openbabel: modify/ob_genProp.xml annotate

annotate modify/ob_genProp.xml @ 22:b4ba90dcfde0 default tip

ChemicalToolBoX update.

author	Bjoern Gruening <bjoern.gruening@gmail.com>
date	Tue, 23 Jul 2013 19:00:18 +0200
parents	3d3e7c1d0f49
children

rev	line source
15 ec87a42dccec ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 10 diff changeset	1 <tool id="ctb_ob_genProp" name="Compute physico-chemical properties" version="1.0">
0 6493d130f018 Uploaded bgruening parents: diff changeset	2 <description>for a set of molecules</description>
6493d130f018 Uploaded bgruening parents: diff changeset	3 <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism>
6493d130f018 Uploaded bgruening parents: diff changeset	4 <requirements>
6493d130f018 Uploaded bgruening parents: diff changeset	5 <requirement type="package" version="2.3.2">openbabel</requirement>
10 cc63a42fd22e Uploaded bgruening parents: 7 diff changeset	6 <requirement type="package" version="0.1">cheminfolib</requirement>
0 6493d130f018 Uploaded bgruening parents: diff changeset	7 </requirements>
6493d130f018 Uploaded bgruening parents: diff changeset	8 <command interpreter="python">
6493d130f018 Uploaded bgruening parents: diff changeset	9 ob_genProp.py
6493d130f018 Uploaded bgruening parents: diff changeset	10 -i "${infile}"
7 12822efbd4a4 Uploaded bgruening parents: 1 diff changeset	11 --iformat "${infile.ext}"
12822efbd4a4 Uploaded bgruening parents: 1 diff changeset	12 --oformat "${output_opts.output_format_types}"
0 6493d130f018 Uploaded bgruening parents: diff changeset	13 #if $output_opts.header.value:
6493d130f018 Uploaded bgruening parents: diff changeset	14 --header $output_opts.header
6493d130f018 Uploaded bgruening parents: diff changeset	15 #end if
6493d130f018 Uploaded bgruening parents: diff changeset	16 -o "${outfile}"
6493d130f018 Uploaded bgruening parents: diff changeset	17 </command>
6493d130f018 Uploaded bgruening parents: diff changeset	18 <inputs>
6493d130f018 Uploaded bgruening parents: diff changeset	19 <param name="infile" type="data" format="sdf,mol,mol2,cml,inchi,smi" label="Select input file with multiple molecules."/>
6493d130f018 Uploaded bgruening parents: diff changeset	20 <conditional name="output_opts">
6493d130f018 Uploaded bgruening parents: diff changeset	21 <param name="output_format_types" type="select" label="Specify output format file">
6493d130f018 Uploaded bgruening parents: diff changeset	22 <option value="table">Tabular format</option>
6493d130f018 Uploaded bgruening parents: diff changeset	23 <option value="sdf" selected="True">sdf</option>
6493d130f018 Uploaded bgruening parents: diff changeset	24 </param>
6493d130f018 Uploaded bgruening parents: diff changeset	25 <when value="table">
6493d130f018 Uploaded bgruening parents: diff changeset	26 <param name="header" type="boolean" checked="False" label="Print the headers of the table as the first row of the table"/>
6493d130f018 Uploaded bgruening parents: diff changeset	27 </when>
6493d130f018 Uploaded bgruening parents: diff changeset	28 <when value="sdf">
6493d130f018 Uploaded bgruening parents: diff changeset	29 <param name="header" type="hidden"/>
6493d130f018 Uploaded bgruening parents: diff changeset	30 </when>
6493d130f018 Uploaded bgruening parents: diff changeset	31 </conditional>
6493d130f018 Uploaded bgruening parents: diff changeset	32 </inputs>
6493d130f018 Uploaded bgruening parents: diff changeset	33 <outputs>
1 e8dce9596b4c Uploaded bgruening parents: 0 diff changeset	34 <data format="tabular" name="outfile" label="${tool.name} on ${on_string}">
0 6493d130f018 Uploaded bgruening parents: diff changeset	35 <change_format>
1 e8dce9596b4c Uploaded bgruening parents: 0 diff changeset	36 <when input="output_opts.output_format_types" value="sdf" format="sdf"/>
0 6493d130f018 Uploaded bgruening parents: diff changeset	37 </change_format>
6493d130f018 Uploaded bgruening parents: diff changeset	38 </data>
6493d130f018 Uploaded bgruening parents: diff changeset	39 </outputs>
6493d130f018 Uploaded bgruening parents: diff changeset	40 <tests>
6493d130f018 Uploaded bgruening parents: diff changeset	41 <test>
6493d130f018 Uploaded bgruening parents: diff changeset	42 <param name="infile" ftype="sdf" value="CID_2244.sdf"/>
6493d130f018 Uploaded bgruening parents: diff changeset	43 <param name="output_format_types" value="sdf" />
6493d130f018 Uploaded bgruening parents: diff changeset	44 <output name="outfile" ftype="sdf" file="ob_genprop_on_CID2244.sdf" />
6493d130f018 Uploaded bgruening parents: diff changeset	45 </test>
6493d130f018 Uploaded bgruening parents: diff changeset	46 <test>
6493d130f018 Uploaded bgruening parents: diff changeset	47 <param name="infile" ftype="sdf" value="CID_2244.sdf"/>
6493d130f018 Uploaded bgruening parents: diff changeset	48 <param name="output_format_types" value="table" />
6493d130f018 Uploaded bgruening parents: diff changeset	49 <param name="header" value="true" />
6493d130f018 Uploaded bgruening parents: diff changeset	50 <output name="outfile" ftype="sdf" file="ob_genprop_on_CID2244.tabular" />
6493d130f018 Uploaded bgruening parents: diff changeset	51 </test>
6493d130f018 Uploaded bgruening parents: diff changeset	52 </tests>
6493d130f018 Uploaded bgruening parents: diff changeset	53 <help>
6493d130f018 Uploaded bgruening parents: diff changeset	54
6493d130f018 Uploaded bgruening parents: diff changeset	55 .. class:: infomark
6493d130f018 Uploaded bgruening parents: diff changeset	56
16 3d3e7c1d0f49 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 15 diff changeset	57 What this tool does
0 6493d130f018 Uploaded bgruening parents: diff changeset	58
16 3d3e7c1d0f49 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 15 diff changeset	59 Computes several physico-chemical properties for a set of molecules.
3d3e7c1d0f49 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 15 diff changeset	60
3d3e7c1d0f49 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 15 diff changeset	61 The following physico-chemical properties and descriptors are computed for each molecule:
0 6493d130f018 Uploaded bgruening parents: diff changeset	62
16 3d3e7c1d0f49 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 15 diff changeset	63 - number of hydrogen-bond donor and acceptor groups
3d3e7c1d0f49 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 15 diff changeset	64
3d3e7c1d0f49 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 15 diff changeset	65 - number of rotatable bonds
0 6493d130f018 Uploaded bgruening parents: diff changeset	66
16 3d3e7c1d0f49 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 15 diff changeset	67 - logP
3d3e7c1d0f49 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 15 diff changeset	68
3d3e7c1d0f49 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 15 diff changeset	69 - number of rings
0 6493d130f018 Uploaded bgruening parents: diff changeset	70
16 3d3e7c1d0f49 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 15 diff changeset	71 - number of heavy atoms
3d3e7c1d0f49 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 15 diff changeset	72
3d3e7c1d0f49 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 15 diff changeset	73 - molecular weight
0 6493d130f018 Uploaded bgruening parents: diff changeset	74
16 3d3e7c1d0f49 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 15 diff changeset	75 - total Polar Surface Area
3d3e7c1d0f49 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 15 diff changeset	76
3d3e7c1d0f49 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 15 diff changeset	77 - molecular refractivity
0 6493d130f018 Uploaded bgruening parents: diff changeset	78
16 3d3e7c1d0f49 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 15 diff changeset	79 - Canonical SMILES
3d3e7c1d0f49 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 15 diff changeset	80
3d3e7c1d0f49 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 15 diff changeset	81 - InChI string
0 6493d130f018 Uploaded bgruening parents: diff changeset	82
16 3d3e7c1d0f49 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 15 diff changeset	83 - InChI-Key
0 6493d130f018 Uploaded bgruening parents: diff changeset	84
16 3d3e7c1d0f49 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 15 diff changeset	85 - Spectrophores(TM)
0 6493d130f018 Uploaded bgruening parents: diff changeset	86
6493d130f018 Uploaded bgruening parents: diff changeset	87 -----
6493d130f018 Uploaded bgruening parents: diff changeset	88
6493d130f018 Uploaded bgruening parents: diff changeset	89 .. class:: infomark
6493d130f018 Uploaded bgruening parents: diff changeset	90
16 3d3e7c1d0f49 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 15 diff changeset	91 Input
0 6493d130f018 Uploaded bgruening parents: diff changeset	92
16 3d3e7c1d0f49 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 15 diff changeset	93 - SDF_
3d3e7c1d0f49 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 15 diff changeset	94 - MOL2_
0 6493d130f018 Uploaded bgruening parents: diff changeset	95
16 3d3e7c1d0f49 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 15 diff changeset	96 .. _SDF: http://en.wikipedia.org/wiki/Chemical_table_file
3d3e7c1d0f49 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 15 diff changeset	97 .. _MOL2: http://www.tripos.com/index.php?family=modules,SimplePage,Mol2_File_Format2009
0 6493d130f018 Uploaded bgruening parents: diff changeset	98
16 3d3e7c1d0f49 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 15 diff changeset	99 3D coordinates of the molecules have to be provided.
0 6493d130f018 Uploaded bgruening parents: diff changeset	100
16 3d3e7c1d0f49 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 15 diff changeset	101 -----
0 6493d130f018 Uploaded bgruening parents: diff changeset	102
16 3d3e7c1d0f49 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 15 diff changeset	103 .. class:: warningmark
0 6493d130f018 Uploaded bgruening parents: diff changeset	104
16 3d3e7c1d0f49 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 15 diff changeset	105 Hint the generation of Spectrophores(TM) requires the previous addition of explicit hydrogen atoms and the proper definition of 3D coordinates. The user is directed towards the corresponding tools if accurate Spectrophores(TM) descriptors are required.
0 6493d130f018 Uploaded bgruening parents: diff changeset	106
6493d130f018 Uploaded bgruening parents: diff changeset	107 -----
6493d130f018 Uploaded bgruening parents: diff changeset	108
16 3d3e7c1d0f49 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 15 diff changeset	109 .. class:: infomark
3d3e7c1d0f49 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 15 diff changeset	110
3d3e7c1d0f49 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 15 diff changeset	111 Output
3d3e7c1d0f49 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 15 diff changeset	112
3d3e7c1d0f49 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 15 diff changeset	113 Either a SD-file containing several computed physico-chemical properties stored as metadata or a tabular file with the metadata stored in columns.
3d3e7c1d0f49 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 15 diff changeset	114
3d3e7c1d0f49 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 15 diff changeset	115 -----
3d3e7c1d0f49 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 15 diff changeset	116
3d3e7c1d0f49 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 15 diff changeset	117 .. class:: infomark
3d3e7c1d0f49 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 15 diff changeset	118
3d3e7c1d0f49 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 15 diff changeset	119 Cite
0 6493d130f018 Uploaded bgruening parents: diff changeset	120
16 3d3e7c1d0f49 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 15 diff changeset	121 N M O'Boyle, C Morley and G R Hutchison - `Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`_
3d3e7c1d0f49 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 15 diff changeset	122
3d3e7c1d0f49 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 15 diff changeset	123 Silicos_ - \|Spectrophores (TM)\| is a registered tool implemented in the open-source OpenBabel.
3d3e7c1d0f49 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 15 diff changeset	124
3d3e7c1d0f49 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 15 diff changeset	125 .. \|Spectrophores (TM)\| unicode:: Spectrophores U+2122
3d3e7c1d0f49 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 15 diff changeset	126
3d3e7c1d0f49 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 15 diff changeset	127 `Open Babel`_
3d3e7c1d0f49 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 15 diff changeset	128
3d3e7c1d0f49 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 15 diff changeset	129 .. _Open Babel: http://openbabel.org/wiki/Main_Page
3d3e7c1d0f49 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 15 diff changeset	130 .. _`Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`: http://www.biomedcentral.com/content/pdf/1752-153X-2-5.pdf
3d3e7c1d0f49 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 15 diff changeset	131 .. _Silicos: http://openbabel.org/docs/dev/Fingerprints/spectrophore.html
3d3e7c1d0f49 ChemicalToolBoX update. Bjoern Gruening <bjoern.gruening@gmail.com> parents: 15 diff changeset	132
0 6493d130f018 Uploaded bgruening parents: diff changeset	133
6493d130f018 Uploaded bgruening parents: diff changeset	134 </help>
6493d130f018 Uploaded bgruening parents: diff changeset	135 </tool>

Mercurial > repos > bgruening > openbabel

annotate modify/ob_genProp.xml @ 22:b4ba90dcfde0 default tip