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annotate packmol.xml @ 1:ddb1ae2cf028 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit b1b74e91a242f2de250761a79b17d77e68b1045f"
author chemteam
date Fri, 30 Aug 2019 15:02:54 -0400
parents 0b8a0ce446f5
children 539fb45630e6
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0b8a0ce446f5 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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1 <tool id="packmol" name="PACKMOL" version="18.169">
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ddb1ae2cf028 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit b1b74e91a242f2de250761a79b17d77e68b1045f"
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2 <description>Initial configurations for Molecular Dynamics simulations by packing optimization</description>
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3 <macros>
0b8a0ce446f5 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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4 <import>macros_packmol.xml</import>
0b8a0ce446f5 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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5 </macros>
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6 <requirements>
0b8a0ce446f5 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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7 <requirement type="package" version="18.169">packmol</requirement>
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8 </requirements>
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9 <command detect_errors="exit_code">
0b8a0ce446f5 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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10 <![CDATA[
0b8a0ce446f5 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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11 python '$packmol_script' '$inputs' &&
0b8a0ce446f5 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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12 packmol < '$parameteroutfile'
0b8a0ce446f5 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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13 ]]>
0b8a0ce446f5 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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14 </command>
0b8a0ce446f5 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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15 <configfiles>
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16 <inputs name="inputs" />
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17 <configfile name="packmol_script"><![CDATA[
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18
0b8a0ce446f5 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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19 import os
0b8a0ce446f5 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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20 import sys
0b8a0ce446f5 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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21 import json
0b8a0ce446f5 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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0b8a0ce446f5 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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23 from jinja2 import Environment, FileSystemLoader
0b8a0ce446f5 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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0b8a0ce446f5 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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25 input_json_path = sys.argv[1]
0b8a0ce446f5 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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26 params = json.load(open(input_json_path, "r"))
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27
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28 # get the inputs
0b8a0ce446f5 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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29 input_iter = []
0b8a0ce446f5 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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30 #for $i, $s in enumerate( $packmol_format.packmol_inputs )
0b8a0ce446f5 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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31 pmfile_index = $i
0b8a0ce446f5 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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32 pmfile_path = "${s.input.file_name}"
0b8a0ce446f5 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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33 input_iter.append(pmfile_path)
0b8a0ce446f5 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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34 params["packmol_format"]["packmol_inputs"][pmfile_index]["file"] = pmfile_path
0b8a0ce446f5 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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35 params["packmol_format"]["packmol_inputs"][pmfile_index]["datasetname"] = "${s.input.name}"
0b8a0ce446f5 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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36 #end for
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37
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38 params["outfile"] = "$outfile"
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39
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40 currentpath = "$__tool_directory__" # should work generally
0b8a0ce446f5 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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41 template_environment = Environment(loader=FileSystemLoader(currentpath),lstrip_blocks=True, trim_blocks=True)
0b8a0ce446f5 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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42 template = template_environment.get_template('template.j2')
0b8a0ce446f5 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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43 print(params)
0b8a0ce446f5 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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44
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45 with open("$parameteroutfile",'w+') as f:
0b8a0ce446f5 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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46 f.write(template.render(params))
0b8a0ce446f5 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem commit 11519cd4ef5f8ac5864cdc8b3e93ff30115f2e27
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47
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48 ]]>
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49 </configfile>
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50 </configfiles>
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51 <inputs>
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52 <conditional name="packmol_format">
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53 <param name="selected_format" type="select" label="Select a file format:">
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54 <option value="pdb" selected="true">pdb</option>
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55 <!--option value="xyz">xyz</option>
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56 <option value="tinker">tinker</option>
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57 <option value="moldy">moldy</option-->
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58 </param>
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59 <when value="pdb">
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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"/>
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61 </when>
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62 <!--when value="xyz">
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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"/>
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64 </when>
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65 <when value="tinker">
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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"/>
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67 </when>
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68 <when value="moldy">
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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"/>
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70 </when-->
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71 </conditional>
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72 <section name="allparams" title="General Parameters" expanded="false">
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73 <param name="tolerance" type="float" value="2.0" label="distance tolerance" min="0.0" max="100.0"/>
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74 <param name="nloop" type="integer" value="20" label="maximum number of optimisation loops" min="1" max="10000"/>
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75 <param name="maxit" type="integer" value="20" label="maximum number of gencan iterations per loop" min="1" max="10000"/>
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76 <param name="seed" type="integer" value="-1" label="random number generator seed, default of -1 used the computer time to set the seed" />
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77 </section>
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78 </inputs>
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79 <outputs>
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80 <data format="pdb" name="outfile" label="${tool.name}: structure output">
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81 <change_format>
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82 <when input="selected_format" value="pdb" format="pdb"/>
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83 <!-- <when input="selected_format" value="xyz" format="xyz"/>
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84 <when input="selected_format" value="tinker" format="tinker"/>
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85 <when input="selected_format" value="moldy" format="moldy"/> -->
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86 </change_format>
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87 </data>
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88 <data format="txt" name="parameteroutfile" label="${tool.name}: parameter output"/>
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89 </outputs>
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90 <tests>
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91 <test>
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92 <param name="selected_format" value="pdb"/>
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93 <param name="packmol_inputs_0|input" value="water.pdb" ftype="pdb"/>
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94 <param name="allparams.seed" value="101"/>
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95 <output name="outfile" file="packmol_outfile1.pdb" compare="sim_size" delta="100000">
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96 <assert_contents>
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97 <has_text text="HETATM 300 O HOH"/>
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98 </assert_contents>
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99 </output>
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100 <output name="parameteroutfile" file="packmol_parameteroutfile_1.txt" compare="diff" lines_diff="6"/>
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101 </test>
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102 <test>
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103 <param name="selected_format" value="pdb"/>
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104 <param name="packmol_inputs_0|input" value="water.pdb" ftype="pdb"/>
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105 <param name="packmol_inputs_1|input" value="urea.pdb" ftype="pdb"/>
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106 <param name="packmol_inputs_0|structureparams|number" value="1000"/>
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107 <param name="packmol_inputs_1|structureparams|number" value="400"/>
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108 <param name="packmol_inputs_0|structureparams|constraints_repeat_0|constraints|constraint" value="box"/>
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109 <param name="packmol_inputs_0|structureparams|constraints_repeat_0|constraints|xmax" value="40.0"/>
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110 <param name="packmol_inputs_0|structureparams|constraints_repeat_0|constraints|ymax" value="40.0"/>
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111 <param name="packmol_inputs_0|structureparams|constraints_repeat_0|constraints|zmax" value="40.0"/>
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112 <param name="packmol_inputs_1|structureparams|constraints_repeat_0|constraints|constraint" value="box"/>
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113 <param name="packmol_inputs_1|structureparams|constraints_repeat_0|constraints|xmax" value="40.0"/>
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114 <param name="packmol_inputs_1|structureparams|constraints_repeat_0|constraints|ymax" value="40.0"/>
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115 <param name="packmol_inputs_1|structureparams|constraints_repeat_0|constraints|zmax" value="40.0"/>
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116 <param name="allparams.seed" value="-1"/>
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117 <output name="outfile" file="packmol_outfile2.pdb" compare="sim_size" delta="100000">
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118 <assert_contents>
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119 <has_text text="HETATM 3000 O HOH"/>
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120 <has_text text="HETATM 6200 H 2 B"/>
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121 </assert_contents>
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122 </output>
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123 <output name="parameteroutfile" file="packmol_parameteroutfile_2.txt" compare="diff" lines_diff="6"/>
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124 </test>
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125 </tests>
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126 <help><![CDATA[
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127 .. class:: infomark
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128
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129 **What it does**
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130
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131 Packmol creates initial MD configurations from input molecules. For example, create a water and urea mixture.
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132
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133 .. class:: infomark
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134
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135 **How it works**
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136
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137 - Select a molecule file type e.g. pdb,xyz
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138 - Select single molecule from your history (can select multiple)
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139 - For each molecule:
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140 - choose how many molecules to create (number variable)
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141 - optionally choose:
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142 - molecular radius
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143 - how to number the molecules (resnumber variable)
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144 - choose one or more placement constraint(s). Each constraint has different parameters:
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145 - for example, specify placement inside a cube of size 40 Angstroms placed at the origin
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146 - all units are in Angstroms for distances and degrees for angles
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147
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148 .. class:: infomark
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149
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150 **Outputs created**
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151
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152 - A pdb file, view this in Galaxy by clicking on visualise and choosing a viewer. The NGLViewer works well for small molecules.
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153 - A packmol input script (for debugging and repeatability)
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154
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155 .. class:: infomark
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156
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157 **User guide and documentation**
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158
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159 - Packmol `userguide`_
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160 - Calculating the number of molecules using the `volume guesser`_
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161
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162 .. class:: infomark
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163
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164 **Known issues**
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165
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166 - fixed constraint only allows 1 atom but this is not set for the user. user has to set this. Job may fail.
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167
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168 .. _`userguide`: http://m3g.iqm.unicamp.br/packmol/userguide.shtml#more
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169 .. _`volume guesser`: http://m3g.iqm.unicamp.br/packmol/utilities.shtml
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170
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171 ]]>
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172 </help>
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173 <citations>
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174 <citation type="doi">10.1002/jcc.21224</citation>
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175 </citations>
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176 </tool>