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1 <tool id="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 does this tool do?**
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36
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37 This tool parses a molecular file and adds hydrogen atoms at a certain pH value.
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38
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39 -----
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40
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41 .. class:: infomark
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42
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43 **Protocol:**
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44
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45 **1.** The hydrogen atoms included in the input molecule are deleted.
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46
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47 **2.** Protonation state is predicted at the target pH and the corresponding hydrogen atoms added accordingly.
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48
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49 **Hint:** to avoid possible crashes, only molecules with >5 heavy atoms are parsed.
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50
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51 -----
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52
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53 .. class:: infomark
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54
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55 **Output:** the output format is the same as the input format. 3D format files are required for this tool.
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56
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57 -----
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58
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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.
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60
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61 </help>
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62 </tool>
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