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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
author chemteam
date Mon, 07 Oct 2019 12:39:21 -0400
parents f739a9e4ed06
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0:f739a9e4ed06 1:b923959babb6
1 <tool id="mdanalysis_ramachandran_plot" name="Ramachandran Plots" version="0.1.3"> 1 <tool id="mdanalysis_ramachandran_plot" name="Ramachandran Plots" version="@VERSION@">
2 <description>Calculate and plot the distribution of two diheadrals in a trajectory</description> 2 <description>- calculate and plot the distribution of two dihedrals in a trajectory</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"> 6 <expand macro="requirements">
7 <requirement type="package" version="1.2.1">scipy</requirement> 7 <requirement type="package" version="1.3.1">scipy</requirement>
8 <requirement type="package" version="0.9.0">seaborn</requirement> 8 <requirement type="package" version="0.9.0">seaborn</requirement>
9 <requirement type="package" version="1.0.5">nbdime</requirement> 9 <requirement type="package" version="1.1.0">nbdime</requirement>
10 </expand> 10 </expand>
11 <command detect_errors="exit_code"> 11 <command detect_errors="exit_code">
12 <![CDATA[ 12 <![CDATA[
13 python '$__tool_directory__/ramachandran_plots.py' 13 python '$__tool_directory__/ramachandran_plots.py'
14 --idcd '$dcdin' 14 --itraj '$trajin'
15 --ipdb '$pdbin' 15 --istr '$strin'
16 --isegid1 '$phi.segid1' 16 --itrajext '$trajin.ext'
17 --iresid1 '$phi.resid1' 17 --istrext '$strin.ext'
18 --iname1 '$phi.name1' 18 --isegid1 '$phi.phi_segid1'
19 --isegid2 '$phi.segid2' 19 --iresid1 '$phi.phi_resid1'
20 --iresid2 '$phi.resid2' 20 --iname1 '$phi.phi_name1'
21 --iname2 '$phi.name2' 21 --isegid2 '$phi.phi_segid2'
22 --isegid3 '$phi.segid3' 22 --iresid2 '$phi.phi_resid2'
23 --iresid3 '$phi.resid3' 23 --iname2 '$phi.phi_name2'
24 --iname3 '$phi.name3' 24 --isegid3 '$phi.phi_segid3'
25 --isegid4 '$phi.segid4' 25 --iresid3 '$phi.phi_resid3'
26 --iresid4 '$phi.resid4' 26 --iname3 '$phi.phi_name3'
27 --iname4 '$phi.name4' 27 --isegid4 '$phi.phi_segid4'
28 --isegid5 '$psi.segid1' 28 --iresid4 '$phi.phi_resid4'
29 --iresid5 '$psi.resid1' 29 --iname4 '$phi.phi_name4'
30 --iname5 '$psi.name1' 30 --isegid5 '$psi.psi_segid1'
31 --isegid6 '$psi.segid2' 31 --iresid5 '$psi.psi_resid1'
32 --iresid6 '$psi.resid2' 32 --iname5 '$psi.psi_name1'
33 --iname6 '$psi.name2' 33 --isegid6 '$psi.psi_segid2'
34 --isegid7 '$psi.segid3' 34 --iresid6 '$psi.psi_resid2'
35 --iresid7 '$psi.resid3' 35 --iname6 '$psi.psi_name2'
36 --iname7 '$psi.name3' 36 --isegid7 '$psi.psi_segid3'
37 --isegid8 '$psi.segid4' 37 --iresid7 '$psi.psi_resid3'
38 --iresid8 '$psi.resid4' 38 --iname7 '$psi.psi_name3'
39 --iname8 '$psi.name4' 39 --isegid8 '$psi.psi_segid4'
40 --iresid8 '$psi.psi_resid4'
41 --iname8 '$psi.psi_name4'
40 --output '$output' 42 --output '$output'
41 --oramachandran_plot '$ramachandran_plot' 43 --oramachandran_plot '$ramachandran_plot'
42 2>&1 44 2>&1
43 ]]></command> 45 ]]></command>
44 <inputs> 46 <inputs>
45 <expand macro="analysis_inputs"/> 47 <expand macro="analysis_inputs"/>
46 <section name="phi" title="Phi" expanded="False"> 48 <section name="phi" title="Phi" expanded="False">
47 <param name="segid1" type="text" value="HET" label="Segid of atom 1"> 49 <param name="phi_segid1" type="text" value="HET" label="Segment ID of atom 1">
48 <expand macro="sanitizer"/> 50 <expand macro="sanitizer"/>
49 </param> 51 </param>
50 <param name="resid1" type="text" value="3" label="Resid of atom 1"> 52 <param name="phi_resid1" type="text" value="3" label="Residue ID of atom 1">
51 <expand macro="sanitizer_resids"/> 53 <expand macro="sanitizer_resids"/>
52 </param> 54 </param>
53 <param name="name1" type="text" value="O5" label="Atom name of atom 1"> 55 <param name="phi_name1" type="text" value="O5" label="Atom name of atom 1">
54 <expand macro="sanitizer"/> 56 <expand macro="sanitizer"/>
55 </param> 57 </param>
56 <param name="segid2" type="text" value="HET" label="Segid of atom 2"> 58 <param name="phi_segid2" type="text" value="HET" label="Segment ID of atom 2">
57 <expand macro="sanitizer"/> 59 <expand macro="sanitizer"/>
58 </param> 60 </param>
59 <param name="resid2" type="text" value="3" label="Resid of atom 2"> 61 <param name="phi_resid2" type="text" value="3" label="Residue ID of atom 2">
60 <expand macro="sanitizer_resids"/> 62 <expand macro="sanitizer_resids"/>
61 </param> 63 </param>
62 <param name="name2" type="text" value="C1" label="Atom name of atom 2"> 64 <param name="phi_name2" type="text" value="C1" label="Atom name of atom 2">
63 <expand macro="sanitizer"/> 65 <expand macro="sanitizer"/>
64 </param> 66 </param>
65 <param name="segid3" type="text" value="HET" label="Segid of atom 3"> 67 <param name="phi_segid3" type="text" value="HET" label="Segment ID of atom 3">
66 <expand macro="sanitizer"/> 68 <expand macro="sanitizer"/>
67 </param> 69 </param>
68 <param name="resid3" type="text" value="2" label="Resid of atom 3"> 70 <param name="phi_resid3" type="text" value="2" label="Residue ID of atom 3">
69 <expand macro="sanitizer_resids"/> 71 <expand macro="sanitizer_resids"/>
70 </param> 72 </param>
71 <param name="name3" type="text" value="O4" label="Atom name of atom 3"> 73 <param name="phi_name3" type="text" value="O4" label="Atom name of atom 3">
72 <expand macro="sanitizer"/> 74 <expand macro="sanitizer"/>
73 </param> 75 </param>
74 <param name="segid4" type="text" value="HET" label="Segid of atom 4"> 76 <param name="phi_segid4" type="text" value="HET" label="Segment ID of atom 4">
75 <expand macro="sanitizer"/> 77 <expand macro="sanitizer"/>
76 </param> 78 </param>
77 <param name="resid4" type="text" value="2" label="Resid of atom 4"> 79 <param name="phi_resid4" type="text" value="2" label="Residue ID of atom 4">
78 <expand macro="sanitizer_resids"/> 80 <expand macro="sanitizer_resids"/>
79 </param> 81 </param>
80 <param name="name4" type="text" value="C4" label="Atom name of atom 4"> 82 <param name="phi_name4" type="text" value="C4" label="Atom name of atom 4">
81 <expand macro="sanitizer"/> 83 <expand macro="sanitizer"/>
82 </param> 84 </param>
83 </section> 85 </section>
84 <section name="psi" title="Psi" expanded="False"> 86 <section name="psi" title="Psi" expanded="False">
85 <param name="segid1" type="text" value="HET" label="Segid of atom 1"> 87 <param name="psi_segid1" type="text" value="HET" label="Segment ID of atom 1">
86 <expand macro="sanitizer"/> 88 <expand macro="sanitizer"/>
87 </param> 89 </param>
88 <param name="resid1" type="text" value="3" label="Resid of atom 1"> 90 <param name="psi_resid1" type="text" value="3" label="Residue ID of atom 1">
89 <expand macro="sanitizer_resids"/> 91 <expand macro="sanitizer_resids"/>
90 </param> 92 </param>
91 <param name="name1" type="text" value="C1" label="Atom name of atom 1"> 93 <param name="psi_name1" type="text" value="C1" label="Atom name of atom 1">
92 <expand macro="sanitizer"/> 94 <expand macro="sanitizer"/>
93 </param> 95 </param>
94 <param name="segid2" type="text" value="HET" label="Segid of atom 2"> 96 <param name="psi_segid2" type="text" value="HET" label="Segment ID of atom 2">
95 <expand macro="sanitizer"/> 97 <expand macro="sanitizer"/>
96 </param> 98 </param>
97 <param name="resid2" type="text" value="2" label="Resid of atom 2"> 99 <param name="psi_resid2" type="text" value="2" label="Residue ID of atom 2">
98 <expand macro="sanitizer_resids"/> 100 <expand macro="sanitizer_resids"/>
99 </param> 101 </param>
100 <param name="name2" type="text" value="O4" label="Atom name of atom 2"> 102 <param name="psi_name2" type="text" value="O4" label="Atom name of atom 2">
101 <expand macro="sanitizer"/> 103 <expand macro="sanitizer"/>
102 </param> 104 </param>
103 <param name="segid3" type="text" value="HET" label="Segid of atom 3"> 105 <param name="psi_segid3" type="text" value="HET" label="Segment ID of atom 3">
104 <expand macro="sanitizer"/> 106 <expand macro="sanitizer"/>
105 </param> 107 </param>
106 <param name="resid3" type="text" value="2" label="Resid of atom 3"> 108 <param name="psi_resid3" type="text" value="2" label="Residue ID of atom 3">
107 <expand macro="sanitizer_resids"/> 109 <expand macro="sanitizer_resids"/>
108 </param> 110 </param>
109 <param name="name3" type="text" value="C4" label="Atom name of atom 3"> 111 <param name="psi_name3" type="text" value="C4" label="Atom name of atom 3">
110 <expand macro="sanitizer"/> 112 <expand macro="sanitizer"/>
111 </param> 113 </param>
112 <param name="segid4" type="text" value="HET" label="Segid of atom 4"> 114 <param name="psi_segid4" type="text" value="HET" label="Segment ID of atom 4">
113 <expand macro="sanitizer"/> 115 <expand macro="sanitizer"/>
114 </param> 116 </param>
115 <param name="resid4" type="text" value="2" label="Resid of atom 4"> 117 <param name="psi_resid4" type="text" value="2" label="Residue ID of atom 4">
116 <expand macro="sanitizer_resids"/> 118 <expand macro="sanitizer_resids"/>
117 </param> 119 </param>
118 <param name="name4" type="text" value="C3" label="Atom name of atom 4"> 120 <param name="psi_name4" type="text" value="C3" label="Atom name of atom 4">
119 <expand macro="sanitizer"/> 121 <expand macro="sanitizer"/>
120 </param> 122 </param>
121 </section> 123 </section>
122 </inputs> 124 </inputs>
123 <outputs> 125 <outputs>
125 <data format="png" name="ramachandran_plot" label="Ramachandran Plot"/> 127 <data format="png" name="ramachandran_plot" label="Ramachandran Plot"/>
126 </outputs> 128 </outputs>
127 <tests> 129 <tests>
128 <test> 130 <test>
129 <expand macro="tests_inputs"/> 131 <expand macro="tests_inputs"/>
130 <param name="phi.segid1" value="HET"/> 132 <param name="phi_segid1" value="HET"/>
131 <param name="phi.resid1" value="3"/> 133 <param name="phi_resid1" value="3"/>
132 <param name="phi.name1" value="O5"/> 134 <param name="phi_name1" value="O5"/>
133 <param name="phi.segid2" value="HET"/> 135 <param name="phi_segid2" value="HET"/>
134 <param name="phi.resid2" value="3"/> 136 <param name="phi_resid2" value="3"/>
135 <param name="phi.name2" value="C1"/> 137 <param name="phi_name2" value="C1"/>
136 <param name="phi.segid3" value="HET"/> 138 <param name="phi_segid3" value="HET"/>
137 <param name="phi.resid3" value="2"/> 139 <param name="phi_resid3" value="2"/>
138 <param name="phi.name3" value="O4"/> 140 <param name="phi_name3" value="O4"/>
139 <param name="phi.segid4" value="HET"/> 141 <param name="phi_segid4" value="HET"/>
140 <param name="phi.resid4" value="2"/> 142 <param name="phi_resid4" value="2"/>
141 <param name="phi.name4" value="C4"/> 143 <param name="phi_name4" value="C4"/>
142 <param name="psi.segid1" value="HET"/> 144 <param name="psi_segid1" value="HET"/>
143 <param name="psi.resid1" value="3"/> 145 <param name="psi_resid1" value="3"/>
144 <param name="psi.name1" value="C1"/> 146 <param name="psi_name1" value="C1"/>
145 <param name="psi.segid2" value="HET"/> 147 <param name="psi_segid2" value="HET"/>
146 <param name="psi.resid2" value="2"/> 148 <param name="psi_resid2" value="2"/>
147 <param name="psi.name2" value="O4"/> 149 <param name="psi_name2" value="O4"/>
148 <param name="psi.segid3" value="HET"/> 150 <param name="psi_segid3" value="HET"/>
149 <param name="psi.resid3" value="2"/> 151 <param name="psi_resid3" value="2"/>
150 <param name="psi.name3" value="C4"/> 152 <param name="psi_name3" value="C4"/>
151 <param name="psi.segid4" value="HET"/> 153 <param name="psi_segid4" value="HET"/>
152 <param name="psi.resid4" value="2"/> 154 <param name="psi_resid4" value="2"/>
153 <param name="psi.name4" value="C3"/> 155 <param name="psi_name4" value="C3"/>
154 <output name="output" file="Ramachandran_Plot_raw_data.tabular" /> 156 <output name="output" file="Ramachandran_Plot_raw_data.tabular" />
157 </test>
158 <test>
159 <expand macro="tests_inputs_gmx"/>
160 <param name="phi_segid1" value="SYSTEM"/>
161 <param name="phi_resid1" value="3"/>
162 <param name="phi_name1" value="O5"/>
163 <param name="phi_segid2" value="SYSTEM"/>
164 <param name="phi_resid2" value="3"/>
165 <param name="phi_name2" value="C1"/>
166 <param name="phi_segid3" value="SYSTEM"/>
167 <param name="phi_resid3" value="2"/>
168 <param name="phi_name3" value="O4"/>
169 <param name="phi_segid4" value="SYSTEM"/>
170 <param name="phi_resid4" value="2"/>
171 <param name="phi_name4" value="C4"/>
172 <param name="psi_segid1" value="SYSTEM"/>
173 <param name="psi_resid1" value="3"/>
174 <param name="psi_name1" value="C1"/>
175 <param name="psi_segid2" value="SYSTEM"/>
176 <param name="psi_resid2" value="2"/>
177 <param name="psi_name2" value="O4"/>
178 <param name="psi_segid3" value="SYSTEM"/>
179 <param name="psi_resid3" value="2"/>
180 <param name="psi_name3" value="C4"/>
181 <param name="psi_segid4" value="SYSTEM"/>
182 <param name="psi_resid4" value="2"/>
183 <param name="psi_name4" value="C3"/>
184 <output name="output" file="Ramachandran_Plot_raw_data_gmx.tabular" />
155 </test> 185 </test>
156 </tests> 186 </tests>
157 <help><![CDATA[ 187 <help><![CDATA[
158 .. class:: infomark 188 .. class:: infomark
159 189
160 **What it does** 190 **What it does**
161 191
162 A Ramachandran plot ([φ,ψ] plot), originally developed as a way to visualize energetically allowed regions for backbone dihedral angles ψ against φ of amino acid. 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.
163 This 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 define φ and ψ angles of a trajectory. 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.
164 194
165 - For protien φ and ψ diheadral definitions see https://proteinstructures.com/Structure/Structure/Ramachandran-plot.html. 195 - For protein φ and ψ dihedral definitions see https://proteinstructures.com/Structure/Structure/Ramachandran-plot.html.
166 196 - For glycan φ and ψ dihedral definitions see http://www.glycanstructure.org/
167 - For glycan φ and ψ diheadral definitions see http://www.glycanstructure.org/
168 197
169 _____ 198 _____
170 199
171 200
172 .. class:: infomark 201 .. class:: infomark
173 202
174 **Input** 203 **Input**
175 204
176 - Trajectory file (DCD). 205 - Trajectory file (DCD).
177 - PDB file. 206 - PDB file.
178 - Segids, resids and names of the four atoms to calculate diheadrals. 207 - Segment IDs, residue IDs and names of the four atoms to calculate dihedrals.
179 208
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.
210
180 _____ 211 _____
181 212
182 213
183 .. class:: infomark 214 .. class:: infomark
184 215
185 **Output** 216 **Output**
186 217
187 - Tab-separated file of raw data of the φ,ψ angles time series. 218 - Tab-separated file of raw data of the φ,ψ angles over time.
188 - Image (as png) of the Ramachandran Plot. 219 - Image (as png) of the Ramachandran plot.
189 220
190 221
191 ]]></help> 222 ]]></help>
192 <expand macro="citations" /> 223 <expand macro="citations" />
193 </tool> 224 </tool>