 1st backbone atom of 1st residue of 'nml':
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| 22 | !
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| 23 | ! - it's position: from 'gbpr(1-3,nml)'
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| 24 | ! - it's axes: from 'setgbl' according to
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| 25 | ! global angles 'gbpr(4-5,nml)'
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| 26 | !
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| 27 | ! CALLS: eyring, fnd3ba,setgbl,setsys
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| 28 | ! .................................................
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| 29 |
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| 30 | include 'INCL.H'
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| 31 |
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| 32 | dimension xg(3),zg(3)
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| 33 |
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| 34 |
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| 35 | call fnd3ba(nml,i1,i2,i3)
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| 36 | ! ------------------------------ first 3 bb atoms of 'nml'
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| 37 | ixrfpt(1,nml)=i1
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| 38 | ixrfpt(2,nml)=i2
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| 39 | ixrfpt(3,nml)=i3
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| 40 |
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| 41 | ! ------------------------------ position of 1st bb atom
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| 42 | xat(i1) = gbpr(1,nml)
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| 43 | yat(i1) = gbpr(2,nml)
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| 44 | zat(i1) = gbpr(3,nml)
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| 45 |
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| 46 | rfpt(1,nml)=xat(i1)
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| 47 | rfpt(2,nml)=yat(i1)
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| 48 | rfpt(3,nml)=zat(i1)
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| 49 |
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| 50 | call setgbl(nml,i1,i2,i3, xg, zg)
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| 51 |
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| 52 | xbaat(i1) = zg(1)
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| 53 | ybaat(i1) = zg(2)
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| 54 | zbaat(i1) = zg(3)
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| 55 |
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| 56 | xtoat(i1) = xg(1)
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| 57 | ytoat(i1) = xg(2)
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| 58 | ztoat(i1) = xg(3)
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| 59 |
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| 60 | ifirs=irsml1(nml)
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| 61 |
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| 62 | do i=ifirs,irsml2(nml)
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| 63 | if (i.eq.ifirs) then ! not construct
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| 64 | jj=iatrs1(i)+1 ! 1st bb atom again
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| 65 | else
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| 66 | jj=iatrs1(i)
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| 67 | endif
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| 68 | do j=jj,iatrs2(i)
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| 69 | jow=iowat(j)
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| 70 | call eyring(j,jow)
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| 71 | enddo
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| 72 | enddo
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| 73 |
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| 74 | call setsys(i1,i2,i3, x1,x2,x3,y1,y2,y3,z1,z2,z3)
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| 75 |
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| 76 | xrfax(1,nml)=x1 ! J
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| 77 | xrfax(2,nml)=x2
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| 78 | xrfax(3,nml)=x3
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| 79 | yrfax(1,nml)=-y1 ! K
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| 80 | yrfax(2,nml)=-y2
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| 81 | yrfax(3,nml)=-y3
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| 82 | zrfax(1,nml)=-z1 ! L
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| 83 | zrfax(2,nml)=-z2
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| 84 | zrfax(3,nml)=-z3
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| 85 |
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| 86 | return
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| 87 | end
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| 88 | ! ***********************************
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| 89 | subroutine fnd3ba(nml,i1,i2,i3)
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| 90 |
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| 91 | ! .................................................
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| 92 | ! PURPOSE: return indices 'i1,i2,i3' of
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| 93 | ! first 3 backbone atoms in molecule 'nml'
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| 94 | !
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| 95 | ! CALLS: fndbrn
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| 96 | ! .................................................
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| 97 |
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| 98 | include 'INCL.H'
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| 99 |
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| 100 | dimension ibd(4)
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| 101 | logical bb
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| 102 |
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| 103 |
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| 104 | irs=irsml1(nml)
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| 105 |
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| 106 | ! --------------------------- 1st bb atom
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| 107 | i1=iatrs1(irs)
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| 108 |
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| 109 | call fndbrn(nml,irs,i1,i,ix,i2,bb)
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| 110 |
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| 111 | ! --------------------------- 2nd bb atom
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| 112 | i2=i+1
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| 113 |
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| 114 | ! ------------------------ check for ring
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| 115 |
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| 116 | ibd(1)=iowat(i1)
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| 117 | ibd(2)=ibdat(1,i1)
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| 118 | ibd(3)=ibdat(2,i1)
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| 119 | ibd(4)=ibdat(3,i1)
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| 120 |
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| 121 | ix = 0
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| 122 | do i=1,nbdat(i1)+1
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| 123 |
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| 124 | if (iowat(ibd(i)).ne.i1) then
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| 125 |
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| 126 | if (ix.ne.0) then
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| 127 | write (*,'(2a,i3)')
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| 128 | & ' fnd3ba> Can handle only simple ring at 1st',
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| 129 | & ' atom of molecule #',nml
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| 130 | stop
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| 131 | endif
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| 132 |
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| 133 | ix=ibd(i)
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| 134 | endif
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| 135 | enddo
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| 136 |
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| 137 | ! --------------------------- 3rd bb atom
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| 138 |
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| 139 | ix=ixatrs(irs)
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| 140 |
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| 141 | if (i2.eq.ix) then
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| 142 |
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| 143 | if (irs.lt.irsml2(nml)) then
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| 144 | i3 = iatrs1(irs+1)
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| 145 | return
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| 146 | endif
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| 147 |
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| 148 | else
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| 149 |
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| 150 | do i = ix,i2+1,-1
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| 151 | if (iowat(i).eq.i2) then
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| 152 | i3=i
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| 153 | return
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| 154 | endif
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| 155 | enddo
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| 156 |
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| 157 | endif
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| 158 |
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| 159 | write (*,'(4a,i4,a,i4)')
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| 160 | & ' fnd3ba> Cannot find backbone atom following ',nmat(i2),
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| 161 | & ' of residue ',seq(irs),irs,' in molecule #',nml
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| 162 | stop
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| 163 |
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| 164 | end
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| 165 | ! ***************************
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| 166 | subroutine eyring(i,ia)
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| 167 |
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| 168 | ! .........................................................
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| 169 | ! PURPOSE: calculate cartesian coordinates of atom 'i'
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| 170 | ! using EYRING's algorithm
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| 171 | ! INPUT: i - index of atom to be constructed
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| 172 | ! for 'i': blat,csbaat,snbaat,cstoat,sntoat
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| 173 | ! ia- index of atom from which 'i' is to be built
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| 174 | ! OUTPUT: for 'i': xat,yat,zat,xbaat,ybaat,zbaat,xtoat,ytoat,ztoat
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| 175 | !
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| 176 | ! CALLS: none
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| 177 | ! .........................................................
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| 178 |
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| 179 | include 'INCL.H'
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| 180 |
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| 181 | ct=cstoat(i)
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| 182 | st=sntoat(i)
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| 183 | ca=csbaat(i)
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| 184 | sa=snbaat(i)
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| 185 | bl=blat(i)
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| 186 |
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| 187 | x1=xtoat(ia)
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| 188 | x2=ytoat(ia)
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| 189 | x3=ztoat(ia)
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| 190 |
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| 191 | z1=xbaat(ia)
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| 192 | z2=ybaat(ia)
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| 193 | z3=zbaat(ia)
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| 194 |
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| 195 | y1=z2*x3-z3*x2
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| 196 | y2=z3*x1-z1*x3
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| 197 | y3=z1*x2-z2*x1
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| 198 |
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| 199 | h2=-sa*ct
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| 200 | h3=-sa*st
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| 201 |
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| 202 | x1=-ca*x1+h2*y1+h3*z1
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| 203 | x2=-ca*x2+h2*y2+h3*z2
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| 204 | x3=-ca*x3+h2*y3+h3*z3
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| 205 |
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| 206 | dx=one/sqrt(x1*x1+x2*x2+x3*x3)
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| 207 | x1=x1*dx
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| 208 | x2=x2*dx
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| 209 | x3=x3*dx
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| 210 |
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| 211 | xtoat(i)=x1
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| 212 | ytoat(i)=x2
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| 213 | ztoat(i)=x3
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| 214 |
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| 215 | z1=-st*y1+ct*z1
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| 216 | z2=-st*y2+ct*z2
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| 217 | z3=-st*y3+ct*z3
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| 218 |
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| 219 | dz=one/sqrt(z1*z1+z2*z2+z3*z3)
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| 220 | xbaat(i)=z1*dz
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| 221 | ybaat(i)=z2*dz
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| 222 | zbaat(i)=z3*dz
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| 223 |
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| 224 | xat(i)=xat(ia)+x1*bl
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| 225 | yat(i)=yat(ia)+x2*bl
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| 226 | zat(i)=zat(ia)+x3*bl
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| 227 |
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| 228 | return
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| 229 | end
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| 230 | ! ***********************************************************
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| 231 | subroutine setsys(i1,i2,i3, x1,x2,x3,y1,y2,y3,z1,z2,z3)
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| 232 |
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| 233 | ! ..........................................................
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| 234 | ! PURPOSE: calculate axes X,Y,Z of right-handed orthogonal
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| 235 | ! system given by three atom positions R1, R2, R3
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| 236 | !
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| 237 | ! X = (R2-R1)/ |( )|
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| 238 | ! Z = {X x (R2-R3)} / |{ }|
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| 239 | ! Y = Z x X
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| 240 | !
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| 241 | ! INPUT: i1, i2, i3 - indices of three atoms
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| 242 | ! OUTPUT: x1,x2,x3 |
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| 243 | ! y1,y2,y3 | -direction cosines of X,Y,Z
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| 244 | ! z1,z2,z3 |
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| 245 | !
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| 246 | ! CALLS: none
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| 247 | ! ...................................................
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| 248 |
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| 249 |
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| 250 | include 'INCL.H'
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| 251 |
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| 252 | h1=xat(i2)
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| 253 | h2=yat(i2)
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| 254 | h3=zat(i2)
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| 255 |
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| 256 | x1=h1-xat(i1)
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| 257 | x2=h2-yat(i1)
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| 258 | x3=h3-zat(i1)
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| 259 |
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| 260 | y1=h1-xat(i3)
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| 261 | y2=h2-yat(i3)
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| 262 | y3=h3-zat(i3)
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| 263 |
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| 264 | z1=x2*y3-x3*y2
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| 265 | z2=x3*y1-x1*y3
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| 266 | z3=x1*y2-x2*y1
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| 267 |
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| 268 | dx=one/sqrt(x1*x1+x2*x2+x3*x3)
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| 269 | x1=x1*dx
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| 270 | x2=x2*dx
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| 271 | x3=x3*dx
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| 272 |
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| 273 | dz=one/sqrt(z1*z1+z2*z2+z3*z3)
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| 274 | z1=z1*dz
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| 275 | z2=z2*dz
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| 276 | z3=z3*dz
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| 277 |
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| 278 | y1=z2*x3-z3*x2
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| 279 | y2=z3*x1-z1*x3
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| 280 | y3=z1*x2-z2*x1
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| 281 |
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| 282 | return
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| 283 | end
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| 284 |
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| 285 | ! *****************************************
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| 286 | subroutine setgbl(nml,i1,i2,i3,xg,zg)
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| 287 |
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| 288 | ! ...................................................
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| 289 | !
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| 290 | ! PURPOSE: 1. Obtain global axes (J,K,L)
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| 291 | ! related to x(1 0 0),y(0 1 0),z(0 0 1)
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| 292 | ! by 3 rotations (gbl. parameters #4-#6):
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| 293 | !
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| 294 | ! - round z by angle alpha
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| 295 | ! - round x' by a. beta
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| 296 | ! - round y" by a. gamma
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| 297 | !
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| 298 | ! 2. Return x-axis (xg) & z-axis (zg)
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| 299 | ! for atom #1 in order to orientate J
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| 300 | ! along the bond from backbone atom #1
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| 301 | ! to bb.a. #2 and L according to the
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| 302 | ! cross product [ bond(#1->#2) x
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| 303 | ! bond(#2->#3) ] when using Eyring's
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| 304 | ! algorithm to get the coordinates
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| 305 | !
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| 306 | ! CALLS: none
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| 307 | ! ..............................................
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| 308 |
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| 309 | include 'INCL.H'
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| 310 |
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| 311 | dimension xg(3),zg(3),ag(3,3)
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| 312 |
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| 313 |
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| 314 | ca = cos(gbpr(4,nml)) ! alpha
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| 315 | sa = sin(gbpr(4,nml))
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| 316 | cb = cos(gbpr(5,nml)) ! beta
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| 317 | sb = sin(gbpr(5,nml))
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| 318 | cg = cos(gbpr(6,nml)) ! gamma
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| 319 | sg = sin(gbpr(6,nml))
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| 320 |
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| 321 | ! ----------------------------- J
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| 322 | x1 = ca*cg - sa*sb*sg
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| 323 | x2 = sa*cg + ca*sb*sg
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| 324 | x3 = -cb*sg
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| 325 |
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| 326 | d = sqrt(x1**2+x2**2+x3**2)
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| 327 | ag(1,1) = x1/d
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| 328 | ag(2,1) = x2/d
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| 329 | ag(3,1) = x3/d
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| 330 | ! ----------------------------- K
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| 331 | y1 = -sa*cb
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| 332 | y2 = ca*cb
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| 333 | y3 = sb
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| 334 |
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| 335 | d = sqrt(y1**2+y2**2+y3**2)
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| 336 | ag(1,2) = y1/d
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| 337 | ag(2,2) = y2/d
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| 338 | ag(3,2) = y3/d
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| 339 | ! ----------------------------- L
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| 340 | z1 = ca*sg + sa*sb*cg
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| 341 | z2 = sa*sg - ca*sb*cg
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| 342 | z3 = cb*cg
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| 343 |
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| 344 | d = sqrt(z1**2+z2**2+z3**2)
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| 345 | ag(1,3) = z1/d
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| 346 | ag(2,3) = z2/d
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| 347 | ag(3,3) = z3/d
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| 348 |
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| 349 | ! ------------------------------------ X1
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| 350 | ct2 = cstoat(i2)
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| 351 | st2 = sntoat(i2)
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| 352 | sa2 = snbaat(i2)
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| 353 |
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| 354 | x1 = -csbaat(i2)
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| 355 | x2 = -sa2*ct2
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| 356 | x3 = -sa2*st2
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| 357 |
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| 358 | dx = sqrt(x1**2+x2**2+x3**2)
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| 359 | x1 = x1/dx
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| 360 | x2 = x2/dx
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| 361 | x3 = x3/dx
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| 362 | ! ------------------------------------- Z1
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| 363 | st3 = sntoat(i3)
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| 364 | ct3 = cstoat(i3)
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| 365 |
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| 366 | z1 = -st3*(st2*x3+ct2*x2)
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| 367 | z2 = st3*ct2*x1 + ct3*st2
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| 368 | z3 = st3*st2*x1 - ct3*ct2
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| 369 |
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| 370 | dz = sqrt(z1**2+z2**2+z3**2)
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| 371 | z1 = z1/dz
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| 372 | z2 = z2/dz
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| 373 | z3 = z3/dz
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| 374 | ! ------------------------------------- Y1
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| 375 | y1 = z2 * x3 - z3 * x2
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| 376 | y3 = z1 * x2 - z2 * x1 ! do not need y2
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| 377 |
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| 378 | ! ----------------------------- into global system
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| 379 |
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| 380 | xg(1) = ag(1,1)*x1 + ag(1,2)*y1 + ag(1,3)*z1
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| 381 | xg(2) = ag(2,1)*x1 + ag(2,2)*y1 + ag(2,3)*z1
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| 382 | xg(3) = ag(3,1)*x1 + ag(3,2)*y1 + ag(3,3)*z1
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| 383 |
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| 384 | dx = sqrt(xg(1)**2+xg(2)**2+xg(3)**2)
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| 385 |
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| 386 | zg(1) = ag(1,1)*x3 + ag(1,2)*y3 + ag(1,3)*z3
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| 387 | zg(2) = ag(2,1)*x3 + ag(2,2)*y3 + ag(2,3)*z3
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| 388 | zg(3) = ag(3,1)*x3 + ag(3,2)*y3 + ag(3,3)*z3
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| 389 |
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| 390 | dz = sqrt(zg(1)**2+zg(2)**2+zg(3)**2)
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| 391 |
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| 392 | do i=1,3
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| 393 | xg(i) = xg(i)/dx
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| 394 | zg(i) = zg(i)/dz
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| 395 | enddo
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| 396 |
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| 397 | return
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| 398 | end
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| 399 |
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