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comparison ramachandran_plots.xml @ 4:70a2d548e62c draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
author chemteam
date Mon, 24 Aug 2020 16:23:14 -0400
parents ce0728b92289
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3:8bd0e29927da 4:70a2d548e62c
1 <tool id="mdanalysis_ramachandran_plot" name="Ramachandran Plots" version="@VERSION@"> 1 <tool id="mdanalysis_ramachandran_plot" name="Ramachandran Plots" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
2 <description>- calculate and plot the distribution of two dihedrals 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 <token name="@GALAXY_VERSION@">0</token>
5 </macros> 6 </macros>
6 <expand macro="requirements"> 7 <expand macro="requirements">
7 <requirement type="package" version="1.3.1">scipy</requirement> 8 <requirement type="package" version="1.5.2">scipy</requirement>
8 <requirement type="package" version="0.9.0">seaborn</requirement> 9 <requirement type="package" version="0.10.0">seaborn</requirement>
9 <requirement type="package" version="1.1.0">nbdime</requirement> 10 <requirement type="package" version="2.0.0">nbdime</requirement>
11 <requirement type="package" version="5.3.1">pyyaml</requirement>
10 </expand> 12 </expand>
11 <command detect_errors="exit_code"> 13 <command detect_errors="exit_code"><![CDATA[
12 <![CDATA[
13 python '$__tool_directory__/ramachandran_plots.py' 14 python '$__tool_directory__/ramachandran_plots.py'
14 --itraj '$trajin' 15 --itraj '$trajin'
15 --istr '$strin' 16 --istr '$strin'
16 --itrajext '$trajin.ext' 17 --itrajext '$trajin.ext'
17 --istrext '$strin.ext' 18 --istrext '$strin.ext'
18 --isegid1 '$phi.phi_segid1' 19 --iyml '$ymlin'
19 --iresid1 '$phi.phi_resid1' 20 --output '$output'
20 --iname1 '$phi.phi_name1'
21 --isegid2 '$phi.phi_segid2'
22 --iresid2 '$phi.phi_resid2'
23 --iname2 '$phi.phi_name2'
24 --isegid3 '$phi.phi_segid3'
25 --iresid3 '$phi.phi_resid3'
26 --iname3 '$phi.phi_name3'
27 --isegid4 '$phi.phi_segid4'
28 --iresid4 '$phi.phi_resid4'
29 --iname4 '$phi.phi_name4'
30 --isegid5 '$psi.psi_segid1'
31 --iresid5 '$psi.psi_resid1'
32 --iname5 '$psi.psi_name1'
33 --isegid6 '$psi.psi_segid2'
34 --iresid6 '$psi.psi_resid2'
35 --iname6 '$psi.psi_name2'
36 --isegid7 '$psi.psi_segid3'
37 --iresid7 '$psi.psi_resid3'
38 --iname7 '$psi.psi_name3'
39 --isegid8 '$psi.psi_segid4'
40 --iresid8 '$psi.psi_resid4'
41 --iname8 '$psi.psi_name4'
42 --output '$output'
43 --oramachandran_plot '$ramachandran_plot' 21 --oramachandran_plot '$ramachandran_plot'
44 2>&1 22 2>&1
45 ]]></command> 23 ]]></command>
46 <inputs> 24 <inputs>
47 <expand macro="analysis_inputs"/> 25 <expand macro="analysis_inputs" />
48 <section name="phi" title="Phi" expanded="False"> 26 <section name="ymlparam" title="Torsion Parameters" expanded="False">
49 <param name="phi_segid1" type="text" value="HET" label="Segment ID of atom 1"> 27 <param format="txt" name="ymlin" type="data" label="Torsion parameters in yml format" help="Information in YAML format about the segid, resid, and name for atoms 1-4 of the phi and psi angles. Example formatting included in the main help text"/>
50 <expand macro="sanitizer"/>
51 </param>
52 <param name="phi_resid1" type="text" value="3" label="Residue ID of atom 1">
53 <expand macro="sanitizer_resids"/>
54 </param>
55 <param name="phi_name1" type="text" value="O5" label="Atom name of atom 1">
56 <expand macro="sanitizer"/>
57 </param>
58 <param name="phi_segid2" type="text" value="HET" label="Segment ID of atom 2">
59 <expand macro="sanitizer"/>
60 </param>
61 <param name="phi_resid2" type="text" value="3" label="Residue ID of atom 2">
62 <expand macro="sanitizer_resids"/>
63 </param>
64 <param name="phi_name2" type="text" value="C1" label="Atom name of atom 2">
65 <expand macro="sanitizer"/>
66 </param>
67 <param name="phi_segid3" type="text" value="HET" label="Segment ID of atom 3">
68 <expand macro="sanitizer"/>
69 </param>
70 <param name="phi_resid3" type="text" value="2" label="Residue ID of atom 3">
71 <expand macro="sanitizer_resids"/>
72 </param>
73 <param name="phi_name3" type="text" value="O4" label="Atom name of atom 3">
74 <expand macro="sanitizer"/>
75 </param>
76 <param name="phi_segid4" type="text" value="HET" label="Segment ID of atom 4">
77 <expand macro="sanitizer"/>
78 </param>
79 <param name="phi_resid4" type="text" value="2" label="Residue ID of atom 4">
80 <expand macro="sanitizer_resids"/>
81 </param>
82 <param name="phi_name4" type="text" value="C4" label="Atom name of atom 4">
83 <expand macro="sanitizer"/>
84 </param>
85 </section>
86 <section name="psi" title="Psi" expanded="False">
87 <param name="psi_segid1" type="text" value="HET" label="Segment ID of atom 1">
88 <expand macro="sanitizer"/>
89 </param>
90 <param name="psi_resid1" type="text" value="3" label="Residue ID of atom 1">
91 <expand macro="sanitizer_resids"/>
92 </param>
93 <param name="psi_name1" type="text" value="C1" label="Atom name of atom 1">
94 <expand macro="sanitizer"/>
95 </param>
96 <param name="psi_segid2" type="text" value="HET" label="Segment ID of atom 2">
97 <expand macro="sanitizer"/>
98 </param>
99 <param name="psi_resid2" type="text" value="2" label="Residue ID of atom 2">
100 <expand macro="sanitizer_resids"/>
101 </param>
102 <param name="psi_name2" type="text" value="O4" label="Atom name of atom 2">
103 <expand macro="sanitizer"/>
104 </param>
105 <param name="psi_segid3" type="text" value="HET" label="Segment ID of atom 3">
106 <expand macro="sanitizer"/>
107 </param>
108 <param name="psi_resid3" type="text" value="2" label="Residue ID of atom 3">
109 <expand macro="sanitizer_resids"/>
110 </param>
111 <param name="psi_name3" type="text" value="C4" label="Atom name of atom 3">
112 <expand macro="sanitizer"/>
113 </param>
114 <param name="psi_segid4" type="text" value="HET" label="Segment ID of atom 4">
115 <expand macro="sanitizer"/>
116 </param>
117 <param name="psi_resid4" type="text" value="2" label="Residue ID of atom 4">
118 <expand macro="sanitizer_resids"/>
119 </param>
120 <param name="psi_name4" type="text" value="C3" label="Atom name of atom 4">
121 <expand macro="sanitizer"/>
122 </param>
123 </section> 28 </section>
124 </inputs> 29 </inputs>
125 <outputs> 30 <outputs>
126 <data format="tabular" name="output" label="Ramachandran Plot raw data"/> 31 <data format="tabular" name="output" label="Ramachandran Plot raw data" />
127 <data format="png" name="ramachandran_plot" label="Ramachandran Plot"/> 32 <data format="png" name="ramachandran_plot" label="Ramachandran Plot" />
128 </outputs> 33 </outputs>
129 <tests> 34 <tests>
130 <test> 35 <test>
131 <expand macro="tests_inputs"/> 36 <param name="trajin" value="test.dcd" ftype="dcd" />
132 <param name="phi_segid1" value="HET"/> 37 <param name="strin" value="test.pdb" ftype="pdb" />
133 <param name="phi_resid1" value="3"/> 38 <section name="ymlparam">
134 <param name="phi_name1" value="O5"/> 39 <param name="ymlin" value="test.yml" />
135 <param name="phi_segid2" value="HET"/> 40 </section>
136 <param name="phi_resid2" value="3"/> 41 <output name="output">
137 <param name="phi_name2" value="C1"/> 42 <assert_contents>
138 <param name="phi_segid3" value="HET"/> 43 <has_text text="-144.503" />
139 <param name="phi_resid3" value="2"/> 44 <has_text text="-140.553" />
140 <param name="phi_name3" value="O4"/> 45 </assert_contents>
141 <param name="phi_segid4" value="HET"/> 46 </output>
142 <param name="phi_resid4" value="2"/> 47 <output name="ramachandran_plot">
143 <param name="phi_name4" value="C4"/> 48 <assert_contents>
144 <param name="psi_segid1" value="HET"/> 49 <has_size value="18522" delta="2000" />
145 <param name="psi_resid1" value="3"/> 50 </assert_contents>
146 <param name="psi_name1" value="C1"/> 51 </output>
147 <param name="psi_segid2" value="HET"/>
148 <param name="psi_resid2" value="2"/>
149 <param name="psi_name2" value="O4"/>
150 <param name="psi_segid3" value="HET"/>
151 <param name="psi_resid3" value="2"/>
152 <param name="psi_name3" value="C4"/>
153 <param name="psi_segid4" value="HET"/>
154 <param name="psi_resid4" value="2"/>
155 <param name="psi_name4" value="C3"/>
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" />
185 </test> 52 </test>
186 </tests> 53 </tests>
187 <help><![CDATA[ 54 <help><![CDATA[
188 .. class:: infomark 55 .. class:: infomark
189 56
190 **What it does** 57 **What it does**
191 58
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. 59 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.
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. 60 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.
194 61
195 - For protein φ and ψ dihedral definitions see https://proteinstructures.com/Structure/Structure/Ramachandran-plot.html.
196 - For glycan φ and ψ dihedral definitions see http://www.glycanstructure.org/
197 62
198 _____ 63 _____
199 64
200 65
201 .. class:: infomark 66 .. class:: infomark
202 67
203 **Input** 68 **Input**
204 69
205 - Trajectory file (DCD). 70 - Trajectory file (DCD).
206 - PDB file. 71 - PDB file.
207 - Segment IDs, residue IDs and names of the four atoms to calculate dihedrals. 72 - Text file in YAML format with Segment IDs, residue IDs and names of the four atoms to calculate dihedrals.
208 73
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. 74 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 75
76 - For protein φ and ψ dihedral definitions see https://proteinstructures.com/Structure/Structure/Ramachandran-plot.html
77 - For glycan φ and ψ dihedral definitions, see
78 - `Glycan Structure Website`_ - The glycosidic torsion angle definition is adopted from the crystallographic definition; O5-C1-O1-C'x (Φ; phi), C1-O1-C'x-C'x-1 (Ψ; psi), and O1-C'6-C'5-O'5 (ω; omega). The torsion angle between the first residue of the N-glycan chain and the side chain of the asparagine residue is defined as O5-C1-N'D2-C'G (Φ; phi) and C1-N'D2-C'G-C'B (Ψ; psi). The torsion angle between the first residue of the O-glycan chain and the side chain of the serine residue is defined as O5-C1-O'G-C'B (Φ; phi) and C1-O'G-C'B-C'A (Ψ; psi). For threonine residue, OG1 is used instead of OG. The atom names are based on the CHARMM topology.
79 - `Glycosciences Website`_ - NMR definition - Φ phi: H1-C1-O1-C′X Ψ psi: C1-O1-C′X-H′X ω omega: O1-C′6-C′5-H′5 Crystallographic definition - Φ phi: O5-C1-O1-C′X Ψ psi: C1-O1-C′X-C′X+1 ω omega: O1-C′6-C′5-O′5
80
81 - An example of a yaml formatted selection for φ-ψ of a small glycoprotein called PROF with a carbohydrate portion called CARA where φ=O5-C1-OG1-CB1 and ψ=C1-OG1-CB-CA for the selected segment and residue ids.
82
83 .. code-block:: yaml
84
85 ramachandran1:
86 phi:
87 atom1:
88 segid: CARA
89 resid: 1
90 name: O5
91 atom2:
92 segid: CARA
93 resid: 1
94 name: C1
95 atom3:
96 segid: PROF
97 resid: 4
98 name: OG1
99 atom4:
100 segid: PROF
101 resid: 4
102 name: CB
103 psi:
104 atom1:
105 segid: CARA
106 resid: 1
107 name: C1
108 atom2:
109 segid: PROF
110 resid: 4
111 name: OG1
112 atom3:
113 segid: PROF
114 resid: 4
115 name: CB
116 atom4:
117 segid: PROF
118 resid: 4
119 name: CA
120 comment: pick visually using VMD using labels. Go to labels, dihedral to see the information about resname resid and atomname and then lookup the segname for ach atom.
121
211 _____ 122 _____
212 123
213 124
214 .. class:: infomark 125 .. class:: infomark
215 126
216 **Output** 127 **Output**
217 128
218 - Tab-separated file of raw data of the φ,ψ angles over time. 129 - Tab-separated file of raw data of the φ,ψ angles over time.
219 - Image (as png) of the Ramachandran plot. 130 - Image (as png) of the Ramachandran plot.
220 131
221 132 .. _`Glycan Structure Website`: http://www.glycanstructure.org/fragment-db/howto
133 .. _`Glycosciences Website`: http://www.glycosciences.de/tools/glytorsion/
222 ]]></help> 134 ]]></help>
223 <expand macro="citations" /> 135 <expand macro="citations" />
224 </tool> 136 </tool>