Mercurial > repos > chemteam > mdanalysis_rdf
diff rdf.xml @ 4:36babbdd7818 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
author | chemteam |
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date | Mon, 07 Oct 2019 12:51:57 -0400 |
parents | 57a3d6f94bcd |
children |
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--- a/rdf.xml Wed Apr 03 15:47:16 2019 -0400 +++ b/rdf.xml Mon Oct 07 12:51:57 2019 -0400 @@ -1,5 +1,5 @@ <tool id="mdanalysis_rdf" name="RDF Analysis" version="@VERSION@"> - <description>Radial Distribution Function between two atoms</description> + <description>- Radial Distribution Function between two atoms</description> <macros> <import>macros.xml</import> </macros> @@ -7,8 +7,10 @@ <command detect_errors="exit_code"> <![CDATA[ python '$__tool_directory__/rdf.py' - --idcd '$dcdin' - --ipdb '$pdbin' + --itraj '$trajin' + --istr '$strin' + --itrajext '$trajin.ext' + --istrext '$strin.ext' --isegid1 '$segid1' --iresid1 '$resid1' --iname1 '$name1' @@ -24,15 +26,17 @@ ]]></command> <inputs> <expand macro="analysis_inputs"/> - <param name="segid1" type="text" value="PRO" label="Segid of atom 1"/> - <param name="resid1" type="text" value="212" label="Resid of atom 1"/> + <param name="segid1" type="text" value="PRO" label="Segment ID of atom 1"/> + <param name="resid1" type="text" value="212" label="Residue ID of atom 1"/> <param name="name1" type="text" value="OE2" label="Atom name of atom 1"/> - <param name="segid2" type="text" value="HET" label="Segid of atom 2"/> - <param name="resid2" type="text" value="3" label="Resid of atom 2"/> + <param name="segid2" type="text" value="HET" label="Segment ID of atom 2"/> + <param name="resid2" type="text" value="3" label="Residue ID of atom 2"/> <param name="name2" type="text" value="C1" label="Atom name of atom 2"/> <param name="nbins" type="text" value="100" label="Number of bins in the histogram"/> - <param name="start" type="text" value="0.0" label="Starting Point"/> - <param name="end" type="text" value="5.0" label="End Point"/> + <param name="start" type="text" min="0.0" value="0.0" label="Starting point (angstroms)" + help="Minimum value of r to calculate RDF for"/> + <param name="end" type="text" value="15.0" label="End point (angstroms)" + help="Maximum value of r to calculate RDF for"/> </inputs> <outputs> <data format="tabular" name="output" label="RDF raw data"/> @@ -58,13 +62,32 @@ </assert_contents> </output> </test> + <test> + <expand macro="tests_inputs_gmx"/> + <param name="segid1" value="SYSTEM"/> + <param name="resid1" value="212"/> + <param name="name1" value="OE2"/> + <param name="segid2" value="SYSTEM"/> + <param name="resid2" value="3"/> + <param name="name2" value="C1"/> + <param name="nbins" value="100"/> + <param name="start" value="0.0"/> + <param name="end" value="5.0"/> + <output name="output"> + <assert_contents> + <has_n_columns n="2" /> + <not_has_text text="nan" /> + <has_line_matching expression="3.275\s+6336.*" /> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[ .. class:: infomark **What it does** -The Radial Distribution Function (RDF) , g(r), also called pair distribution function or pair correlation function function can be used to find how density varies as a function of distance from a reference atom. +The Radial Distribution Function (RDF), g(r), also called pair distribution function or pair correlation function, can be used to find how density varies as a function of distance from a reference atom. _____ @@ -73,10 +96,13 @@ **Input** - - Trajectory file (DCD). + - Trajectory file (DCD). - PDB file. - - Segids, resids and names of two atoms to calculate distances. - + - Segment IDs, residue IDs and names of two atoms to calculate RDF values. + +Note that a MDAnalysis 'segment' is a larger organizational unit, for example one protein or all the solvent molecules or simply the whole system. + +Other parameters can also be specified: the number of bins in the RDF histogram, and the start and end points for the calculation (i.e. the values of r between which RDF will be calculated). _____