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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11 |
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12 | subroutine contacts(ncn,nham2,dham)
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13 |
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14 | ! ..............................................................
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15 | !
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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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20 | !
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21 | ! CALLS: c_cont
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22 | ! ..............................................................
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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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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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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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64 | ! *********************************
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65 | subroutine c_alfa(nmol,ncode)
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66 |
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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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80 |
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81 | include 'INCL.H'
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82 | integer nmol
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83 |
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84 | integer ncode, ia, n_res
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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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89 | ! Check for C_alpha atoms
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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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101 | ! **********************************
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102 | subroutine c_cont (nmol,ncode)
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103 |
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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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138 |
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139 | include 'INCL.H'
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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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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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163 | ! write (logString, '(2i3)'),nr_i,nr_j
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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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171 | & +(yat(ialf)-yat(jalf))**2
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172 | & + (zat(ialf)-zat(jalf))**2
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173 | if(sqrt(rij2).lt.rcut) ic=1
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174 |
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175 | ! write (logString, '(2i3)'),nr_i,nr_j
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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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