Mercurial > repos > bgruening > confab

comparison confab.xml @ 18:a396884f933a

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ChemicalToolBoX update.
author Bjoern Gruening <bjoern.gruening@gmail.com>
date Fri, 19 Jul 2013 16:28:23 +0200
parents 6eb2a0358b9c
children ff23947232d0
comparison
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17:6eb2a0358b9c 18:a396884f933a
34 <output name="outfile" file='confab_on_CID_3033.sdf' ftype='sdf' /> 34 <output name="outfile" file='confab_on_CID_3033.sdf' ftype='sdf' />
35 </test> 35 </test>
36 </tests> 36 </tests>
37 <help> 37 <help>
38 38
39 .. class:: infomark
39 40
40 **What it does** 41 **What this tool does**
41 42
42 confab is an application to systematically generate diverse low-energy conformers for molecules. 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/
43 46
44 ----- 47 -----
45 48
46 **Example** 49 .. class:: infomark
47 50
48 * input: 51 **Input**
49 52
50 Dataset:: 53 * Example::
51 54
52 21.2060 9.9350 63.0810 C 0 0 0 0 0 0 0 0 0 0 0 0 55 21.2060 9.9350 63.0810 C 0 0 0 0 0 0 0 0 0 0 0 0
53 21.2410 9.4460 64.5510 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
54 22.0000 8.1250 64.6300 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
55 21.7010 7.3010 65.5120 O 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
56 23.1180 7.8720 63.7340 C 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
57 23.4530 8.7270 62.7850 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
58 24.6970 8.4430 61.9510 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
59 .......
60 1 2 1 0 0 0 0
61 1 11 1 0 0 0 0
62 2 3 1 0 0 0 0
63 3 4 2 0 0 0 0
64 3 5 1 0 0 0 0
65 5 6 2 0 0 0 0
66 6 7 1 0 0 0 0
67 62
68 - RMSD cutoff (in Angstrom) 0.5 63 .......
69 - Energy cutoff (in kcal/mol) 50.0
70 - Max number of conformers to test 100000
71 - Include the input conformation as the first conformer False
72 64
73 * output:: 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::
74 85
75 23 26 0 0 0 0 0 0 0 0999 V2000 86 23 26 0 0 0 0 0 0 0 0999 V2000
76 21.2060 9.9350 63.0810 C 0 0 0 0 0 0 0 0 0 0 0 0 87 21.2060 9.9350 63.0810 C 0 0 0 0 0 0 0 0 0 0 0 0
77 21.2410 9.4460 64.5510 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
78 22.0000 8.1250 64.6300 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
109 6 11 1 0 0 0 0 120 6 11 1 0 0 0 0
110 7 8 1 0 0 0 0 121 7 8 1 0 0 0 0
111 9 8 1 6 0 0 0 122 9 8 1 6 0 0 0
112 10 9 1 1 0 0 0 123 10 9 1 1 0 0 0
113 124
125 -----
126
127 .. class:: infomark
128
129 **Cite**
130
131 Confab_
132
133 .. _Confab: https://code.google.com/p/confab/
114 134
115 135
116 </help> 136 </help>
117 137
118 </tool> 138 </tool>