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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
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3 <!--Proposed Tool Section: [Structure Creation]-->
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4 <tool id="CrystalGenerator" name="CrystalGenerator" version="VERSION">
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5 <description>creates crystals</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">CrystalGenerator</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="stdio"/>
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11 <expand macro="requirements"/>
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12 <command>CrystalGenerator
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13
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14 #if $param_i:
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15 -i $param_i
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16 #end if
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17 #if $param_o:
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18 -o $param_o
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19 #end if
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20 #if $param_sg:
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21 -sg
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22 #if " " in str($param_sg):
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23 "$param_sg"
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24 #else
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25 $param_sg
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26 #end if
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27 #end if
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28 #if $param_axis_a:
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29 -axis_a $param_axis_a
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30 #end if
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31 #if $param_axis_b:
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32 -axis_b $param_axis_b
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33 #end if
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34 #if $param_axis_c:
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35 -axis_c $param_axis_c
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36 #end if
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37 #if $param_angle_alpha:
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38 -angle_alpha $param_angle_alpha
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39 #end if
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40 #if $param_angle_beta:
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41 -angle_beta $param_angle_beta
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42 #end if
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43 #if $param_angle_gamma:
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44 -angle_gamma $param_angle_gamma
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45 #end if
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46 #if $param_from_uc_a:
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47 -from_uc_a $param_from_uc_a
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48 #end if
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49 #if $param_from_uc_b:
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50 -from_uc_b $param_from_uc_b
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51 #end if
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52 #if $param_from_uc_c:
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53 -from_uc_c $param_from_uc_c
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54 #end if
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55 #if $param_to_uc_a:
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56 -to_uc_a $param_to_uc_a
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57 #end if
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58 #if $param_to_uc_b:
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59 -to_uc_b $param_to_uc_b
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60 #end if
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61 #if $param_to_uc_c:
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62 -to_uc_c $param_to_uc_c
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63 #end if
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64 </command>
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65 <inputs>
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66 <param name="param_i" type="data" format="pdb" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input pdb file" help="(-i) "/>
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67 <param name="param_sg" type="select" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="space group symbol in Herman-Mauguin notation" help="(-sg) ">
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68 <option value="P 1">P 1</option>
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69 <option value=" P 1-"> P 1-</option>
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70 <option value=" P 2"> P 2</option>
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71 <option value=" P 21"> P 21</option>
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72 <option value=" C 2"> C 2</option>
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73 <option value=" P M"> P M</option>
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74 <option value=" P C"> P C</option>
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75 <option value=" C M"> C M</option>
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76 <option value=" C C"> C C</option>
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77 <option value=" P 2/M"> P 2/M</option>
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78 <option value=" P 21/M"> P 21/M</option>
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79 <option value=" C 2/M"> C 2/M</option>
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80 <option value=" P 2/C"> P 2/C</option>
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81 <option value=" P 21/C"> P 21/C</option>
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82 <option value=" C 2/C"> C 2/C</option>
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83 <option value=" P 2 2 2"> P 2 2 2</option>
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84 <option value=" P 2 2 21"> P 2 2 21</option>
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85 <option value=" P 21 21 2"> P 21 21 2</option>
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86 <option value=" P 21 21 21"> P 21 21 21</option>
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87 <option value=" C 2 2 21"> C 2 2 21</option>
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88 <option value=" C 2 2 2"> C 2 2 2</option>
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89 <option value=" F 2 2 2"> F 2 2 2</option>
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90 <option value=" I 2 2 2"> I 2 2 2</option>
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91 <option value=" I 21 21 21"> I 21 21 21</option>
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92 <option value=" P M M 2"> P M M 2</option>
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93 <option value=" P M C 21"> P M C 21</option>
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94 <option value=" P C C 2"> P C C 2</option>
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95 <option value=" P M A 2"> P M A 2</option>
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96 <option value=" P C A 21"> P C A 21</option>
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97 <option value=" P N C 2"> P N C 2</option>
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98 <option value=" P M N 21"> P M N 21</option>
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99 <option value=" P B A 2"> P B A 2</option>
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100 <option value=" P N A 21"> P N A 21</option>
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101 <option value=" P N N 2"> P N N 2</option>
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102 <option value=" C M M 2"> C M M 2</option>
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103 <option value=" C M C 21"> C M C 21</option>
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104 <option value=" C C C 2"> C C C 2</option>
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105 <option value=" A M M 2"> A M M 2</option>
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106 <option value=" A B M 2"> A B M 2</option>
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107 <option value=" A M A 2"> A M A 2</option>
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108 <option value=" A B A 2"> A B A 2</option>
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109 <option value=" F M M 2"> F M M 2</option>
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110 <option value=" F D D 2"> F D D 2</option>
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111 <option value=" I M M 2"> I M M 2</option>
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112 <option value=" I B A 2"> I B A 2</option>
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113 <option value=" I M A 2"> I M A 2</option>
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114 <option value=" P M M M"> P M M M</option>
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115 <option value=" P N N N"> P N N N</option>
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116 <option value=" P C C M"> P C C M</option>
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117 <option value=" P B A N"> P B A N</option>
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118 <option value=" P M M A"> P M M A</option>
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119 <option value=" P N N A"> P N N A</option>
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120 <option value=" P M N A"> P M N A</option>
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121 <option value=" P C C A"> P C C A</option>
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122 <option value=" P B A M"> P B A M</option>
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123 <option value=" P C C N"> P C C N</option>
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124 <option value=" P B C M"> P B C M</option>
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125 <option value=" P N N M"> P N N M</option>
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126 <option value=" P M M N"> P M M N</option>
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127 <option value=" P B C N"> P B C N</option>
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128 <option value=" P B C A"> P B C A</option>
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129 <option value=" P N M A"> P N M A</option>
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130 <option value=" C M C M"> C M C M</option>
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131 <option value=" C M C A"> C M C A</option>
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132 <option value=" C M M M"> C M M M</option>
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133 <option value=" C C C M"> C C C M</option>
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134 <option value=" C M M A"> C M M A</option>
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135 <option value=" C C C A"> C C C A</option>
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136 <option value=" F M M M"> F M M M</option>
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137 <option value=" F D D D"> F D D D</option>
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138 <option value=" I M M M"> I M M M</option>
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139 <option value=" I B A M"> I B A M</option>
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140 <option value=" I B C A"> I B C A</option>
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141 <option value=" I M M A"> I M M A</option>
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142 <option value=" P 4"> P 4</option>
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143 <option value=" P 41"> P 41</option>
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144 <option value=" P 42"> P 42</option>
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145 <option value=" P 43"> P 43</option>
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146 <option value=" I 4"> I 4</option>
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147 <option value=" I 41"> I 41</option>
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148 <option value=" P -4"> P -4</option>
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149 <option value=" I -4"> I -4</option>
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150 <option value=" P 4/M"> P 4/M</option>
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151 <option value=" P 42/M"> P 42/M</option>
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152 <option value=" P 4/N"> P 4/N</option>
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153 <option value=" P 42/N"> P 42/N</option>
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154 <option value=" I 4/M"> I 4/M</option>
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155 <option value=" I 41/A"> I 41/A</option>
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156 <option value=" P 4 2 2"> P 4 2 2</option>
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157 <option value=" P 4 21 2"> P 4 21 2</option>
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158 <option value=" P 41 2 2"> P 41 2 2</option>
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159 <option value=" P 41 21 2"> P 41 21 2</option>
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160 <option value=" P 42 2 2"> P 42 2 2</option>
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161 <option value=" P 42 21 2"> P 42 21 2</option>
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162 <option value=" P 43 2 2"> P 43 2 2</option>
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163 <option value=" P 43 21 2"> P 43 21 2</option>
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164 <option value=" I 4 2 2"> I 4 2 2</option>
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165 <option value=" I 41 2 2"> I 41 2 2</option>
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166 <option value=" P 4 M M"> P 4 M M</option>
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167 <option value=" P 4 B M"> P 4 B M</option>
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168 <option value=" P 42 C M"> P 42 C M</option>
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169 <option value=" P 42 N M"> P 42 N M</option>
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170 <option value=" P 4 C C"> P 4 C C</option>
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171 <option value=" P 4 N C"> P 4 N C</option>
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172 <option value=" P 42 M C"> P 42 M C</option>
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173 <option value=" P 42 B C"> P 42 B C</option>
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174 <option value=" I 4 M M"> I 4 M M</option>
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175 <option value=" I 4 C M"> I 4 C M</option>
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176 <option value=" I 41 M D"> I 41 M D</option>
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177 <option value=" I 41 C D"> I 41 C D</option>
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178 <option value=" P -4 2 M"> P -4 2 M</option>
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179 <option value=" P -4 2 C"> P -4 2 C</option>
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180 <option value=" P -4 21 M"> P -4 21 M</option>
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181 <option value=" P -4 21 C"> P -4 21 C</option>
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182 <option value=" P -4 M 2"> P -4 M 2</option>
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183 <option value=" P -4 C 2"> P -4 C 2</option>
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184 <option value=" P -4 B 2"> P -4 B 2</option>
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185 <option value=" P -4 N 2"> P -4 N 2</option>
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186 <option value=" I -4 M 2"> I -4 M 2</option>
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187 <option value=" I -4 C 2"> I -4 C 2</option>
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188 <option value=" I -4 2 M"> I -4 2 M</option>
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189 <option value=" I -4 2 D"> I -4 2 D</option>
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190 <option value=" P 4/M M M"> P 4/M M M</option>
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191 <option value=" P 4/M C C"> P 4/M C C</option>
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192 <option value=" P 4/N B M"> P 4/N B M</option>
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193 <option value=" P 4/N N C"> P 4/N N C</option>
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194 <option value=" P 4/M B M"> P 4/M B M</option>
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195 <option value=" P 4/M N C"> P 4/M N C</option>
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196 <option value=" P 4/N M M"> P 4/N M M</option>
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197 <option value=" P 4/N C C"> P 4/N C C</option>
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198 <option value=" P 42/M M C"> P 42/M M C</option>
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199 <option value=" P 42/M C M"> P 42/M C M</option>
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200 <option value=" P 42/N B C"> P 42/N B C</option>
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201 <option value=" P 42/N N M"> P 42/N N M</option>
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202 <option value=" P 42/M B C"> P 42/M B C</option>
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203 <option value=" P 42/M N M"> P 42/M N M</option>
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204 <option value=" P 42/N M C"> P 42/N M C</option>
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205 <option value=" P 42/N C M"> P 42/N C M</option>
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206 <option value=" I 4/M M M"> I 4/M M M</option>
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207 <option value=" I 4/M C M"> I 4/M C M</option>
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208 <option value=" I 41/A M D"> I 41/A M D</option>
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209 <option value=" I 41/A C D"> I 41/A C D</option>
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210 <option value=" P 3"> P 3</option>
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211 <option value=" P 31"> P 31</option>
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212 <option value=" P 32"> P 32</option>
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213 <option value=" R 3"> R 3</option>
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214 <option value=" P -3"> P -3</option>
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215 <option value=" R -3"> R -3</option>
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216 <option value=" P 3 1 2"> P 3 1 2</option>
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217 <option value=" P 3 2 1"> P 3 2 1</option>
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218 <option value=" P 31 1 2"> P 31 1 2</option>
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219 <option value=" P 31 2 1"> P 31 2 1</option>
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220 <option value=" P 32 1 2"> P 32 1 2</option>
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221 <option value=" P 32 2 1"> P 32 2 1</option>
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222 <option value=" R 3 2"> R 3 2</option>
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223 <option value=" P 3 M 1"> P 3 M 1</option>
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224 <option value=" P 3 1 M"> P 3 1 M</option>
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225 <option value=" P 3 C 1"> P 3 C 1</option>
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226 <option value=" P 3 1 C"> P 3 1 C</option>
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227 <option value=" R 3 M"> R 3 M</option>
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228 <option value=" R 3 C"> R 3 C</option>
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229 <option value=" P -3 1 M"> P -3 1 M</option>
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230 <option value=" P -3 1 C"> P -3 1 C</option>
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231 <option value=" P -3 M 1"> P -3 M 1</option>
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232 <option value=" P -3 C 1"> P -3 C 1</option>
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233 <option value=" R -3 M"> R -3 M</option>
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234 <option value=" R -3 C"> R -3 C</option>
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235 <option value=" P 6"> P 6</option>
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236 <option value=" P 61"> P 61</option>
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237 <option value=" P 65"> P 65</option>
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238 <option value=" P 62"> P 62</option>
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239 <option value=" P 64"> P 64</option>
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240 <option value=" P 63"> P 63</option>
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241 <option value=" P -6"> P -6</option>
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242 <option value=" P 6/M"> P 6/M</option>
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243 <option value=" P 63/M"> P 63/M</option>
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244 <option value=" P 6 2 2"> P 6 2 2</option>
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245 <option value=" P 61 2 2"> P 61 2 2</option>
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246 <option value=" P 65 2 2"> P 65 2 2</option>
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247 <option value=" P 62 2 2"> P 62 2 2</option>
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248 <option value=" P 64 2 2"> P 64 2 2</option>
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249 <option value=" P 63 2 2"> P 63 2 2</option>
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250 <option value=" P 6 M M"> P 6 M M</option>
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251 <option value=" P 6 C C"> P 6 C C</option>
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252 <option value=" P 63 C M"> P 63 C M</option>
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253 <option value=" P 63 M C"> P 63 M C</option>
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254 <option value=" P -6 M 2"> P -6 M 2</option>
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255 <option value=" P -6 C 2"> P -6 C 2</option>
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256 <option value=" P -6 2 M"> P -6 2 M</option>
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257 <option value=" P -6 2 C"> P -6 2 C</option>
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258 <option value=" P 6/M M M"> P 6/M M M</option>
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259 <option value=" P 6/M C C"> P 6/M C C</option>
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260 <option value=" P 63/M C M"> P 63/M C M</option>
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261 <option value=" P 63/M M C"> P 63/M M C</option>
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262 <option value=" P 2 3"> P 2 3</option>
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263 <option value=" F 2 3"> F 2 3</option>
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264 <option value=" I 2 3"> I 2 3</option>
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265 <option value=" P 21 3"> P 21 3</option>
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266 <option value=" I 21 3"> I 21 3</option>
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267 <option value=" P M -3"> P M -3</option>
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268 <option value=" P N -3"> P N -3</option>
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269 <option value=" F M -3"> F M -3</option>
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270 <option value=" F D -3"> F D -3</option>
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271 <option value=" I M -3"> I M -3</option>
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272 <option value=" P A -3"> P A -3</option>
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273 <option value=" I A -3"> I A -3</option>
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274 <option value=" P 4 3 2"> P 4 3 2</option>
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275 <option value=" P 42 3 2"> P 42 3 2</option>
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276 <option value=" F 4 3 2"> F 4 3 2</option>
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277 <option value=" F 41 3 2"> F 41 3 2</option>
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278 <option value=" I 4 3 2"> I 4 3 2</option>
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279 <option value=" P 43 3 2"> P 43 3 2</option>
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280 <option value=" P 41 3 2"> P 41 3 2</option>
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281 <option value=" I 41 3 2"> I 41 3 2</option>
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282 <option value=" P -4 3 M"> P -4 3 M</option>
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283 <option value=" F 4 -3 M"> F 4 -3 M</option>
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284 <option value=" I -4 3 M"> I -4 3 M</option>
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285 <option value=" P -4 3 N"> P -4 3 N</option>
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286 <option value=" F -4 3 C"> F -4 3 C</option>
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287 <option value=" I -4 3 D"> I -4 3 D</option>
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288 <option value=" P M -3 M"> P M -3 M</option>
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289 <option value=" P N -3 N"> P N -3 N</option>
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290 <option value=" P M -3 N"> P M -3 N</option>
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291 <option value=" P N -3 M"> P N -3 M</option>
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292 <option value=" F M -3 M"> F M -3 M</option>
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293 <option value=" F M -3 C"> F M -3 C</option>
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294 <option value=" F D -3 M"> F D -3 M</option>
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295 <option value=" F D -3 C"> F D -3 C</option>
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296 <option value=" I M -3 M"> I M -3 M</option>
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297 <option value=" I A -3 D"> I A -3 D</option>
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298 <option value=" B 2"> B 2</option>
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299 <option value=" P 1 1 21"> P 1 1 21</option>
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300 <option value=" P 2 21 21"> P 2 21 21</option>
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301 <option value=" P 21 2 21"> P 21 2 21</option>
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302 <option value=" I 1 2 1"> I 1 2 1</option>
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303 </param>
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304 <param name="param_axis_a" type="float" value="0.0" label="cell axis a" help="(-axis_a) "/>
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305 <param name="param_axis_b" type="float" value="0.0" label="cell axis" help="(-axis_b) "/>
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306 <param name="param_axis_c" type="float" value="0.0" label="cell axis c" help="(-axis_c) "/>
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307 <param name="param_angle_alpha" type="float" min="0.0" max="359.0" optional="True" value="0.0" label="cell angle alpha" help="(-angle_alpha) "/>
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308 <param name="param_angle_beta" type="float" min="0.0" max="359.0" optional="True" value="0.0" label="cell angle beta" help="(-angle_beta) "/>
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309 <param name="param_angle_gamma" type="float" min="0.0" max="359.0" optional="True" value="0.0" label="cell angle gamma" help="(-angle_gamma) "/>
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310 <param name="param_from_uc_a" type="integer" min="0" max="9" optional="False" value="0" label="from unit cell index a" help="(-from_uc_a) "/>
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311 <param name="param_from_uc_b" type="integer" min="0" max="9" optional="False" value="0" label="from unit cell index" help="(-from_uc_b) "/>
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312 <param name="param_from_uc_c" type="integer" min="0" max="9" optional="False" value="0" label="from unit cell index c" help="(-from_uc_c) "/>
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313 <param name="param_to_uc_a" type="integer" value="0" label="to unit cell index a" help="(-to_uc_a) "/>
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314 <param name="param_to_uc_b" type="integer" value="0" label="to unit cell index" help="(-to_uc_b) "/>
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315 <param name="param_to_uc_c" type="integer" value="0" label="to unit cell index c" help="(-to_uc_c) "/>
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316 </inputs>
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317 <expand macro="advanced_options"/>
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318 <outputs>
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319 <data name="param_o" format="pdb"/>
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320 </outputs>
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321 <help>TODO: Manual
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322
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323 </help>
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324 </tool>
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