Mercurial > repos > fmercuri > gmx_editconf_daimoners

changeset 4:770be7b8dddd draft

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Uploaded
author fmercuri
date Fri, 25 Jun 2021 15:55:00 +0000
parents 0876b56a3b3d
children 0e7f3bea714a
files editconf.xml
diffstat 1 files changed, 30 insertions(+), 35 deletions(-) [+]
line wrap: on
line diff
--- a/editconf.xml	Fri Jun 25 15:22:14 2021 +0000
+++ b/editconf.xml	Fri Jun 25 15:55:00 2021 +0000
@@ -14,12 +14,13 @@
             -f ./input.$input_file.ext
             -o ./output.${output_format}
             #if $box.config == "true":
-                -d $box.dim 
-                -bt $box.type
-            #end if
-            #if $sbox.config == "true":
-                -box $sbox.dim 
-                -bt $box.type
+                #if $boxtype.boxtype == "cubic":
+                    -box $boxtype.cubicdim
+                #end if
+                #if $boxtype.boxtype == "custom":
+                    -d $boxtype.boxdim
+                    -bt $boxtype.type
+                #end if
             #end if
             &>> verbose.txt &&
 
@@ -33,43 +34,37 @@
             <option value="gro">GRO file</option>
             <option value="pdb">PDB file</option>
         </param>
-        
+
         <conditional name="box">
-            <param argument="config" type="select" label="Configure distance-based box?">
+            <param argument="config" type="select" label="Configure box?">
                 <option value="true">Yes</option>
                 <option value="false" selected="true">No</option>
             </param>
             <when value="true">
-                <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" />
-                <param argument="type" type="select" label="Box type"
-                    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.">
-                    <option value="cubic">Rectangular box with all sides equal</option>
-                    <option value="triclinic">Triclinic</option>
-                    <option value="dodecahedron">represents a rhombic dodecahedron</option>
-                    <option value="octahedron">truncated octahedron</option>
-                </param>
+                <conditional name="boxtype">
+                    <param argument="boxtype" type="select" label="Box type"/>
+                        <option value="cubic">Standard cubic box</option>
+                        <option value="custom">Custom box type</option>
+                    </param>
+
+                    <when value="cubic">
+                        <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" />
+                    </when>
+
+                    <when value="variable">
+                        <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" />
+                        <param argument="type" type="select" label="Box type" help="Box type">
+                            <option value="cubic">Cubic</option>
+                            <option value="triclinic">Triclinic</option>
+                            <option value="dodecahedron">Rhombic dodecahedron</option>
+                            <option value="octahedron">Truncated octahedron</option>
+                        </param>
+                    </when>
+                </conditional>
             </when>
             <when value="false"/>
         </conditional>
-
-        <conditional name="sbox">
-            <param argument="config" type="select" label="Configure size-based box?">
-                <option value="true">Yes</option>
-                <option value="false" selected="true">No</option>
-            </param>
-            <when value="true">
-                <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" />
-                <param argument="type" type="select" label="Box type"
-                    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.">
-                    <option value="cubic">Rectangular box with all sides equal</option>
-                    <option value="triclinic">Triclinic</option>
-                    <option value="dodecahedron">represents a rhombic dodecahedron</option>
-                    <option value="octahedron">truncated octahedron</option>
-                </param>
-            </when>
-            <when value="false"/>
-        </conditional>
-
+        
     <expand macro="log" />
 
     </inputs>