Mercurial > repos > bgruening > openbabel
annotate filter/multi_obgrep.xml @ 15:ec87a42dccec
ChemicalToolBoX update.
| author | Bjoern Gruening <bjoern.gruening@gmail.com> |
|---|---|
| date | Sat, 01 Jun 2013 20:02:50 +0200 |
| parents | 6493d130f018 |
| children | 3d3e7c1d0f49 |
| rev | line source |
|---|---|
| 0 | 1 <tool id="ctb_multi_obgrep" name="Multi Compound Search" version="0.1"> |
| 2 <description>an advanced molecular grep program using SMARTS</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="2.3.2">openbabel</requirement> | |
| 5 </requirements> | |
| 6 <command interpreter="python"> | |
| 7 | |
| 8 multi_obgrep.py | |
| 9 -i $infile | |
| 10 --iformat ${infile.ext} | |
| 11 -q $query | |
| 12 -o "${outfile}" | |
| 13 $invert_matches | |
| 14 --n-times $n_times | |
| 15 $only_name | |
| 16 $full_match | |
| 17 $number_of_matches | |
| 18 --processors 10 | |
| 19 | |
| 20 </command> | |
| 21 <inputs> | |
| 22 <param name="infile" type="data" format="sdf,mol,mol2,cml,inchi,smi" label="Compound File" help="Specify a compound file in SDF Format"/> | |
| 23 <param name="query" type='data' format="tabular,text" label="Query file" help="One SMARTS pattern in each line."/> | |
| 24 <param name="invert_matches" type="boolean" label="Invert the matching, print non-matching molecules (-v)" truevalue="--invert-matches" falsevalue="" checked="false" /> | |
| 25 <param name="n_times" type="integer" value="0" label="Print a molecule only if the pattern occurs # times inside the molecule" /> | |
| 26 <param name="only_name" type="boolean" label="Only print the name of the molecules (-n)" truevalue="--only-name" falsevalue="" checked="false" /> | |
| 27 <param name="full_match" type="boolean" label="Full match, print matching-molecules only when the number of heavy atoms is also equal to the number of atoms in the SMARTS pattern (-f)" truevalue="--full-match" falsevalue="" checked="false" /> | |
| 28 <param name="number_of_matches" type="boolean" label="Print the number of matches (-c)" truevalue="--number-of-matches" falsevalue="" checked="false" /> | |
| 29 </inputs> | |
| 30 <outputs> | |
| 31 <data name="outfile" format_source="infile" /> | |
| 32 </outputs> | |
| 33 <tests> | |
| 34 <test> | |
| 35 </test> | |
| 36 </tests> | |
| 37 <help> | |
| 38 | |
| 39 | |
| 40 **What it does** | |
| 41 | |
|
15
ec87a42dccec
ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents:
0
diff
changeset
|
42 Providing a query file with SMARTS pattern in each line. These tool will run obgreg_ in parallel and merges the results. |
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ec87a42dccec
ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents:
0
diff
changeset
|
43 It is known that not all SMARTS features from the Daylight Toolkit are supported, please have a look here_. |
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ec87a42dccec
ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents:
0
diff
changeset
|
44 |
|
ec87a42dccec
ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents:
0
diff
changeset
|
45 |
|
ec87a42dccec
ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents:
0
diff
changeset
|
46 .. _obgrep: http://openbabel.org/wiki/Obgrep |
|
ec87a42dccec
ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents:
0
diff
changeset
|
47 .. _here: http://openbabel.org/wiki/SMARTS |
| 0 | 48 |
| 49 ----- | |
| 50 | |
| 51 **Example** | |
| 52 | |
| 53 | |
| 54 | |
| 55 </help> | |
| 56 </tool> |