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comparison pdbfixer.xml @ 0:24bf162ef74b draft default tip

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/openmm commit 78cfada16486c61f1de167ed358f8a52fcbe9f70"
author chemteam
date Wed, 13 Apr 2022 16:21:56 +0000
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1 <tool id="pdbfixer" name="PDBFixer" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
2 <description>to automatically fix a PDB file before performing molecular dynamics simulation</description>
3 <macros>
4 <token name="@TOOL_VERSION@">1.8.1</token>
5 <token name="@GALAXY_VERSION@">0</token>
6 </macros>
7 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">pdbfixer</requirement>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[
11 pdbfixer
12 '$pdb_input'
13 ## --pdbid and --url not implemented here, users can use the get_pdb tool
14 --output '$output'
15 --add-atoms='$add_atoms' ## which missing atoms to add: all, heavy, hydrogen, or none [default: all]
16 --keep-heterogens='$keep_heterogens' ## which heterogens to keep: all, water, or none [default: all]
17 $replace_nonstandard ## replace nonstandard residues with standard equivalents
18 $add_residues ## add missing residues
19 --ph='$ph' ## the pH to use for adding missing hydrogens [default: 7.0]
20
21 #if $solvent.box.water_box == "true":
22 --water-box=$solvent.box.x $solvent.box.y $solvent.box.z ## add a water box. The value is the box dimensions in nm [example: --water-box=2.5 2.4 3.0]
23 --positive-ion='$solvent.positive_ion' ## positive ion to include in the water box: Cs+, K+, Li+, Na+, or Rb+ [default: Na+]
24 --negative-ion='$solvent.negative_ion' ## negative ion to include in the water box: Cl-, Br-, F-, or I- [default: Cl-]
25 --ionic-strength='$solvent.ionic_strength' ## molar concentration of ions to add to the water box [default: 0.0]
26 #end if
27 --verbose
28
29 ]]></command>
30 <inputs>
31 <param format="pdb" name="pdb_input" type="data" label="PDB input file"/>
32 <param name="add_atoms" type="select" label="Missing atoms to be added">
33 <option value="all" selected="true">All</option>
34 <option value="heavy">Heavy atoms only</option>
35 <option value="hydrogen">Hydrogen atoms only</option>
36 <option value="none">None</option>
37 </param>
38 <param name="keep_heterogens" type="select" label="Which heterogens to keep">
39 <option value="all" selected="true">All</option>
40 <option value="water">Only water</option>
41 <option value="none">None</option>
42 </param>
43 <param name="replace_nonstandard" type="boolean" label="Replace nonstandard residues with standard equivalents?" truevalue="--replace-nonstandard" falsevalue="" value=""/>
44 <param name="add_residues" type="boolean" label="Add missing residues?" truevalue="--add-residues" falsevalue="" value=""/>
45 <param name="ph" type="float" min="0" max="14" value="7" label="pH" help="Ignored if not adding hydrogen atoms"/>
46 <section name="solvent" title="Solvent parameters" help="Note that you may prefer to modify solvent parameters using other tools.">
47 <conditional name="box">
48 <param name="water_box" type="select" label="Add a water box?" help="Dimensions in nanometers">
49 <option value="true">Yes</option>
50 <option value="false" selected="true">No</option>
51 </param>
52 <when value="true">
53 <param name="x" type="float" min="0" value="0" label="Size in X dimension"/>
54 <param name="y" type="float" min="0" value="0" label="Size in Y dimension"/>
55 <param name="z" type="float" min="0" value="0" label="Size in Z dimension"/>
56 </when>
57 <when value="false" />
58 </conditional>
59 <param name="positive_ion" type="select" label="Type of positive ion to add">
60 <option value="Li+">Lithium (Li+)</option>
61 <option value="Na+" selected="true">Sodium (Na+)</option>
62 <option value="K+">Potassium (K+)</option>
63 <option value="Rb+">Rubidium (Rb+)</option>
64 <option value="Cs+">Cesium (Cs+)</option>
65 </param>
66 <param name="negative_ion" type="select" label="Type of negative ion to add">
67 <option value="Cl-" selected="true">Chloride (Cl-)</option>
68 <option value="Br-">Bromide (Br-)</option>
69 <option value="F-">Fluoride (F-)</option>
70 <option value="I-">Iodide (I-)</option>
71 </param>
72 <param name="ionic_strength" type="float" min="0" max="10" value="0" label="Ionic strength" help="Molar concentration of ions to add to the water box"/>
73 </section>
74 </inputs>
75 <outputs>
76 <data name="output" format="pdb"/>
77 </outputs>
78 <tests>
79 <!-- pdbfixer test-data/broken.pdb -add-atoms=all -keep-heterogens=all -replace-nonstandard -->
80 <test>
81 <param name="pdb_input" value="broken.pdb"/>
82 <param name="add_atoms" value="all"/>
83 <param name="keep_heterogens" value="all"/>
84 <param name="replace_nonstandard" value="true"/>
85 <param name="add_residues" value="false"/>
86 <param name="ph" value="7"/>
87 <output name="output">
88 <assert_contents>
89 <has_n_lines n="162"/>
90 <!-- check LYS8 is fixed -->
91 <has_text text="CD LYS A 8"/>
92 <has_text text="CE LYS A 8"/>
93 <!-- check hydration -->
94 <has_text_matching expression="H \n" n="81"/>
95 </assert_contents>
96 </output>
97 </test>
98 <!-- pdbfixer test-data/broken.pdb -add-atoms=heavy -keep-heterogens=all -replace-nonstandard -add-residues -->
99 <test>
100 <param name="pdb_input" value="broken.pdb"/>
101 <param name="add_atoms" value="heavy"/>
102 <param name="keep_heterogens" value="all"/>
103 <param name="replace_nonstandard" value="true"/>
104 <param name="add_residues" value="false"/>
105 <output name="output">
106 <assert_contents>
107 <has_n_lines n="81"/>
108 <!-- check LYS8 is fixed -->
109 <has_text text="CD LYS A 8"/>
110 <has_text text="CE LYS A 8"/>
111 <!-- check no hydration -->
112 <has_text_matching expression="H \n" negate="true"/>
113 </assert_contents>
114 </output>
115 </test>
116 <test>
117 <param name="pdb_input" value="broken.pdb"/>
118 <param name="add_atoms" value="all"/>
119 <param name="keep_heterogens" value="all"/>
120 <param name="replace_nonstandard" value="true"/>
121 <param name="add_residues" value="false"/>
122 <param name="ph" value="14"/>
123 <param name="water_box" value="true"/>
124 <param name="x" value="5"/>
125 <param name="y" value="5"/>
126 <param name="z" value="5"/>
127 <param name="positive_ion" value="Li+"/>
128 <param name="negative_ion" value="I-"/>
129 <param name="ionic_strength" value="2"/>
130 <output name="output">
131 <assert_contents>
132 <!-- seems insertion of water is random and not fully reproducible -->
133 <has_n_lines n="11482" delta="100"/>
134 <!-- check LYS8 is fixed -->
135 <has_text text="CD LYS A 8"/>
136 <has_text text="CE LYS A 8"/>
137 <!-- check hydration one less due to raised pH -->
138 <has_text_matching expression="ATOM.* H \n" n="80"/>
139 <!-- check water and ions -->
140 <has_text_matching expression="HOH" n="11041" delta="100"/>
141 <has_text_matching expression=" I .*\n" n="144"/>
142 <has_text_matching expression=" Li .*\n" n="144"/>
143 </assert_contents>
144 </output>
145 </test>
146 </tests>
147 <help><![CDATA[
148 .. class:: infomark
149
150 **What it does**
151
152 Fixes any issues in a PDB file (for example, adding missing residues, or missing atoms) prior to performing molecular dynamics simulations.
153
154 PDBFixer can do any or all of the following:
155
156 - Add missing heavy atoms.
157 - Add missing hydrogen atoms.
158 - Build missing loops.
159 - Convert non-standard residues to their standard equivalents.
160 - Select a single position for atoms with multiple alternate positions listed.
161 - Delete unwanted chains from the model.
162 - Delete unwanted heterogens.
163 - Build a water box for explicit solvent simulations.
164
165 _____
166
167
168 .. class:: infomark
169
170 **Input**
171
172 - PDB file
173
174 _____
175
176
177 .. class:: infomark
178
179 **Output**
180
181 - PDB file
182
183 ]]></help>
184 <citations>
185 <citation type="doi">10.1371/journal.pcbi.1005659</citation>
186 <citation type="bibtex">@misc{pdbfixer, author = {{Peter Eastman et al.}}, title = {PDBFixer}, url={https://github.com/openmm/PDBFixer}, abstract = {PDBFixer is an easy to use application for fixing problems in Protein Data Bank files in preparation for simulating them.}, urldate = {2022-03-25}, publisher = {GitHub}, year = {2022}, month = mar, }</citation>
187 </citations>
188 </tool>
189