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1 <tool id="ctb_ob_addh" name="Add hydrogen atoms" version="1.0">
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2 <description>at a certain pH value</description>
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3 <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism>
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4 <requirements>
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5 <requirement type="package" version="2.3.2">openbabel</requirement>
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6 </requirements>
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7 <command interpreter="python">
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2
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8 <![CDATA[
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9 ob_addh.py
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10 -i "${infile}"
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11 --iformat "${infile.ext}"
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12 -o "${outfile}"
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13 $polar
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14 --pH "${pH_value}"
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15 ]]>
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16 </command>
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17 <inputs>
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18 <param name="infile" type="data" format="sdf,smi,mol,mol2,cml,inchi" label="Select input file"/>
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19 <param name="polar" type="boolean" truevalue="--polar" falsevalue="" label="Add hydrogens to polar atoms only"/>
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20 <param name="pH_value" type="float" size="4" value="7.4" label="Specify pH value"/>
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21 </inputs>
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22 <outputs>
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23 <data format_source="infile" name="outfile" />
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24 </outputs>
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25 <tests>
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26 <test>
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27 <param name="infile" value="CID_2244.can" ftype="smi" />
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28 <param name="polar" value="--polar" />
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29 <param name="pH_value" value="7.4" />
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30 <output name="outfile" file="CID_2244_addh.can" ftype="can" />
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31 </test>
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32 </tests>
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33 <help>
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34 <![CDATA[
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35
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36 .. class:: infomark
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37
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38 **What this tool does**
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39
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40 Parses a molecular file and adds hydrogen atoms at a user-defined pH value.
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41
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42 * Protocol::
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43
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44 1. The hydrogen atoms included in the input molecule are deleted.
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45 2. Protonation state is predicted at the target pH and the corresponding hydrogen atoms added accordingly.
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46
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47 -----
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48
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49 .. class:: infomark
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50
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51 **Input**
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52
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53 3D format files are required, e.g. SDF_
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54
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55 .. _SDF: http://en.wikipedia.org/wiki/Chemical_table_file
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56
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57 -----
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58
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59 .. class:: warningmark
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60
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61 **Hint**
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62
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63 To avoid possible crashes, only molecules with more than five heavy atoms are parsed.
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64
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65 -----
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66
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67 .. class:: infomark
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68
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69 **Output**
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70
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71 Same output format as the input format.
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72
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73 -----
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74
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75 .. class:: infomark
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76
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77 **Cite**
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78
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79 `Open Babel`_
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80
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81 .. _Open Babel: http://openbabel.org/wiki/Main_Page
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82
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83 N M O'Boyle, C Morley and G R Hutchison - `Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`_
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84
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85 .. _`Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`: http://www.biomedcentral.com/content/pdf/1752-153X-2-5.pdf
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86
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87 ]]>
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88 </help>
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89 </tool>
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