annotate ramachandran_plots.xml @ 2:b348dfa55e0a draft

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
author chemteam
date Thu, 06 Feb 2020 19:40:37 -0500
parents ce0728b92289
children 70a2d548e62c
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1 <tool id="mdanalysis_ramachandran_plot" name="Ramachandran Plots" version="@VERSION@">
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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2 <description>- calculate and plot the distribution of two dihedrals in a trajectory</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements">
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7 <requirement type="package" version="1.3.1">scipy</requirement>
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8 <requirement type="package" version="0.9.0">seaborn</requirement>
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9 <requirement type="package" version="1.1.0">nbdime</requirement>
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10 </expand>
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11 <command detect_errors="exit_code">
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12 <![CDATA[
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13 python '$__tool_directory__/ramachandran_plots.py'
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ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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14 --itraj '$trajin'
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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15 --istr '$strin'
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16 --itrajext '$trajin.ext'
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17 --istrext '$strin.ext'
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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18 --isegid1 '$phi.phi_segid1'
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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19 --iresid1 '$phi.phi_resid1'
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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20 --iname1 '$phi.phi_name1'
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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21 --isegid2 '$phi.phi_segid2'
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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22 --iresid2 '$phi.phi_resid2'
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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23 --iname2 '$phi.phi_name2'
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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24 --isegid3 '$phi.phi_segid3'
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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25 --iresid3 '$phi.phi_resid3'
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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26 --iname3 '$phi.phi_name3'
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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27 --isegid4 '$phi.phi_segid4'
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28 --iresid4 '$phi.phi_resid4'
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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29 --iname4 '$phi.phi_name4'
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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30 --isegid5 '$psi.psi_segid1'
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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31 --iresid5 '$psi.psi_resid1'
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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32 --iname5 '$psi.psi_name1'
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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33 --isegid6 '$psi.psi_segid2'
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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34 --iresid6 '$psi.psi_resid2'
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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35 --iname6 '$psi.psi_name2'
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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36 --isegid7 '$psi.psi_segid3'
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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37 --iresid7 '$psi.psi_resid3'
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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38 --iname7 '$psi.psi_name3'
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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39 --isegid8 '$psi.psi_segid4'
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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40 --iresid8 '$psi.psi_resid4'
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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41 --iname8 '$psi.psi_name4'
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42 --output '$output'
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43 --oramachandran_plot '$ramachandran_plot'
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44 2>&1
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45 ]]></command>
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46 <inputs>
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47 <expand macro="analysis_inputs"/>
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48 <section name="phi" title="Phi" expanded="False">
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49 <param name="phi_segid1" type="text" value="HET" label="Segment ID of atom 1">
0
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50 <expand macro="sanitizer"/>
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51 </param>
1
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52 <param name="phi_resid1" type="text" value="3" label="Residue ID of atom 1">
0
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53 <expand macro="sanitizer_resids"/>
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54 </param>
1
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55 <param name="phi_name1" type="text" value="O5" label="Atom name of atom 1">
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56 <expand macro="sanitizer"/>
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57 </param>
1
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58 <param name="phi_segid2" type="text" value="HET" label="Segment ID of atom 2">
0
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59 <expand macro="sanitizer"/>
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60 </param>
1
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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61 <param name="phi_resid2" type="text" value="3" label="Residue ID of atom 2">
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62 <expand macro="sanitizer_resids"/>
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63 </param>
1
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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64 <param name="phi_name2" type="text" value="C1" label="Atom name of atom 2">
0
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65 <expand macro="sanitizer"/>
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66 </param>
1
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67 <param name="phi_segid3" type="text" value="HET" label="Segment ID of atom 3">
0
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68 <expand macro="sanitizer"/>
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69 </param>
1
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70 <param name="phi_resid3" type="text" value="2" label="Residue ID of atom 3">
0
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71 <expand macro="sanitizer_resids"/>
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72 </param>
1
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73 <param name="phi_name3" type="text" value="O4" label="Atom name of atom 3">
0
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74 <expand macro="sanitizer"/>
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75 </param>
1
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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76 <param name="phi_segid4" type="text" value="HET" label="Segment ID of atom 4">
0
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77 <expand macro="sanitizer"/>
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78 </param>
1
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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79 <param name="phi_resid4" type="text" value="2" label="Residue ID of atom 4">
0
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80 <expand macro="sanitizer_resids"/>
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81 </param>
1
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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82 <param name="phi_name4" type="text" value="C4" label="Atom name of atom 4">
0
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83 <expand macro="sanitizer"/>
d710c7f00ae6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
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84 </param>
d710c7f00ae6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
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85 </section>
d710c7f00ae6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
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86 <section name="psi" title="Psi" expanded="False">
1
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents: 0
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87 <param name="psi_segid1" type="text" value="HET" label="Segment ID of atom 1">
0
d710c7f00ae6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
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88 <expand macro="sanitizer"/>
d710c7f00ae6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
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89 </param>
1
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents: 0
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90 <param name="psi_resid1" type="text" value="3" label="Residue ID of atom 1">
0
d710c7f00ae6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
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91 <expand macro="sanitizer_resids"/>
d710c7f00ae6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
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92 </param>
1
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents: 0
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93 <param name="psi_name1" type="text" value="C1" label="Atom name of atom 1">
0
d710c7f00ae6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
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94 <expand macro="sanitizer"/>
d710c7f00ae6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
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95 </param>
1
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents: 0
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96 <param name="psi_segid2" type="text" value="HET" label="Segment ID of atom 2">
0
d710c7f00ae6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
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97 <expand macro="sanitizer"/>
d710c7f00ae6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
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98 </param>
1
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents: 0
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99 <param name="psi_resid2" type="text" value="2" label="Residue ID of atom 2">
0
d710c7f00ae6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
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100 <expand macro="sanitizer_resids"/>
d710c7f00ae6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
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101 </param>
1
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents: 0
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102 <param name="psi_name2" type="text" value="O4" label="Atom name of atom 2">
0
d710c7f00ae6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
chemteam
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103 <expand macro="sanitizer"/>
d710c7f00ae6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
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104 </param>
1
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
parents: 0
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105 <param name="psi_segid3" type="text" value="HET" label="Segment ID of atom 3">
0
d710c7f00ae6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
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106 <expand macro="sanitizer"/>
d710c7f00ae6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
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107 </param>
1
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
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108 <param name="psi_resid3" type="text" value="2" label="Residue ID of atom 3">
0
d710c7f00ae6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
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109 <expand macro="sanitizer_resids"/>
d710c7f00ae6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
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110 </param>
1
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
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111 <param name="psi_name3" type="text" value="C4" label="Atom name of atom 3">
0
d710c7f00ae6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
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112 <expand macro="sanitizer"/>
d710c7f00ae6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
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113 </param>
1
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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114 <param name="psi_segid4" type="text" value="HET" label="Segment ID of atom 4">
0
d710c7f00ae6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
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115 <expand macro="sanitizer"/>
d710c7f00ae6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
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116 </param>
1
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
chemteam
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117 <param name="psi_resid4" type="text" value="2" label="Residue ID of atom 4">
0
d710c7f00ae6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
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118 <expand macro="sanitizer_resids"/>
d710c7f00ae6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
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119 </param>
1
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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120 <param name="psi_name4" type="text" value="C3" label="Atom name of atom 4">
0
d710c7f00ae6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
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121 <expand macro="sanitizer"/>
d710c7f00ae6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
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122 </param>
d710c7f00ae6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
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123 </section>
d710c7f00ae6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
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124 </inputs>
d710c7f00ae6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
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125 <outputs>
d710c7f00ae6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
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126 <data format="tabular" name="output" label="Ramachandran Plot raw data"/>
d710c7f00ae6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
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127 <data format="png" name="ramachandran_plot" label="Ramachandran Plot"/>
d710c7f00ae6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
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128 </outputs>
d710c7f00ae6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
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129 <tests>
d710c7f00ae6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
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130 <test>
d710c7f00ae6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
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131 <expand macro="tests_inputs"/>
1
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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132 <param name="phi_segid1" value="HET"/>
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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133 <param name="phi_resid1" value="3"/>
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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134 <param name="phi_name1" value="O5"/>
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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parents: 0
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135 <param name="phi_segid2" value="HET"/>
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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136 <param name="phi_resid2" value="3"/>
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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diff changeset
137 <param name="phi_name2" value="C1"/>
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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138 <param name="phi_segid3" value="HET"/>
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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139 <param name="phi_resid3" value="2"/>
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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diff changeset
140 <param name="phi_name3" value="O4"/>
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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141 <param name="phi_segid4" value="HET"/>
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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142 <param name="phi_resid4" value="2"/>
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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parents: 0
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143 <param name="phi_name4" value="C4"/>
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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144 <param name="psi_segid1" value="HET"/>
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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145 <param name="psi_resid1" value="3"/>
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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parents: 0
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146 <param name="psi_name1" value="C1"/>
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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147 <param name="psi_segid2" value="HET"/>
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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148 <param name="psi_resid2" value="2"/>
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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149 <param name="psi_name2" value="O4"/>
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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150 <param name="psi_segid3" value="HET"/>
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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151 <param name="psi_resid3" value="2"/>
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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parents: 0
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152 <param name="psi_name3" value="C4"/>
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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153 <param name="psi_segid4" value="HET"/>
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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parents: 0
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154 <param name="psi_resid4" value="2"/>
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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155 <param name="psi_name4" value="C3"/>
0
d710c7f00ae6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
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156 <output name="output" file="Ramachandran_Plot_raw_data.tabular" />
d710c7f00ae6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
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157 </test>
1
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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158 <test>
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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159 <expand macro="tests_inputs_gmx"/>
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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160 <param name="phi_segid1" value="SYSTEM"/>
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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161 <param name="phi_resid1" value="3"/>
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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162 <param name="phi_name1" value="O5"/>
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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163 <param name="phi_segid2" value="SYSTEM"/>
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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164 <param name="phi_resid2" value="3"/>
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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165 <param name="phi_name2" value="C1"/>
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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166 <param name="phi_segid3" value="SYSTEM"/>
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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parents: 0
diff changeset
167 <param name="phi_resid3" value="2"/>
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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168 <param name="phi_name3" value="O4"/>
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169 <param name="phi_segid4" value="SYSTEM"/>
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170 <param name="phi_resid4" value="2"/>
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171 <param name="phi_name4" value="C4"/>
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172 <param name="psi_segid1" value="SYSTEM"/>
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173 <param name="psi_resid1" value="3"/>
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174 <param name="psi_name1" value="C1"/>
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175 <param name="psi_segid2" value="SYSTEM"/>
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176 <param name="psi_resid2" value="2"/>
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177 <param name="psi_name2" value="O4"/>
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178 <param name="psi_segid3" value="SYSTEM"/>
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179 <param name="psi_resid3" value="2"/>
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180 <param name="psi_name3" value="C4"/>
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181 <param name="psi_segid4" value="SYSTEM"/>
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182 <param name="psi_resid4" value="2"/>
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183 <param name="psi_name4" value="C3"/>
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184 <output name="output" file="Ramachandran_Plot_raw_data_gmx.tabular" />
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185 </test>
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186 </tests>
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187 <help><![CDATA[
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188 .. class:: infomark
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189
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190 **What it does**
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191
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192 A Ramachandran plot ([φ,ψ] plot) was originally developed as a way to visualize the energetically allowed regions for backbone dihedral angles ψ and φ of an amino acid.
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193 It can be also used to calculate glycosidic φ and ψ angles formed between carbohydrates. This tool can calculate and plot the histogram (Ramachandran plot) of user-defined φ and ψ angles of a trajectory.
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194
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195 - For protein φ and ψ dihedral definitions see https://proteinstructures.com/Structure/Structure/Ramachandran-plot.html.
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196 - For glycan φ and ψ dihedral definitions see http://www.glycanstructure.org/
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197
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198 _____
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199
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200
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201 .. class:: infomark
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202
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203 **Input**
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204
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205 - Trajectory file (DCD).
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206 - PDB file.
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207 - Segment IDs, residue IDs and names of the four atoms to calculate dihedrals.
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208
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209 Note that a MDAnalysis 'segment' is a larger organizational unit, for example one protein or all the solvent molecules or simply the whole system.
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210
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211 _____
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212
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213
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214 .. class:: infomark
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215
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216 **Output**
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217
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218 - Tab-separated file of raw data of the φ,ψ angles over time.
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219 - Image (as png) of the Ramachandran plot.
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220
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221
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222 ]]></help>
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223 <expand macro="citations" />
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224 </tool>