Mercurial > repos > bgruening > openbabel
comparison visualisation/ob_depiction_svg.xml @ 0:527ecd2fc500 draft
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author | bgruening |
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date | Thu, 15 Aug 2013 03:25:06 -0400 |
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children | 125da3a296ca |
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-1:000000000000 | 0:527ecd2fc500 |
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1 <tool id="ctb_ob_svg_depiction" name="Visualisation"> | |
2 <description>of compounds</description> | |
3 <requirements> | |
4 <requirement type="package" version="2.3.2">openbabel</requirement> | |
5 </requirements> | |
6 <command> | |
7 obabel -i${infile.ext} $infile | |
8 $embed_molecule_as_cml | |
9 $draw_all_carbon_atoms | |
10 -xC | |
11 -O | |
12 $outfile -o$oformat | |
13 #if str($sort) != "none": | |
14 --sort $sort | |
15 #end if | |
16 #if str($display_name) != "None" and len(str($display_name)) > 0 and str($display_name) != 'title': | |
17 --append "$display_name" | |
18 --title "" | |
19 #end if | |
20 $thick_lines | |
21 2>&1 | |
22 </command> | |
23 <inputs> | |
24 <param name="infile" type="data" format="mol,sdf,smi,inchi" label="Input format"/> | |
25 <param name="embed_molecule_as_cml" type="boolean" truevalue="-e" falsevalue="" label="Embed molecule as CML"/> | |
26 <param name="draw_all_carbon_atoms" type="boolean" truevalue="-a" falsevalue="" label="draw all carbon atoms"/> | |
27 <param name="thick_lines" type="boolean" truevalue="-xt" falsevalue="" label="use thicker lines"/> | |
28 | |
29 <param name='display_name' type='select' format='text' label="The property which is displayed under the molecule"> | |
30 <option value='title'>Molecule's title</option> | |
31 <option value='MW'>Molecular Weight</option> | |
32 <option value='abonds'>Number of aromatic bonds</option> | |
33 <option value='atoms'>Number of atoms</option> | |
34 <option value='bonds'>Number of bonds</option> | |
35 <option value='cansmi'>Canonical SMILES</option> | |
36 <option value='cansmiNS'>Canonical SMILES without isotopes or stereo</option> | |
37 <option value='dbonds'>Number of double bonds</option> | |
38 <option value='formula'>Chemical formula</option> | |
39 <option value='HBA1'>Number of Hydrogen Bond Acceptors 1 (JoelLib)</option> | |
40 <option value='HBA2'>Number of Hydrogen Bond Acceptors 2 (JoelLib)</option> | |
41 <option value='HBD'>Number of Hydrogen Bond Donors (JoelLib)</option> | |
42 <option value='InChI'>IUPAC InChI identifier</option> | |
43 <option value='L5'>Lipinski Rule of Five</option> | |
44 <option value='logP'>octanol/water partition coefficient</option> | |
45 <option value='MR'>molar refractivity</option> | |
46 <option value='nF'>Number of Fluorine Atoms</option> | |
47 <option value='s'>SMARTS filter</option> | |
48 <option value='sbonds'>Number of single bonds</option> | |
49 <option value='smarts'>SMARTS filter</option> | |
50 <option value='tbonds'>Number of triple bonds</option> | |
51 <option value='TPSA'>topological polar surface area</option> | |
52 </param> | |
53 | |
54 <param name='sort' type='select' format='text' label="Sorting the displayed molecules by"> | |
55 <option value='none'>No sorting</option> | |
56 <option value='MW'>Molecular Weight</option> | |
57 <option value='abonds'>Number of aromatic bonds</option> | |
58 <option value='atoms'>Number of atoms</option> | |
59 <option value='bonds'>Number of bonds</option> | |
60 <option value='dbonds'>Number of double bonds</option> | |
61 <option value='HBA1'>Number of Hydrogen Bond Acceptors 1 (JoelLib)</option> | |
62 <option value='HBA2'>Number of Hydrogen Bond Acceptors 2 (JoelLib)</option> | |
63 <option value='HBD'>Number of Hydrogen Bond Donors (JoelLib)</option> | |
64 <option value='L5'>Lipinski Rule of Five</option> | |
65 <option value='logP'>octanol/water partition coefficient</option> | |
66 <option value='MR'>molar refractivity</option> | |
67 <option value='nF'>Number of Fluorine Atoms</option> | |
68 <option value='sbonds'>Number of single bonds</option> | |
69 <option value='tbonds'>Number of triple bonds</option> | |
70 <option value='TPSA'>topological polar surface area</option> | |
71 </param> | |
72 | |
73 <param name='oformat' type='select' format='text' label="Format of the resulting picture"> | |
74 <option value='svg'>SVG</option> | |
75 <option value='png'>PNG</option> | |
76 </param> | |
77 | |
78 </inputs> | |
79 <outputs> | |
80 <data name="outfile" type="data" format="png" label="${tool.name} on ${on_string}"> | |
81 <change_format> | |
82 <when input="oformat" value="svg" format="svg"/> | |
83 </change_format> | |
84 </data> | |
85 </outputs> | |
86 <tests> | |
87 <test> | |
88 <param name="infile" ftype="smi" value="8_mol.smi" /> | |
89 <param name="embed_molecule_as_cml" value="" /> | |
90 <param name="draw_all_carbon_atoms" value="-a" /> | |
91 <param name="thick_lines" value="-xt" /> | |
92 <param name='display_name' value="title" /> | |
93 <param name='sort' value='none' /> | |
94 <output name="outfile" ftype="svg" file="ob_depiction_svg_on_8_mol.svg" /> | |
95 </test> | |
96 </tests> | |
97 <help> | |
98 | |
99 .. class:: infomark | |
100 | |
101 **What this tool does** | |
102 | |
103 Creates an .svg or .png image of a small set of molecules (few hundreds). Based on Open Babel PNG_/SVG_ 2D depiction. | |
104 | |
105 .. _PNG: http://openbabel.org/docs/dev/FileFormats/PNG_2D_depiction.html | |
106 .. _SVG: http://openbabel.org/docs/dev/FileFormats/SVG_2D_depiction.html | |
107 | |
108 ----- | |
109 | |
110 .. class:: warningmark | |
111 | |
112 **Hint** | |
113 | |
114 Use only libraries with at most a few hundred molecules. | |
115 | |
116 ----- | |
117 | |
118 .. class:: infomark | |
119 | |
120 **Cite** | |
121 | |
122 `Open Babel`_ | |
123 | |
124 .. _Open Babel: http://openbabel.org/wiki/Main_Page | |
125 | |
126 </help> | |
127 </tool> |