Mercurial > repos > bgruening > chemfp
annotate chemfp_mol2fps/mol2fps.xml @ 24:dce673edc031
ChemicalToolBoX update.
| author | Bjoern Gruening <bjoern.gruening@gmail.com> |
|---|---|
| date | Sat, 20 Jul 2013 19:07:47 +0200 |
| parents | 1868005213a1 |
| children | a2ba3431eca4 |
| rev | line source |
|---|---|
| 9 | 1 <tool id="ctb_chemfp_mol2fps" name="Molecules to Fingerprints" version="0.2.0"> |
| 2 <description>with different fingerprint types</description> | |
| 3 <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism> | |
| 4 <requirements> | |
| 5 <requirement type="package" version="1.1p1">chemfp</requirement> | |
| 6 <requirement type="package" version="2012_12_1">rdkit</requirement> | |
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7 <requirement type="package" version="2.3.2">openbabel</requirement> |
| 9 | 8 </requirements> |
| 9 <command> | |
| 13 | 10 #set $fptype = $fp_opts.fp_opts_selector |
| 11 | |
| 9 | 12 #if $fptype in ['--FP2', '--FP3', '--FP4', '--MACCS']: |
| 13 ## Open Babel fingerprints | |
| 13 | 14 ob2fps $fptype --in "${infile.ext}" "${infile}" -o "${outfile}" |
| 9 | 15 #else: |
| 16 ## RDKit fingerprints | |
| 17 rdkit2fps --in "${infile.ext}" "${infile}" -o "${outfile}" | |
| 13 | 18 #if $fp_opts.fp_opts_selector == "--RDK": |
| 9 | 19 --RDK |
| 20 --fpSize $fp_opts.fpSize | |
| 21 --minPath $fp_opts.minPath | |
| 22 --maxPath $fp_opts.maxPath | |
| 23 --nBitsPerHash $fp_opts.nBitsPerHash | |
| 24 $fp_opts.useHs | |
| 13 | 25 #elif $fp_opts.fp_opts_selector == "--torsions": |
| 9 | 26 --torsions |
| 27 --fpSize $fp_opts.fpSize | |
| 28 --targetSize $fp_opts.targetSize | |
| 13 | 29 #elif $fp_opts.fp_opts_selector == "--morgan": |
| 9 | 30 --morgan |
| 31 --fpSize $fp_opts.fpSize | |
| 32 --radius $fp_opts.radius | |
| 33 $fp_opts.useFeatures | |
| 34 $fp_opts.useChirality | |
| 35 $fp_opts.useBondTypes | |
| 13 | 36 #elif $fp_opts.fp_opts_selector == "--pairs": |
| 9 | 37 --paris |
| 38 --fpSize $fp_opts.fpSize | |
| 39 --minLength $fp_opts.minLength | |
| 40 --maxLength $fp_opts.maxLength | |
| 13 | 41 #elif $fp_opts.fp_opts_selector == "--maccs166": |
| 9 | 42 --maccs166 |
| 13 | 43 #elif $fp_opts.fp_opts_selector == "--substruct": |
| 9 | 44 --substruct |
| 13 | 45 #end if |
| 46 #end if | |
| 47 --errors report 2>&1 | |
| 9 | 48 </command> |
| 49 <inputs> | |
| 50 <param name="infile" type='data' format="sdf,smi,mol,mol2,cml,inchi" label="molecule file"/> | |
| 51 <conditional name="fp_opts"> | |
| 52 <param name="fp_opts_selector" type="select" label="Type of fingerprint"> | |
| 53 <option value='--FP2' selected="True">Open Babel FP2 fingerprints</option> | |
| 54 <option value='--FP3'>Open Babel FP3 fingerprints</option> | |
| 55 <option value='--FP4'>Open Babel FP4 fingerprints</option> | |
| 56 <option value='--MACCS'>Open Babel MACCS fingerprints</option> | |
| 57 <option value='--RDK'>RDKit topological fingerprint</option> | |
| 58 <option value='--torsions'>RDKit topological Torsion fingerprints</option> | |
| 59 <option value='--morgan'>RDKit Morgan fingerprints</option> | |
| 60 <option value='--pairs'>RDKit Atom Pair fingerprints</option> | |
| 61 <option value='--maccs166'>RDKit MACCS fingerprints</option> | |
| 62 <option value='--substruct'>RDKit substructure fingerprints</option> | |
| 63 </param> | |
| 64 <when value="--FP2" /> | |
| 65 <when value="--FP3" /> | |
| 66 <when value="--FP4" /> | |
| 67 <when value="--MACCS" /> | |
| 68 <when value="--RDK"> | |
| 69 <param name="fpSize" type="integer" value="2048" label="number of bits in the fingerprint" help=""> | |
| 70 <validator type="in_range" min="1" /> | |
| 71 </param> | |
| 72 <param name="minPath" type="integer" value="1" label="minimum number of bonds to include in the subgraph" help=""> | |
| 73 <validator type="in_range" min="1" /> | |
| 74 </param> | |
| 75 <param name="maxPath" type="integer" value="7" label="maximum number of bonds to include in the subgraph" help=""> | |
| 76 <validator type="in_range" min="1" /> | |
| 77 </param> | |
| 78 <param name="nBitsPerHash" type="integer" value="4" label="number of bits to set per path" help=""> | |
| 79 <validator type="in_range" min="1" /> | |
| 80 </param> | |
| 81 <param name="useHs" type="boolean" label="include information about the number of hydrogens on each atom" truevalue="--useHs 1" falsevalue="--useHs 0" checked="true" /> | |
| 82 </when> | |
| 83 <when value="--torsions"> | |
| 84 <param name="fpSize" type="integer" value="2048" label="number of bits in the fingerprint" help=""> | |
| 85 <validator type="in_range" min="1" /> | |
| 86 </param> | |
| 87 <param name="targetSize" type="integer" value="4" label="number of target bits in the fingerprint" help=""> | |
| 88 <validator type="in_range" min="1" /> | |
| 89 </param> | |
| 90 </when> | |
| 91 <when value="--morgan"> | |
| 92 <param name="fpSize" type="integer" value="2048" label="number of bits in the fingerprint" help=""> | |
| 93 <validator type="in_range" min="1" /> | |
| 94 </param> | |
| 95 <param name="radius" type="integer" value="2" label="radius for the Morgan algorithm" help=""> | |
| 96 <validator type="in_range" min="1" /> | |
| 97 </param> | |
| 98 <param name="useFeatures" type="boolean" label="include information about the number of hydrogens on each atom" truevalue="--useFeatures 1" falsevalue="--useFeatures 0" checked="false" /> | |
| 99 <param name="useChirality" type="boolean" label="include information about the number of hydrogens on each atom" truevalue="--useChirality 1" falsevalue="--useChirality 0" checked="false" /> | |
| 100 <param name="useBondTypes" type="boolean" label="include information about the number of hydrogens on each atom" truevalue="--useBondTypes 1" falsevalue="--useBondTypes 0" checked="true" /> | |
| 101 </when> | |
| 102 <when value="--pairs"> | |
| 103 <param name="fpSize" type="integer" value="2048" label="number of bits in the fingerprint" help=""> | |
| 104 <validator type="in_range" min="1" /> | |
| 105 </param> | |
| 106 <param name="minLength" type="integer" value="1" label="minimum bond count for a pair" help=""> | |
| 107 <validator type="in_range" min="1" /> | |
| 108 </param> | |
| 109 <param name="maxLength" type="integer" value="30" label="maximum bond count for a pair" help=""> | |
| 110 <validator type="in_range" min="1" /> | |
| 111 </param> | |
| 112 </when> | |
| 113 <when value="--maccs166" /> | |
| 114 <when value="--substruct" /> | |
| 115 </conditional> | |
| 116 | |
| 117 </inputs> | |
| 118 <outputs> | |
| 119 <data name="outfile" format="fps" /> | |
| 120 </outputs> | |
| 121 <tests> | |
| 122 <!-- FP2 --> | |
| 123 <test> | |
| 124 <param name="infile" value="CID_2244.sdf" ftype="sdf" /> | |
| 13 | 125 <param name="fp_opts.fp_opts_selector" value="--FP2" /> |
| 9 | 126 <output name="outfile" file="CID_2244_FP2.fps" ftype="fps" /> |
| 127 </test> | |
| 128 <test> | |
| 129 <param name="infile" value="CID_2244.smi" ftype="smi" /> | |
| 13 | 130 <param name="fp_opts.fp_opts_selector" value="--FP2" /> |
| 9 | 131 <output name="outfile" file="CID_2244_FP2.fps" ftype="fps" /> |
| 132 </test> | |
| 133 <!-- FP3 --> | |
| 134 <test> | |
| 135 <param name="infile" value="CID_2244.sdf" ftype="sdf" /> | |
| 13 | 136 <param name="fp_opts.fp_opts_selector" value="--FP3" /> |
| 9 | 137 <output name="outfile" file="CID_2244_FP3.fps" ftype="fps" /> |
| 138 </test> | |
| 139 <test> | |
| 140 <param name="infile" value="CID_2244.smi" ftype="smi" /> | |
| 13 | 141 <param name="fp_opts.fp_opts_selector" value="--FP3" /> |
| 9 | 142 <output name="outfile" file="CID_2244_FP3.fps" ftype="fps" /> |
| 143 </test> | |
| 144 <!-- FP4 --> | |
| 145 <test> | |
| 146 <param name="infile" value="CID_2244.sdf" ftype="sdf" /> | |
| 13 | 147 <param name="fp_opts.fp_opts_selector" value="--FP4" /> |
| 9 | 148 <output name="outfile" file="CID_2244_FP4.fps" ftype="fps" /> |
| 149 </test> | |
| 150 <test> | |
| 151 <param name="infile" value="CID_2244.smi" ftype="smi" /> | |
| 13 | 152 <param name="fp_opts.fp_opts_selector" value="--FP4" /> |
| 9 | 153 <output name="outfile" file="CID_2244_FP4.fps" ftype="fps" /> |
| 154 </test> | |
| 155 <!-- MACCS --> | |
| 156 <test> | |
| 157 <param name="infile" value="CID_2244.sdf" ftype="sdf" /> | |
| 13 | 158 <param name="fp_opts.fp_opts_selector" value="--MACCS" /> |
| 9 | 159 <output name="outfile" file="CID_2244_MACCS.fps" ftype="fps" /> |
| 160 </test> | |
| 161 <test> | |
| 162 <param name="infile" value="CID_2244.smi" ftype="smi" /> | |
| 13 | 163 <param name="fp_opts.fp_opts_selector" value="--MACCS" /> |
| 9 | 164 <output name="outfile" file="CID_2244_MACCS.fps" ftype="fps" /> |
| 165 </test> | |
| 166 </tests> | |
| 167 <help> | |
| 168 | |
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169 .. class:: infomark |
| 9 | 170 |
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171 **What this tool does** |
| 9 | 172 |
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173 This tool uses chemfp_ to calculate 10 different fingerprints of common file formats. Chemfp uses `Open Babel`_, OpenEye_ and RDKit_. |
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174 |
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175 For more information check the websites listed below:: |
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176 |
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177 - http://code.google.com/p/rdkit/wiki/FingerprintsInTheRDKit |
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178 - http://openbabel.org/wiki/Tutorial:Fingerprints |
| 9 | 179 |
| 180 ----- | |
| 181 | |
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182 .. class:: infomark |
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183 |
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184 **Input** |
| 9 | 185 |
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186 FPS fingerprint file format |
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187 |
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188 * Example:: |
| 9 | 189 |
| 190 - SDF File | |
| 191 | |
| 192 28434379 | |
| 193 -OEChem-02031205132D | |
| 194 | |
| 195 37 39 0 0 0 0 0 0 0999 V2000 | |
| 196 8.1648 -1.8842 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 197 6.0812 -0.2134 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 198 6.0812 -1.8229 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 199 2.5369 -2.0182 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 200 6.3919 0.7371 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 201 7.3704 0.9433 0.0000 C 0 0 0 0 | |
| 202 ...... | |
| 203 1 15 1 0 0 0 0 | |
| 204 1 35 1 0 0 0 0 | |
| 205 2 5 1 0 0 0 0 | |
| 206 2 11 1 0 0 0 0 | |
| 207 2 12 1 0 0 0 0 | |
| 208 3 12 2 0 0 0 0 | |
| 209 3 13 1 0 0 0 0 | |
| 210 4 18 1 0 0 0 0 | |
| 211 ...... | |
| 212 | |
| 213 >PUBCHEM_COMPOUND_CID< | |
| 214 28434379 | |
| 215 | |
| 216 > <PUBCHEM_COMPOUND_CANONICALIZED> | |
| 217 1 | |
| 218 | |
| 219 > <PUBCHEM_CACTVS_COMPLEXITY> | |
| 220 280 | |
| 221 | |
| 222 > <PUBCHEM_CACTVS_HBOND_ACCEPTOR> | |
| 223 2 | |
| 224 | |
| 225 > <PUBCHEM_CACTVS_HBOND_DONOR> | |
| 226 2 | |
| 227 | |
| 228 > <PUBCHEM_CACTVS_ROTATABLE_BOND> | |
| 229 2 | |
| 230 | |
| 231 > <PUBCHEM_CACTVS_SUBSKEYS> | |
| 232 AAADceBzIAAAAAAAAAAAAAAAAAAAAWAAAAAwYAAAAAAAAFgB8AAAHgAQCAAACCjhlwYx0LdMEgCgASZiZASCgC0hEqAJ2CA4dJiKeKLA2dGUJAhokALYyCcQAAAAAACAAAQAACAAAQAACAAAQAAAAAAAAA== | |
| 233 | |
| 234 > | |
| 235 | |
| 236 - type : FP2 | |
| 237 | |
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238 ----- |
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239 |
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240 .. class:: infomark |
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241 |
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242 **Output** |
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243 |
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244 * Example:: |
| 9 | 245 |
| 246 #FPS1 | |
| 247 #num_bits=1021 | |
| 248 #type=OpenBabel-FP2/1 | |
| 249 #software=OpenBabel/2.3.0 | |
| 250 #source=/tmp/dataset_409.dat.sdf | |
| 251 #date=2012-02-03T11:13:39 | |
| 252 c0000000000008c0000846000400000000000010800000000000004000000000100010000700802170000018000000c | |
| 253 0010000000020600208008000008000000c000c02c00002000000c00000100000008001400c800001c0180000000300 | |
| 254 10000000000080000000c0000060000c0000060810000010000000800102000000 28434379 | |
| 255 | |
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256 ----- |
| 9 | 257 |
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258 .. class:: infomark |
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259 |
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260 **Cite** |
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261 |
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262 | `Open Babel`_ |
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263 | RDKit_ project |
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264 | chemfp_ project. |
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265 | |
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266 | N M O'Boyle, M Banck, C A James, C Morley, T Vandermeersch and G R Hutchison. `Open Babel: An open chemical toolbox.`_ |
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267 |
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268 .. _`Open Babel: An open chemical toolbox.`: http://www.jcheminf.com/content/3/1/33 |
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269 .. _OpenEye: http://www.eyesopen.com/ |
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270 .. _chemfp: http://chemfp.com/ |
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271 .. _RDKit: http://www.rdkit.org/ |
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272 .. _`Open Babel`: http://openbabel.org/ |
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273 |
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274 |
| 9 | 275 </help> |
| 276 </tool> |