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comparison confab.xml @ 0:4a73b5059c22 draft

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author bgruening
date Thu, 15 Aug 2013 03:31:39 -0400
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1 <tool id="ctb_confab" name="Conformer calculation" version="0.1">
2 <description>for molecules (confab)</description>
3 <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="100" shared_inputs="" merge_outputs="outfile"></parallelism>
4 <requirements>
5 <requirement type="package" version="1.0.1">confab</requirement>
6 </requirements>
7 <command> confab
8 -i ${infile.ext}
9 -o sdf
10 -r $RMSD
11 -e $energy
12 -c $conformers
13 $first_conformer
14 $infile
15 $outfile 2>&#38;1
16 </command>
17 <inputs>
18 <param name="infile" type="data" format="sdf,mol2" label="Input molecule with 3D coordinates" help="Dataset missing? See TIP below"/>
19 <param name='RMSD' type='float' value='0.5' label='RMSD cutoff (in Angstrom)' />
20 <param name='energy' type='float' value='50.0' label='Energy cutoff (in kcal/mol)' />
21 <param name='conformers' type='integer' value='100' label='Max number of conformers to test' />
22 <param name='first_conformer' type='boolean' truevalue='-a' falsevalue='' label='Include the input conformation as the first conformer' />
23 </inputs>
24 <outputs>
25 <data format="sdf" name="outfile" label="${tool.name} on ${on_string}"/>
26 </outputs>
27 <tests>
28 <test>
29 <param name="infile" value='CID_3033.sdf' ftype='sdf' />
30 <param name='RMSD' value='0.5' />
31 <param name='energy' value='50.0' />
32 <param name='conformers' value='100000' />
33 <param name='first_conformer' value='-a' />
34 <output name="outfile" file='confab_on_CID_3033.sdf' ftype='sdf' />
35 </test>
36 </tests>
37 <help>
38
39 .. class:: infomark
40
41 **What this tool does**
42
43 Confab_ is a conformation generator. The algorithm starts with an input 3D structure which, after some initialisation steps, is used to generate multiple conformers which are filtered on-the-fly to identify diverse low energy conformers.
44
45 .. _Confab: https://code.google.com/p/confab/
46
47 -----
48
49 .. class:: infomark
50
51 **Input**
52
53 * Example::
54
55 21.2060 9.9350 63.0810 C 0 0 0 0 0 0 0 0 0 0 0 0
56 21.2410 9.4460 64.5510 C 0 0 0 0 0 0 0 0 0 0 0 0
57 22.0000 8.1250 64.6300 C 0 0 0 0 0 0 0 0 0 0 0 0
58 21.7010 7.3010 65.5120 O 0 0 0 0 0 0 0 0 0 0 0 0
59 23.1180 7.8720 63.7340 C 0 0 0 0 0 0 0 0 0 0 0 0
60 23.4530 8.7270 62.7850 C 0 0 0 0 0 0 0 0 0 0 0 0
61 24.6970 8.4430 61.9510 C 0 0 0 0 0 0 0 0 0 0 0 0
62
63 .......
64
65 1 2 1 0 0 0 0
66 1 11 1 0 0 0 0
67 2 3 1 0 0 0 0
68 3 4 2 0 0 0 0
69 3 5 1 0 0 0 0
70 5 6 2 0 0 0 0
71 6 7 1 0 0 0 0
72
73 RMSD cutoff (in Angstrom) 0.5
74 Energy cutoff (in kcal/mol) 50.0
75 Max number of conformers to test 100000
76 Include the input conformation as the first conformer False
77
78 -----
79
80 .. class:: infomark
81
82 **Output**
83
84 * Example::
85
86 23 26 0 0 0 0 0 0 0 0999 V2000
87 21.2060 9.9350 63.0810 C 0 0 0 0 0 0 0 0 0 0 0 0
88 21.2410 9.4460 64.5510 C 0 0 0 0 0 0 0 0 0 0 0 0
89 22.0000 8.1250 64.6300 C 0 0 0 0 0 0 0 0 0 0 0 0
90 21.7010 7.3010 65.5120 O 0 0 0 0 0 0 0 0 0 0 0 0
91 23.1180 7.8720 63.7340 C 0 0 0 0 0 0 0 0 0 0 0 0
92 23.4530 8.7270 62.7850 C 0 0 0 0 0 0 0 0 0 0 0 0
93 24.6970 8.4430 61.9510 C 0 0 0 0 0 0 0 0 0 0 0 0
94 24.4490 8.6370 60.4430 C 0 0 0 0 0 0 0 0 0 0 0 0
95 23.7890 9.9970 60.0980 C 0 0 2 0 0 0 0 0 0 0 0 0
96 22.4340 10.0950 60.8720 C 0 0 1 0 0 0 0 0 0 0 0 0
97 22.6140 10.0230 62.4340 C 0 0 1 0 0 0 0 0 0 0 0 0
98 21.6330 11.3540 60.4500 C 0 0 0 0 0 0 0 0 0 0 0 0
99 21.4320 11.4340 58.9110 C 0 0 0 0 0 0 0 0 0 0 0 0
100 22.7860 11.4040 58.1690 C 0 0 1 0 0 0 0 0 0 0 0 0
101 23.4830 10.0600 58.5980 C 0 0 1 0 0 0 0 0 0 0 0 0
102 24.6740 9.9180 57.6180 C 0 0 0 0 0 0 0 0 0 0 0 0
103 24.0720 10.4500 56.2670 C 0 0 0 0 0 0 0 0 0 0 0 0
104 22.7140 11.1490 56.6270 C 0 0 2 0 0 0 0 0 0 0 0 0
105 23.6590 12.6770 58.4540 C 0 0 0 0 0 0 0 0 0 0 0 0
106 23.4270 11.2460 63.0070 C 0 0 0 0 0 0 0 0 0 0 0 0
107 22.3750 12.3880 55.7810 C 0 0 0 0 0 0 0 0 0 0 0 0
108 23.2120 12.8760 55.0520 O 0 0 0 0 0 0 0 0 0 0 0 0
109 21.0090 12.9760 55.8570 C 0 0 0 0 0 0 0 0 0 0 0 0
110
111 ::
112
113 1 2 1 0 0 0 0
114 1 11 1 0 0 0 0
115 2 3 1 0 0 0 0
116 3 4 2 0 0 0 0
117 3 5 1 0 0 0 0
118 5 6 2 0 0 0 0
119 6 7 1 0 0 0 0
120 6 11 1 0 0 0 0
121 7 8 1 0 0 0 0
122 9 8 1 6 0 0 0
123 10 9 1 1 0 0 0
124
125 -----
126
127 .. class:: infomark
128
129 **Cite**
130
131 Confab_
132
133 .. _Confab: https://code.google.com/p/confab/
134
135
136 </help>
137
138 </tool>