Mercurial > repos > bgruening > openbabel
comparison filter/ob_filter.xml @ 2:125da3a296ca draft default tip
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author | bgruening |
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date | Wed, 15 Jul 2015 12:13:08 -0400 |
parents | 527ecd2fc500 |
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1:b52872a1755a | 2:125da3a296ca |
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4 <requirements> | 4 <requirements> |
5 <requirement type="package" version="2.3.2">openbabel</requirement> | 5 <requirement type="package" version="2.3.2">openbabel</requirement> |
6 <requirement type="package" version="0.1">cheminfolib</requirement> | 6 <requirement type="package" version="0.1">cheminfolib</requirement> |
7 </requirements> | 7 </requirements> |
8 <command interpreter="python"> | 8 <command interpreter="python"> |
9 <![CDATA[ | |
9 ob_filter.py | 10 ob_filter.py |
10 -i "${infile}" | 11 -i "${infile}" |
11 -o "${outfile}" | 12 -o "${outfile}" |
12 -iformat "${infile.ext}" | 13 -iformat "${infile.ext}" |
13 -oformat "${infile.ext}" | 14 -oformat "${infile.ext}" |
38 #set $filter_max = $filter_selected + "_max" | 39 #set $filter_max = $filter_selected + "_max" |
39 "$filter_selected" : [$filter.filter_sel[$filter_min], $filter.filter_sel[$filter_max] ], | 40 "$filter_selected" : [$filter.filter_sel[$filter_min], $filter.filter_sel[$filter_max] ], |
40 #end for | 41 #end for |
41 #end if | 42 #end if |
42 }' | 43 }' |
44 ]]> | |
43 </command> | 45 </command> |
44 <inputs> | 46 <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"/> | 47 <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"> | 48 <conditional name="filter_methods"> |
47 <param name="filter_methods_opts" type="select" label="Select a pre-defined filtering set"> | 49 <param name="filter_methods_opts" type="select" label="Select a pre-defined filtering set"> |
134 <output name="outfile" ftype="smi" file="ob_filter_on_CID2244_2.smi" /> | 136 <output name="outfile" ftype="smi" file="ob_filter_on_CID2244_2.smi" /> |
135 </test> | 137 </test> |
136 --> | 138 --> |
137 </tests> | 139 </tests> |
138 <help> | 140 <help> |
141 <![CDATA[ | |
139 | 142 |
140 | 143 |
141 .. class:: infomark | 144 .. class:: infomark |
142 | 145 |
143 **What this tool does** | 146 **What this tool does** |
144 | 147 |
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. | 148 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. |
146 | 149 |
147 ----- | 150 ----- |
148 | 151 |
149 .. class:: warningmark | 152 .. class:: warningmark |
150 | 153 |
151 **Hint** | 154 **Hint** |
152 | 155 |
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. | 156 | 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. |
154 | | 157 | |
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). | 158 | 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). |
156 | | 159 | |
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). | 160 | 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). |
158 | 161 |
159 ----- | 162 ----- |
160 | 163 |
161 .. class:: infomark | 164 .. class:: infomark |
162 | 165 |
163 **Definition of the pre-defined filtering rules** | 166 **Definition of the pre-defined filtering rules** |
164 | 167 |
165 **# Lipinski's Rule of Five:** | 168 **# Lipinski's Rule of Five:** |
166 =< 5 Hydrogen-bond donor groups | 169 =< 5 Hydrogen-bond donor groups |
167 | 170 |
168 =< 10 Hydrogen-bond acceptor groups | 171 =< 10 Hydrogen-bond acceptor groups |
169 | 172 |
170 =< 500 Molecular weight | 173 =< 500 Molecular weight |
171 | 174 |
172 =< 5 octanol/water partition coefficient (log P) | 175 =< 5 octanol/water partition coefficient (log P) |
173 | 176 |
174 **# Lead Like properties** (Teague, Davis, Leeson, Oprea, Angew Chem Int Ed Engl. 1999 Dec 16;38(24):3743-3748): | 177 **# Lead Like properties** (Teague, Davis, Leeson, Oprea, Angew Chem Int Ed Engl. 1999 Dec 16;38(24):3743-3748): |
175 =< 7 rotatable bonds | 178 =< 7 rotatable bonds |
176 | 179 |
177 =< 350 Molecular weight | 180 =< 350 Molecular weight |
178 | 181 |
179 =< 3.5 octanol/water partition coefficient (log P) | 182 =< 3.5 octanol/water partition coefficient (log P) |
180 | 183 |
181 **# Drug Like properties** (Lipinski, J Pharmacol Toxicol Methods. 2000 Jul-Aug;44(1):235-49): | 184 **# Drug Like properties** (Lipinski, J Pharmacol Toxicol Methods. 2000 Jul-Aug;44(1):235-49): |
182 =< 10 Hydrogen-bond acceptor groups | 185 =< 10 Hydrogen-bond acceptor groups |
183 | 186 |
184 =< 8 rotatable bonds | 187 =< 8 rotatable bonds |
185 | 188 |
186 150 =< Molecular weight =< 500 | 189 150 =< Molecular weight =< 500 |
187 | 190 |
188 =< 150 Polar Surface Area | 191 =< 150 Polar Surface Area |
189 | 192 |
190 =< 5 octanol/water partition coefficient (log P) | 193 =< 5 octanol/water partition coefficient (log P) |
191 | 194 |
192 **# Fragment Like properties** (Carr RA, Congreve M, Murray CW, Rees DC, Drug Discov Today. 2005 Jul 15;10(14):987): | 195 **# Fragment Like properties** (Carr RA, Congreve M, Murray CW, Rees DC, Drug Discov Today. 2005 Jul 15;10(14):987): |
193 =< 5 rotatable bonds | 196 =< 5 rotatable bonds |
194 | 197 |
195 =< 250 Molecular weight | 198 =< 250 Molecular weight |
196 | 199 |
197 =< 2.5 octanol/water partition coefficient (log P) | 200 =< 2.5 octanol/water partition coefficient (log P) |
198 | 201 |
199 ----- | 202 ----- |
200 | 203 |
201 .. class:: infomark | 204 .. class:: infomark |
202 | 205 |
210 | 213 |
211 ----- | 214 ----- |
212 | 215 |
213 .. class:: infomark | 216 .. class:: infomark |
214 | 217 |
215 **Output** | 218 **Output** |
216 | 219 |
217 | SDF formatted coordinates of the molecules, with selected properties stored as meta-data for each compound. | 220 | SDF formatted coordinates of the molecules, with selected properties stored as meta-data for each compound. |
218 | | 221 | |
219 | SMILES, InChI or mol2 formatted files containing the 1D strings or 3D coordinates of each compound. | 222 | SMILES, InChI or mol2 formatted files containing the 1D strings or 3D coordinates of each compound. |
220 | 223 |
221 ----- | 224 ----- |
222 | 225 |
223 .. class:: infomark | 226 .. class:: infomark |
234 | 237 |
235 `Open Babel`_ | 238 `Open Babel`_ |
236 | 239 |
237 .. _`Open Babel`: http://openbabel.org/wiki/Main_Page | 240 .. _`Open Babel`: http://openbabel.org/wiki/Main_Page |
238 | 241 |
242 ]]> | |
239 </help> | 243 </help> |
240 </tool> | 244 </tool> |