Mercurial > repos > chemteam > vmd_hbonds

annotate hbonds/hbonds.xml @ 0:8aa5e465b043 draft default tip

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"planemo upload for repository https://github.com/thatchristoph/vmd-cvs-github/tree/master/vmd commit a48d8046b8d9c8093daaa35bfedafa62fc5c5fd9"
author chemteam
date Thu, 24 Oct 2019 07:00:24 -0400
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8aa5e465b043 "planemo upload for repository https://github.com/thatchristoph/vmd-cvs-github/tree/master/vmd commit a48d8046b8d9c8093daaa35bfedafa62fc5c5fd9"
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1 <tool id="vmd_hbonds" name="Hydrogen Bond Analysis using VMD" version="1.9.3">
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2 <description>between two segments of a trajectory</description>
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3 <requirements>
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4 <requirement type="package" version="1.9.3">vmd</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code">
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7 <![CDATA[
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8 ln -s '$__tool_directory__/hbonds.tcl' ./hbonds.tcl &&
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9 #if $trajin.is_of_type("dcd"):
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10 vmd -pdb '$strin' -dcd '$trajin' -dispdev text -e '$hbonds_inp' &>> verbose.txt
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11 #elif $trajin.is_of_type("xtc"):
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12 vmd -gro '$strin' -xtc '$trajin' -dispdev text -e '$hbonds_inp' &>> verbose.txt
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13 #end if
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14 ]]></command>
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15 <configfiles>
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16 <configfile name="hbonds_inp">
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17 source hbonds.tcl
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19 set sele1 [atomselect $molid "$sele1"]
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20 set sele2 [atomselect $molid "$sele2"]
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22 hbonds -sel1 \$sele1 -sel2 \$sele2 -writefile yes -ang $angle -dist $distance -plot no -DA both -type all -outfile hbond.txt -detailout detail.txt
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23 quit
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24 </configfile>
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25 </configfiles>
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26 <inputs>
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27 <param format="dcd,xtc" name="trajin" type="data" label="DCD/XTC trajectory input"/>
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28 <param format="pdb,gro" name="strin" type="data" label="PDB/GRO input"/>
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29 <param name="molid" type="integer" value="0" label="Molecule ID"/>
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30 <param name="sele1" type="text" value="segid PRO" label="Selection 1" help="Definition of a segment with VMD atom selection language"/>
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31 <param name="sele2" type="text" value="segid HET" label="Selection 2" help="Definition of a segment with VMD atom selection language"/>
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32 <param name="angle" type="float" value="20.0" label="Angle cutoff"/>
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33 <param name="distance" type="float" value="3.0" label="Distance cutoff"/>
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34 </inputs>
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35 <outputs>
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36 <data format="txt" name="detail" from_work_dir="detail.txt" label="Percentage occupancy of the H-bond"/>
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37 <data format="txt" name="hbond" from_work_dir="hbond.txt" label="Number of H-bonds"/>
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38 <data name="report" format="txt" from_work_dir="verbose.txt"/>
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39 </outputs>
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40 <tests>
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41 <test>
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42 <param name="trajin" value="test.dcd" ftype="dcd"/>
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43 <param name="strin" value="test.pdb" ftype="pdb"/>
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44 <param name="molid" value="0"/>
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45 <param name="distance" value="3.0"/>
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46 <param name="angle" value="20.0"/>
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47 <param name="sele1" value="water"/>
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48 <param name="sele2" value="not water"/>
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49 <output name="hbond" value="Number_of_H-bonds.txt"/>
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50 </test>
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51 <test>
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52 <param name="trajin" value="test.xtc" ftype="xtc"/>
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53 <param name="strin" value="test.gro" ftype="gro"/>
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54 <param name="molid" value="0"/>
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55 <param name="distance" value="3.0"/>
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56 <param name="angle" value="20.0"/>
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57 <param name="sele1" value="water"/>
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58 <param name="sele2" value="not water"/>
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59 <output name="hbond" value="Number_of_H-bonds_gro.txt"/>
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60 </test>
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61 </tests>
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62 <help><![CDATA[
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63 .. class:: infomark
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64
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65 **What it does**
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66
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67 This tool calculates hydrogen bonds between two segments of a system in a molecular dynamics trajectory.
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68
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69 _____
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72 .. class:: infomark
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74 **Input**
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76 - Trajectory file (DCD/XTC).
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77 - PDB or GRO file.
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78 - Atom selection commands for two regions to be compared - e.g. 'not water' or 'segid PRO'. See here_ for more information on the VMD atom selection language.
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80 .. _here: https://www.ks.uiuc.edu/Research/vmd/vmd-1.3/ug/node132.html
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82 _____
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84
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85 .. class:: infomark
8aa5e465b043 "planemo upload for repository https://github.com/thatchristoph/vmd-cvs-github/tree/master/vmd commit a48d8046b8d9c8093daaa35bfedafa62fc5c5fd9"
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86
8aa5e465b043 "planemo upload for repository https://github.com/thatchristoph/vmd-cvs-github/tree/master/vmd commit a48d8046b8d9c8093daaa35bfedafa62fc5c5fd9"
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87 **Output**
8aa5e465b043 "planemo upload for repository https://github.com/thatchristoph/vmd-cvs-github/tree/master/vmd commit a48d8046b8d9c8093daaa35bfedafa62fc5c5fd9"
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88
8aa5e465b043 "planemo upload for repository https://github.com/thatchristoph/vmd-cvs-github/tree/master/vmd commit a48d8046b8d9c8093daaa35bfedafa62fc5c5fd9"
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89 - Number of H-bonds for each time step and and their occupancy.
8aa5e465b043 "planemo upload for repository https://github.com/thatchristoph/vmd-cvs-github/tree/master/vmd commit a48d8046b8d9c8093daaa35bfedafa62fc5c5fd9"
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90
8aa5e465b043 "planemo upload for repository https://github.com/thatchristoph/vmd-cvs-github/tree/master/vmd commit a48d8046b8d9c8093daaa35bfedafa62fc5c5fd9"
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91
8aa5e465b043 "planemo upload for repository https://github.com/thatchristoph/vmd-cvs-github/tree/master/vmd commit a48d8046b8d9c8093daaa35bfedafa62fc5c5fd9"
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92 ]]></help>
8aa5e465b043 "planemo upload for repository https://github.com/thatchristoph/vmd-cvs-github/tree/master/vmd commit a48d8046b8d9c8093daaa35bfedafa62fc5c5fd9"
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93 <citations>
8aa5e465b043 "planemo upload for repository https://github.com/thatchristoph/vmd-cvs-github/tree/master/vmd commit a48d8046b8d9c8093daaa35bfedafa62fc5c5fd9"
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94 <citation type="doi">10.1016/0263-7855(96)00018-5</citation>
8aa5e465b043 "planemo upload for repository https://github.com/thatchristoph/vmd-cvs-github/tree/master/vmd commit a48d8046b8d9c8093daaa35bfedafa62fc5c5fd9"
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95 <citation type="doi">10.1093/bioinformatics/btz107</citation>
8aa5e465b043 "planemo upload for repository https://github.com/thatchristoph/vmd-cvs-github/tree/master/vmd commit a48d8046b8d9c8093daaa35bfedafa62fc5c5fd9"
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96 </citations>
8aa5e465b043 "planemo upload for repository https://github.com/thatchristoph/vmd-cvs-github/tree/master/vmd commit a48d8046b8d9c8093daaa35bfedafa62fc5c5fd9"
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97 </tool>