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1 <tool id="ctb_chemfp_mol2fps" name="Molecules to Fingerprints" version="0.2.0">
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2 <description>with different fingerprint types</description>
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3 <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism>
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4 <requirements>
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5 <requirement type="package" version="1.1p1">chemfp</requirement>
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6 <requirement type="package" version="2012_12_1">rdkit</requirement>
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7 </requirements>
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8 <command>
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13
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9 #set $fptype = $fp_opts.fp_opts_selector
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10
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9
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11 #if $fptype in ['--FP2', '--FP3', '--FP4', '--MACCS']:
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12 ## Open Babel fingerprints
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13
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13 ob2fps $fptype --in "${infile.ext}" "${infile}" -o "${outfile}"
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9
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14 #else:
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15 ## RDKit fingerprints
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16 rdkit2fps --in "${infile.ext}" "${infile}" -o "${outfile}"
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13
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17 #if $fp_opts.fp_opts_selector == "--RDK":
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9
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18 --RDK
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19 --fpSize $fp_opts.fpSize
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20 --minPath $fp_opts.minPath
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21 --maxPath $fp_opts.maxPath
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22 --nBitsPerHash $fp_opts.nBitsPerHash
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23 $fp_opts.useHs
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13
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24 #elif $fp_opts.fp_opts_selector == "--torsions":
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9
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25 --torsions
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26 --fpSize $fp_opts.fpSize
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27 --targetSize $fp_opts.targetSize
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13
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28 #elif $fp_opts.fp_opts_selector == "--morgan":
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9
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29 --morgan
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30 --fpSize $fp_opts.fpSize
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31 --radius $fp_opts.radius
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32 $fp_opts.useFeatures
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33 $fp_opts.useChirality
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34 $fp_opts.useBondTypes
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13
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35 #elif $fp_opts.fp_opts_selector == "--pairs":
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9
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36 --paris
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37 --fpSize $fp_opts.fpSize
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38 --minLength $fp_opts.minLength
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39 --maxLength $fp_opts.maxLength
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13
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40 #elif $fp_opts.fp_opts_selector == "--maccs166":
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9
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41 --maccs166
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13
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42 #elif $fp_opts.fp_opts_selector == "--substruct":
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9
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43 --substruct
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13
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44 #end if
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45 #end if
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46 --errors report 2>&1
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9
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47 </command>
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48 <inputs>
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49 <param name="infile" type='data' format="sdf,smi,mol,mol2,cml,inchi" label="molecule file"/>
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50 <conditional name="fp_opts">
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51 <param name="fp_opts_selector" type="select" label="Type of fingerprint">
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52 <option value='--FP2' selected="True">Open Babel FP2 fingerprints</option>
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53 <option value='--FP3'>Open Babel FP3 fingerprints</option>
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54 <option value='--FP4'>Open Babel FP4 fingerprints</option>
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55 <option value='--MACCS'>Open Babel MACCS fingerprints</option>
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56 <option value='--RDK'>RDKit topological fingerprint</option>
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57 <option value='--torsions'>RDKit topological Torsion fingerprints</option>
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58 <option value='--morgan'>RDKit Morgan fingerprints</option>
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59 <option value='--pairs'>RDKit Atom Pair fingerprints</option>
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60 <option value='--maccs166'>RDKit MACCS fingerprints</option>
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61 <option value='--substruct'>RDKit substructure fingerprints</option>
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62 </param>
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63 <when value="--FP2" />
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64 <when value="--FP3" />
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65 <when value="--FP4" />
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66 <when value="--MACCS" />
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67 <when value="--RDK">
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68 <param name="fpSize" type="integer" value="2048" label="number of bits in the fingerprint" help="">
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69 <validator type="in_range" min="1" />
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70 </param>
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71 <param name="minPath" type="integer" value="1" label="minimum number of bonds to include in the subgraph" help="">
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72 <validator type="in_range" min="1" />
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73 </param>
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74 <param name="maxPath" type="integer" value="7" label="maximum number of bonds to include in the subgraph" help="">
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75 <validator type="in_range" min="1" />
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76 </param>
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77 <param name="nBitsPerHash" type="integer" value="4" label="number of bits to set per path" help="">
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78 <validator type="in_range" min="1" />
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79 </param>
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80 <param name="useHs" type="boolean" label="include information about the number of hydrogens on each atom" truevalue="--useHs 1" falsevalue="--useHs 0" checked="true" />
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81 </when>
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82 <when value="--torsions">
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83 <param name="fpSize" type="integer" value="2048" label="number of bits in the fingerprint" help="">
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84 <validator type="in_range" min="1" />
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85 </param>
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86 <param name="targetSize" type="integer" value="4" label="number of target bits in the fingerprint" help="">
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87 <validator type="in_range" min="1" />
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88 </param>
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89 </when>
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90 <when value="--morgan">
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91 <param name="fpSize" type="integer" value="2048" label="number of bits in the fingerprint" help="">
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92 <validator type="in_range" min="1" />
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93 </param>
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94 <param name="radius" type="integer" value="2" label="radius for the Morgan algorithm" help="">
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95 <validator type="in_range" min="1" />
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96 </param>
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97 <param name="useFeatures" type="boolean" label="include information about the number of hydrogens on each atom" truevalue="--useFeatures 1" falsevalue="--useFeatures 0" checked="false" />
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98 <param name="useChirality" type="boolean" label="include information about the number of hydrogens on each atom" truevalue="--useChirality 1" falsevalue="--useChirality 0" checked="false" />
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99 <param name="useBondTypes" type="boolean" label="include information about the number of hydrogens on each atom" truevalue="--useBondTypes 1" falsevalue="--useBondTypes 0" checked="true" />
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100 </when>
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101 <when value="--pairs">
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102 <param name="fpSize" type="integer" value="2048" label="number of bits in the fingerprint" help="">
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103 <validator type="in_range" min="1" />
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104 </param>
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105 <param name="minLength" type="integer" value="1" label="minimum bond count for a pair" help="">
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106 <validator type="in_range" min="1" />
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107 </param>
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108 <param name="maxLength" type="integer" value="30" label="maximum bond count for a pair" help="">
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109 <validator type="in_range" min="1" />
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110 </param>
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111 </when>
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112 <when value="--maccs166" />
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113 <when value="--substruct" />
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114 </conditional>
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115
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116 </inputs>
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117 <outputs>
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118 <data name="outfile" format="fps" />
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119 </outputs>
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120 <tests>
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121 <!-- FP2 -->
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122 <test>
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123 <param name="infile" value="CID_2244.sdf" ftype="sdf" />
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124 <param name="fp_opts.fp_opts_selector" value="--FP2" />
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125 <output name="outfile" file="CID_2244_FP2.fps" ftype="fps" />
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126 </test>
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127 <test>
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128 <param name="infile" value="CID_2244.smi" ftype="smi" />
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129 <param name="fp_opts.fp_opts_selector" value="--FP2" />
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130 <output name="outfile" file="CID_2244_FP2.fps" ftype="fps" />
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131 </test>
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132 <!-- FP3 -->
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133 <test>
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134 <param name="infile" value="CID_2244.sdf" ftype="sdf" />
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135 <param name="fp_opts.fp_opts_selector" value="--FP3" />
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136 <output name="outfile" file="CID_2244_FP3.fps" ftype="fps" />
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137 </test>
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138 <test>
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139 <param name="infile" value="CID_2244.smi" ftype="smi" />
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140 <param name="fp_opts.fp_opts_selector" value="--FP3" />
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141 <output name="outfile" file="CID_2244_FP3.fps" ftype="fps" />
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142 </test>
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143 <!-- FP4 -->
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144 <test>
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145 <param name="infile" value="CID_2244.sdf" ftype="sdf" />
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146 <param name="fp_opts.fp_opts_selector" value="--FP4" />
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147 <output name="outfile" file="CID_2244_FP4.fps" ftype="fps" />
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148 </test>
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149 <test>
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150 <param name="infile" value="CID_2244.smi" ftype="smi" />
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151 <param name="fp_opts.fp_opts_selector" value="--FP4" />
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152 <output name="outfile" file="CID_2244_FP4.fps" ftype="fps" />
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153 </test>
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154 <!-- MACCS -->
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155 <test>
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156 <param name="infile" value="CID_2244.sdf" ftype="sdf" />
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157 <param name="fp_opts.fp_opts_selector" value="--MACCS" />
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158 <output name="outfile" file="CID_2244_MACCS.fps" ftype="fps" />
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159 </test>
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160 <test>
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161 <param name="infile" value="CID_2244.smi" ftype="smi" />
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162 <param name="fp_opts.fp_opts_selector" value="--MACCS" />
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163 <output name="outfile" file="CID_2244_MACCS.fps" ftype="fps" />
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164 </test>
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165 </tests>
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166 <help>
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167
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168
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169 **What it does**
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170
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171 Generate fingerprints using OpenBabel
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172
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173 -----
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174
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175 **Example**
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176
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177 * input::
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178
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179 - SDF File
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180
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181 28434379
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182 -OEChem-02031205132D
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183
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184 37 39 0 0 0 0 0 0 0999 V2000
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185 8.1648 -1.8842 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
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186 6.0812 -0.2134 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
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187 6.0812 -1.8229 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
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188 2.5369 -2.0182 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
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189 6.3919 0.7371 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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190 7.3704 0.9433 0.0000 C 0 0 0 0
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191 ......
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192 1 15 1 0 0 0 0
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193 1 35 1 0 0 0 0
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194 2 5 1 0 0 0 0
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195 2 11 1 0 0 0 0
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196 2 12 1 0 0 0 0
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197 3 12 2 0 0 0 0
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198 3 13 1 0 0 0 0
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199 4 18 1 0 0 0 0
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200 ......
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201
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202 >PUBCHEM_COMPOUND_CID<
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203 28434379
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204
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205 > <PUBCHEM_COMPOUND_CANONICALIZED>
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206 1
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207
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208 > <PUBCHEM_CACTVS_COMPLEXITY>
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209 280
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210
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211 > <PUBCHEM_CACTVS_HBOND_ACCEPTOR>
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212 2
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213
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214 > <PUBCHEM_CACTVS_HBOND_DONOR>
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215 2
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216
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217 > <PUBCHEM_CACTVS_ROTATABLE_BOND>
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218 2
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219
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220 > <PUBCHEM_CACTVS_SUBSKEYS>
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221 AAADceBzIAAAAAAAAAAAAAAAAAAAAWAAAAAwYAAAAAAAAFgB8AAAHgAQCAAACCjhlwYx0LdMEgCgASZiZASCgC0hEqAJ2CA4dJiKeKLA2dGUJAhokALYyCcQAAAAAACAAAQAACAAAQAACAAAQAAAAAAAAA==
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222
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223 >
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224
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225 - type : FP2
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226
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227 * output::
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228
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229 #FPS1
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230 #num_bits=1021
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231 #type=OpenBabel-FP2/1
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232 #software=OpenBabel/2.3.0
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233 #source=/tmp/dataset_409.dat.sdf
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234 #date=2012-02-03T11:13:39
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235 c0000000000008c0000846000400000000000010800000000000004000000000100010000700802170000018000000c
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236 0010000000020600208008000008000000c000c02c00002000000c00000100000008001400c800001c0180000000300
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237 10000000000080000000c0000060000c0000060810000010000000800102000000 28434379
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238
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239
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240 </help>
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241 </tool>
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