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1 <macros>
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2 <xml name="multiple_input" token_name="input_files" token_max_num="10" token_format="txt" token_label="Sparse matrix file (.mtx, .txt)" token_help_text="Specify a sparse matrix file in .txt format.">
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3 <repeat name="@NAME@" min="1" max="@MAX_NUM@" title="Select input file(s):">
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4 <param name="input" type="data" format="@FORMAT@" label="@LABEL@" help="@HELP_TEXT@"/>
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5 <section name="structureparams" title="Structure Parameters (Make Changes!)" expanded="false">
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6 <param name="number" label="Number" type="integer" multiple="True" value="100" help="How many molecules to create"/>
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7 <param name="radius" label="Radius" type="float" multiple="True" value="1.0" help="Molecular radius (angstroms)"/>
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8 <param name="resnumbers" label="Resnumbers" type="integer" multiple="True" value="0" help="Default is to number 1 to n for type 1 and 1 to n for type 2"/>
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9 <repeat name="constraints_repeat" min="1" max="3" title="Select constraint(s) to apply:">
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10 <conditional name="constraints">
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11 <param name="constraint" type="select" label="Shape constraint selection" help="Choose the constraint for the molecules">
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12 <option value="fixed">fixed - hold 1 molecule in fixed position (hardcoded number=1) Exclusive other constraints not possible</option>
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13 <option selected="True" value="cube">cube</option>
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14 <option value="box">box</option>
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15 <option value="sphere">sphere</option>
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16 <option value="ellipsoid">ellipsoid </option>
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17 <option value="plane">plane</option>
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18 <option value="cylinder">cylinder</option>
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19 </param>
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20 <when value="fixed">
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21 <param name="center" type="select" label="Center" help="center">
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22 <option value="Yes">yes</option>
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23 <option value="No">no</option>
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24 </param>
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25 <param name="x" type="float" value="0.0" label="x" />
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26 <param name="y" type="float" value="0.0" label="y" />
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27 <param name="z" type="float" value="0.0" label="z" />
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28 <param name="a" type="float" value="0.0" label="a" />
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29 <param name="b" type="float" value="0.0" label="b" />
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30 <param name="g" type="float" value="0.0" label="g" />
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31 </when>
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32 <when value="cube">
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33 <param name="placement" type="select" label="Choose placement of molecules" help="Choose the placement of the molecules">
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34 <option value="inside">inside</option>
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35 <option value="outside">outside</option>
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36 </param>
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37 <param name="xmin" type="float" value="0.0" label="xmin" />
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38 <param name="ymin" type="float" value="0.0" label="ymin" />
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39 <param name="zmin" type="float" value="0.0" label="zmin" />
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40 <param name="d" type="float" value="40.0" label="d" />
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41 </when>
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42 <when value="box">
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43 <param name="placement" type="select" label="Choose placement of molecules" help="Choose the placement of the molecules">
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44 <option value="inside">inside</option>
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45 <option value="outside">outside</option>
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46 </param>
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47 <param name="xmin" type="float" value="0.0" label="xmin" />
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48 <param name="ymin" type="float" value="0.0" label="ymin" />
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49 <param name="zmin" type="float" value="0.0" label="zmin" />
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50 <param name="xmax" type="float" value="40.0" label="xmax" />
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51 <param name="ymax" type="float" value="40.0" label="ymax" />
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52 <param name="zmax" type="float" value="40.0" label="zmax" />
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53 </when>
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54 <when value="sphere">
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55 <param name="placement" type="select" label="Choose placement of molecules" help="Choose the placement of the molecules">
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56 <option value="inside">inside</option>
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57 <option value="outside">outside</option>
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58 </param>
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59 <param name="a" type="float" value="0.0" label="a" />
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60 <param name="b" type="float" value="0.0" label="b" />
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61 <param name="c" type="float" value="0.0" label="c" />
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62 <param name="d" type="float" value="40.0" label="d" />
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63 </when>
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64 <when value="ellipsoid">
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65 <param name="placement" type="select" label="Choose placement of molecules" help="Choose the placement of the molecules">
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66 <option value="inside">inside</option>
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67 <option value="outside">outside</option>
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68 </param>
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69 <param name="a1" type="float" value="0.0" label="a1" />
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70 <param name="b1" type="float" value="0.0" label="b1" />
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71 <param name="c1" type="float" value="0.0" label="c1" />
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72 <param name="a2" type="float" value="20.0" label="a2" />
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73 <param name="b2" type="float" value="20.0" label="b2" />
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74 <param name="c2" type="float" value="20.0" label="c2" />
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75 <param name="d" type="float" value="40.0" label="d" />
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76 </when>
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77 <when value="plane">
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78 <param name="placement" type="select" label="Choose placement of molecules" help="Choose the placement of the molecules">
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79 <option value="over">over</option>
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80 <option value="below">below</option>
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81 </param>
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82 <param name="a" type="float" value="0.0" label="a" />
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83 <param name="b" type="float" value="0.0" label="b" />
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84 <param name="c" type="float" value="0.0" label="c" />
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85 <param name="d" type="float" value="10.0" label="d" />
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86 </when>
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87 <when value="cylinder">
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88 <param name="placement" type="select" label="Choose placement of molecules" help="Choose the placement of the molecules">
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89 <option value="inside">inside</option>
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90 <option value="outside">outside</option>
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91 </param>
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92 <param name="a1" type="float" value="0.0" label="a1" />
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93 <param name="b1" type="float" value="0.0" label="b1" />
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94 <param name="c1" type="float" value="0.0" label="c1" />
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95 <param name="a2" type="float" value="40.0" label="a2" />
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96 <param name="b2" type="float" value="40.0" label="b2" />
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97 <param name="c2" type="float" value="40.0" label="c2" />
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98 <param name="d" type="float" value="10.0" label="d" />
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99 <param name="l" type="float" value="10.0" label="l" />
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100 </when>
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101 </conditional>
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102 </repeat>
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103 </section>
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104 </repeat>
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105 </xml>
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106 </macros>
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