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author | fmercuri |
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date | Wed, 23 Jun 2021 21:28:24 +0000 |
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<tool id="packmol_daimoners" name="PACKMOL daimoners version" version="18.169.1"> <description>- initial configurations for molecular dynamics simulations by packing optimization</description> <macros> <import>macros_packmol.xml</import> </macros> <requirements> <requirement type="package" version="18.169">packmol</requirement> </requirements> <command detect_errors="exit_code"> <![CDATA[ python3 '$packmol_script' '$inputs' && packmol < '$parameteroutfile' ]]> </command> <configfiles> <inputs name="inputs" /> <configfile name="packmol_script"><![CDATA[ import os import sys import json from jinja2 import Environment, FileSystemLoader input_json_path = sys.argv[1] params = json.load(open(input_json_path, "r")) # get the inputs input_iter = [] #for $i, $s in enumerate( $packmol_inputs ) ## enumerate( $packmol_format.packmol_inputs ) pmfile_index = $i pmfile_path = "${s.input.file_name}" input_iter.append(pmfile_path) params["packmol_inputs"][pmfile_index]["file"] = pmfile_path ## params["packmol_format"]["packmol_inputs"] params["packmol_inputs"][pmfile_index]["datasetname"] = "${s.input.name}" ## params["packmol_format"]["packmol_inputs"] #end for params["outfile"] = "$outfile" currentpath = "$__tool_directory__" # should work generally template_environment = Environment(loader=FileSystemLoader(currentpath),lstrip_blocks=True, trim_blocks=True) template = template_environment.get_template('template.j2') print(params) with open("$parameteroutfile",'w+') as f: f.write(template.render(params)) ]]> </configfile> </configfiles> <inputs> <!-- <conditional name="packmol_format"> <param name="selected_format" type="select" label="Select a file format:"> <option value="pdb" selected="true">pdb</option> <option value="xyz">xyz</option> <option value="tinker">tinker</option> <option value="moldy">moldy</option> </param> <when value="pdb"> <expand macro="multiple_input" name="packmol_inputs" format="pdb" label="pdb input with molecule type" help_text="Select a pdb file in .pdb format"/> </when> <when value="xyz"> <expand macro="multiple_input" name="packmol_inputs" format="xyz" label="xyz input with molecule type" help_text="Select a xyz file in .xyz format"/> </when> <when value="tinker"> <expand macro="multiple_input" name="packmol_inputs" format="tinker" label="tinker input with molecule type" help_text="Select a tinker file in .tinker format"/> </when> <when value="moldy"> <expand macro="multiple_input" name="packmol_inputs" format="moldy" label="moldy input with molecule type" help_text="Select a moldy file in .moldy format"/> </when> </conditional> --> <expand macro="multiple_input" name="packmol_inputs" format="pdb" label="PDB input with molecule type" help_text="Select a PDB file in .pdb format"/> <section name="allparams" title="General parameters" expanded="false"> <param name="tolerance" type="float" value="2.0" label="Distance tolerance" min="0.0" max="100.0"/> <param name="nloop" type="integer" value="20" label="Maximum number of optimisation loops" min="1" max="10000"/> <param name="maxit" type="integer" value="20" label="Maximum number of gencan iterations per loop" min="1" max="10000"/> <param name="seed" type="integer" value="-1" label="Random number generator seed, default of -1 uses the computer time to set the seed" /> </section> </inputs> <outputs> <data format="pdb" name="outfile" label="${tool.name}: structure output"> <!-- <change_format> <when input="selected_format" value="pdb" format="pdb"/> <when input="selected_format" value="xyz" format="xyz"/> <when input="selected_format" value="tinker" format="tinker"/> <when input="selected_format" value="moldy" format="moldy"/> </change_format> --> </data> <data format="txt" name="parameteroutfile" label="${tool.name}: parameter output"/> </outputs> <tests> <test> <param name="selected_format" value="pdb"/> <param name="packmol_inputs_0|input" value="water.pdb" ftype="pdb"/> <param name="allparams.seed" value="101"/> <output name="outfile" file="packmol_outfile1.pdb" compare="sim_size" delta="100000"> <assert_contents> <has_text text="HETATM 300 O HOH"/> </assert_contents> </output> <output name="parameteroutfile" file="packmol_parameteroutfile_1.txt" compare="diff" lines_diff="6"/> </test> <test> <param name="selected_format" value="pdb"/> <param name="packmol_inputs_0|input" value="water.pdb" ftype="pdb"/> <param name="packmol_inputs_1|input" value="urea.pdb" ftype="pdb"/> <param name="packmol_inputs_0|structureparams|number" value="1000"/> <param name="packmol_inputs_1|structureparams|number" value="400"/> <param name="packmol_inputs_0|structureparams|constraints_repeat_0|constraints|constraint" value="box"/> <param name="packmol_inputs_0|structureparams|constraints_repeat_0|constraints|xmax" value="40.0"/> <param name="packmol_inputs_0|structureparams|constraints_repeat_0|constraints|ymax" value="40.0"/> <param name="packmol_inputs_0|structureparams|constraints_repeat_0|constraints|zmax" value="40.0"/> <param name="packmol_inputs_1|structureparams|constraints_repeat_0|constraints|constraint" value="box"/> <param name="packmol_inputs_1|structureparams|constraints_repeat_0|constraints|xmax" value="40.0"/> <param name="packmol_inputs_1|structureparams|constraints_repeat_0|constraints|ymax" value="40.0"/> <param name="packmol_inputs_1|structureparams|constraints_repeat_0|constraints|zmax" value="40.0"/> <param name="allparams.seed" value="-1"/> <output name="outfile" file="packmol_outfile2.pdb" compare="sim_size" delta="100000"> <assert_contents> <has_text text="HETATM 3000 O HOH"/> <has_text text="HETATM 6200 H 2 B"/> </assert_contents> </output> <output name="parameteroutfile" file="packmol_parameteroutfile_2.txt" compare="diff" lines_diff="6"/> </test> </tests> <help><![CDATA[ .. class:: infomark **What it does** Packmol creates initial MD configurations from input molecules - for example, creating a water and urea mixture. .. class:: infomark **How it works** - Select a molecule file type e.g. pdb, xyz - Select a single molecule from your history (can select multiple) - For each molecule: - choose how many molecules to create (number variable) - optionally choose: - molecular radius - how to number the molecules (resnumber variable) - choose one or more placement constraint(s). Each constraint has different parameters: - for example, specify placement inside a cube of size 40 Angstroms placed at the origin - all units are in Angstroms for distances and degrees for angles .. class:: infomark **Outputs created** - A pdb file; view this in Galaxy by clicking on the 'visualize' icon and choosing a viewer. The NGLViewer works well for small molecules. - A packmol input script (for debugging and repeatability) .. class:: infomark **User guide and documentation** - Packmol `userguide`_ - Calculating the number of molecules using the `volume guesser`_ .. class:: infomark **Known issues** - 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. .. _`userguide`: http://m3g.iqm.unicamp.br/packmol/userguide.shtml#more .. _`volume guesser`: http://m3g.iqm.unicamp.br/packmol/utilities.shtml ]]> </help> <citations> <citation type="doi">10.1002/jcc.21224</citation> </citations> </tool>