|
3
|
1 <tool id="ANARCI" name="ANARCI" version="3.0">
|
|
2
|
2 <description>Use ANARCI tools to use HADDOCK-antibody-antigen after.</description>
|
|
0
|
3 <command detect_errors="exit_code"><![CDATA[
|
|
2
|
4 source /home/galaxy/data/_conda/bin/activate Ab-HADDOCK;
|
|
3
|
5 python2.7 /home/galaxy/HADDOCK-antibody-antigen/ImmunoPDB.py -i '${input}' -o '${output}' --scheme ${scheme} --splitscfv
|
|
0
|
6 #if $receptor
|
|
|
7 --receptor ${receptor}
|
|
|
8 #end if;
|
|
|
9 #if $fvonly
|
|
|
10 --fvonly
|
|
|
11 #end if;
|
|
|
12 #if $rename
|
|
|
13 --rename
|
|
|
14 #end if;
|
|
|
15 #if $splitscfv
|
|
|
16 --splitscfv
|
|
|
17 #end if;
|
|
2
|
18 ;
|
|
|
19 source /home/galaxy/data/_conda/bin/deactivate
|
|
0
|
20 ]]></command>
|
|
|
21 <inputs>
|
|
|
22 <param format="pdb" name="input" type="data" label="Select your PDB file."/>
|
|
|
23 <param name="scheme" type="select" label="Scheme to use - default is 'IMGT'" help="Which numbering scheme should be used.">
|
|
|
24 <option value="imgt" selected="true">IMGT</option>
|
|
|
25 <option value="kabat">Kabat</option>
|
|
|
26 <option value="aho">Aho</option>
|
|
|
27 <option value="wolfguy">Wolfguy</option>
|
|
|
28 <option value="chothia">Chothia</option>
|
|
|
29 <option value="martin">Martin</option>
|
|
|
30 <option value="pdb">PDB</option>
|
|
|
31 </param>
|
|
|
32 <param name="receptor" type="select" optional="true" label="Choose ig or tr domains" help="Choose whether to number Antibody (ig) or TCR (tr) domains. (Optional)">
|
|
|
33 <option value="ig" >Antibody domains</option>
|
|
|
34 <option value="tr" >TCR domains</option>
|
|
|
35 </param>
|
|
1
|
36 <param name="fvonly" type="boolean" optional="true" label="Only output Fv regions." help="Only output Fv regions."/>
|
|
|
37 <param name="rename" type="boolean" optional="true" label="Rename the receptor chains." help="Rename the receptor chains with H and L (ig) or B and A (tr). Only receptor chains output. First pair identified used."/>
|
|
|
38 <param name="splitscfv" type="boolean" optional="true" label="Split chain." help="When they are found split single chain fvs into two seperate chains (fvonly becomes true)."/>
|
|
0
|
39 </inputs>
|
|
|
40 <outputs>
|
|
|
41 <data name="output" format="pdb" />
|
|
|
42 </outputs>
|
|
|
43 <help>
|
|
|
44 usage: ImmunoPDB [-h] [-i INPUTSTRUCTURE] [-o OUTFILE]
|
|
|
45 [--scheme {kabat,aho,wolfguy,imgt,a,c,chothia,i,k,m,w,martin,pdb}]
|
|
|
46 [--receptor {ig,tr}] [--rename] [--fvonly] [--splitscfv]
|
|
|
47 [--warnings]
|
|
|
48
|
|
|
49 ANARCI - ImmunoPDB \\ //
|
|
|
50 Antibody Numbering and Antigen Receptor ClassIfication \\ //
|
|
|
51 ||
|
|
|
52 (c) Oxford Protein Informatics Group (OPIG). 2015-16 ||
|
|
|
53
|
|
|
54 Example script to number Antibody and TCR PDB structures.
|
|
|
55
|
|
|
56 ANARCI must be installed and in the path
|
|
|
57 opig.stats.ox.ac.uk/webapps/anarci
|
|
|
58
|
|
|
59 Requirements: Biopython (version >= 1.66)
|
|
|
60 Muscle
|
|
|
61
|
|
|
62 This script extends the BioPython PDBParser and Structure classes so that a numbering scheme can be applied to the variable domain
|
|
|
63 of an antigen receptor chain.
|
|
|
64
|
|
|
65 o Where available the Seqres record is used as the full sequence. Missing residues are recognised by comparing this to the residues
|
|
|
66 with coordinates.
|
|
|
67
|
|
|
68 o *Only* variable domains are numbered consistently in the chosen scheme.
|
|
|
69
|
|
|
70 o Residues before the domain are numbered '0' with reverse alphabetical insertions if there are less than 28 (all 0 otherwise - this
|
|
|
71 will break some PDB parsers...)
|
|
|
72
|
|
|
73 o Residues after the variable domain are numbered sequentially from 1001.
|
|
|
74
|
|
|
75 o By default when more than one variable domain is found on a single chain (e.g. single chain Fv, diabody...) the numbering will be
|
|
|
76 with respect to the first domain identified.
|
|
|
77
|
|
|
78 o CDR recognition is performed and regions are annotated in the xtra dictionary attributes of residue objects.
|
|
|
79
|
|
|
80 o Pairing is performed using the distance between the interface cysteine positions (imgt 104).
|
|
|
81
|
|
|
82 Basic useage
|
|
|
83
|
|
|
84 Renumber antibody chains with imgt numbering scheme
|
|
|
85 python ImmunoPDB.py -i infile.pdb -o outfile.pdb -s imgt
|
|
|
86
|
|
|
87 Renumber tcr chains with imgt numbering scheme
|
|
|
88 python ImmunoPDB.py -i infile.pdb -o outfile.pdb -s imgt --receptor tr
|
|
|
89
|
|
|
90 optional arguments:
|
|
|
91 -h, --help show this help message and exit
|
|
|
92 -i INPUTSTRUCTURE A structure to be numbered
|
|
|
93 -o OUTFILE The output file to use. Default is stdout
|
|
|
94 --scheme {kabat,aho,wolfguy,imgt,a,c,chothia,i,k,m,w,martin,pdb}, -s {kabat,aho,wolfguy,imgt,a,c,chothia,i,k,m,w,martin,pdb}
|
|
|
95 Which numbering scheme should be used. i, k, c, m, w
|
|
|
96 and a are shorthand for IMGT, Kabat, Chothia, Martin
|
|
|
97 (Extended Chothia), Wolfguy and Aho respectively.
|
|
|
98 Default IMGT. Use pdb to retain the numbering but get
|
|
|
99 the annotations as remarks
|
|
|
100 --receptor {ig,tr}, -r {ig,tr}
|
|
|
101 Choose whether to number Antibody (ig) or TCR (tr)
|
|
|
102 domains.
|
|
|
103 --rename Rename the receptor chains with H and L (ig) or B and
|
|
|
104 A (tr). Only receptor chains output. First pair
|
|
|
105 identified used.
|
|
|
106 --fvonly Only output Fv regions.
|
|
|
107 --splitscfv When they are found split single chain fvs into two
|
|
|
108 seperate chains (fvonly becomes true)
|
|
|
109 --warnings Report warnings about missing residues
|
|
|
110
|
|
|
111 Author: James Dunbar (dunbar@stats.ox.ac.uk)
|
|
|
112 Charlotte Deane (deane@stats.ox.ac.uk)
|
|
|
113
|
|
|
114 Copyright (C) 2016 Oxford Protein Informatics Group (OPIG)
|
|
|
115 Freely distributed under the GNU General Public License (GPLv3).
|
|
|
116 </help>
|
|
|
117 </tool>
|
|
|
118
|
