Mercurial > repos > bgruening > ctb_rdkit_describtors
annotate rdkit_descriptors.xml @ 1:2f212f34b80c draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 9a3dc91fa984be18fabc0d968360634d787c9589
author | bgruening |
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date | Wed, 24 May 2017 09:51:36 -0400 |
parents | d7ea4e8cb1f3 |
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d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
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1 <tool id="ctb_rdkit_describtors" name="Descriptors" version="0.3"> |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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2 <description>calculated with RDKit</description> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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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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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
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4 <requirements> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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5 <requirement type="package" version="2016.03.3">rdkit</requirement> |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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6 </requirements> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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7 <command> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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8 <![CDATA[ |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
parents:
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9 python '$__tool_directory__/rdkit_descriptors.py' |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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10 -i '${infile}' |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
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11 --iformat '${infile.ext}' |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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12 -o '${outfile}' |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
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13 $header |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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14 ]]> |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
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15 </command> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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16 <inputs> |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
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17 <param name="infile" format="smi,sdf,mol2" type="data" label="Molecule data" |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
parents:
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18 help="In SD- or SMILES-format"/> |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
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19 <param name="header" type="boolean" label="Include the descriptor name as header" |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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20 truevalue="--header" falsevalue="" checked="false" /> |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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21 </inputs> |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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22 <outputs> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
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23 <data format="tabular" name="outfile" /> |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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parents:
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24 </outputs> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
parents:
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25 <tests> |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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parents:
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26 <test> |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
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27 <param name="infile" ftype='sdf' value="CID_3037.sdf" /> |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
parents:
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28 <param name="header" value="True" /> |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
parents:
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29 <output name="outfile" ftype='tabular' file="rdkit_descriptors_result1.tab" /> |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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parents:
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30 </test> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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31 </tests> |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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32 <help> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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33 <![CDATA[ |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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34 |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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35 .. class:: infomark |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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36 |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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37 **What this tool does** |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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38 |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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39 | RDKit is an open source toolkit for cheminformatics and machine learning. |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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40 | This implementation focuses on descriptor calculation, though, RDKit offers a vast number of other functions. |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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41 | |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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42 | The table below shows a brief overview of the descriptors. |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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43 | |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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44 |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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45 +-----------------------------------+------------+ |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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46 | Descriptor/Descriptor Family | Language | |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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47 +===================================+============+ |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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48 | Gasteiger/Marsili Partial Charges | C++ | |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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49 +-----------------------------------+------------+ |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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50 | BalabanJ | Python | |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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51 +-----------------------------------+------------+ |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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52 | BertzCT | Python | |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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53 +-----------------------------------+------------+ |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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54 | Ipc | Python | |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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55 +-----------------------------------+------------+ |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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56 | HallKierAlpha | Python | |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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57 +-----------------------------------+------------+ |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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58 | Kappa1 - Kappa3 | Python | |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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59 +-----------------------------------+------------+ |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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60 | Chi0, Chi1 | Python | |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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61 +-----------------------------------+------------+ |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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62 | Chi0n - Chi4n | Python | |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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63 +-----------------------------------+------------+ |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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64 | Chi0v - Chi4v | Python | |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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65 +-----------------------------------+------------+ |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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66 | MolLogP | C++ | |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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67 +-----------------------------------+------------+ |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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68 | MolMR | C++ | |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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69 +-----------------------------------+------------+ |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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70 | MolWt | C++ | |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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71 +-----------------------------------+------------+ |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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72 | HeavyAtomCount | Python | |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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73 +-----------------------------------+------------+ |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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74 | HeavyAtomMolWt | Python | |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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75 +-----------------------------------+------------+ |
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76 | NHOHCount | C++ | |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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77 +-----------------------------------+------------+ |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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78 | NOCount | C++ | |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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79 +-----------------------------------+------------+ |
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80 | NumHAcceptors | C++ | |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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81 +-----------------------------------+------------+ |
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82 | NumHDonors | C++ | |
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83 +-----------------------------------+------------+ |
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84 | NumHeteroatoms | C++ | |
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85 +-----------------------------------+------------+ |
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86 | NumRotatableBonds | C++ | |
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87 +-----------------------------------+------------+ |
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88 | NumValenceElectrons | Python | |
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89 +-----------------------------------+------------+ |
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90 | RingCount | C++ | |
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91 +-----------------------------------+------------+ |
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92 | TPSA | C++ | |
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93 +-----------------------------------+------------+ |
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94 | LabuteASA | C++ | |
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95 +-----------------------------------+------------+ |
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96 | PEOE_VSA1 - PEOE_VSA14 | Python/C++ | |
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97 +-----------------------------------+------------+ |
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98 | SMR_VSA1 - SMR_VSA10 | Python/C++ | |
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99 +-----------------------------------+------------+ |
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100 | SlogP_VSA1 - SlogP_VSA12 | Python/C++ | |
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101 +-----------------------------------+------------+ |
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102 | EState_VSA1 - EState_VSA11 | Python | |
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103 +-----------------------------------+------------+ |
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104 | VSA_EState1 - VSA_EState10 | Python | |
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105 +-----------------------------------+------------+ |
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106 | Topliss fragments | Python | |
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107 +-----------------------------------+------------+ |
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108 |
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109 | |
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110 | A full list of the descriptors can be obtained here_. |
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111 |
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112 .. _here: https://rdkit.readthedocs.org/en/latest/GettingStartedInPython.html#list-of-available-descriptors |
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113 |
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114 ----- |
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115 |
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116 .. class:: warningmark |
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117 |
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118 **HINT** |
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119 |
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120 Use the **cut columns from a table** tool to select just the desired descriptors. |
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121 |
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122 ----- |
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123 |
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124 .. class:: infomark |
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125 |
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126 **Input** |
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127 |
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128 | - `SD-Format`_ |
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129 | - `SMILES Format`_ |
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130 | - `Corina MOL2`_ |
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131 |
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132 .. _SD-Format: http://en.wikipedia.org/wiki/Chemical_table_file |
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133 .. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification |
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134 .. _Corina MOL2: http://www.molecular-networks.com/products/corina |
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135 |
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136 ----- |
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137 |
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138 .. class:: infomark |
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139 |
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140 **Output** |
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141 |
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142 Tabularfile, where each descriptor (value) is shown in a seperate column. |
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143 |
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144 |
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145 ]]> |
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146 </help> |
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147 <citations> |
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148 <citation type="bibtex"> |
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149 @article{rdkit, |
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150 author = {Greg Landrum}, |
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151 title = {RDKit: Open-source cheminformatics}, |
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152 url ={http://www.rdkit.org} |
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153 }</citation> |
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154 </citations> |
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155 </tool> |