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comparison smina.xml @ 2:958fa7ba4715 draft

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planemo upload commit 489ad526806f22eefcb73e8d8efe44d648e8185e-dirty
author marpiech
date Wed, 14 Sep 2016 09:47:48 -0400
parents dc6fb5c5d4c8
children 8c2e85bb2ce9
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1:dc6fb5c5d4c8 2:958fa7ba4715
3 <stdio> 3 <stdio>
4 <exit_code range="1:" /> 4 <exit_code range="1:" />
5 </stdio> 5 </stdio>
6 <command> 6 <command>
7 <![CDATA[ 7 <![CDATA[
8 cat $receptor > receptor.pdbqt; 8 cat $input.receptor > receptor.pdbqt;
9 cat $ligand > ligand.pdbqt; 9 cat $input.ligand > ligand.pdbqt;
10 $__tool_directory__/tools/smina/smina.static 10 $__tool_directory__/tools/smina/smina.static
11 --receptor receptor.pdbqt 11 --receptor receptor.pdbqt
12 --ligand ligand.pdbqt 12 --ligand ligand.pdbqt
13 13
14 #if $flex 14 #if $input.flex
15 --flex $flex 15 --flex $input.flex
16 #end if 16 #end if
17 #if $flexres 17 #if $input.flexres
18 --flexres $flexres 18 --flexres $input.flexres
19 #end if 19 #end if
20 #if $flexdist_ligand 20 #if $input.flexdist_ligand
21 --flexdist_ligand $flexdist_ligand 21 --flexdist_ligand $input.flexdist_ligand
22 #end if 22 #end if
23 #if $flexdist 23 #if $input.flexdist
24 --flexdist $flexdist 24 --flexdist $input.flexdist
25 #end if 25 #end if
26 26
27 --center_x $center_x 27 --center_x $search_space.center_x
28 --center_y $center_y 28 --center_y $search_space.center_y
29 --center_z $center_z 29 --center_z $search_space.center_z
30 --size_x $size_x 30 --size_x $search_space.size_x
31 --size_y $size_y 31 --size_y $search_space.size_y
32 --size_z $size_z 32 --size_z $search_space.size_z
33 33
34 #if $autobox_ligand 34 #if $search_space.autobox_ligand
35 --autobox_ligand $autobox_ligand 35 --autobox_ligand $search_space.autobox_ligand
36 #end if 36 #end if
37 #if $autobox_add 37 #if $search_space.autobox_add
38 --autobox_add $autobox_add 38 --autobox_add $search_space.autobox_add
39 #end if 39 #end if
40 #if $no_lig=="true" 40 #if $search_space.no_lig=="true"
41 --no_lig 41 --no_lig
42 #end if 42 #end if
43 43
44 --scoring $scoring 44 --out ligand_out.pdbqt
45 #if $custom_scoring 45 #if $output_sect.out_flex=="true"
46 --custom_scoring $custom_scoring 46 --out_flex output_flex
47 #end if 47 #end if
48 #if $custom_atoms 48 #if $output_sect.log=="true"
49 --custom_atoms $custom_atoms 49 --log output_log
50 #end if 50 #end if
51 #if $score_only=="true" 51 #if $output_sect.atom_terms=="true"
52 --atom_terms output_atom_terms
53 #end if
54 #if $output_sect.atom_term_data=="true"
55 --atom_term_data
56 #end if
57
58 --scoring $scoring_and_minimization.scoring
59 #if $scoring_and_minimization.custom_scoring
60 --custom_scoring $scoring_and_minimization.custom_scoring
61 #end if
62 #if $scoring_and_minimization.custom_atoms
63 --custom_atoms $scoring_and_minimization.custom_atoms
64 #end if
65 #if $scoring_and_minimization.score_only=="true"
52 --score_only 66 --score_only
53 #end if 67 #end if
54 #if $local_only=="true" 68 #if $scoring_and_minimization.local_only=="true"
55 --local_only 69 --local_only
56 #end if 70 #end if
57 #if $minimize=="true" 71 #if $scoring_and_minimization.minimize=="true"
58 --minimize 72 --minimize
59 #end if 73 #end if
60 #if $randomize_only=="true" 74 #if $scoring_and_minimization.randomize_only=="true"
61 --randomize_only 75 --randomize_only
62 #end if 76 #end if
63 #if $minimize_iters 77 --minimize_iters $scoring_and_minimization.minimize_iters
64 --minimize_iters $minimize_iters 78 #if $scoring_and_minimization.accurate_line=="true"
65 #end if
66 #if $accurate_line=="true"
67 --accurate_line 79 --accurate_line
68 #end if 80 #end if
69 #if $minimize_early_term=="true" 81 #if $scoring_and_minimization.minimize_early_term=="true"
70 --minimize_early_term 82 --minimize_early_term
71 #end if 83 #end if
72 #if $approximation 84 #if $scoring_and_minimization.approximation
73 --approximation $approximation 85 --approximation $scoring_and_minimization.approximation
74 #end if 86 #end if
75 #if $factor 87 #if $scoring_and_minimization.factor
76 --factor $factor 88 --factor $scoring_and_minimization.factor
77 #end if 89 #end if
78 #if $force_cap 90 #if $scoring_and_minimization.force_cap
79 --force_cap $force_cap 91 --force_cap $scoring_and_minimization.force_cap
80 #end if 92 #end if
81 #if $user_grid 93 #if $scoring_and_minimization.user_grid
82 --user_grid $user_grid 94 --user_grid $scoring_and_minimization.user_grid
83 #end if 95 #end if
84 #if $user_grid_lambda 96 --user_grid_lambda $scoring_and_minimization.user_grid_lambda
85 --user_grid_lambda $user_grid_lambda 97 #if $scoring_and_minimization.print_terms=="true"
86 #end if
87 #if $print_terms=="true"
88 --print_terms 98 --print_terms
89 #end if 99 #end if
90 #if $print_atom_types=="true" 100 #if $scoring_and_minimization.print_atom_types=="true"
91 --print_atom_types 101 --print_atom_types
92 #end if 102 #end if
93 103
94 #if $out 104 #if $misc.cpu
95 --out $out 105 --cpu $misc.cpu
96 #end if 106 #end if
97 #if $out_flex 107 #if $misc.seed
98 --out_flex $out_flex 108 --seed $misc.seed
99 #end if 109 #end if
100 #if $atom_terms 110 --exhaustiveness $misc.exhaustiveness
101 --atom_terms $atom_terms 111 --num_modes $misc.num_modes
102 #end if 112 --energy_range $misc.energy_range
103 #if $atom_term_data=="true" 113 --min_rmsd_filter $misc.min_rmsd_filter
104 --atom_term_data 114 #if $misc.addH=="false"
105 #end if
106
107 #if $seed
108 --seed $seed
109 #end if
110 #if $exhaustiveness
111 --exhaustiveness $exhaustiveness
112 #end if
113 #if $num_modes
114 --num_modes $num_modes
115 #end if
116 #if $energy_range
117 --energy_range $energy_range
118 #end if
119 #if $min_rmsd_filter
120 --min_rmsd_filter $min_rmsd_filter
121 #end if
122 #if $addH=="false"
123 --addH false 115 --addH false
124 #end if 116 #end if
125 117 ;
126 > $stand_output; 118 #if $output_sect.out_flex=="true" #
127 #if $out # cat $out > $out_output; #end if # 119 cat output_flex > $out_flex_output;
128 #if $out_flex # cat $out_flex > $out_flex_output; #end if # 120 #end if #
129 #if $atom_terms # cat $atom_terms > $atom_terms_output; #end if # 121 #if $output_sect.log=="true" #
130 122 cat output_log > $output_log;
131 cat $stand_output > /tmp/ouput 123 #end if #
124 #if $output_sect.atom_terms=="true" #
125 cat output_atom_terms > $atom_terms_output;
126 #end if #
127
128 cat ligand_out.pdbqt > $output
132 ]]> 129 ]]>
133 </command> 130 </command>
134 <inputs> 131 <inputs>
135 <param name="receptor" type="data" format="pdbqt" label="rigid part of the receptore" help="(--receptor)"/> 132 <section name="input" title="Input" expanded="True">
136 <param name="ligand" type="data" format="data" label="ligand(s)" help="(--ligand)"/> 133 <param name="receptor" type="data" format="pdbqt" label="rigid part of the receptore" help="(--receptor)"/>
137 134 <param name="ligand" type="data" format="data" label="ligand(s)" help="(--ligand)"/>
138 <param name="flex" type="data" format="pdbqt" label="flexible side chains, if any" optional="true" help="(--flex"/> 135 <param name="flex" type="data" format="pdbqt" label="flexible side chains, if any" optional="true" help="(--flex)"/>
139 <param name="flexres" type="text" label="flexible side chains specified by comma separated list of chain:resid" optional="true" help="(--flexres)"/> 136 <param name="flexres" type="text" label="flexible side chains specified by comma separated list of chain:resid" optional="true" help="(--flexres)"/>
140 <param name="flexdist_ligand" type="data" format="data" label="Ligand to use for flexdist" optional="true" help="(--flexdist_ligand)"/> 137 <param name="flexdist_ligand" type="data" format="data" label="Ligand to use for flexdist" optional="true" help="(--flexdist_ligand)"/>
141 <param name="flexdist" type="float" label="set all side chains within specified distance to flexdist_ligand to flexible" optional="true" help="(flexdist)"/> 138 <param name="flexdist" type="float" label="set all side chains within specified distance to flexdist_ligand to flexible" optional="true" help="(--flexdist)"/>
142 139 </section>
143 <param name="center_x" type="float" value="0" label="X coordinate of the center" help="(--center_x)"/> 140 <section name="search_space" title="Search space" expanded="True">
144 <param name="center_y" type="float" value="0" label="Y coordinate of the center" help="(--center_y)"/> 141 <param name="center_x" type="float" value="0" label="X coordinate of the center" help="(--center_x)"/>
145 <param name="center_z" type="float" value="0" label="Z coordinate of the center" help="(--center_z)"/> 142 <param name="center_y" type="float" value="0" label="Y coordinate of the center" help="(--center_y)"/>
146 <param name="size_x" type="integer" value="1" label="size in the X dimension" help="(--size_x)"/> 143 <param name="center_z" type="float" value="0" label="Z coordinate of the center" help="(--center_z)"/>
147 <param name="size_y" type="integer" value="1" label="size in the Y dimension" help="(--size_y)"/> 144 <param name="size_x" type="integer" value="1" label="size in the X dimension" help="(--size_x)"/>
148 <param name="size_z" type="integer" value="1" label="size in the Z dimension" help="(--size_z)"/> 145 <param name="size_y" type="integer" value="1" label="size in the Y dimension" help="(--size_y)"/>
149 146 <param name="size_z" type="integer" value="1" label="size in the Z dimension" help="(--size_z)"/>
150 <param name="autobox_ligand" type="data" format="data" label="Ligand to use for autobox" optional="true" help="(--autobox_ligand)"/> 147
151 <param name="autobox_add" type="float" label="Amount of buffer space to add to auto-generated box text(default +4 on all six sides)" optional="true" help="(autobox_add)"/> 148 <param name="autobox_ligand" type="data" format="data" label="Ligand to use for autobox" optional="true" help="(--autobox_ligand)"/>
152 <param name="no_lig" type="select" label="no ligand; for sampling/minimizing flexible residues (Type true if you want to use it)" help="(no_lig)"> 149 <param name="autobox_add" type="float" label="Amount of buffer space to add to auto-generated box text(default +4 on all six sides)" optional="true" help="(--autobox_add)"/>
153 <option value="false" selected="true">Don't use this option</option> 150 <param name="no_lig" type="select" label="no ligand; for sampling/minimizing flexible residues (Type true if you want to use it)" help="(--no_lig)">
154 <option value="true">Use this option</option> 151 <option value="false" selected="true">Do not use this option</option>
155 </param> 152 <option value="true">Use this option</option>
156 153 </param>
157 <param name="scoring" type="select" label="specify alternative builtin scoring function" help="(--scoring)"> 154 </section>
158 <option value="default" selected="true">default</option> 155 <section name="output_sect" title="Output" >
159 <option value="ad4_scoring">ad4_scoring</option> 156 <param name="out_flex" type="select" label="Write flexible receptor residues" help="(--out_flex)">
160 <option value="dkoes_fast">dkoes_fast</option> 157 <option value="false" selected="true" >No </option>
161 <option value="dkoes_scoring">dkoes_scoring</option> 158 <option value="true" >Yes </option>
162 <option value="dkoes_scoring_old">dkoes_scoring_old</option> 159 </param>
163 <option value="vina">vina</option> 160 <param name="log" type="select" label="Write log file" help="(--log)">
164 <option value="vinardo">vinardo</option> 161 <option value="false" selected="true" >No </option>
165 </param> 162 <option value="true" >Yes </option>
166 <param name="custom_scoring" type="data" format="data" label="custom scoring function file" optional="true" help="(--custom_scoring)"/> 163 </param>
167 <param name="custom_atoms" type="data" format="data" label="custom atom type parameters file" optional="true" help="(--custom_atoms)"/> 164 <param name="atom_terms" type="select" label="Write per-atom interaction term values" help="(--atom_terms)">
168 <param name="score_only" type="select" label="score provided ligand pose" help="(--score_only)"> 165 <option value="false" selected="true" >No </option>
169 <option value="false" selected="true">Don't use this option</option> 166 <option value="true" >Yes </option>
170 <option value="true">Use this option</option> 167 </param>
171 </param> 168 <param name="atom_term_data" type="select" label="embedded per-atom interaction terms in output sd data" help="(--atom_term_data)">
172 <param name="local_only" type="select" label="local search only using autobox (you probably want to use --minimize)" help="(--local_only)"> 169 <option value="false" selected="true">Do not use this option</option>
173 <option value="false" selected="true">Don't use this option</option> 170 <option value="true">Use this option</option>
174 <option value="true">Use this option</option> 171 </param>
175 </param> 172 </section>
176 <param name="minimize" type="select" label="energy minimization" help="(--minimize)"> 173 <section name="scoring_and_minimization" title="Scoring and minimization options" >
177 <option value="false" selected="true">Don't use this option</option> 174 <param name="scoring" type="select" label="specify alternative builtin scoring function" help="(--scoring)">
178 <option value="true">Use this option</option> 175 <option value="default" selected="true">default</option>
179 </param> 176 <option value="ad4_scoring">ad4_scoring</option>
180 <param name="randomize_only" type="select" label="generate random poses, attempting to avoid clashes" help="(--randomize_only)"> 177 <option value="dkoes_fast">dkoes_fast</option>
181 <option value="false" selected="true">Don't use this option</option> 178 <option value="dkoes_scoring">dkoes_scoring</option>
182 <option value="true">Use this option</option> 179 <option value="dkoes_scoring_old">dkoes_scoring_old</option>
183 </param> 180 <option value="vina">vina</option>
184 <param name="minimize_iters" type="integer" label="number iterations of steepest descent; default scales with rotors and usually isn't sufficient for convergence" optional="true" help="(--minimize_iters)"/> 181 <option value="vinardo">vinardo</option>
185 <param name="accurate_line" type="select" label="use accurate line search" help="(--accurate_line)"> 182 </param>
186 <option value="false" selected="true">Don't use this option</option> 183 <param name="custom_scoring" type="data" format="data" label="custom scoring function file" optional="true" help="(--custom_scoring)"/>
187 <option value="true">Use this option</option> 184 <param name="custom_atoms" type="data" format="data" label="custom atom type parameters file" optional="true" help="(--custom_atoms)"/>
188 </param> 185 <param name="score_only" type="select" label="score provided ligand pose" help="(--score_only)">
189 <param name="minimize_early_term" type="select" label="Stop minimization before convergence conditions are fully met" help="(--minimize_early_term)"> 186 <option value="false" selected="true">Do not use this option</option>
190 <option value="false" selected="true">Don't use this option</option> 187 <option value="true">Use this option</option>
191 <option value="true">Use this option</option> 188 </param>
192 </param> 189 <param name="local_only" type="select" label="local search only using autobox (you probably want to use --minimize)" help="(--local_only)">
193 <param name="approximation" type="select" label="approximation (linear, spline, or exact) to use" optional="true" help="(--approximation)"> 190 <option value="false" selected="true">Do not use this option</option>
194 <option value="linear">linear</option> 191 <option value="true">Use this option</option>
195 <option value="spline">spline</option> 192 </param>
196 <option value="exact">exact</option> 193 <param name="minimize" type="select" label="energy minimization" help="(--minimize)">
197 </param> 194 <option value="false" selected="true">Do not use this option</option>
198 <param name="factor" type="float" label="approximation factor: higher results in a finer-grained approximation" optional="true" help="(--factor)"> 195 <option value="true">Use this option</option>
199 <validator type="in_range" min="0"/> 196 </param>
200 </param> 197 <param name="randomize_only" type="select" label="generate random poses, attempting to avoid clashes" help="(--randomize_only)">
201 <param name="force_cap" type="float" label="max allowed force; lower values more gently minimize clashing structures" optional="true" help="(--force_cap)"/> 198 <option value="false" selected="true">Do not use this option</option>
202 <param name="user_grid" type="float" label="Autodock map file for user grid data based calculations" optional="true" help="(--user_grid)"/> 199 <option value="true">Use this option</option>
203 <param name="user_grid_lambda" type="float" label="Scales user_grid and functional scoring" optional="true" help="(--user_grid)"/> 200 </param>
204 <param name="print_terms" type="select" label="Print all available terms with default parameterizations" help="(--print_terms)"> 201 <param name="minimize_iters" type="integer" value="0" label="number iterations of steepest descent; default scales with rotors and usually isn't sufficient for convergence" help="(--minimize_iters)"/>
205 <option value="false" selected="true">Don't use this option</option> 202 <param name="accurate_line" type="select" label="use accurate line search" help="(--accurate_line)">
206 <option value="true">Use this option</option> 203 <option value="false" selected="true">Do not use this option</option>
207 </param> 204 <option value="true">Use this option</option>
208 <param name="print_atom_types" type="select" label="Print all available atom types" help="(--print_atom_types)"> 205 </param>
209 <option value="false" selected="true">Don't use this option</option> 206 <param name="minimize_early_term" type="select" label="Stop minimization before convergence conditions are fully met" help="(--minimize_early_term)">
210 <option value="true">Use this option</option> 207 <option value="false" selected="true">Do not use this option</option>
211 </param> 208 <option value="true">Use this option</option>
212 209 </param>
213 <param name="out" type="text" label="output file name, format taken from file extension" optional="true" help="(--out)"/> 210 <param name="approximation" type="select" label="approximation (linear, spline, or exact) to use" optional="true" help="(--approximation)">
214 <param name="out_flex" type="text" label="output file for flexible receptor residues" optional="true" help="(--out_flex)"/> 211 <option value="linear">linear</option>
215 <param name="atom_terms" type="text" label="output file for flexible receptor residues" optional="true" help="(--atom_terms)"/> 212 <option value="spline">spline</option>
216 <param name="atom_term_data" type="select" label="embedded per-atom interaction terms in output sd data" help="(--atom_term_data)"> 213 <option value="exact">exact</option>
217 <option value="false" selected="true">Don't use this option</option> 214 </param>
218 <option value="true">Use this option</option> 215 <param name="factor" type="float" label="approximation factor: higher results in a finer-grained approximation" optional="true" help="(--factor)">
219 </param> 216 <validator type="in_range" min="0"/>
220 217 </param>
221 <param name="seed" type="float" label="explicit random seed" optional="true" help="(--seed)"/> 218 <param name="force_cap" type="float" label="max allowed force; lower values more gently minimize clashing structures" optional="true" help="(--force_cap)"/>
222 <param name="exhaustiveness" type="integer" label="exhaustiveness of the global search (roughly proportional to time)" optional="true" help="(--exhaustiveness)"/> 219 <param name="user_grid" type="float" label="Autodock map file for user grid data based calculations" optional="true" help="(--user_grid)"/>
223 <param name="num_modes" type="integer" label="exhaustiveness of the global search (roughly proportional to time)" optional="true" help="(--num_modes)"> 220 <param name="user_grid_lambda" type="float" value="-1" label="Scales user_grid and functional scoring" help="(--user_grid_lambda)"/>
224 <validator type="in_range" min="1"/> 221 <param name="print_terms" type="select" label="Print all available terms with default parameterizations" help="(--print_terms)">
225 </param> 222 <option value="false" selected="true">Do not use this option</option>
226 <param name="energy_range" type="float" label="maximum energy difference between the best binding mode and the worst one displayed (kcal/mol)" optional="true" help="(--energy_range)"/> 223 <option value="true">Use this option</option>
227 <param name="min_rmsd_filter" type="float" label="rmsd value used to filter final poses to remove redundancy" optional="true" help="(--min_rmsd_filter)"/> 224 </param>
228 <param name="addH" type="select" label="automatically add hydrogens in ligands (on by default)" help="(--addH)"> 225 <param name="print_atom_types" type="select" label="Print all available atom types" help="(--print_atom_types)">
229 <option value="false" >Don't use this option</option> 226 <option value="false" selected="true">Do not use this option</option>
230 <option value="true" selected="true">Use this option</option> 227 <option value="true">Use this option</option>
231 </param> 228 </param>
232 229 </section>
230 <section name="misc" title="Misc" >
231 <param name="cpu" type="integer" label="the number of CPUs to use (the default is to try to detect the number of CPUs or, failing that, use 1)" optional="true" help="(--cpu)"/>
232 <param name="seed" type="float" label="explicit random seed" optional="true" help="(--seed)"/>
233 <param name="exhaustiveness" type="integer" value="8" label="exhaustiveness of the global search (roughly proportional to time)" help="(--exhaustiveness)"/>
234 <param name="num_modes" type="integer" value="9" label="exhaustiveness of the global search (roughly proportional to time)" help="(--num_modes)">
235 <validator type="in_range" min="1"/>
236 </param>
237 <param name="energy_range" type="float" value="3" label="maximum energy difference between the best binding mode and the worst one displayed (kcal/mol)" help="(--energy_range)"/>
238 <param name="min_rmsd_filter" type="float" value="1" label="rmsd value used to filter final poses to remove redundancy" help="(--min_rmsd_filter)"/>
239 <param name="addH" type="select" label="automatically add hydrogens in ligands (on by default)" help="(--addH)">
240 <option value="false" >Do not use this option</option>
241 <option value="true" selected="true">Use this option</option>
242 </param>
243 </section>
233 </inputs> 244 </inputs>
234 <outputs> 245 <outputs>
235 <data name="stand_output" format="data" /> 246 <data name="output" format="txt" />
236 <data name="out_output" format="data" /> 247 <data name="out_flex_output" format="txt" label="smina: flexible receptor residues">
237 <data name="out_flex_output" format="data" /> 248 <filter>output_sect['out_flex']=="true"</filter>
238 <data name="atom_terms_output" format="data" /> 249 </data>
250 <data name="output_log" format="txt" label="smina: log file">
251 <filter>output_sect['log']=="true"</filter>
252 </data>
253 <data name="atom_terms_output" format="txt" label="smima: per-atom interaction term values">
254 <filter>output_sect['atom_terms']=="true"</filter>
255 </data>
239 </outputs> 256 </outputs>
240 <tests> 257 <tests>
241 <test> 258 <test>
242 <param name="receptor" value="smina/protein.pdbqt" /> 259 <param name="receptor" value="smina/protein.pdbqt" />
243 <param name="ligand" value="smina/ligand.pdbqt" /> 260 <param name="ligand" value="smina/ligand.pdbqt" />
247 <param name="size_x" value="22" /> 264 <param name="size_x" value="22" />
248 <param name="size_y" value="24" /> 265 <param name="size_y" value="24" />
249 <param name="size_z" value="28" /> 266 <param name="size_z" value="28" />
250 <output name="stand_output" > 267 <output name="stand_output" >
251 <assert_contents> 268 <assert_contents>
252 <has_text_matching expression="Using random seed" /> 269 <has_text_matching expression="END" />
253 </assert_contents> 270 </assert_contents>
254 </output> 271 </output>
255 </test> 272 </test>
256 </tests> 273 </tests>
257 <help> 274 <help>
333 350
334 ]]> 351 ]]>
335 </help> 352 </help>
336 <citations> 353 <citations>
337 <citation type="bibtex"> 354 <citation type="bibtex">
338 @misc{url = {https://sourceforge.net/projects/smina/}, } 355 @article{Koes2013,
356 doi = {10.1021/ci300604z},
357 url = {http://dx.doi.org/10.1021/ci300604z},
358 year = {2013},
359 month = {aug},
360 publisher = {American Chemical Society ({ACS})},
361 volume = {53},
362 number = {8},
363 pages = {1893--1904},
364 author = {David Ryan Koes and Matthew P. Baumgartner and Carlos J. Camacho},
365 title = {Lessons Learned in Empirical Scoring with smina from the {CSAR} 2011 Benchmarking Exercise},
366 journal = {Journal of Chemical Information and Modeling}
367 }
368 @misc{url = {https://sourceforge.net/projects/smina/}}
339 </citation> 369 </citation>
340 </citations> 370 </citations>
341 </tool> 371 </tool>