Mercurial > repos > bgruening > openbabel
annotate modify/ob_addh.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 |
|---|---|
|
15
ec87a42dccec
ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents:
0
diff
changeset
|
1 <tool id="ctb_ob_addh" name="Add hydrogen atoms" version="1.0"> |
| 0 | 2 <description>at a certain pH value</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> | |
| 6 </requirements> | |
| 7 <command interpreter="python"> | |
| 8 ob_addh.py | |
| 9 -i "${infile}" | |
| 10 --iformat "${infile.ext}" | |
| 11 -o "${outfile}" | |
| 12 $polar | |
| 13 --pH "${pH_value}" | |
| 14 </command> | |
| 15 <inputs> | |
| 16 <param name="infile" type="data" format="sdf,smi,mol,mol2,cml,inchi" label="Select input file"/> | |
| 17 <param name="polar" type="boolean" truevalue="--polar" falsevalue="" label="Add hydrogens to polar atoms only"/> | |
| 18 <param name="pH_value" type="float" size="4" value="7.4" label="Specify pH value"/> | |
| 19 </inputs> | |
| 20 <outputs> | |
| 21 <data format_source="infile" name="outfile" /> | |
| 22 </outputs> | |
| 23 <tests> | |
| 24 <test> | |
| 25 <param name="infile" value="CID_2244.can" ftype="smi" /> | |
| 26 <param name="polar" value="--polar" /> | |
| 27 <param name="pH_value" value="7.4" /> | |
| 28 <output name="outfile" file="CID_2244_addh.can" ftype="can" /> | |
| 29 </test> | |
| 30 </tests> | |
| 31 <help> | |
| 32 | |
| 33 .. class:: infomark | |
| 34 | |
| 35 **What does this tool do?** | |
| 36 | |
| 37 This tool parses a molecular file and adds hydrogen atoms at a certain pH value. | |
| 38 | |
| 39 ----- | |
| 40 | |
| 41 .. class:: infomark | |
| 42 | |
| 43 **Protocol:** | |
| 44 | |
| 45 **1.** The hydrogen atoms included in the input molecule are deleted. | |
| 46 | |
| 47 **2.** Protonation state is predicted at the target pH and the corresponding hydrogen atoms added accordingly. | |
| 48 | |
| 49 **Hint:** to avoid possible crashes, only molecules with >5 heavy atoms are parsed. | |
| 50 | |
| 51 ----- | |
| 52 | |
| 53 .. class:: infomark | |
| 54 | |
| 55 **Output:** the output format is the same as the input format. 3D format files are required for this tool. | |
| 56 | |
| 57 ----- | |
| 58 | |
| 59 **This tool uses Pybel:** N. M. O'Boyle, C. Morley and G. R. Hutchison. Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit Chem. Cent. J. 2008, 2, 5. | |
| 60 | |
| 61 </help> | |
| 62 </tool> |