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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
author chemteam
date Tue, 07 Apr 2020 11:53:51 +0000
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-1:000000000000 0:1c4b26fe9a88
1 <tool id="parmconv" name="Convert Parameters" version="@VERSION@">
2 <description>to AMBER prmtop in preparation for MMPBSA</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements">
7 <requirement type="package" version="3.2.0">parmed</requirement>
8 <requirement type="package" version="2019.1">gromacs</requirement>
9 <requirement type="package" version="2.11.1">jinja2</requirement>
10 </expand>
11 <command detect_errors="exit_code">
12 <![CDATA[
13 python '$templating_script' '$inputs' &&
14 PATH_TO_PARMED=\$(dirname `which parmed`) &&
15 export AMBERHOME=\$(dirname \$PATH_TO_PARMED) &&
16 export GMXDATA=\$AMBERHOME/share/gromacs/top/ &&
17 parmed -i ligand.script -O &&
18 parmed -i receptor.script -O &&
19 parmed -i complex.script -O &&
20 parmed -i solvatedcomplex.script -O
21
22 ]]>
23 </command>
24 <configfiles>
25 <inputs name="inputs"/>
26 <configfile name="templating_script">
27 <![CDATA[
28
29 import os
30 import sys
31 import json
32
33 from jinja2 import Environment, FileSystemLoader
34 input_json_path = sys.argv[1]
35 params = json.load(open(input_json_path, "r"))
36 currentpath = "$__tool_directory__" # should work generally
37 template_environment = Environment(loader=FileSystemLoader(currentpath),lstrip_blocks=True, trim_blocks=True)
38 template = template_environment.get_template('template_parmconv.j2')
39 params['fmt'] = '$param_inputs.fmt'
40 #if str($param_inputs.fmt) == 'AMBER':
41 params["top_in"] = '$param_inputs.top_in'
42 #else:
43 params["top_in"] = '$param_inputs.top_in'
44 params["str_in"] = '$param_inputs.str_in'
45 #end if
46 params['prmtop_ligand'] = '$prmtop_ligand'
47 params['prmtop_receptor'] = '$prmtop_receptor'
48 params['prmtop_complex'] = '$prmtop_complex'
49 params['prmtop_solvatedcomplex'] = '$prmtop_solvatedcomplex'
50 print(params)
51
52
53 def unescape(cond_text):
54 """
55 # Unescape if input has been escaped - credit @bgruening //github.com/bgruening/galaxytools.git get_online_data.py
56 """
57 mapped_chars = { '>' :'__gt__',
58 '<' :'__lt__',
59 "'" :'__sq__',
60 '"' :'__dq__',
61 '[' :'__ob__',
62 ']' :'__cb__',
63 '{' :'__oc__',
64 '}' :'__cc__',
65 '@' : '__at__',
66 '\n' : '__cn__',
67 '\r' : '__cr__',
68 '\t' : '__tc__',
69 '&' : '__and__'
70 }
71 for key, value in mapped_chars.items():
72 cond_text = cond_text.replace( value, key )
73 return cond_text
74
75 def run_template(params=params, system="ligand"):
76 """
77 # Render template on a selected system using a local parameter copy
78 """
79 localparams=params.copy() # shallow copy ok for simple variables
80 localparams['stripmask']=unescape(localparams['stripmask_'+system])
81 localparams['prmtop_out']=localparams['prmtop_'+system]
82 print(localparams)
83 with open(system+'.script','w+') as f:
84 f.write(template.render(localparams))
85
86 systems = ['ligand', 'receptor', 'complex', 'solvatedcomplex']
87 for system in systems:
88 run_template(system=system)
89
90 ]]>
91 </configfile>
92 </configfiles>
93 <inputs>
94 <conditional name="param_inputs">
95 <param name="fmt" type="select" label="Force Field format">
96 <option selected="True" value="AMBER">AMBER</option>
97 <option value="GROMACS">GROMACS</option>
98 </param>
99 <when value="AMBER">
100 <param name="top_in" type="data" label="Input topology (prmtop) file" format="txt"/>
101 </when>
102 <when value="GROMACS">
103 <param name="top_in" type="data" label="Input topology (top) file" format="top"/>
104 <param name="str_in" type="data" label="Input structure (gro) file" format="gro"/>
105 </when>
106 </conditional>
107 <param name="stripmask_ligand" type="text" label="Ligand selection" value="!:UNL" help="Define a valid AMBER stripmask that will select only the ligand">
108 <sanitizer>
109 <valid initial="string.printable">
110 <remove value="&amp;"/>
111 </valid>
112 <mapping initial="none">
113 <add source="&amp;" target="__and__"/>
114 </mapping>
115 </sanitizer>
116 </param>
117 <param name="stripmask_receptor" type="text" label="Receptor selection" value=":NA,SOL,UNL" help="Define a valid AMBER stripmask that will select only the receptor">
118 <sanitizer>
119 <valid initial="string.printable">
120 <remove value="&amp;"/>
121 </valid>
122 <mapping initial="none">
123 <add source="&amp;" target="__and__"/>
124 </mapping>
125 </sanitizer>
126 </param>
127 <param name="stripmask_complex" type="text" label="Complex selection" value=":NA,SOL" help="Define a valid AMBER stripmask that will select the complex (receptor with ligand)">
128 <sanitizer>
129 <valid initial="string.printable">
130 <remove value="&amp;"/>
131 </valid>
132 <mapping initial="none">
133 <add source="&amp;" target="__and__"/>
134 </mapping>
135 </sanitizer>
136 </param>
137 <param name="stripmask_solvatedcomplex" type="text" label="Solvated complex selection" help="Define a valid AMBER stripmask that will select the solvated complex (includes water and ions)">
138 <sanitizer>
139 <valid initial="string.printable">
140 <remove value="&amp;"/>
141 </valid>
142 <mapping initial="none">
143 <add source="&amp;" target="__and__"/>
144 </mapping>
145 </sanitizer>
146 </param>
147 </inputs>
148 <outputs>
149 <data format="txt" name="prmtop_ligand" label="ligand prmtop"/>
150 <data format="txt" name="prmtop_receptor" label="receptor prmtop"/>
151 <data format="txt" name="prmtop_complex" label="complex prmtop"/>
152 <data format="txt" name="prmtop_solvatedcomplex" label="solvated complex prmtop"/>
153 </outputs>
154 <tests>
155 <test>
156 <!--example in this test is not solvated but sufficient -->
157 <param name="fmt" value="AMBER"/>
158 <conditional name="param_inputs">
159 <param name="top_in" value="complex.prmtop"/>
160 </conditional>
161 <param name="stripmask_ligand" value="!:RAL"/>
162 <param name="stripmask_receptor" value=":NA,CL,SOL,WAT,RAL"/>
163 <param name="stripmask_complex" value=":NA,CL,SOL,WAT"/>
164 <output name="prmtop_ligand">
165 <assert_contents>
166 <has_text text=" 61 15"/>
167 <has_text text="%FLAG MASS"/>
168 <has_text text="RAL"/>
169 </assert_contents>
170 </output>
171 <output name="prmtop_receptor">
172 <assert_contents>
173 <has_text text=" 3880 15"/>
174 <has_text text="%FLAG MASS"/>
175 <has_text text="ALA LEU"/>
176 <not_has_text text="RAL "/>
177 </assert_contents>
178 </output>
179 <output name="prmtop_complex">
180 <assert_contents>
181 <has_text text=" 3941 15"/>
182 <has_text text="%FLAG MASS"/>
183 <has_text text="ALA LEU"/>
184 <has_text text="RAL"/>
185 </assert_contents>
186 </output>
187 </test>
188 <test>
189 <!--example in this test is from @sbrays' gromacs tests. It has no ligand but is sufficient and will not take extra space in the repo! -->
190 <param name="fmt" value="GROMACS"/>
191 <conditional name="param_inputs">
192 <param name="top_in" value="topol_solv.top"/>
193 <param name="str_in" value="solv_ions.gro"/>
194 </conditional>
195 <!-- pretending CL is a ligand -->
196 <param name="stripmask_ligand" value="!:CL"/>
197 <param name="stripmask_receptor" value=":NA,CL,SOL,WAT"/>
198 <!-- test a fairly complex selection. All backbone oxygens in residues 1-500 but not in water, lysine or arginine -->
199 <param name="stripmask_solvatedcomplex" value=":1-500@O&amp;!(:WAT|:LYS,ARG)"/>
200 <output name="prmtop_ligand">
201 <assert_contents>
202 <has_text text=" 8 59"/>
203 <has_text text="%FLAG MASS"/>
204 <has_text text="CL"/>
205 </assert_contents>
206 </output>
207 <output name="prmtop_receptor">
208 <assert_contents>
209 <has_text text=" 1960 59"/>
210 <has_text text="%FLAG MASS"/>
211 <has_text text="LYS VAL PHE "/>
212 <not_has_text text="CL "/>
213 </assert_contents>
214 </output>
215 <output name="prmtop_solvatedcomplex">
216 <assert_contents>
217 <has_text text=" 38265 59"/>
218 <has_text text="%FLAG MASS"/>
219 <has_text text="LYS VAL PHE"/>
220 </assert_contents>
221 </output>
222 </test>
223 </tests>
224 <help>
225 <![CDATA[
226 .. class:: infomark
227
228 **What it does**
229
230 This tool converts parameter and topology files that represent a solvated complex into parameter files for the ligand, receptor, complex and solvated complex in AMBER prmtop format. These files are needed for MMPBSA calculations.
231
232 .. class:: infomark
233
234 **How it works**
235
236 AmberTools ParmEd is used to strip unneeded atoms and save out the parameter files. The stripmasks are defined by the user.
237
238 .. class:: infomark
239
240 **Outputs created**
241
242 prmtop files for the ligand, receptor, complex and solvated complex.
243
244 .. class:: infomark
245
246 **User guide and documentation**
247
248 - The `AmberTools Manual`_
249 - The `Parmed Documentation`_
250
251
252 .. _`AmberTools Manual`: https://ambermd.org/doc12/Amber18.pdf
253 .. _`Parmed Documentation`: https://parmed.github.io/ParmEd/html/index.html
254
255
256 ]]>
257 </help>
258 <expand macro="citations">
259 <citation type="bibtex">@misc{parmed_2020, author = {ParmEd}, title = {ParmEd/ParmEd}, url={https://github.com/ParmEd/ParmEd}, abstract = {Parameter/topology editor and molecular simulator. Contribute to ParmEd/ParmEd development by creating an
260 account on GitHub.}, urldate = {2020-04-03}, publisher = {GitHub}, year = {2020}, month = mar, }</citation>
261 </expand>
262 </tool>