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1 <tool id="ctb_confab" name="Conformer calculation" version="0.1">
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2 <description>for molecules (confab)</description>
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3 <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="100" shared_inputs="" merge_outputs="outfile"></parallelism>
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4 <requirements>
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5 <requirement type="package" version="1.0.1">confab</requirement>
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6 </requirements>
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7 <command> confab
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8 -i ${infile.ext}
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9 -o sdf
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10 -r $RMSD
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11 -e $energy
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12 -c $conformers
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13 $first_conformer
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14 $infile
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15 $outfile 2>&1
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16 </command>
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17 <inputs>
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18 <param name="infile" type="data" format="sdf,mol2" label="Input molecule with 3D coordinates" help="Dataset missing? See TIP below"/>
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19 <param name='RMSD' type='float' value='0.5' label='RMSD cutoff (in Angstrom)' />
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20 <param name='energy' type='float' value='50.0' label='Energy cutoff (in kcal/mol)' />
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21 <param name='conformers' type='integer' value='100' label='Max number of conformers to test' />
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22 <param name='first_conformer' type='boolean' truevalue='-a' falsevalue='' label='Include the input conformation as the first conformer' />
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23 </inputs>
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24 <outputs>
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25 <data format="sdf" name="outfile" label="${tool.name} on ${on_string}"/>
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26 </outputs>
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27 <tests>
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28 <test>
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29 <param name="infile" value='CID_3033.sdf' ftype='sdf' />
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30 <param name='RMSD' value='0.5' />
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31 <param name='energy' value='50.0' />
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32 <param name='conformers' value='100000' />
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33 <param name='first_conformer' value='-a' />
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34 <output name="outfile" file='confab_on_CID_3033.sdf' ftype='sdf' />
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35 </test>
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36 </tests>
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37 <help>
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38
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39 .. class:: infomark
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40
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41 **What this tool does**
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42
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43 Confab_ is a conformation generator. The algorithm starts with an input 3D structure which, after some initialisation steps, is used to generate multiple conformers which are filtered on-the-fly to identify diverse low energy conformers.
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44
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45 .. _Confab: https://code.google.com/p/confab/
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46
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47 -----
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48
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49 .. class:: infomark
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50
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51 **Input**
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52
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53 * Example::
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54
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55 21.2060 9.9350 63.0810 C 0 0 0 0 0 0 0 0 0 0 0 0
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56 21.2410 9.4460 64.5510 C 0 0 0 0 0 0 0 0 0 0 0 0
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57 22.0000 8.1250 64.6300 C 0 0 0 0 0 0 0 0 0 0 0 0
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58 21.7010 7.3010 65.5120 O 0 0 0 0 0 0 0 0 0 0 0 0
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59 23.1180 7.8720 63.7340 C 0 0 0 0 0 0 0 0 0 0 0 0
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60 23.4530 8.7270 62.7850 C 0 0 0 0 0 0 0 0 0 0 0 0
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61 24.6970 8.4430 61.9510 C 0 0 0 0 0 0 0 0 0 0 0 0
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62
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63 .......
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64
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65 1 2 1 0 0 0 0
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66 1 11 1 0 0 0 0
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67 2 3 1 0 0 0 0
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68 3 4 2 0 0 0 0
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69 3 5 1 0 0 0 0
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70 5 6 2 0 0 0 0
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71 6 7 1 0 0 0 0
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72
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73 RMSD cutoff (in Angstrom) 0.5
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74 Energy cutoff (in kcal/mol) 50.0
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75 Max number of conformers to test 100000
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76 Include the input conformation as the first conformer False
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77
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78 -----
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79
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80 .. class:: infomark
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81
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82 **Output**
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83
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84 * Example::
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85
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86 23 26 0 0 0 0 0 0 0 0999 V2000
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87 21.2060 9.9350 63.0810 C 0 0 0 0 0 0 0 0 0 0 0 0
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88 21.2410 9.4460 64.5510 C 0 0 0 0 0 0 0 0 0 0 0 0
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89 22.0000 8.1250 64.6300 C 0 0 0 0 0 0 0 0 0 0 0 0
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90 21.7010 7.3010 65.5120 O 0 0 0 0 0 0 0 0 0 0 0 0
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91 23.1180 7.8720 63.7340 C 0 0 0 0 0 0 0 0 0 0 0 0
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92 23.4530 8.7270 62.7850 C 0 0 0 0 0 0 0 0 0 0 0 0
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93 24.6970 8.4430 61.9510 C 0 0 0 0 0 0 0 0 0 0 0 0
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94 24.4490 8.6370 60.4430 C 0 0 0 0 0 0 0 0 0 0 0 0
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95 23.7890 9.9970 60.0980 C 0 0 2 0 0 0 0 0 0 0 0 0
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96 22.4340 10.0950 60.8720 C 0 0 1 0 0 0 0 0 0 0 0 0
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97 22.6140 10.0230 62.4340 C 0 0 1 0 0 0 0 0 0 0 0 0
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98 21.6330 11.3540 60.4500 C 0 0 0 0 0 0 0 0 0 0 0 0
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99 21.4320 11.4340 58.9110 C 0 0 0 0 0 0 0 0 0 0 0 0
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100 22.7860 11.4040 58.1690 C 0 0 1 0 0 0 0 0 0 0 0 0
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101 23.4830 10.0600 58.5980 C 0 0 1 0 0 0 0 0 0 0 0 0
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102 24.6740 9.9180 57.6180 C 0 0 0 0 0 0 0 0 0 0 0 0
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103 24.0720 10.4500 56.2670 C 0 0 0 0 0 0 0 0 0 0 0 0
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104 22.7140 11.1490 56.6270 C 0 0 2 0 0 0 0 0 0 0 0 0
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105 23.6590 12.6770 58.4540 C 0 0 0 0 0 0 0 0 0 0 0 0
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106 23.4270 11.2460 63.0070 C 0 0 0 0 0 0 0 0 0 0 0 0
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107 22.3750 12.3880 55.7810 C 0 0 0 0 0 0 0 0 0 0 0 0
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108 23.2120 12.8760 55.0520 O 0 0 0 0 0 0 0 0 0 0 0 0
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109 21.0090 12.9760 55.8570 C 0 0 0 0 0 0 0 0 0 0 0 0
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110
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111 ::
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112
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113 1 2 1 0 0 0 0
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114 1 11 1 0 0 0 0
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115 2 3 1 0 0 0 0
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116 3 4 2 0 0 0 0
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117 3 5 1 0 0 0 0
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118 5 6 2 0 0 0 0
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119 6 7 1 0 0 0 0
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120 6 11 1 0 0 0 0
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121 7 8 1 0 0 0 0
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122 9 8 1 6 0 0 0
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123 10 9 1 1 0 0 0
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124
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125 -----
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126
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127 .. class:: infomark
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128
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129 **Cite**
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130
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131 Confab_
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132
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133 .. _Confab: https://code.google.com/p/confab/
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134
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135
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136 </help>
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137
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138 </tool>
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