Mercurial > repos > bgruening > openbabel
annotate filter/ob_filter.xml @ 22:b4ba90dcfde0 default tip
ChemicalToolBoX update.
| author | Bjoern Gruening <bjoern.gruening@gmail.com> |
|---|---|
| date | Tue, 23 Jul 2013 19:00:18 +0200 |
| parents | 3d3e7c1d0f49 |
| children |
| rev | line source |
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| 0 | 1 <tool id="ctb_filter" name="Filter" version="1.0"> |
| 2 <description> a set of molecules from a file</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="2.3.2">openbabel</requirement> | |
| 10 | 6 <requirement type="package" version="0.1">cheminfolib</requirement> |
| 0 | 7 </requirements> |
| 8 <command interpreter="python"> | |
| 9 ob_filter.py | |
| 10 -i "${infile}" | |
| 11 -o "${outfile}" | |
| 12 -iformat "${infile.ext}" | |
| 13 -oformat "${infile.ext}" | |
| 14 --filters '{ | |
| 15 #if $filter_methods.filter_methods_opts == "ruleof5": | |
| 16 "hbd" : [0, 5], | |
| 17 "hba" : [0, 10], | |
| 18 "molwt" : [0, 500], | |
| 19 "logp" : [-5, 5], | |
| 20 #elif $filter_methods.filter_methods_opts == "LeadLike": | |
| 21 "rotbonds" : [0, 7], | |
| 22 "molwt" : [0, 350], | |
| 23 "logp" : [-5, 3.5], | |
| 24 #elif $filter_methods.filter_methods_opts == "DrugLike": | |
| 25 "hba" : [0, 10], | |
| 26 "rotbonds" : [0, 8], | |
| 27 "molwt" : [150, 500], | |
| 28 "logp" : [-5, 5], | |
| 29 "psa" : [0, 150], | |
| 30 #elif $filter_methods.filter_methods_opts == "FragmentLike": | |
| 31 "rotbonds" : [0, 5], | |
| 32 "molwt" : [0, 250], | |
| 33 "logp" : [-5, 2.5], | |
| 34 #else: | |
| 35 #for $filter in $filter_methods.filter_set: | |
| 36 #set $filter_selected = $filter.filter_sel.filter_sel_opts | |
| 37 #set $filter_min = $filter_selected + "_min" | |
| 38 #set $filter_max = $filter_selected + "_max" | |
| 39 "$filter_selected" : [$filter.filter_sel[$filter_min], $filter.filter_sel[$filter_max] ], | |
| 40 #end for | |
| 41 #end if | |
| 42 }' | |
| 43 </command> | |
| 44 <inputs> | |
| 45 <param name="infile" type="data" format="sdf,smi,mol,mol2,cml,inchi" label="Select input file previously created with the 'Compute physico-chemical properties' tool"/> | |
| 46 <conditional name="filter_methods"> | |
| 47 <param name="filter_methods_opts" type="select" label="Select a pre-defined filtering set"> | |
| 48 <option value="user">User-defined properties</option> | |
| 49 <option value="ruleof5">Lipinski's Rule-of-Five</option> | |
| 50 <option value="LeadLike">Lead-like properties</option> | |
| 51 <option value="DrugLike">Drug-like properties</option> | |
| 52 <option value="FragmentLike">Fragment-like properties</option> | |
| 53 </param> | |
| 7 | 54 <when value="ruleof5" /> |
| 55 <when value="LeadLike" /> | |
| 56 <when value="DrugLike" /> | |
| 57 <when value="FragmentLike" /> | |
| 0 | 58 <when value="user"> |
| 59 <repeat name="filter_set" title="Filters selection"> | |
| 60 <conditional name="filter_sel"> | |
| 61 <param name="filter_sel_opts" type="select" label="Select properties to filter"> | |
| 62 <option value="hbd">Number of Hydrogen-bond donor groups</option> | |
| 63 <option value="hba">Number of Hydrogen-bond acceptor groups</option> | |
| 64 <option value="psa">Total polar Surface Area</option> | |
| 65 <option value="rotbonds">Number of rotatable bonds</option> | |
| 66 <option value="molwt">Molecular weight</option> | |
| 67 <option value="logp">Predicted value of LogP</option> | |
| 68 <option value="mr">Predicted value for the Molecular Refractivity</option> | |
| 69 <option value="atoms">Number of atoms</option> | |
| 7 | 70 <!-- Add later, we need to add a new smarts pattern to plugindefines.txt |
| 71 <option value="hatoms">Number of heavy atoms</option>--> | |
| 0 | 72 <!-- We skip that options, for further information please read: http://www.dalkescientific.com/writings/diary/archive/2011/06/04/dealing_with_sssr.html --> |
| 73 <!--<option value="rings">Number of rings</option>--> | |
| 74 </param> | |
| 75 <when value="hbd"> | |
| 76 <param name="hbd_min" size="3" type="integer" value="" label="Minimum number of HB donors"/> | |
| 77 <param name="hbd_max" size="3" type="integer" value="" label="Maximum number of HB donors"/> | |
| 78 </when> | |
| 79 <when value="hba"> | |
| 80 <param name="hba_min" size="3" type="integer" value="" label="Minimum number of HB acceptors"/> | |
| 81 <param name="hba_max" size="3" type="integer" value="" label="Maximum number of HB acceptors"/> | |
| 82 </when> | |
| 83 <when value="psa"> | |
| 84 <param name="psa_min" size="5" type="integer" value="" label="Minimum threshold for the Total Polar Surface Area"/> | |
| 85 <param name="psa_max" size="5" type="integer" value="" label="Maximum threshold for the Total Polar Surface Area"/> | |
| 86 </when> | |
| 87 <when value="rotbonds"> | |
| 88 <param name="rotbonds_min" size="3" type="integer" value="" label="Minimum number of rotatable bonds"/> | |
| 89 <param name="rotbonds_max" size="3" type="integer" value="" label="Maximum number of rotatable bonds"/> | |
| 90 </when> | |
| 91 <when value="molwt"> | |
| 92 <param name="molwt_min" size="5" type="integer" value="" label="Minimum threshold value for the Molecular Weight"/> | |
| 93 <param name="molwt_max" size="5" type="integer" value="" label="Maximum threshold value for the Molecular Weight"/> | |
| 94 </when> | |
| 95 <when value="logp"> | |
| 96 <param name="logp_min" size="4" type="float" value="" label="Minimum threshold value for the log-P"/> | |
| 97 <param name="logp_max" size="4" type="float" value="" label="Maximum threshold value for the log-P"/> | |
| 98 </when> | |
| 99 <when value="mr"> | |
| 100 <param name="mr_min" size="4" type="float" value="" label="Minimum threshold value for the Molecular Refractivity"/> | |
| 101 <param name="mr_max" size="4" type="float" value="" label="Maximum threshold value for the Molecular Refractivity"/> | |
| 102 </when> | |
| 103 <when value="atoms"> | |
| 104 <param name="atoms_min" size="3" type="integer" value="" label="Minimum number of atoms"/> | |
| 105 <param name="atoms_max" size="3" type="integer" value="" label="Maximum number of atoms"/> | |
| 106 </when> | |
| 107 <!--<when value="rings"> | |
| 108 <param name="rings_min" size="3" type="integer" value="" label="Minimum number of rings"/> | |
| 109 <param name="rings_max" size="3" type="integer" value="" label="Maximum number of rings"/> | |
| 110 </when>--> | |
| 111 </conditional> | |
| 112 </repeat> | |
| 113 </when> | |
| 114 </conditional> | |
| 115 </inputs> | |
| 116 <outputs> | |
| 117 <data format_source="infile" name="outfile" /> | |
| 118 </outputs> | |
| 119 <tests> | |
| 120 <test> | |
| 121 <param name="infile" ftype="smi" value="CID_2244.smi"/> | |
| 122 <param name="filter_methods_opts" value="ruleof5" /> | |
| 123 <output name="outfile" ftype="smi" file="ob_filter_on_CID2244.smi" /> | |
| 124 </test> | |
| 7 | 125 <!-- |
| 126 Limitation of the test framework: | |
| 127 https://trello.com/card/disambiguated-conditional-parameters-not-supported-in-unit-tests/506338ce32ae458f6d15e4b3/820 | |
| 0 | 128 <test> |
| 129 <param name="infile" ftype="smi" value="CID_2244.smi"/> | |
| 130 <param name="filter_methods_opts" value="user" /> | |
| 131 <param name="filter_sel_opts" value="hba" /> | |
| 132 <param name="hbd_min" value="0" /> | |
| 133 <param name="hbd_max" value="5" /> | |
| 134 <output name="outfile" ftype="smi" file="ob_filter_on_CID2244_2.smi" /> | |
| 135 </test> | |
| 7 | 136 --> |
| 0 | 137 </tests> |
| 138 <help> | |
| 139 | |
| 140 | |
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141 .. class:: infomark |
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142 |
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143 **What this tool does** |
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144 |
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145 Filters a library of compounds based on user-defined physico-chemical parameters or predefined options (e.g. Ro5, lead-like properties, etc.). Multiple parameters can be selected for more specific queries. |
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146 |
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147 ----- |
| 0 | 148 |
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149 .. class:: warningmark |
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150 |
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151 **Hint** |
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152 |
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153 | If your input file is in SDF format you can use the *Compute physico-chemical properties* tool to precalulate the properties and use the filter on that precomputed dataset. It should be faster and can be reused but it's bigger than a SMILES file. |
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154 | |
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155 | For exact matches please use the target value for both minimum and maximum parameters (e.g. a selection of exactly 4 rotatable bonds can be performed by selecting 4 as minimum and maximum value). |
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156 | |
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157 | Selecting the same property multiple times with different parameters will result in querying the largest overlapping subset of values for the parameter (e.g. a selection of between 0 and 3 rotatable bonds plus a selection between 2 and 4 will result in a query for compounds between 2 and 3 rotatable bonds). |
| 0 | 158 |
| 159 ----- | |
| 160 | |
| 161 .. class:: infomark | |
| 162 | |
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163 **Definition of the pre-defined filtering rules** |
| 0 | 164 |
| 165 **# Lipinski's Rule of Five:** | |
| 166 =< 5 Hydrogen-bond donor groups | |
| 167 | |
| 168 =< 10 Hydrogen-bond acceptor groups | |
| 169 | |
| 170 =< 500 Molecular weight | |
| 171 | |
| 172 =< 5 octanol/water partition coefficient (log P) | |
| 173 | |
| 174 **# Lead Like properties** (Teague, Davis, Leeson, Oprea, Angew Chem Int Ed Engl. 1999 Dec 16;38(24):3743-3748): | |
| 175 =< 7 rotatable bonds | |
| 176 | |
| 177 =< 350 Molecular weight | |
| 178 | |
| 179 =< 3.5 octanol/water partition coefficient (log P) | |
| 180 | |
| 181 **# Drug Like properties** (Lipinski, J Pharmacol Toxicol Methods. 2000 Jul-Aug;44(1):235-49): | |
| 182 =< 10 Hydrogen-bond acceptor groups | |
| 183 | |
| 184 =< 8 rotatable bonds | |
| 185 | |
| 186 150 =< Molecular weight =< 500 | |
| 187 | |
| 188 =< 150 Polar Surface Area | |
| 189 | |
| 190 =< 5 octanol/water partition coefficient (log P) | |
| 191 | |
| 192 **# Fragment Like properties** (Carr RA, Congreve M, Murray CW, Rees DC, Drug Discov Today. 2005 Jul 15;10(14):987): | |
| 193 =< 5 rotatable bonds | |
| 194 | |
| 195 =< 250 Molecular weight | |
| 196 | |
| 197 =< 2.5 octanol/water partition coefficient (log P) | |
| 198 | |
| 199 ----- | |
| 200 | |
| 201 .. class:: infomark | |
| 202 | |
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203 **Input** |
| 0 | 204 |
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205 | - `SD-Format`_ |
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206 | - `SMILES Format`_ |
| 0 | 207 |
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208 .. _SD-Format: http://en.wikipedia.org/wiki/Chemical_table_file |
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209 .. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification |
| 0 | 210 |
| 211 ----- | |
| 212 | |
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213 .. class:: infomark |
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214 |
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215 **Output** |
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216 |
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217 | SDF formatted coordinates of the molecules, with selected properties stored as meta-data for each compound. |
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218 | |
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219 | SMILES, InChI or mol2 formatted files containing the 1D strings or 3D coordinates of each compound. |
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220 |
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221 ----- |
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222 |
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223 .. class:: infomark |
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224 |
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225 **Cite** |
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226 |
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227 N M O'Boyle, C Morley and G R Hutchison - `Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`_ |
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228 |
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229 .. _`Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`: http://journal.chemistrycentral.com/content/2/1/5 |
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230 |
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231 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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232 |
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233 .. _`Open Babel: An open chemical toolbox.`: http://www.jcheminf.com/content/3/1/33 |
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234 |
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235 `Open Babel`_ |
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236 |
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237 .. _`Open Babel`: http://openbabel.org/wiki/Main_Page |
| 0 | 238 |
| 239 </help> | |
| 240 </tool> |