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annotate modify/ob_addh.xml @ 16:3d3e7c1d0f49

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ChemicalToolBoX update.
author Bjoern Gruening <bjoern.gruening@gmail.com>
date Fri, 19 Jul 2013 16:27:52 +0200
parents ec87a42dccec
children
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ec87a42dccec ChemicalToolBoX update.
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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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8 ob_addh.py
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9 -i "${infile}"
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10 --iformat "${infile.ext}"
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11 -o "${outfile}"
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12 $polar
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13 --pH "${pH_value}"
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14 </command>
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15 <inputs>
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16 <param name="infile" type="data" format="sdf,smi,mol,mol2,cml,inchi" label="Select input file"/>
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17 <param name="polar" type="boolean" truevalue="--polar" falsevalue="" label="Add hydrogens to polar atoms only"/>
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18 <param name="pH_value" type="float" size="4" value="7.4" label="Specify pH value"/>
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19 </inputs>
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20 <outputs>
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21 <data format_source="infile" name="outfile" />
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22 </outputs>
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23 <tests>
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24 <test>
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25 <param name="infile" value="CID_2244.can" ftype="smi" />
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26 <param name="polar" value="--polar" />
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27 <param name="pH_value" value="7.4" />
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28 <output name="outfile" file="CID_2244_addh.can" ftype="can" />
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29 </test>
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30 </tests>
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31 <help>
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32
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33 .. class:: infomark
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34
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35 **What this tool does**
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36
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37 Parses a molecular file and adds hydrogen atoms at a user-defined pH value.
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38
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39 * Protocol::
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40
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41 1. The hydrogen atoms included in the input molecule are deleted.
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42 2. Protonation state is predicted at the target pH and the corresponding hydrogen atoms added accordingly.
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43
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44 -----
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45
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46 .. class:: infomark
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47
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48 **Input**
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49
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50 3D format files are required, e.g. SDF_
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51
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52 .. _SDF: http://en.wikipedia.org/wiki/Chemical_table_file
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54 -----
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55
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56 .. class:: warningmark
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57
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58 **Hint**
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59
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60 To avoid possible crashes, only molecules with more than five heavy atoms are parsed.
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61
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62 -----
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64 .. class:: infomark
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65
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66 **Output**
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67
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68 Same output format as the input format.
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70 -----
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72 .. class:: infomark
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73
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74 **Cite**
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75
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76 `Open Babel`_
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77
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78 .. _Open Babel: http://openbabel.org/wiki/Main_Page
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79
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80 N M O'Boyle, C Morley and G R Hutchison - `Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`_
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81
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82 .. _`Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`: http://www.biomedcentral.com/content/pdf/1752-153X-2-5.pdf
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83
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84 </help>
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85 </tool>