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comparison 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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1 <tool id="vmd_hbonds" name="Hydrogen Bond Analysis using VMD" version="1.9.3">
2 <description>between two segments of a trajectory</description>
3 <requirements>
4 <requirement type="package" version="1.9.3">vmd</requirement>
5 </requirements>
6 <command detect_errors="exit_code">
7 <![CDATA[
8 ln -s '$__tool_directory__/hbonds.tcl' ./hbonds.tcl &&
9 #if $trajin.is_of_type("dcd"):
10 vmd -pdb '$strin' -dcd '$trajin' -dispdev text -e '$hbonds_inp' &>> verbose.txt
11 #elif $trajin.is_of_type("xtc"):
12 vmd -gro '$strin' -xtc '$trajin' -dispdev text -e '$hbonds_inp' &>> verbose.txt
13 #end if
14 ]]></command>
15 <configfiles>
16 <configfile name="hbonds_inp">
17 source hbonds.tcl
18
19 set sele1 [atomselect $molid "$sele1"]
20 set sele2 [atomselect $molid "$sele2"]
21
22 hbonds -sel1 \$sele1 -sel2 \$sele2 -writefile yes -ang $angle -dist $distance -plot no -DA both -type all -outfile hbond.txt -detailout detail.txt
23 quit
24 </configfile>
25 </configfiles>
26 <inputs>
27 <param format="dcd,xtc" name="trajin" type="data" label="DCD/XTC trajectory input"/>
28 <param format="pdb,gro" name="strin" type="data" label="PDB/GRO input"/>
29 <param name="molid" type="integer" value="0" label="Molecule ID"/>
30 <param name="sele1" type="text" value="segid PRO" label="Selection 1" help="Definition of a segment with VMD atom selection language"/>
31 <param name="sele2" type="text" value="segid HET" label="Selection 2" help="Definition of a segment with VMD atom selection language"/>
32 <param name="angle" type="float" value="20.0" label="Angle cutoff"/>
33 <param name="distance" type="float" value="3.0" label="Distance cutoff"/>
34 </inputs>
35 <outputs>
36 <data format="txt" name="detail" from_work_dir="detail.txt" label="Percentage occupancy of the H-bond"/>
37 <data format="txt" name="hbond" from_work_dir="hbond.txt" label="Number of H-bonds"/>
38 <data name="report" format="txt" from_work_dir="verbose.txt"/>
39 </outputs>
40 <tests>
41 <test>
42 <param name="trajin" value="test.dcd" ftype="dcd"/>
43 <param name="strin" value="test.pdb" ftype="pdb"/>
44 <param name="molid" value="0"/>
45 <param name="distance" value="3.0"/>
46 <param name="angle" value="20.0"/>
47 <param name="sele1" value="water"/>
48 <param name="sele2" value="not water"/>
49 <output name="hbond" value="Number_of_H-bonds.txt"/>
50 </test>
51 <test>
52 <param name="trajin" value="test.xtc" ftype="xtc"/>
53 <param name="strin" value="test.gro" ftype="gro"/>
54 <param name="molid" value="0"/>
55 <param name="distance" value="3.0"/>
56 <param name="angle" value="20.0"/>
57 <param name="sele1" value="water"/>
58 <param name="sele2" value="not water"/>
59 <output name="hbond" value="Number_of_H-bonds_gro.txt"/>
60 </test>
61 </tests>
62 <help><![CDATA[
63 .. class:: infomark
64
65 **What it does**
66
67 This tool calculates hydrogen bonds between two segments of a system in a molecular dynamics trajectory.
68
69 _____
70
71
72 .. class:: infomark
73
74 **Input**
75
76 - Trajectory file (DCD/XTC).
77 - PDB or GRO file.
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.
79
80 .. _here: https://www.ks.uiuc.edu/Research/vmd/vmd-1.3/ug/node132.html
81
82 _____
83
84
85 .. class:: infomark
86
87 **Output**
88
89 - Number of H-bonds for each time step and and their occupancy.
90
91
92 ]]></help>
93 <citations>
94 <citation type="doi">10.1016/0263-7855(96)00018-5</citation>
95 <citation type="doi">10.1093/bioinformatics/btz107</citation>
96 </citations>
97 </tool>