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1 <tool id="ctb_ob_svg_depiction" name="Visualisation">
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2 <description>of compounds</description>
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3 <requirements>
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4 <requirement type="package" version="2.3.2">openbabel</requirement>
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5 </requirements>
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6 <command>
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7 obabel -i${infile.ext} $infile
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8 $embed_molecule_as_cml
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9 $draw_all_carbon_atoms
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10 -xC
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11 -O
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12 $outfile -o$oformat
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13 #if str($sort) != "none":
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14 --sort $sort
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15 #end if
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16 #if str($display_name) != "None" and len(str($display_name)) > 0 and str($display_name) != 'title':
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17 --append "$display_name"
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18 --title ""
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19 #end if
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20 $thick_lines
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21 2>&1
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22 </command>
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23 <inputs>
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24 <param name="infile" type="data" format="mol,sdf,smi,inchi" label="Input format"/>
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25 <param name="embed_molecule_as_cml" type="boolean" truevalue="-e" falsevalue="" label="Embed molecule as CML"/>
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26 <param name="draw_all_carbon_atoms" type="boolean" truevalue="-a" falsevalue="" label="draw all carbon atoms"/>
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27 <param name="thick_lines" type="boolean" truevalue="-xt" falsevalue="" label="use thicker lines"/>
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28
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29 <param name='display_name' type='select' format='text' label="The property which is displayed under the molecule">
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30 <option value='title'>Molecule's title</option>
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31 <option value='MW'>Molecular Weight</option>
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32 <option value='abonds'>Number of aromatic bonds</option>
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33 <option value='atoms'>Number of atoms</option>
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34 <option value='bonds'>Number of bonds</option>
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35 <option value='cansmi'>Canonical SMILES</option>
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36 <option value='cansmiNS'>Canonical SMILES without isotopes or stereo</option>
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37 <option value='dbonds'>Number of double bonds</option>
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38 <option value='formula'>Chemical formula</option>
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39 <option value='HBA1'>Number of Hydrogen Bond Acceptors 1 (JoelLib)</option>
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40 <option value='HBA2'>Number of Hydrogen Bond Acceptors 2 (JoelLib)</option>
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41 <option value='HBD'>Number of Hydrogen Bond Donors (JoelLib)</option>
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42 <option value='InChI'>IUPAC InChI identifier</option>
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43 <option value='L5'>Lipinski Rule of Five</option>
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44 <option value='logP'>octanol/water partition coefficient</option>
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45 <option value='MR'>molar refractivity</option>
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46 <option value='nF'>Number of Fluorine Atoms</option>
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47 <option value='s'>SMARTS filter</option>
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48 <option value='sbonds'>Number of single bonds</option>
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49 <option value='smarts'>SMARTS filter</option>
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50 <option value='tbonds'>Number of triple bonds</option>
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51 <option value='TPSA'>topological polar surface area</option>
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52 </param>
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53
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54 <param name='sort' type='select' format='text' label="Sorting the displayed molecules by">
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55 <option value='none'>No sorting</option>
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56 <option value='MW'>Molecular Weight</option>
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57 <option value='abonds'>Number of aromatic bonds</option>
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58 <option value='atoms'>Number of atoms</option>
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59 <option value='bonds'>Number of bonds</option>
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60 <option value='dbonds'>Number of double bonds</option>
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61 <option value='HBA1'>Number of Hydrogen Bond Acceptors 1 (JoelLib)</option>
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62 <option value='HBA2'>Number of Hydrogen Bond Acceptors 2 (JoelLib)</option>
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63 <option value='HBD'>Number of Hydrogen Bond Donors (JoelLib)</option>
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64 <option value='L5'>Lipinski Rule of Five</option>
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65 <option value='logP'>octanol/water partition coefficient</option>
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66 <option value='MR'>molar refractivity</option>
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67 <option value='nF'>Number of Fluorine Atoms</option>
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68 <option value='sbonds'>Number of single bonds</option>
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69 <option value='tbonds'>Number of triple bonds</option>
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70 <option value='TPSA'>topological polar surface area</option>
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71 </param>
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72
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73 <param name='oformat' type='select' format='text' label="Format of the resulting picture">
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74 <option value='svg'>SVG</option>
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75 <option value='png'>PNG</option>
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76 </param>
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77
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78 </inputs>
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79 <outputs>
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80 <data name="outfile" type="data" format="png" label="${tool.name} on ${on_string}">
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81 <change_format>
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82 <when input="oformat" value="svg" format="svg"/>
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83 </change_format>
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84 </data>
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85 </outputs>
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86 <tests>
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87 <test>
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88 <param name="infile" ftype="smi" value="8_mol.smi" />
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89 <param name="embed_molecule_as_cml" value="" />
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90 <param name="draw_all_carbon_atoms" value="-a" />
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91 <param name="thick_lines" value="-xt" />
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92 <param name='display_name' value="title" />
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93 <param name='sort' value='none' />
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94 <output name="outfile" ftype="svg" file="ob_depiction_svg_on_8_mol.svg" />
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95 </test>
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96 </tests>
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97 <help>
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98
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99 .. class:: infomark
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100
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101 **What this tool does**
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102
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103 Creates an .svg or .png image of a small set of molecules (few hundreds). Based on Open Babel PNG_/SVG_ 2D depiction.
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104
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105 .. _PNG: http://openbabel.org/docs/dev/FileFormats/PNG_2D_depiction.html
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106 .. _SVG: http://openbabel.org/docs/dev/FileFormats/SVG_2D_depiction.html
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107
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108 -----
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109
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110 .. class:: warningmark
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111
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112 **Hint**
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113
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114 Use only libraries with at most a few hundred molecules.
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115
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116 -----
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117
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118 .. class:: infomark
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119
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120 **Cite**
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121
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122 `Open Babel`_
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123
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124 .. _Open Babel: http://openbabel.org/wiki/Main_Page
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125
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126 </help>
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127 </tool>
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