Mercurial > repos > fmercuri > gmx_editconf_daimoners
comparison editconf.xml @ 4:770be7b8dddd draft
Uploaded
| author | fmercuri |
|---|---|
| date | Fri, 25 Jun 2021 15:55:00 +0000 |
| parents | 0876b56a3b3d |
| children | 0e7f3bea714a |
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| 3:0876b56a3b3d | 4:770be7b8dddd |
|---|---|
| 12 ln -s '$input_file' ./input.$input_file.ext && | 12 ln -s '$input_file' ./input.$input_file.ext && |
| 13 gmx editconf | 13 gmx editconf |
| 14 -f ./input.$input_file.ext | 14 -f ./input.$input_file.ext |
| 15 -o ./output.${output_format} | 15 -o ./output.${output_format} |
| 16 #if $box.config == "true": | 16 #if $box.config == "true": |
| 17 -d $box.dim | 17 #if $boxtype.boxtype == "cubic": |
| 18 -bt $box.type | 18 -box $boxtype.cubicdim |
| 19 #end if | 19 #end if |
| 20 #if $sbox.config == "true": | 20 #if $boxtype.boxtype == "custom": |
| 21 -box $sbox.dim | 21 -d $boxtype.boxdim |
| 22 -bt $box.type | 22 -bt $boxtype.type |
| 23 #end if | |
| 23 #end if | 24 #end if |
| 24 &>> verbose.txt && | 25 &>> verbose.txt && |
| 25 | 26 |
| 26 cp ./output.${output_format} '$output' | 27 cp ./output.${output_format} '$output' |
| 27 | 28 |
| 31 <param argument="input_file" type="data" format='gro,pdb' label="Input structure"/> | 32 <param argument="input_file" type="data" format='gro,pdb' label="Input structure"/> |
| 32 <param argument="output_format" type="select" label="Output format"> | 33 <param argument="output_format" type="select" label="Output format"> |
| 33 <option value="gro">GRO file</option> | 34 <option value="gro">GRO file</option> |
| 34 <option value="pdb">PDB file</option> | 35 <option value="pdb">PDB file</option> |
| 35 </param> | 36 </param> |
| 36 | 37 |
| 37 <conditional name="box"> | 38 <conditional name="box"> |
| 38 <param argument="config" type="select" label="Configure distance-based box?"> | 39 <param argument="config" type="select" label="Configure box?"> |
| 39 <option value="true">Yes</option> | 40 <option value="true">Yes</option> |
| 40 <option value="false" selected="true">No</option> | 41 <option value="false" selected="true">No</option> |
| 41 </param> | 42 </param> |
| 42 <when value="true"> | 43 <when value="true"> |
| 43 <param argument="dim" type="float" label="Size to be added to the dimensions of the system" value="0.0" min="0.0" max="1000.0" help="Size to be added to the dimension of the system" /> | 44 <conditional name="boxtype"> |
| 44 <param argument="type" type="select" label="Box type" | 45 <param argument="boxtype" type="select" label="Box type"/> |
| 45 help="triclinic is a triclinic box, cubic is a rectangular box with all sides equal dodecahedron represents a rhombic dodecahedron and octahedron is a truncated octahedron. The last two are special cases of a triclinic box. The length of the three box vectors of the truncated octahedron is the shortest distance between two opposite hexagons. Relative to a cubic box with some periodic image distance, the volume of a dodecahedron with this same periodic distance is 0.71 times that of the cube, and that of a truncated octahedron is 0.77 times."> | 46 <option value="cubic">Standard cubic box</option> |
| 46 <option value="cubic">Rectangular box with all sides equal</option> | 47 <option value="custom">Custom box type</option> |
| 47 <option value="triclinic">Triclinic</option> | 48 </param> |
| 48 <option value="dodecahedron">represents a rhombic dodecahedron</option> | 49 |
| 49 <option value="octahedron">truncated octahedron</option> | 50 <when value="cubic"> |
| 50 </param> | 51 <param argument="cubicdim" type="float" label="Box dimensions in nanometers" value="0.0" min="0.0" max="1000.0" help="Dimensions of the box in which simulation will take place" /> |
| 52 </when> | |
| 53 | |
| 54 <when value="variable"> | |
| 55 <param argument="boxdim" type="float" label="Size to be added to the dimensions of the system" value="0.0" min="0.0" max="1000.0" help="Size to be added to the dimension of the system" /> | |
| 56 <param argument="type" type="select" label="Box type" help="Box type"> | |
| 57 <option value="cubic">Cubic</option> | |
| 58 <option value="triclinic">Triclinic</option> | |
| 59 <option value="dodecahedron">Rhombic dodecahedron</option> | |
| 60 <option value="octahedron">Truncated octahedron</option> | |
| 61 </param> | |
| 62 </when> | |
| 63 </conditional> | |
| 51 </when> | 64 </when> |
| 52 <when value="false"/> | 65 <when value="false"/> |
| 53 </conditional> | 66 </conditional> |
| 54 | 67 |
| 55 <conditional name="sbox"> | |
| 56 <param argument="config" type="select" label="Configure size-based box?"> | |
| 57 <option value="true">Yes</option> | |
| 58 <option value="false" selected="true">No</option> | |
| 59 </param> | |
| 60 <when value="true"> | |
| 61 <param argument="dim" type="float" label="Box dimensions in nanometers" value="0.0" min="0.0" max="1000.0" help="Dimensions of the box in which simulation will take place" /> | |
| 62 <param argument="type" type="select" label="Box type" | |
| 63 help="triclinic is a triclinic box, cubic is a rectangular box with all sides equal dodecahedron represents a rhombic dodecahedron and octahedron is a truncated octahedron. The last two are special cases of a triclinic box. The length of the three box vectors of the truncated octahedron is the shortest distance between two opposite hexagons. Relative to a cubic box with some periodic image distance, the volume of a dodecahedron with this same periodic distance is 0.71 times that of the cube, and that of a truncated octahedron is 0.77 times."> | |
| 64 <option value="cubic">Rectangular box with all sides equal</option> | |
| 65 <option value="triclinic">Triclinic</option> | |
| 66 <option value="dodecahedron">represents a rhombic dodecahedron</option> | |
| 67 <option value="octahedron">truncated octahedron</option> | |
| 68 </param> | |
| 69 </when> | |
| 70 <when value="false"/> | |
| 71 </conditional> | |
| 72 | |
| 73 <expand macro="log" /> | 68 <expand macro="log" /> |
| 74 | 69 |
| 75 </inputs> | 70 </inputs> |
| 76 <outputs> | 71 <outputs> |
| 77 <data name="output" format="gro"> | 72 <data name="output" format="gro"> |