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comparison confab.xml @ 0:ea7816847e5e

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author bgruening
date Tue, 26 Mar 2013 14:52:53 -0400
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1 <tool id="confab" name="Conformer calculation" >
2 <description>for molecules (confab)</description>
3 <requirements>
4 <requirement type="package" version="1.0.1">confab</requirement>
5 </requirements>
6 <command> confab
7 -i ${infile.ext}
8 -o sdf
9 -r $RMSD
10 -e $energy
11 -c $conformers
12 $first_conformer
13 $infile
14 $outfile 2>&#38;1
15 </command>
16 <inputs>
17 <param name="infile" type="data" format="sdf,pdb,mol2" label="Dataset" help="Dataset missing? See TIP below"/>
18 <param name='RMSD' type='float' value='0.5' label='RMSD cutoff (in Angstrom)' />
19 <param name='energy' type='float' value='50.0' label='Energy cutoff (in kcal/mol)' />
20 <param name='conformers' type='integer' value='100000' label='Max number of conformers to test' />
21 <param name='first_conformer' type='boolean' label='Include the input conformation as the first conformer' truevalue='-a' falsevalue='' />
22 </inputs>
23 <outputs>
24 <data format="sdf" name="outfile"/>
25 </outputs>
26 <tests>
27 <test>
28 <param name="infile" value='CID_3033.sdf' ftype='sdf' />
29 <param name='RMSD' value='0.5' />
30 <param name='energy' value='50.0' />
31 <param name='conformers' value='100000' />
32 <param name='first_conformer' value='-a' />
33 <output name="outfile" file='confab_on_CID_3033.sdf' ftype='sdf' />
34 </test>
35 </tests>
36 <help>
37
38
39 **What it does**
40
41 confab is an application to systematically generate diverse low-energy conformers for molecules.
42
43 -----
44
45 **Example**
46
47 * input:
48
49 Dataset::
50
51 21.2060 9.9350 63.0810 C 0 0 0 0 0 0 0 0 0 0 0 0
52 21.2410 9.4460 64.5510 C 0 0 0 0 0 0 0 0 0 0 0 0
53 22.0000 8.1250 64.6300 C 0 0 0 0 0 0 0 0 0 0 0 0
54 21.7010 7.3010 65.5120 O 0 0 0 0 0 0 0 0 0 0 0 0
55 23.1180 7.8720 63.7340 C 0 0 0 0 0 0 0 0 0 0 0 0
56 23.4530 8.7270 62.7850 C 0 0 0 0 0 0 0 0 0 0 0 0
57 24.6970 8.4430 61.9510 C 0 0 0 0 0 0 0 0 0 0 0 0
58 .......
59 1 2 1 0 0 0 0
60 1 11 1 0 0 0 0
61 2 3 1 0 0 0 0
62 3 4 2 0 0 0 0
63 3 5 1 0 0 0 0
64 5 6 2 0 0 0 0
65 6 7 1 0 0 0 0
66
67 - RMSD cutoff (in Angstrom) 0.5
68 - Energy cutoff (in kcal/mol) 50.0
69 - Max number of conformers to test 100000
70 - Include the input conformation as the first conformer False
71
72 * output::
73
74 23 26 0 0 0 0 0 0 0 0999 V2000
75 21.2060 9.9350 63.0810 C 0 0 0 0 0 0 0 0 0 0 0 0
76 21.2410 9.4460 64.5510 C 0 0 0 0 0 0 0 0 0 0 0 0
77 22.0000 8.1250 64.6300 C 0 0 0 0 0 0 0 0 0 0 0 0
78 21.7010 7.3010 65.5120 O 0 0 0 0 0 0 0 0 0 0 0 0
79 23.1180 7.8720 63.7340 C 0 0 0 0 0 0 0 0 0 0 0 0
80 23.4530 8.7270 62.7850 C 0 0 0 0 0 0 0 0 0 0 0 0
81 24.6970 8.4430 61.9510 C 0 0 0 0 0 0 0 0 0 0 0 0
82 24.4490 8.6370 60.4430 C 0 0 0 0 0 0 0 0 0 0 0 0
83 23.7890 9.9970 60.0980 C 0 0 2 0 0 0 0 0 0 0 0 0
84 22.4340 10.0950 60.8720 C 0 0 1 0 0 0 0 0 0 0 0 0
85 22.6140 10.0230 62.4340 C 0 0 1 0 0 0 0 0 0 0 0 0
86 21.6330 11.3540 60.4500 C 0 0 0 0 0 0 0 0 0 0 0 0
87 21.4320 11.4340 58.9110 C 0 0 0 0 0 0 0 0 0 0 0 0
88 22.7860 11.4040 58.1690 C 0 0 1 0 0 0 0 0 0 0 0 0
89 23.4830 10.0600 58.5980 C 0 0 1 0 0 0 0 0 0 0 0 0
90 24.6740 9.9180 57.6180 C 0 0 0 0 0 0 0 0 0 0 0 0
91 24.0720 10.4500 56.2670 C 0 0 0 0 0 0 0 0 0 0 0 0
92 22.7140 11.1490 56.6270 C 0 0 2 0 0 0 0 0 0 0 0 0
93 23.6590 12.6770 58.4540 C 0 0 0 0 0 0 0 0 0 0 0 0
94 23.4270 11.2460 63.0070 C 0 0 0 0 0 0 0 0 0 0 0 0
95 22.3750 12.3880 55.7810 C 0 0 0 0 0 0 0 0 0 0 0 0
96 23.2120 12.8760 55.0520 O 0 0 0 0 0 0 0 0 0 0 0 0
97 21.0090 12.9760 55.8570 C 0 0 0 0 0 0 0 0 0 0 0 0
98
99 ::
100
101 1 2 1 0 0 0 0
102 1 11 1 0 0 0 0
103 2 3 1 0 0 0 0
104 3 4 2 0 0 0 0
105 3 5 1 0 0 0 0
106 5 6 2 0 0 0 0
107 6 7 1 0 0 0 0
108 6 11 1 0 0 0 0
109 7 8 1 0 0 0 0
110 9 8 1 6 0 0 0
111 10 9 1 1 0 0 0
112
113
114
115 </help>
116
117 </tool>