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1 <tool id="ctb_shapeit" name="Shape alignment" version="0.1">
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2 <description>against a database of molecules (Shape-it)</description>
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3 <requirements>
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4 <requirement type="package" version="1.0.1">silicos_it</requirement>
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5 <requirement type="package" version="2.3.2">openbabel</requirement>
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6 </requirements>
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7 <command >
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8 shape-it
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9 --format ${database.ext}
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10 --dbase $database
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11 --reference $reference
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12 --addIterations $addIterations
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13 #if int($best) > 0:
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14 --best $best
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15 #end if
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16 --cutoff $cutoff
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17 #if $scores == 'yes':
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18 --scores $output_scores
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19 #end if
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20 --rankBy $rankBy
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21 $noref
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22 --out $output 2>&1
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23 </command>
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24 <inputs>
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25 <param name="reference" type="data" format='sdf,mol,mol2' label="Refrence molecule (with 3D coordinates)" />
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26 <param name="database" type="data" format='sdf,mol,mol2' label="Database of molecules (with 3D coordinates)" />
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27 <param name="cutoff" type="float" value="0.0" label="Only molecules with a score higher than the cutoff are reported." help="The scoring function is defined by the scoring scheme.">
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28 <validator type="in_range" min="0.0" />
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29 </param>
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30 <param name='addIterations' type='integer' value='0' label='Perform N additional optimization steps with the simulated annealing procedure' help="The default value is set to 0, which refers to only a local gradient ascent."/>
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31 <param name='best' type='integer' value='0' label='The N best scoring molecules are reported' help="0 means all molecules are reported"/>
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32 <param name='scores' type='boolean' truevalue='yes' falsevalue='' label='Output a Tab-delimited text file with the scores of molecules' checked="false" />
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33 <param name='noref' type='boolean' truevalue='--noRef' falsevalue='' label='The reference molecule is not written into the output files' checked="false" />
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34 <param name='rankBy' type='select' format='text' label="This option defines the used scoring scheme">
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35 <option value='TANIMOTO'>Tanimoto</option>
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36 <option value='TVERSKY_REF'>TVERSKY_REF</option>
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37 <option value='TVERSKY_DB'>TVERSKY_DB</option>
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38 </param>
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39 </inputs>
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40 <outputs>
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41 <data name="output" format_source='database' />
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42 <data name="output_scores" format="tabular">
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43 <filter>scores == "yes"</filter>
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44 </data>
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45 </outputs>
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46 <tests>
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47 <test>
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48 <param name="database" ftype='sdf' value="CID_3033.sdf" />
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49 <param name="reference" type="sdf" value='CID_3037.sdf' />
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50 <param name="cutoff" value="0.0" />
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51 <param name='addIterations' value='0' />
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52 <param name='best' value='0' />
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53 <output name="output" ftype='sdf' file="shapeit_on_CID3033_and_CID3037.sdf" />
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54 </test>
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55 </tests>
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56 <help>
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57
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58
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59 .. class:: infomark
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60
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61 **What this tool does**
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62
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63 Shape-it_ is a tool that aligns a reference molecule against a set of database
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64 molecules using the shape of the molecules as the align criterion.
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65 It is based on the use of `gaussian volumes as descriptor for molecular shape`_ as it was introduced by Grant and Pickup.
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66
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67 The program expects one reference molecule with
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68 its three-dimensional coordinates and one database files containing one
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69 or more molecules in three dimensions. The results are either the alignment
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70 of all database molecules and their respective scores or the N best
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71 scoring molecules of the complete database.
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72
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73 .. _gaussian volumes as descriptor for molecular shape: http://pubs.acs.org/doi/abs/10.1021/j100011a016
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74 .. _Shape-it: http://silicos-it.com/software/shape-it/1.0.1/shape-it.html
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75
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76 -----
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77
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78 .. class:: infomark
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79
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80 **Input**
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81
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82
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83 | - `formates recognized by OpenBabel`_
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84
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85 .. _formates recognized by OpenBabel: http://openbabel.org/wiki/Category:Formats
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86
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87 * Example::
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88
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89 - database
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90 27 28 0 0 0 0 0 0 0999 V2000
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91 -4.8550 1.3401 0.2120 Cl 0 0 0 0 0 0 0 0 0 0 0 0
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92 4.8529 -1.3406 0.2121 Cl 0 0 0 0 0 0 0 0 0 0 0 0
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93 -0.1809 -2.1668 -0.3789 O 0 0 0 0 0 0 0 0 0 0 0 0
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94 0.1788 2.1664 -0.3787 O 0 0 0 0 0 0 0 0 0 0 0 0
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95 -0.0011 -0.0002 1.4744 C 0 0 0 0 0 0 0 0 0 0 0 0
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96 -1.2222 -0.2738 0.6597 C 0 0 0 0 0 0 0 0 0 0 0 0
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97 1.2377 0.2772 0.6480 C 0 0 0 0 0 0 0 0 0 0 0 0
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98 -1.2586 -1.3462 -0.2316 C 0 0 0 0 0 0 0 0 0 0 0 0
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99 1.2565 1.3457 -0.2314 C 0 0 0 0 0 0 0 0 0 0 0 0
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100 -2.3343 0.5568 0.7972 C 0 0 0 0 0 0 0 0 0 0 0 0
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101 2.3322 -0.5574 0.7972 C 0 0 0 0 0 0 0 0 0 0 0 0
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102 -2.4069 -1.5879 -0.9855 C 0 0 0 0 0 0 0 0 0 0 0 0
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103 2.4048 1.5875 -0.9852 C 0 0 0 0 0 0 0 0 0 0 0 0
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104 -3.4827 0.3152 0.0433 C 0 0 0 0 0 0 0 0 0 0 0 0
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105 3.4807 -0.3156 0.0435 C 0 0 0 0 0 0 0 0 0 0 0 0
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106 -3.5190 -0.7571 -0.8481 C 0 0 0 0 0 0 0 0 0 0 0 0
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107 3.5170 0.7568 -0.8478 C 0 0 0 0 0 0 0 0 0 0 0 0
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108 -0.1548 0.8649 2.1342 H 0 0 0 0 0 0 0 0 0 0 0 0
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109 0.1601 -0.8435 2.1593 H 0 0 0 0 0 0 0 0 0 0 0 0
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110 -2.3089 1.3938 1.4913 H 0 0 0 0 0 0 0 0 0 0 0 0
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111 2.3053 -1.3909 1.4943 H 0 0 0 0 0 0 0 0 0 0 0 0
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112 -2.4415 -2.4213 -1.6818 H 0 0 0 0 0 0 0 0 0 0 0 0
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113 2.4469 2.4191 -1.6835 H 0 0 0 0 0 0 0 0 0 0 0 0
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114 -4.4070 -0.9574 -1.4422 H 0 0 0 0 0 0 0 0 0 0 0 0
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115 4.4050 0.9570 -1.4418 H 0 0 0 0 0 0 0 0 0 0 0 0
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116 0.2961 -2.2262 0.4641 H 0 0 0 0 0 0 0 0 0 0 0 0
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117 0.3872 2.8487 -1.0397 H 0 0 0 0 0 0 0 0 0 0 0 0
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118 1 14 1 0 0 0 0
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119 2 15 1 0 0 0 0
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120 3 8 1 0 0 0 0
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121 3 26 1 0 0 0 0
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122 4 9 1 0 0 0 0
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123 4 27 1 0 0 0 0
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124 5 6 1 0 0 0 0
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125 5 7 1 0 0 0 0
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126 .....
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127
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128 - reference
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129
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130 30 31 0 0 0 0 0 0 0999 V2000
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131 1.9541 1.1500 -2.5078 Cl 0 0 0 0 0 0 0 0 0 0 0 0
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132 1.1377 -1.6392 2.1136 Cl 0 0 0 0 0 0 0 0 0 0 0 0
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133 -3.2620 -2.9284 -1.0647 O 0 0 0 0 0 0 0 0 0 0 0 0
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134 -2.7906 -1.9108 0.9092 O 0 0 0 0 0 0 0 0 0 0 0 0
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135 0.2679 -0.2051 -0.3990 N 0 0 0 0 0 0 0 0 0 0 0 0
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136 -2.0640 0.5139 -0.3769 C 0 0 0 0 0 0 0 0 0 0 0 0
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137 -0.7313 0.7178 -0.0192 C 0 0 0 0 0 0 0 0 0 0 0 0
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138 -2.4761 -0.6830 -1.1703 C 0 0 0 0 0 0 0 0 0 0 0 0
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139 1.6571 -0.2482 -0.1795 C 0 0 0 0 0 0 0 0 0 0 0 0
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140 -3.0382 1.4350 0.0081 C 0 0 0 0 0 0 0 0 0 0 0 0
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141 -0.3728 1.8429 0.7234 C 0 0 0 0 0 0 0 0 0 0 0 0
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142 -2.6797 2.5600 0.7506 C 0 0 0 0 0 0 0 0 0 0 0 0
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143 -1.3470 2.7640 1.1083 C 0 0 0 0 0 0 0 0 0 0 0 0
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144 2.5353 0.3477 -1.0918 C 0 0 0 0 0 0 0 0 0 0 0 0
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145 2.1740 -0.8865 0.9534 C 0 0 0 0 0 0 0 0 0 0 0 0
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146 -2.8480 -1.8749 -0.3123 C 0 0 0 0 0 0 0 0 0 0 0 0
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147 3.9124 0.3058 -0.8739 C 0 0 0 0 0 0 0 0 0 0 0 0
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148 3.5511 -0.9285 1.1713 C 0 0 0 0 0 0 0 0 0 0 0 0
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149 4.4203 -0.3324 0.2576 C 0 0 0 0 0 0 0 0 0 0 0 0
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150 -1.7086 -0.9792 -1.8930 H 0 0 0 0 0 0 0 0 0 0 0 0
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151 -3.3614 -0.4266 -1.7676 H 0 0 0 0 0 0 0 0 0 0 0 0
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152 -0.0861 -1.1146 -0.6780 H 0 0 0 0 0 0 0 0 0 0 0 0
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153 -4.0812 1.2885 -0.2604 H 0 0 0 0 0 0 0 0 0 0 0 0
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154 0.6569 2.0278 1.0167 H 0 0 0 0 0 0 0 0 0 0 0 0
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155 -3.4382 3.2769 1.0511 H 0 0 0 0 0 0 0 0 0 0 0 0
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156 -1.0683 3.6399 1.6868 H 0 0 0 0 0 0 0 0 0 0 0 0
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157 4.6037 0.7654 -1.5758 H 0 0 0 0 0 0 0 0 0 0 0 0
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158 3.9635 -1.4215 2.0480 H 0 0 0 0 0 0 0 0 0 0 0 0
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159 5.4925 -0.3651 0.4274 H 0 0 0 0 0 0 0 0 0 0 0 0
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160 -3.5025 -3.7011 -0.5102 H 0 0 0 0 0 0 0 0 0 0 0 0
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161 1 14 1 0 0 0 0
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162 2 15 1 0 0 0 0
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163 3 16 1 0 0 0 0
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164 3 30 1 0 0 0 0
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165 4 16 2 0 0 0 0
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166 5 7 1 0 0 0 0
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167 5 9 1 0 0 0 0
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168 5 22 1 0 0 0 0
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169 6 7 1 0 0 0 0
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170 6 8 1 0 0 0 0
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171 ......
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172
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173 - cutoff : 0.0
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174
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175 -----
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176
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177 .. class:: infomark
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178
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179 **Output**
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180
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181 * Example::
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182
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183 27 28 0 0 0 0 0 0 0 0999 V2000
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184 -4.8550 1.3401 0.2120 Cl 0 0 0 0 0 0 0 0 0 0 0 0
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185 4.8529 -1.3406 0.2121 Cl 0 0 0 0 0 0 0 0 0 0 0 0
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186 -0.1809 -2.1668 -0.3789 O 0 0 0 0 0 0 0 0 0 0 0 0
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187 0.1788 2.1664 -0.3787 O 0 0 0 0 0 0 0 0 0 0 0 0
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188 -0.0011 -0.0002 1.4744 C 0 0 0 0 0 0 0 0 0 0 0 0
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189 -1.2222 -0.2738 0.6597 C 0 0 0 0 0 0 0 0 0 0 0 0
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190 1.2377 0.2772 0.6480 C 0 0 0 0 0 0 0 0 0 0 0 0
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191 -1.2586 -1.3462 -0.2316 C 0 0 0 0 0 0 0 0 0 0 0 0
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192 1.2565 1.3457 -0.2314 C 0 0 0 0 0 0 0 0 0 0 0 0
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193 -2.3343 0.5568 0.7972 C 0 0 0 0 0 0 0 0 0 0 0 0
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194 2.3322 -0.5574 0.7972 C 0 0 0 0 0 0 0 0 0 0 0 0
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195 -2.4069 -1.5879 -0.9855 C 0 0 0 0 0 0 0 0 0 0 0 0
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196 2.4048 1.5875 -0.9852 C 0 0 0 0 0 0 0 0 0 0 0 0
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197 -3.4827 0.3152 0.0433 C 0 0 0 0 0 0 0 0 0 0 0 0
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198 3.4807 -0.3156 0.0435 C 0 0 0 0 0 0 0 0 0 0 0 0
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199 -3.5190 -0.7571 -0.8481 C 0 0 0 0 0 0 0 0 0 0 0 0
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200 3.5170 0.7568 -0.8478 C 0 0 0 0 0 0 0 0 0 0 0 0
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201 -0.1548 0.8649 2.1342 H 0 0 0 0 0 0 0 0 0 0 0 0
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202 0.1601 -0.8435 2.1593 H 0 0 0 0 0 0 0 0 0 0 0 0
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203 -2.3089 1.3938 1.4913 H 0 0 0 0 0 0 0 0 0 0 0 0
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204 2.3053 -1.3909 1.4943 H 0 0 0 0 0 0 0 0 0 0 0 0
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205 -2.4415 -2.4213 -1.6818 H 0 0 0 0 0 0 0 0 0 0 0 0
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206 2.4469 2.4191 -1.6835 H 0 0 0 0 0 0 0 0 0 0 0 0
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207 -4.4070 -0.9574 -1.4422 H 0 0 0 0 0 0 0 0 0 0 0 0
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208 4.4050 0.9570 -1.4418 H 0 0 0 0 0 0 0 0 0 0 0 0
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209 0.2961 -2.2262 0.4641 H 0 0 0 0 0 0 0 0 0 0 0 0
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210 0.3872 2.8487 -1.0397 H 0 0 0 0 0 0 0 0 0 0 0 0
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211 1 14 1 0 0 0 0
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212 2 15 1 0 0 0 0
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213 3 8 1 0 0 0 0
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214 3 26 1 0 0 0 0
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215 4 9 1 0 0 0 0
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216 4 27 1 0 0 0 0
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217 5 6 1 0 0 0 0
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218 5 7 1 0 0 0 0
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219 5 18 1 0 0 0 0
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220 5 19 1 0 0 0 0
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221 6 8 2 0 0 0 0
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222 ......
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223
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224 -----
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225
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226 .. class:: infomark
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227
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228 **Cite**
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229
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230 `Silicos-it`_ - shape-it
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231
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232 .. _Silicos-it: http://silicos-it.com/software/shape-it/1.0.1/shape-it.html
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233
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234
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235 </help>
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236 </tool>
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