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comparison packmol.xml @ 2:539fb45630e6 draft default tip

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
author chemteam
date Mon, 07 Oct 2019 12:46:54 -0400
parents ddb1ae2cf028
children
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1:ddb1ae2cf028 2:539fb45630e6
1 <tool id="packmol" name="PACKMOL" version="18.169"> 1 <tool id="packmol" name="PACKMOL" version="18.169.1">
2 <description>Initial configurations for Molecular Dynamics simulations by packing optimization</description> 2 <description>- initial configurations for molecular dynamics simulations by packing optimization</description>
3 <macros> 3 <macros>
4 <import>macros_packmol.xml</import> 4 <import>macros_packmol.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="18.169">packmol</requirement> 7 <requirement type="package" version="18.169">packmol</requirement>
25 input_json_path = sys.argv[1] 25 input_json_path = sys.argv[1]
26 params = json.load(open(input_json_path, "r")) 26 params = json.load(open(input_json_path, "r"))
27 27
28 # get the inputs 28 # get the inputs
29 input_iter = [] 29 input_iter = []
30 #for $i, $s in enumerate( $packmol_format.packmol_inputs ) 30 #for $i, $s in enumerate( $packmol_inputs ) ## enumerate( $packmol_format.packmol_inputs )
31 pmfile_index = $i 31 pmfile_index = $i
32 pmfile_path = "${s.input.file_name}" 32 pmfile_path = "${s.input.file_name}"
33 input_iter.append(pmfile_path) 33 input_iter.append(pmfile_path)
34 params["packmol_format"]["packmol_inputs"][pmfile_index]["file"] = pmfile_path 34 params["packmol_inputs"][pmfile_index]["file"] = pmfile_path ## params["packmol_format"]["packmol_inputs"]
35 params["packmol_format"]["packmol_inputs"][pmfile_index]["datasetname"] = "${s.input.name}" 35 params["packmol_inputs"][pmfile_index]["datasetname"] = "${s.input.name}" ## params["packmol_format"]["packmol_inputs"]
36 #end for 36 #end for
37 37
38 params["outfile"] = "$outfile" 38 params["outfile"] = "$outfile"
39 39
40 currentpath = "$__tool_directory__" # should work generally 40 currentpath = "$__tool_directory__" # should work generally
47 47
48 ]]> 48 ]]>
49 </configfile> 49 </configfile>
50 </configfiles> 50 </configfiles>
51 <inputs> 51 <inputs>
52 <conditional name="packmol_format"> 52
53 <!-- <conditional name="packmol_format">
53 <param name="selected_format" type="select" label="Select a file format:"> 54 <param name="selected_format" type="select" label="Select a file format:">
54 <option value="pdb" selected="true">pdb</option> 55 <option value="pdb" selected="true">pdb</option>
55 <!--option value="xyz">xyz</option> 56 <option value="xyz">xyz</option>
56 <option value="tinker">tinker</option> 57 <option value="tinker">tinker</option>
57 <option value="moldy">moldy</option--> 58 <option value="moldy">moldy</option>
58 </param> 59 </param>
59 <when value="pdb"> 60 <when value="pdb">
60 <expand macro="multiple_input" name="packmol_inputs" format="pdb" label="pdb input with molecule type" help_text="Select a pdb file in .pdb format"/> 61 <expand macro="multiple_input" name="packmol_inputs" format="pdb" label="pdb input with molecule type" help_text="Select a pdb file in .pdb format"/>
61 </when> 62 </when>
62 <!--when value="xyz"> 63 <when value="xyz">
63 <expand macro="multiple_input" name="packmol_inputs" format="xyz" label="xyz input with molecule type" help_text="Select a xyz file in .xyz format"/> 64 <expand macro="multiple_input" name="packmol_inputs" format="xyz" label="xyz input with molecule type" help_text="Select a xyz file in .xyz format"/>
64 </when> 65 </when>
65 <when value="tinker"> 66 <when value="tinker">
66 <expand macro="multiple_input" name="packmol_inputs" format="tinker" label="tinker input with molecule type" help_text="Select a tinker file in .tinker format"/> 67 <expand macro="multiple_input" name="packmol_inputs" format="tinker" label="tinker input with molecule type" help_text="Select a tinker file in .tinker format"/>
67 </when> 68 </when>
68 <when value="moldy"> 69 <when value="moldy">
69 <expand macro="multiple_input" name="packmol_inputs" format="moldy" label="moldy input with molecule type" help_text="Select a moldy file in .moldy format"/> 70 <expand macro="multiple_input" name="packmol_inputs" format="moldy" label="moldy input with molecule type" help_text="Select a moldy file in .moldy format"/>
70 </when--> 71 </when>
71 </conditional> 72 </conditional> -->
72 <section name="allparams" title="General Parameters" expanded="false"> 73 <expand macro="multiple_input" name="packmol_inputs" format="pdb" label="PDB input with molecule type" help_text="Select a PDB file in .pdb format"/>
73 <param name="tolerance" type="float" value="2.0" label="distance tolerance" min="0.0" max="100.0"/> 74 <section name="allparams" title="General parameters" expanded="false">
74 <param name="nloop" type="integer" value="20" label="maximum number of optimisation loops" min="1" max="10000"/> 75 <param name="tolerance" type="float" value="2.0" label="Distance tolerance" min="0.0" max="100.0"/>
75 <param name="maxit" type="integer" value="20" label="maximum number of gencan iterations per loop" min="1" max="10000"/> 76 <param name="nloop" type="integer" value="20" label="Maximum number of optimisation loops" min="1" max="10000"/>
76 <param name="seed" type="integer" value="-1" label="random number generator seed, default of -1 used the computer time to set the seed" /> 77 <param name="maxit" type="integer" value="20" label="Maximum number of gencan iterations per loop" min="1" max="10000"/>
78 <param name="seed" type="integer" value="-1" label="Random number generator seed, default of -1 uses the computer time to set the seed" />
77 </section> 79 </section>
78 </inputs> 80 </inputs>
79 <outputs> 81 <outputs>
80 <data format="pdb" name="outfile" label="${tool.name}: structure output"> 82 <data format="pdb" name="outfile" label="${tool.name}: structure output">
81 <change_format> 83 <!-- <change_format>
82 <when input="selected_format" value="pdb" format="pdb"/> 84 <when input="selected_format" value="pdb" format="pdb"/>
83 <!-- <when input="selected_format" value="xyz" format="xyz"/> 85 <when input="selected_format" value="xyz" format="xyz"/>
84 <when input="selected_format" value="tinker" format="tinker"/> 86 <when input="selected_format" value="tinker" format="tinker"/>
85 <when input="selected_format" value="moldy" format="moldy"/> --> 87 <when input="selected_format" value="moldy" format="moldy"/>
86 </change_format> 88 </change_format> -->
87 </data> 89 </data>
88 <data format="txt" name="parameteroutfile" label="${tool.name}: parameter output"/> 90 <data format="txt" name="parameteroutfile" label="${tool.name}: parameter output"/>
89 </outputs> 91 </outputs>
90 <tests> 92 <tests>
91 <test> 93 <test>
126 <help><![CDATA[ 128 <help><![CDATA[
127 .. class:: infomark 129 .. class:: infomark
128 130
129 **What it does** 131 **What it does**
130 132
131 Packmol creates initial MD configurations from input molecules. For example, create a water and urea mixture. 133 Packmol creates initial MD configurations from input molecules - for example, creating a water and urea mixture.
132 134
133 .. class:: infomark 135 .. class:: infomark
134 136
135 **How it works** 137 **How it works**
136 138
137 - Select a molecule file type e.g. pdb,xyz 139 - Select a molecule file type e.g. pdb, xyz
138 - Select single molecule from your history (can select multiple) 140 - Select a single molecule from your history (can select multiple)
139 - For each molecule: 141 - For each molecule:
140 - choose how many molecules to create (number variable) 142 - choose how many molecules to create (number variable)
141 - optionally choose: 143 - optionally choose:
142 - molecular radius 144 - molecular radius
143 - how to number the molecules (resnumber variable) 145 - how to number the molecules (resnumber variable)
147 149
148 .. class:: infomark 150 .. class:: infomark
149 151
150 **Outputs created** 152 **Outputs created**
151 153
152 - A pdb file, view this in Galaxy by clicking on visualise and choosing a viewer. The NGLViewer works well for small molecules. 154 - A pdb file; view this in Galaxy by clicking on the 'visualize' icon and choosing a viewer. The NGLViewer works well for small molecules.
153 - A packmol input script (for debugging and repeatability) 155 - A packmol input script (for debugging and repeatability)
154 156
155 .. class:: infomark 157 .. class:: infomark
156 158
157 **User guide and documentation** 159 **User guide and documentation**
161 163
162 .. class:: infomark 164 .. class:: infomark
163 165
164 **Known issues** 166 **Known issues**
165 167
166 - fixed constraint only allows 1 atom but this is not set for the user. user has to set this. Job may fail. 168 - fixed constraint only allows 1 atom but this is not set for the user. The user has to set this parameter. The job may fail.
167 169
168 .. _`userguide`: http://m3g.iqm.unicamp.br/packmol/userguide.shtml#more 170 .. _`userguide`: http://m3g.iqm.unicamp.br/packmol/userguide.shtml#more
169 .. _`volume guesser`: http://m3g.iqm.unicamp.br/packmol/utilities.shtml 171 .. _`volume guesser`: http://m3g.iqm.unicamp.br/packmol/utilities.shtml
170 172
171 ]]> 173 ]]>