Mercurial > repos > bgruening > confab
annotate confab.xml @ 17:6eb2a0358b9c
ChemicalToolBoX update.
| author | Bjoern Gruening <bjoern.gruening@gmail.com> |
|---|---|
| date | Sat, 01 Jun 2013 20:03:28 +0200 |
| parents | 6c8f72ee4a51 |
| children | a396884f933a |
| rev | line source |
|---|---|
|
17
6eb2a0358b9c
ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents:
4
diff
changeset
|
1 <tool id="ctb_confab" name="Conformer calculation" version="0.1"> |
| 0 | 2 <description>for molecules (confab)</description> |
| 4 | 3 <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="100" shared_inputs="" merge_outputs="outfile"></parallelism> |
| 0 | 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 $outfile 2>&1 | |
| 16 </command> | |
| 17 <inputs> | |
|
17
6eb2a0358b9c
ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents:
4
diff
changeset
|
18 <param name="infile" type="data" format="sdf,mol2" label="Input molecule with 3D coordinates" help="Dataset missing? See TIP below"/> |
| 0 | 19 <param name='RMSD' type='float' value='0.5' label='RMSD cutoff (in Angstrom)' /> |
| 20 <param name='energy' type='float' value='50.0' label='Energy cutoff (in kcal/mol)' /> | |
|
17
6eb2a0358b9c
ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents:
4
diff
changeset
|
21 <param name='conformers' type='integer' value='100' label='Max number of conformers to test' /> |
|
6eb2a0358b9c
ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents:
4
diff
changeset
|
22 <param name='first_conformer' type='boolean' truevalue='-a' falsevalue='' label='Include the input conformation as the first conformer' /> |
| 0 | 23 </inputs> |
| 24 <outputs> | |
| 2 | 25 <data format="sdf" name="outfile" label="${tool.name} on ${on_string}"/> |
| 0 | 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 | |
| 40 **What it does** | |
| 41 | |
| 42 confab is an application to systematically generate diverse low-energy conformers for molecules. | |
| 43 | |
| 44 ----- | |
| 45 | |
| 46 **Example** | |
| 47 | |
| 48 * input: | |
| 49 | |
| 50 Dataset:: | |
| 51 | |
| 52 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 | |
| 54 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 | |
| 56 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 | |
| 58 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 | |
| 68 - RMSD cutoff (in Angstrom) 0.5 | |
| 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 | |
| 73 * output:: | |
| 74 | |
| 75 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 | |
| 77 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 | |
| 79 21.7010 7.3010 65.5120 O 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 80 23.1180 7.8720 63.7340 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 81 23.4530 8.7270 62.7850 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 82 24.6970 8.4430 61.9510 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 83 24.4490 8.6370 60.4430 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 84 23.7890 9.9970 60.0980 C 0 0 2 0 0 0 0 0 0 0 0 0 | |
| 85 22.4340 10.0950 60.8720 C 0 0 1 0 0 0 0 0 0 0 0 0 | |
| 86 22.6140 10.0230 62.4340 C 0 0 1 0 0 0 0 0 0 0 0 0 | |
| 87 21.6330 11.3540 60.4500 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 88 21.4320 11.4340 58.9110 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 89 22.7860 11.4040 58.1690 C 0 0 1 0 0 0 0 0 0 0 0 0 | |
| 90 23.4830 10.0600 58.5980 C 0 0 1 0 0 0 0 0 0 0 0 0 | |
| 91 24.6740 9.9180 57.6180 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 92 24.0720 10.4500 56.2670 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 93 22.7140 11.1490 56.6270 C 0 0 2 0 0 0 0 0 0 0 0 0 | |
| 94 23.6590 12.6770 58.4540 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 95 23.4270 11.2460 63.0070 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 96 22.3750 12.3880 55.7810 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 97 23.2120 12.8760 55.0520 O 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 98 21.0090 12.9760 55.8570 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 99 | |
| 100 :: | |
| 101 | |
| 102 1 2 1 0 0 0 0 | |
| 103 1 11 1 0 0 0 0 | |
| 104 2 3 1 0 0 0 0 | |
| 105 3 4 2 0 0 0 0 | |
| 106 3 5 1 0 0 0 0 | |
| 107 5 6 2 0 0 0 0 | |
| 108 6 7 1 0 0 0 0 | |
| 109 6 11 1 0 0 0 0 | |
| 110 7 8 1 0 0 0 0 | |
| 111 9 8 1 6 0 0 0 | |
| 112 10 9 1 1 0 0 0 | |
| 113 | |
| 114 | |
| 115 | |
| 116 </help> | |
| 117 | |
| 118 </tool> |