| 1 | ! **************************
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| 2 | ! **************************************************************
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| 3 | !
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| 4 | ! This file contains the subroutines: getmol,redres
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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 |
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| 14 | subroutine getmol(nml)
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| 15 |
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| 16 | ! ...................................................................
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| 17 | ! PURPOSE: assemble data for molecule 'nml' according to
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| 18 | ! its sequence using residue library 'reslib'
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| 19 | !
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| 20 | ! ! Molecules must be assembled in sequential order (1 -> ntlml)
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| 21 | ! (or number of atoms & variables must remain the same)
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| 22 | !
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| 23 | ! INPUT: irsml1(nml),irsml2(nml),seq(irsml1()...irsml2())
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| 24 | ! nml>1: irsml1(nml-1),iatrs2(irsml2(nml-1))
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| 25 | ! ivrrs1(irsml2(nml-1)),nvrrs(irsml2(nml-1))
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| 26 | !
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| 27 | ! OUTPUT: molecule - ivrml1,nvrml
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| 28 | ! residues - iatrs1,ixatrs,iatrs2,ivrrs1,nvrrs
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| 29 | ! atoms - nmat,ityat,cgat,blat,baat,csbaat,snbaat,
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| 30 | ! toat,cstoat,sntoat
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| 31 | ! bonds - nbdat,iowat,iyowat,ibdat(1-mxbd,),iybdat(1-mxbd,)
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| 32 | ! ! 1st atom of 'nml': iowat indicates 1st bond
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| 33 | ! to a FOLLOWING atom (not previous) !
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| 34 | ! variables - ityvr,iclvr,iatvr,nmvr
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| 35 | !
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| 36 | ! CALLS: iopfil,redres,iendst
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| 37 | ! ...................................................................
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| 38 |
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| 39 | include 'INCL.H'
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| 40 | ! arguments
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| 41 | integer nml
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| 42 | ! functions
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| 43 | integer iopfil, iendst
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| 44 |
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| 45 | integer i, iat, iow, ifirs, ibd, ilars, j, mvr, nbd, n, nbd1, nj
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| 46 | integer nh, nrs, ntlat, ntlvr, nat, nxt
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| 47 | double precision ba, t, to
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| 48 | character res*4
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| 49 |
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| 50 | if (iopfil(lunlib,reslib,'old','formatted').le.izero) then
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| 51 | write (logString, '(a,/,a,i3,2a)')
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| 52 | & ' getmol> ERROR opening library of residues:',
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| 53 | & ' LUN=',lunlib,' FILE=',reslib(1:iendst(reslib))
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| 54 | stop
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| 55 | endif
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| 56 |
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| 57 | if (nml.eq.1) then
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| 58 | ntlat=0
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| 59 | ntlvr=0
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| 60 | else
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| 61 | i=irsml2(nml-1) ! last res. of previous mol.
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| 62 | ntlat=iatrs2(i)
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| 63 | ntlvr=ivrrs1(i)+nvrrs(i)-1
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| 64 | endif
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| 65 | ivrml1(nml)=ntlvr + 1
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| 66 |
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| 67 | ilars=irsml2(nml)
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| 68 | ifirs=irsml1(nml)
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| 69 |
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| 70 | do nrs=ifirs,ilars ! Residues in molecule
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| 71 |
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| 72 | res = seq(nrs)
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| 73 | call tolost(res) ! ensure lower case for residue name
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| 74 |
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| 75 | if (res(:3).eq.'nme'.and.nrs.ne.ilars) then
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| 76 | write (logString, '(3a)') ' getmol> residue >',res,
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| 77 | & '< allowed at C-terminus only !'
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| 78 | close(lunlib)
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| 79 | stop
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| 80 | elseif (res(:3).eq.'ace'.and.nrs.ne.ifirs) then
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| 81 | write (logString, '(3a)') ' getmol> residue >',res,
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| 82 | & '< allowed at N-terminus only !'
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| 83 | close(lunlib)
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| 84 | stop
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| 85 | endif
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| 86 |
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| 87 | call redres(res,nat,nxt,nvr)
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| 88 |
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| 89 | if ((nat+ntlat).gt.mxat) then
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| 90 | write (logString, '(a,i5)') ' getmol> number of atoms > ',mxat
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| 91 | close(lunlib)
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| 92 | stop
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| 93 | endif
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| 94 | if ((nvr+ntlvr).gt.mxvr) then
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| 95 | write (logString, '(a,i5)') ' getmol> number of variables > '
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| 96 | & ,mxvr
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| 97 | close(lunlib)
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| 98 | stop
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| 99 | endif
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| 100 |
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| 101 | rewind lunlib
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| 102 |
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| 103 | ! ___________________________________________________________ Atoms
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| 104 | do i=1,nat
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| 105 | n=i+ntlat
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| 106 | nmat(n)=nmath(i)
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| 107 | ityat(n)=ityath(i)
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| 108 | cgat(n)=cgath(i)
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| 109 | blat(n)=blath(i)
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| 110 | ba=baath(i)
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| 111 | baat(n)=ba
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| 112 | csbaat(n)=cos(ba)
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| 113 | snbaat(n)=sin(ba)
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| 114 | to=toath(i)
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| 115 | toat(n)=to
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| 116 | cstoat(n)=cos(to)
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| 117 | sntoat(n)=sin(to)
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| 118 | ! ______________________________ bonds to previous & following atoms
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| 119 | iow=iowath(i)
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| 120 | if (iow.eq.0) then ! 1st atom of residue
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| 121 | if (nrs.eq.ifirs) then ! 1st atom of 'nml'
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| 122 |
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| 123 | iowat(n)=ibdath(1,i)+ntlat
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| 124 | iyowat(n)=iybdath(1,i)
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| 125 |
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| 126 | do j = 1,mxbd-1
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| 127 | ibdath(j,i)=ibdath(j+1,i)
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| 128 | iybdath(j,i)=iybdath(j+1,i)
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| 129 | enddo
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| 130 | ibdath(mxbd,i)=0
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| 131 | iybdath(mxbd,i)=1
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| 132 |
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| 133 | nbdath(i)=nbdath(i)-1
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| 134 | else ! connected with prev. res.
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| 135 | nh=ixatrs(nrs-1) ! atom to 'next' residue of prev.res.
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| 136 | iowat(n)=nh
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| 137 | iyowat(n)=1 !!! only single bonds assumed !!!
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| 138 |
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| 139 | ! ___________________________ correct atom to 'next' res.
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| 140 | nbd=nbdat(nh)
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| 141 | if (nbd.eq.mxbd) then
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| 142 | write (logString, '(a,i2,a,i4,2a,i4,a)')
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| 143 | & ' getmol> need ',(mxbd+2),
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| 144 | & 'th bond to connect residues ',
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| 145 | & nrs-1,seq(nrs-1),' and ',nrs,seq(nrs)
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| 146 | close(lunlib)
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| 147 | stop
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| 148 | else ! correct atom to 'next' res.
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| 149 | ! _______________________________!! dihedrals for atoms bound to 'nh'
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| 150 | ! are assumed to be phase angles !!
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| 151 | do j=1,nbd
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| 152 |
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| 153 | nj=ibdat(j,nh)
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| 154 | t=toat(nj)
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| 155 |
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| 156 | if (t.eq.0.0) then
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| 157 | write (logString, '(3a,/,2a)')
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| 158 | & ' getmol> DIHEDRAL for atom ',nmat(nj),
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| 159 | & ' should be PHASE angle with respect to atom ',
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| 160 | & nmat(n),' & therefore must be not 0.0 !!'
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| 161 | close(lunlib)
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| 162 | stop
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| 163 | endif
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| 164 |
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| 165 | t=t+to
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| 166 | if (abs(t).gt.pi) t=t-sign(pi2,t)
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| 167 | toat(nj)=t
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| 168 | cstoat(nj)=cos(t)
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| 169 | sntoat(nj)=sin(t)
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| 170 |
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| 171 | enddo
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| 172 |
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| 173 | nbd1=nbd+1
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| 174 | ibdat(nbd1,nh)=n
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| 175 | iybdat(nbd1,nh)=1 ! (only single bonds !)
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| 176 | nbdat(nh)=nbd1
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| 177 |
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| 178 | endif
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| 179 |
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| 180 | endif
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| 181 |
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| 182 | else ! connected within res.
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| 183 |
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| 184 | iowat(n)=ntlat+iow
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| 185 | iyowat(n)=iyowath(i)
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| 186 |
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| 187 | endif
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| 188 |
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| 189 | nbdat(n)=nbdath(i)
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| 190 |
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| 191 | do j=1,mxbd
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| 192 |
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| 193 | ibd=ibdath(j,i)
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| 194 |
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| 195 | if (ibd.ne.0) then
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| 196 | ibdat(j,n)=ibd+ntlat
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| 197 | iybdat(j,n)=iybdath(j,i)
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| 198 | else
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| 199 | ibdat(j,n)=0
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| 200 | iybdat(j,n)=1
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| 201 | endif
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| 202 |
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| 203 | enddo
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| 204 |
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| 205 | enddo ! ... atoms
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| 206 |
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| 207 | ! ________________________________________________________ Variables
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| 208 | ivrrs1(nrs)=ntlvr+1
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| 209 | mvr=0
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| 210 |
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| 211 | do i=1,nvr
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| 212 |
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| 213 | if (nrs.eq.ifirs) then
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| 214 |
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| 215 | iat=iatvrh(i)
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| 216 | ! ____________________________________ Exclude all variables for 1st atom
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| 217 | ! & torsion for atoms bound to it
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| 218 | if ( iat.eq.1.or.
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| 219 | & (iowath(iat).eq.1.and.ityvrh(i).eq.3)) goto 1
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| 220 |
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| 221 | endif
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| 222 |
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| 223 | mvr=mvr+1
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| 224 | ntlvr=ntlvr+1
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| 225 | ityvr(ntlvr)=ityvrh(i)
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| 226 | iclvr(ntlvr)=iclvrh(i)
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| 227 | iatvr(ntlvr)=iatvrh(i)+ntlat
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| 228 | nmvr(ntlvr)=nmvrh(i)
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| 229 |
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| 230 | 1 enddo ! ... Variables
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| 231 |
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| 232 | nvrrs(nrs)=mvr
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| 233 |
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| 234 | iatrs1(nrs)=ntlat+1 ! first backbone atom of res.
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| 235 | ixatrs(nrs)=ntlat+nxt ! last backbone atom
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| 236 | ntlat=ntlat+nat
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| 237 | iatrs2(nrs)=ntlat ! last atom of res.
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| 238 |
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| 239 | enddo ! ... residues
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| 240 |
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| 241 | close(lunlib)
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| 242 |
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| 243 | ! _______________________________ Variables
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| 244 | if (nml.eq.1) then
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| 245 | nvrml(nml)=ntlvr
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| 246 | else
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| 247 | nvrml(nml)=ntlvr-ivrml1(nml) + 1
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| 248 | endif
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| 249 |
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| 250 | return
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| 251 | end
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| 252 | ! **************************************
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| 253 | subroutine redres(res,nat,nxt,nvrr)
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| 254 |
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| 255 | ! .......................................................
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| 256 | ! PURPOSE: read atom data for residue 'res' from library
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| 257 | ! (file 'lunlib' 'reslib' opened in routine calling
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| 258 | ! this one)
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| 259 | !
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| 260 | ! OUTPUT: nat - number of atoms in residue
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| 261 | ! nxt - atom which may bind to following residue
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| 262 | ! nvrr - number of variables in residue
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| 263 | ! for atoms - nmath,blath,baath(rad),toath(rad),
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| 264 | ! ityath,iyowath,iowath (INSIDE residue,
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| 265 | ! =0 if 1st atom)
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| 266 | ! for variables - ityvrh (1=bl/2=ba/3=to),iclvrh,iatvrh,nmvrh
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| 267 | !
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| 268 | ! LIBRARY: residue-lines:
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| 269 | ! '#', res, nat, nxt; Format: a1,a4,2i4
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| 270 | ! atom-lines:
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| 271 | ! nmat,3{"fix" =' ', clvr,nmvr, blat/baat(deg)/toat(deg)},
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| 272 | ! cgat, ityat, iowat,ibdat1,ibdat2,ibdat3;
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| 273 | ! Format: a4, 3(1x,i2,a1,a3,f9.3), f7.4, i4,4i4
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| 274 | !
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| 275 | ! CALLS: iendst,tolost
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| 276 | !
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| 277 | ! .......................................................
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| 278 |
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| 279 | include 'INCL.H'
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| 280 | ! arguments
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| 281 | integer nat, nxt, nvrr
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| 282 |
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| 283 | ! functions
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| 284 | integer iendst
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| 285 |
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| 286 | integer icl, ibd, ib3, i, ib1, ib2, ic, iow, iexcp, ity, jow, lg
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| 287 | integer nln, j
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| 288 | dimension icl(3),ibd(mxbd)
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| 289 | character blnk,fix(3),nm(3)*3,res*4,resl*4,line*132
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| 290 | data blnk/' '/
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| 291 |
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| 292 | double precision ba, to
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| 293 |
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| 294 | nln=0
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| 295 | do i=1,mxbd
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| 296 | ibd(i)=0
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| 297 | enddo
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| 298 |
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| 299 | resl=res
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| 300 |
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| 301 | call tolost(resl) ! ensure lower case for residue name
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| 302 |
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| 303 | ! ________________________________ find residue 'resl'
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| 304 | 1 line=blnk
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| 305 | nln=nln+1
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| 306 |
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| 307 | read (lunlib,'(a)',end=2,err=3) line
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| 308 | lg=iendst(line)
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| 309 |
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| 310 | if (lg.ge.13.and.line(1:1).eq.'#'.and.line(2:5).eq.resl) then
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| 311 | ! _____________________________________________ read atom data for 'resl'
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| 312 | read (line(6:13),'(2i4)',err=3) nat,nxt
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| 313 |
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| 314 | if (nat.gt.mxath) then
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| 315 | write (logString, '(a,i5)') ' redres> number of atoms > ',mxath
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| 316 | close(lunlib)
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| 317 | stop
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| 318 | endif
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| 319 |
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| 320 | nvrr=0
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| 321 | do i=1,nat
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| 322 |
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| 323 | nln=nln+1
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| 324 |
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| 325 | read (lunlib,'(a4,3(1x,i2,a1,a3,d9.3),d7.4,i4,4i4)',
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| 326 | & end=3,err=3)
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| 327 | & nmath(i),icl(1),fix(1),nm(1),blath(i),icl(2),fix(2),nm(2),ba,
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| 328 | & icl(3),fix(3),nm(3),to,cgath(i),ity,iow,(ibd(j),j=1,mxbd)
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| 329 |
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| 330 | if (ity.le.0.or.ity.gt.mxtyat) goto 6
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| 331 | ityath(i)=ity
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| 332 |
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| 333 | jow=abs(iow)
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| 334 |
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| 335 | if (res(:3).eq.'ace'.and.i.eq.1) then ! exception from following check
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| 336 | iexcp = 1
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| 337 | else
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| 338 | iexcp = 0
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| 339 | endif
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| 340 |
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| 341 | if (iexcp.eq.0.and.i.le.jow) then
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| 342 | if (i.eq.jow) then
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| 343 | write(logString,'(5a)') ' redres> atom ',nmath(i),' of ',
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| 344 | & resl,' cannot preceed itself '
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| 345 | else
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| 346 | write (logString, '(5a,i4)')
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| 347 | & ' redres> atom ',nmath(i),' of ',
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| 348 | & resl,' should be placed AFTER atom #',jow
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| 349 | endif
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| 350 | goto 5
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| 351 | endif
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| 352 |
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| 353 | iowath(i)=jow
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| 354 | iyowath(i)=sign(1,iow)
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| 355 | ! ____________________________________ check order & find number of bonds
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| 356 | ! (bonds closing ring must be last !)
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| 357 | ib1=abs(ibd(1))
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| 358 | ib2=abs(ibd(2))
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| 359 | ib3=abs(ibd(3))
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| 360 |
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| 361 | if (ib1.eq.i.or.ib2.eq.i.or.ib3.eq.i) goto 4
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| 362 |
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| 363 | if (ib1.eq.0) then ! no bond to following
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| 364 | if (ib2.ne.0.or.ib3.ne.0) goto 4
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| 365 | nbdath(i)=0
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| 366 | else
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| 367 | if (ib1.eq.jow) goto 4
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| 368 | if (ib2.eq.0) then
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| 369 | if (ib3.ne.0) goto 4
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| 370 | nbdath(i)=1
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| 371 | else
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| 372 | if ( ib2.eq.jow.or.ib2.eq.ib1.or.
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| 373 | & (ib2.gt.i.and.ib2.lt.ib1) ) goto 4
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| 374 | if (ib3.eq.0) then
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| 375 | nbdath(i)=2
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| 376 | else
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| 377 | if (ib3.eq.jow.or.ib3.eq.ib1.or.ib3.eq.ib2.or.
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| 378 | & (ib3.gt.i.and.(ib3.lt.ib1.or.ib3.lt.ib2)) ) goto 4
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| 379 | nbdath(i)=3
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| 380 | endif
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| 381 | endif
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| 382 | endif
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| 383 |
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| 384 | do j=1,mxbd
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| 385 | ibdath(j,i)=abs(ibd(j))
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| 386 | iybdath(j,i)=sign(1,ibd(j))
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| 387 | enddo
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| 388 |
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| 389 | baath(i)=ba*cdr ! convert angles into 'radians'
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| 390 | toath(i)=to*cdr
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| 391 |
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| 392 | ! ______________________________ internal degrees of freedom
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| 393 | do j=1,3
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| 394 | if (fix(j).ne.blnk) then
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| 395 | nvrr=nvrr+1
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|---|
| 396 |
|
|---|
| 397 | if (nvrr.gt.mxvrh) then
|
|---|
| 398 | write (logString, '(a,i5)')
|
|---|
| 399 | & ' redres> number of variables > ',
|
|---|
| 400 | & mxvrh
|
|---|
| 401 | close(lunlib)
|
|---|
| 402 | stop
|
|---|
| 403 | endif
|
|---|
| 404 |
|
|---|
| 405 | ic=icl(j)
|
|---|
| 406 |
|
|---|
| 407 | if ( ic.le.0
|
|---|
| 408 | & .or.(j.eq.3.and.ic.gt.mxtyto) ! dihedral
|
|---|
| 409 | & .or.(j.eq.2.and.ic.gt.mxtyba) ! bond angle
|
|---|
| 410 | & .or.(j.eq.1.and.ic.gt.mxtybl) ) goto 7 ! b. length
|
|---|
| 411 |
|
|---|
| 412 | ityvrh(nvrr)=j
|
|---|
| 413 | iclvrh(nvrr)=ic
|
|---|
| 414 | iatvrh(nvrr)=i
|
|---|
| 415 | nmvrh(nvrr)=nm(j)
|
|---|
| 416 |
|
|---|
| 417 | endif
|
|---|
| 418 |
|
|---|
| 419 | enddo
|
|---|
| 420 | enddo ! ... atoms
|
|---|
| 421 |
|
|---|
| 422 | return
|
|---|
| 423 | endif
|
|---|
| 424 |
|
|---|
| 425 | goto 1
|
|---|
| 426 |
|
|---|
| 427 | ! ____________________________________________________________ ERRORS
|
|---|
| 428 | 2 write (logString, '(4a)') ' redres> residue >',resl,
|
|---|
| 429 | & '< NOT FOUND in ',
|
|---|
| 430 | &reslib(1:iendst(reslib))
|
|---|
| 431 | close(lunlib)
|
|---|
| 432 | stop
|
|---|
| 433 |
|
|---|
| 434 | 3 write (logString, '(a,i4,2a)') ' redres> ERROR reading line No. ',
|
|---|
| 435 | & nln,
|
|---|
| 436 | & ' in ',reslib(1:iendst(reslib))
|
|---|
| 437 | close(lunlib)
|
|---|
| 438 | stop
|
|---|
| 439 |
|
|---|
| 440 | 4 write (logString, '(4a)')
|
|---|
| 441 | & ' redres> Incorrect order of bonds for atom ',
|
|---|
| 442 | & nmath(i),' of ',resl
|
|---|
| 443 |
|
|---|
| 444 | 5 write (logString, '(8x,2a)') '... must correct ',
|
|---|
| 445 | & reslib(1:iendst(reslib))
|
|---|
| 446 | close(lunlib)
|
|---|
| 447 | stop
|
|---|
| 448 |
|
|---|
| 449 | 6 write (logString, '(a,i2,4a)') ' redres> unknown type :',ity,
|
|---|
| 450 | & ': for atom ',nmath(i),' in residue ',resl
|
|---|
| 451 | close(lunlib)
|
|---|
| 452 | stop
|
|---|
| 453 |
|
|---|
| 454 | 7 write (logString, '(a,i2,4a)') ' redres> unknown class :',ic,
|
|---|
| 455 | & ': for variable ',nm(j),' in residue ',resl
|
|---|
| 456 | close(lunlib)
|
|---|
| 457 | stop
|
|---|
| 458 |
|
|---|
| 459 | end
|
|---|
| 460 |
|
|---|
