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1 <tool id="chemfp_mol2fps" name="Molecules to Fingerprints" version="0.2.0">
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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
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6 <requirement type="package" version="2012_12_1">rdkit</requirement>
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0
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7 </requirements>
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8 <command>
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6
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9 #if $fptype in ['--FP2', '--FP3', '--FP4', '--MACCS']:
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10 ## Open Babel fingerprints
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11 ob2fps $fptype --in "${infile.ext}" "${infile}" -o "${outfile}" --errors report 2>&1
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12 #else:
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13 ## RDKit fingerprints
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14 rdkit2fps --in "${infile.ext}" "${infile}" -o "${outfile}"
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15 #if $fp_opts.fp_opts_selector=="--RDK":
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16 --RDK
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17 --fpSize $fp_opts.fpSize
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18 --minPath $fp_opts.minPath
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19 --maxPath $fp_opts.maxPath
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20 --nBitsPerHash $fp_opts.nBitsPerHash
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21 $fp_opts.useHs
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22 #elif $fp_opts.fp_opts_selector=="--torsions":
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23 --torsions
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24 --fpSize $fp_opts.fpSize
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25 --targetSize $fp_opts.targetSize
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26 #elif $fp_opts.fp_opts_selector=="--morgan":
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27 --morgan
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28 --fpSize $fp_opts.fpSize
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29 --radius $fp_opts.radius
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30 $fp_opts.useFeatures
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31 $fp_opts.useChirality
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32 $fp_opts.useBondTypes
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33 #elif $fp_opts.fp_opts_selector=="--pairs":
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34 --paris
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35 --fpSize $fp_opts.fpSize
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36 --minLength $fp_opts.minLength
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37 --maxLength $fp_opts.maxLength
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38 #elif $fp_opts.fp_opts_selector=="--maccs166":
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39 --maccs166
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40 #elif $fp_opts.fp_opts_selector=="--substruct":
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41 --substruct
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42 #endif
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43 --errors report 2>&1
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44 #endif
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0
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45 </command>
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46 <inputs>
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47 <param name="infile" type='data' format="sdf,smi,mol,mol2,cml,inchi" label="molecule file"/>
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6
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48 <conditional name="fp_opts">
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49 <param name="fp_opts_selector" type="select" label="Type of fingerprint">
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50 <option value='--FP2' selected="True">Open Babel FP2 fingerprints</option>
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51 <option value='--FP3'>Open Babel FP3 fingerprints</option>
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52 <option value='--FP4'>Open Babel FP4 fingerprints</option>
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53 <option value='--MACCS'>Open Babel MACCS fingerprints</option>
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54 <option value='--RDK'>RDKit topological fingerprint</option>
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55 <option value='--torsions'>RDKit topological Torsion fingerprints</option>
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56 <option value='--morgan'>RDKit Morgan fingerprints</option>
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57 <option value='--pairs'>RDKit Atom Pair fingerprints</option>
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58 <option value='--maccs166'>RDKit MACCS fingerprints</option>
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59 <option value='--substruct'>RDKit substructure fingerprints</option>
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60 </param>
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61 <when value="--FP2" />
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62 <when value="--FP3" />
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63 <when value="--FP4" />
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64 <when value="--MACCS" />
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65 <when value="--RDK">
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66 <param name="fpSize" type="integer" value="2048" label="number of bits in the fingerprint" help="">
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67 <validator type="in_range" min="1" />
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68 </param>
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69 <param name="minPath" type="integer" value="1" label="minimum number of bonds to include in the subgraph" help="">
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70 <validator type="in_range" min="1" />
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71 </param>
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72 <param name="maxPath" type="integer" value="7" label="maximum number of bonds to include in the subgraph" help="">
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73 <validator type="in_range" min="1" />
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74 </param>
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75 <param name="nBitsPerHash" type="integer" value="4" label="number of bits to set per path" help="">
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76 <validator type="in_range" min="1" />
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77 </param>
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78 <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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79 </when>
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80 <when value="--torsions">
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81 <param name="fpSize" type="integer" value="2048" label="number of bits in the fingerprint" help="">
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82 <validator type="in_range" min="1" />
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83 </param>
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84 <param name="targetSize" type="integer" value="4" label="number of target bits in the fingerprint" help="">
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85 <validator type="in_range" min="1" />
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86 </param>
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87 </when>
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88 <when value="--morgan">
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89 <param name="fpSize" type="integer" value="2048" label="number of bits in the fingerprint" help="">
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90 <validator type="in_range" min="1" />
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91 </param>
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92 <param name="radius" type="integer" value="2" label="radius for the Morgan algorithm" help="">
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93 <validator type="in_range" min="1" />
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94 </param>
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95 <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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96 <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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97 <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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98 </when>
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99 <when value="--pairs">
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100 <param name="fpSize" type="integer" value="2048" label="number of bits in the fingerprint" help="">
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101 <validator type="in_range" min="1" />
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102 </param>
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103 <param name="minLength" type="integer" value="1" label="minimum bond count for a pair" help="">
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104 <validator type="in_range" min="1" />
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105 </param>
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106 <param name="maxLength" type="integer" value="30" label="maximum bond count for a pair" help="">
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107 <validator type="in_range" min="1" />
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108 </param>
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109 </when>
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110 <when value="--maccs166" />
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111 <when value="--substruct" />
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112 </conditional>
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113
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0
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114 </inputs>
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115 <outputs>
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116 <data name="outfile" format="fps" />
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117 </outputs>
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118 <tests>
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119 <!-- FP2 -->
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120 <test>
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121 <param name="infile" value="CID_2244.sdf" ftype="sdf" />
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122 <param name="fptype" value="--FP2" />
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123 <output name="outfile" file="CID_2244_FP2.fps" ftype="fps" />
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124 </test>
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125 <test>
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126 <param name="infile" value="CID_2244.smi" ftype="smi" />
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127 <param name="fptype" value="--FP2" />
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128 <output name="outfile" file="CID_2244_FP2.fps" ftype="fps" />
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129 </test>
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130 <!-- FP3 -->
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131 <test>
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132 <param name="infile" value="CID_2244.sdf" ftype="sdf" />
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133 <param name="fptype" value="--FP3" />
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134 <output name="outfile" file="CID_2244_FP3.fps" ftype="fps" />
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135 </test>
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136 <test>
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137 <param name="infile" value="CID_2244.smi" ftype="smi" />
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138 <param name="fptype" value="--FP3" />
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139 <output name="outfile" file="CID_2244_FP3.fps" ftype="fps" />
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140 </test>
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141 <!-- FP4 -->
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142 <test>
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143 <param name="infile" value="CID_2244.sdf" ftype="sdf" />
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144 <param name="fptype" value="--FP4" />
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145 <output name="outfile" file="CID_2244_FP4.fps" ftype="fps" />
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146 </test>
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147 <test>
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148 <param name="infile" value="CID_2244.smi" ftype="smi" />
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149 <param name="fptype" value="--FP4" />
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150 <output name="outfile" file="CID_2244_FP4.fps" ftype="fps" />
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151 </test>
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152 <!-- MACCS -->
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153 <test>
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154 <param name="infile" value="CID_2244.sdf" ftype="sdf" />
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155 <param name="fptype" value="--MACCS" />
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156 <output name="outfile" file="CID_2244_MACCS.fps" ftype="fps" />
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157 </test>
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158 <test>
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159 <param name="infile" value="CID_2244.smi" ftype="smi" />
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160 <param name="fptype" value="--MACCS" />
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161 <output name="outfile" file="CID_2244_MACCS.fps" ftype="fps" />
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162 </test>
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163 </tests>
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164 <help>
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165
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166
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167 **What it does**
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168
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169 Generate fingerprints using OpenBabel
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170
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171 -----
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172
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173 **Example**
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174
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175 * input::
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176
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177 - SDF File
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178
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179 28434379
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180 -OEChem-02031205132D
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181
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182 37 39 0 0 0 0 0 0 0999 V2000
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183 8.1648 -1.8842 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
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184 6.0812 -0.2134 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
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185 6.0812 -1.8229 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
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186 2.5369 -2.0182 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
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187 6.3919 0.7371 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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188 7.3704 0.9433 0.0000 C 0 0 0 0
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189 ......
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190 1 15 1 0 0 0 0
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191 1 35 1 0 0 0 0
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192 2 5 1 0 0 0 0
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193 2 11 1 0 0 0 0
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194 2 12 1 0 0 0 0
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195 3 12 2 0 0 0 0
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196 3 13 1 0 0 0 0
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197 4 18 1 0 0 0 0
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198 ......
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199
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200 >PUBCHEM_COMPOUND_CID<
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201 28434379
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202
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203 > <PUBCHEM_COMPOUND_CANONICALIZED>
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204 1
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205
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206 > <PUBCHEM_CACTVS_COMPLEXITY>
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207 280
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208
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209 > <PUBCHEM_CACTVS_HBOND_ACCEPTOR>
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210 2
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211
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212 > <PUBCHEM_CACTVS_HBOND_DONOR>
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213 2
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214
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215 > <PUBCHEM_CACTVS_ROTATABLE_BOND>
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216 2
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217
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218 > <PUBCHEM_CACTVS_SUBSKEYS>
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219 AAADceBzIAAAAAAAAAAAAAAAAAAAAWAAAAAwYAAAAAAAAFgB8AAAHgAQCAAACCjhlwYx0LdMEgCgASZiZASCgC0hEqAJ2CA4dJiKeKLA2dGUJAhokALYyCcQAAAAAACAAAQAACAAAQAACAAAQAAAAAAAAA==
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220
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221 >
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222
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223 - type : FP2
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224
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225 * output::
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226
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227 #FPS1
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228 #num_bits=1021
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229 #type=OpenBabel-FP2/1
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230 #software=OpenBabel/2.3.0
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231 #source=/tmp/dataset_409.dat.sdf
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232 #date=2012-02-03T11:13:39
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233 c0000000000008c0000846000400000000000010800000000000004000000000100010000700802170000018000000c
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234 0010000000020600208008000008000000c000c02c00002000000c00000100000008001400c800001c0180000000300
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235 10000000000080000000c0000060000c0000060810000010000000800102000000 28434379
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236
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237
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238 </help>
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239 </tool>
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