[bd2278d] | 1 | ! **************************************************************
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| 2 | !
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| 3 | ! This file contains the subroutines: contacts,c_alfa,c_cont
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| 4 | !
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| 5 | ! Copyright 2003-2005 Frank Eisenmenger, U.H.E. Hansmann,
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| 6 | ! Shura Hayryan, Chin-Ku
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| 7 | ! Copyright 2007 Frank Eisenmenger, U.H.E. Hansmann,
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| 8 | ! Jan H. Meinke, Sandipan Mohanty
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| 9 | !
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| 10 | ! **************************************************************
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[e40e335] | 11 |
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| 12 | subroutine contacts(ncn,nham2,dham)
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| 13 |
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[bd2278d] | 14 | ! ..............................................................
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| 15 | !
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[4e219a3] | 16 | ! Calculates number of contacts in given conformation, number of
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| 17 | ! contacts which are the same in given and reference conformation,
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| 18 | ! and the hamming distance between given conformation and the
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| 19 | ! reference conformation.
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[bd2278d] | 20 | !
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| 21 | ! CALLS: c_cont
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| 22 | ! ..............................................................
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[e40e335] | 23 |
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| 24 | include 'INCL.H'
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| 25 |
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| 26 | !f2py integer, intent(out) :: ncn, nham2
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| 27 | !f2py double precistion, intent(out) :: dham
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[2019dff] | 28 | integer ncn
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| 29 |
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| 30 | integer nham2
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| 31 |
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| 32 | double precision dham
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| 33 |
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| 34 | integer i, j, nham, ncode, nresi
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[e40e335] | 35 |
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| 36 | call c_cont(1,ncode)
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| 37 |
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| 38 | ncn=0
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| 39 | nham=0
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| 40 | nham2=0
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| 41 | nresi=irsml2(1)-irsml1(1)+1
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| 42 | do i=1,nresi
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| 43 | do j=nresi,i+3,-1
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| 44 |
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| 45 | if (ijcont(i,j).eq.1) then
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| 46 | ncn=ncn+1
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| 47 | if (iref(i,j).eq.1) nham2 = nham2+1
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| 48 | end if
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| 49 |
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| 50 | nham = nham + abs(ijcont(i,j)-iref(i,j))
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| 51 | end do
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| 52 | end do
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| 53 |
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| 54 | if (ncn.ne.0.and.nci.ne.0) then
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| 55 | dham = float(nham)/float(ncn)/float(nci)
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| 56 | else
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| 57 | dham = 1.0
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| 58 | end if
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| 59 |
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| 60 | return
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| 61 | end
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| 62 |
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| 63 |
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[bd2278d] | 64 | ! *********************************
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[e40e335] | 65 | subroutine c_alfa(nmol,ncode)
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| 66 |
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[bd2278d] | 67 | ! ......................................................
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| 68 | ! Calculates the indices of C-alpha atoms and
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| 69 | ! stores in the array ind_alf(mxrs)
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| 70 | !
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| 71 | ! Usage: call c_alfa(nmol,ncode)
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| 72 | !
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| 73 | ! nmol - index of the molecule
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| 74 | ! ncode ---> not in use in the current version
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| 75 | !
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| 76 | ! OUTPUT: ind_alf(mxrs)
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| 77 | !
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| 78 | ! CALLS: none
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| 79 | ! ......................................................
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[e40e335] | 80 |
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| 81 | include 'INCL.H'
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[2019dff] | 82 | integer nmol
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| 83 |
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| 84 | integer ncode, ia, n_res
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[e40e335] | 85 |
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| 86 | do n_res=irsml1(nmol),irsml2(nmol) ! Over res.
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| 87 | do ia=iatrs1(n_res),iatrs2(n_res) ! Over the atoms of res.
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| 88 |
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[bd2278d] | 89 | ! Check for C_alpha atoms
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[e40e335] | 90 |
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| 91 | if (nmat(ia)(1:2).eq.'ca') then
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| 92 | ind_alf(n_res)=ia
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| 93 | endif
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| 94 |
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| 95 | enddo ! Over the atoms of res.
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| 96 | enddo ! Over the res.
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| 97 |
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| 98 | return
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| 99 | end
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| 100 |
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[bd2278d] | 101 | ! **********************************
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[e40e335] | 102 | subroutine c_cont (nmol,ncode)
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| 103 |
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[bd2278d] | 104 | !..............................................................
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| 105 | ! Calculates the matrix of contacts between aminoacid residues
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| 106 | ! of the molecule "nmol" according to L.Mirny and E.Domany,
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| 107 | ! PROTEINS:Structure, Function, and Genetics 26:391-410 (1996)
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| 108 | !
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| 109 | ! Two residues are in contact if their C_alpha atoms are
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| 110 | ! closer than 8.5 Angstrem
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| 111 | !
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| 112 | ! Usage: call c_cont(nmol,ncode)
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| 113 | !
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| 114 | ! Where nmol is the index of the molecule (always 1, in the
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| 115 | ! current version of SMM)
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| 116 | ! ncode ---> not in use in the current version
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| 117 | !
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| 118 | ! IMPORTANT: Before the first call of this subroutine "c_alfa"
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| 119 | ! must be called to calculate the inices of C_alpha atoms.
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| 120 | ! (ONLY ONCE)
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| 121 | !
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| 122 | ! OUTPUT: The output of this routine is the contact matrix
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| 123 | ! ijcont(mxrs,mxrs)
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| 124 | !
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| 125 | ! ijcont(i,j)=0---> residues i and j are not in contact
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| 126 | ! ijcont(i,j)=1---> ---------''----- are in contact
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| 127 | ! ijcont(i,j)=2---> residues i and j are adjacent
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| 128 | !
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| 129 | ! NOTE: Adjacent residues are always in contact (and therefore not
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| 130 | ! counted)
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| 131 | !
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| 132 | ! Here "mxrs" is the maximum number of residues for SMM
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| 133 | ! Obviously, this subroutine calculates only NxN part
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| 134 | ! of that matrix, N -is the number of res. in "nmol"
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| 135 | !
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| 136 | ! CALLS: none
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| 137 | !..............................................................
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[e40e335] | 138 |
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| 139 | include 'INCL.H'
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[2019dff] | 140 | integer nmol
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| 141 |
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| 142 | double precision rcut, rij2
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| 143 |
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| 144 | integer ncode, ic, ialf, jalf, nr_j, nr_i
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[e40e335] | 145 |
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| 146 | rcut=8.5 ! Domany
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| 147 |
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| 148 |
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| 149 | do nr_i=irsml1(nmol),irsml2(nmol) ! Over res. i
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| 150 |
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| 151 | ijcont(nr_i,nr_i)=2
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| 152 | if(nr_i+1.le.irsml2(nmol)) then
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| 153 | ijcont(nr_i,nr_i+1)=2
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| 154 | ijcont(nr_i+1,nr_i)=2
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| 155 | if(nr_i+2.le.irsml2(nmol)) then
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| 156 | ijcont(nr_i,nr_i+2)=2
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| 157 | ijcont(nr_i+2,nr_i)=2
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| 158 | end if
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| 159 | end if
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| 160 |
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| 161 | do nr_j=nr_i+3,irsml2(nmol) ! Over res. j
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| 162 |
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[38d77eb] | 163 | ! write (logString, '(2i3)'),nr_i,nr_j
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[e40e335] | 164 |
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| 165 | ic=0
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| 166 |
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| 167 | ialf=ind_alf(nr_i)
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| 168 | jalf=ind_alf(nr_j)
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| 169 |
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| 170 | rij2=(xat(ialf)-xat(jalf))**2
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[bd2278d] | 171 | & +(yat(ialf)-yat(jalf))**2
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| 172 | & + (zat(ialf)-zat(jalf))**2
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[e40e335] | 173 | if(sqrt(rij2).lt.rcut) ic=1
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| 174 |
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[38d77eb] | 175 | ! write (logString, '(2i3)'),nr_i,nr_j
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[e40e335] | 176 |
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| 177 | ijcont(nr_i,nr_j)=ic
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| 178 | ijcont(nr_j,nr_i)=ic ! The matrix is symmetrical
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| 179 |
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| 180 | end do ! Over res. j
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| 181 | end do ! Over res. i
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| 182 |
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| 183 | return
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| 184 | end
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| 185 |
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