1
|
1 {
|
|
2 "a_galaxy_workflow": "true",
|
|
3 "annotation": "Water finding, contraints generation, pocket detection and grid building",
|
|
4 "format-version": "0.1",
|
|
5 "name": "Docking-preparation: constraints, water, pocket-detection",
|
|
6 "steps": {
|
|
7 "0": {
|
|
8 "annotation": "",
|
|
9 "id": 0,
|
|
10 "input_connections": {},
|
|
11 "inputs": [
|
|
12 {
|
|
13 "description": "",
|
|
14 "name": "Receptor"
|
|
15 }
|
|
16 ],
|
|
17 "name": "Input dataset",
|
|
18 "outputs": [],
|
|
19 "position": {
|
|
20 "left": 200,
|
|
21 "top": 251.5
|
|
22 },
|
|
23 "tool_errors": null,
|
|
24 "tool_id": null,
|
|
25 "tool_state": "{\"name\": \"Receptor\"}",
|
|
26 "tool_version": null,
|
|
27 "type": "data_input",
|
|
28 "user_outputs": []
|
|
29 },
|
|
30 "1": {
|
|
31 "annotation": "",
|
|
32 "id": 1,
|
|
33 "input_connections": {},
|
|
34 "inputs": [
|
|
35 {
|
|
36 "description": "",
|
|
37 "name": "pdb-file w/ water molecules"
|
|
38 }
|
|
39 ],
|
|
40 "name": "Input dataset",
|
|
41 "outputs": [],
|
|
42 "position": {
|
|
43 "left": 198,
|
|
44 "top": 325
|
|
45 },
|
|
46 "tool_errors": null,
|
|
47 "tool_id": null,
|
|
48 "tool_state": "{\"name\": \"pdb-file w/ water molecules\"}",
|
|
49 "tool_version": null,
|
|
50 "type": "data_input",
|
|
51 "user_outputs": []
|
|
52 },
|
|
53 "2": {
|
|
54 "annotation": "",
|
|
55 "id": 2,
|
|
56 "input_connections": {},
|
|
57 "inputs": [
|
|
58 {
|
|
59 "description": "",
|
|
60 "name": "Reference ligand"
|
|
61 }
|
|
62 ],
|
|
63 "name": "Input dataset",
|
|
64 "outputs": [],
|
|
65 "position": {
|
|
66 "left": 254.5,
|
|
67 "top": 491
|
|
68 },
|
|
69 "tool_errors": null,
|
|
70 "tool_id": null,
|
|
71 "tool_state": "{\"name\": \"Reference ligand\"}",
|
|
72 "tool_version": null,
|
|
73 "type": "data_input",
|
|
74 "user_outputs": []
|
|
75 },
|
|
76 "3": {
|
|
77 "annotation": "",
|
|
78 "id": 3,
|
|
79 "input_connections": {
|
|
80 "i": {
|
|
81 "id": 0,
|
|
82 "output_name": "output"
|
|
83 }
|
|
84 },
|
|
85 "inputs": [],
|
|
86 "name": "ProteinProtonator",
|
|
87 "outputs": [
|
|
88 {
|
|
89 "name": "o",
|
|
90 "type": "pdb"
|
|
91 }
|
|
92 ],
|
|
93 "position": {
|
|
94 "left": 388.5,
|
|
95 "top": 255
|
|
96 },
|
|
97 "tool_errors": null,
|
|
98 "tool_id": "proteinprotonator",
|
|
99 "tool_state": "{\"i\": \"null\", \"input\": \"null\", \"ph\": \"\\\"7.0\\\"\", \"__page__\": 0}",
|
|
100 "tool_version": "1.0",
|
|
101 "type": "tool",
|
|
102 "user_outputs": []
|
|
103 },
|
|
104 "4": {
|
|
105 "annotation": "",
|
|
106 "id": 4,
|
|
107 "input_connections": {
|
|
108 "rec": {
|
|
109 "id": 3,
|
|
110 "output_name": "o"
|
|
111 },
|
|
112 "rl": {
|
|
113 "id": 2,
|
|
114 "output_name": "output"
|
|
115 },
|
|
116 "wat": {
|
|
117 "id": 1,
|
|
118 "output_name": "output"
|
|
119 }
|
|
120 },
|
|
121 "inputs": [],
|
|
122 "name": "WaterFinder",
|
|
123 "outputs": [
|
|
124 {
|
|
125 "name": "o",
|
|
126 "type": "pdb"
|
|
127 }
|
|
128 ],
|
|
129 "position": {
|
|
130 "left": 600,
|
|
131 "top": 212
|
|
132 },
|
|
133 "tool_errors": null,
|
|
134 "tool_id": "waterfinder",
|
|
135 "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"input1\": \"null\", \"ai\": \"\\\"False\\\"\", \"ini\": \"null\", \"water_pdb\": \"null\", \"rl\": \"null\", \"rec\": \"null\", \"wat\": \"null\"}",
|
|
136 "tool_version": "1.0",
|
|
137 "type": "tool",
|
|
138 "user_outputs": []
|
|
139 },
|
|
140 "5": {
|
|
141 "annotation": "",
|
|
142 "id": 5,
|
|
143 "input_connections": {
|
|
144 "rec": {
|
|
145 "id": 4,
|
|
146 "output_name": "o"
|
|
147 },
|
|
148 "rl": {
|
|
149 "id": 2,
|
|
150 "output_name": "output"
|
|
151 }
|
|
152 },
|
|
153 "inputs": [],
|
|
154 "name": "ConstraintsFinder",
|
|
155 "outputs": [
|
|
156 {
|
|
157 "name": "o",
|
|
158 "type": "ini"
|
|
159 }
|
|
160 ],
|
|
161 "position": {
|
|
162 "left": 544.5,
|
|
163 "top": 425
|
|
164 },
|
|
165 "tool_errors": null,
|
|
166 "tool_id": "constraintsfinder",
|
|
167 "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"input1\": \"null\", \"ini\": \"null\", \"rec\": \"null\", \"rl\": \"null\", \"configfile_input\": \"null\"}",
|
|
168 "tool_version": "1.0",
|
|
169 "type": "tool",
|
|
170 "user_outputs": []
|
|
171 },
|
|
172 "6": {
|
|
173 "annotation": "",
|
|
174 "id": 6,
|
|
175 "input_connections": {
|
|
176 "i": {
|
|
177 "id": 4,
|
|
178 "output_name": "o"
|
|
179 }
|
|
180 },
|
|
181 "inputs": [],
|
|
182 "name": "ProteinCheck",
|
|
183 "outputs": [
|
|
184 {
|
|
185 "name": "o",
|
|
186 "type": "pdf"
|
|
187 }
|
|
188 ],
|
|
189 "position": {
|
|
190 "left": 912.5,
|
|
191 "top": 244
|
|
192 },
|
|
193 "tool_errors": null,
|
|
194 "tool_id": "proteincheck",
|
|
195 "tool_state": "{\"i\": \"null\", \"ignorebrokenchains\": \"\\\"False\\\"\", \"__page__\": 0, \"input\": \"null\", \"bc\": \"\\\"False\\\"\"}",
|
|
196 "tool_version": "1.0",
|
|
197 "type": "tool",
|
|
198 "user_outputs": []
|
|
199 },
|
|
200 "7": {
|
|
201 "annotation": "",
|
|
202 "id": 7,
|
|
203 "input_connections": {
|
|
204 "ini": {
|
|
205 "id": 5,
|
|
206 "output_name": "o"
|
|
207 },
|
|
208 "rec": {
|
|
209 "id": 4,
|
|
210 "output_name": "o"
|
|
211 },
|
|
212 "rl": {
|
|
213 "id": 2,
|
|
214 "output_name": "output"
|
|
215 }
|
|
216 },
|
|
217 "inputs": [],
|
|
218 "name": "PocketDetector",
|
|
219 "outputs": [
|
|
220 {
|
|
221 "name": "o",
|
|
222 "type": "ini"
|
|
223 }
|
|
224 ],
|
|
225 "position": {
|
|
226 "left": 773,
|
|
227 "top": 420
|
|
228 },
|
|
229 "tool_errors": null,
|
|
230 "tool_id": "pocketdetector",
|
|
231 "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"input1\": \"null\", \"ini\": \"null\", \"rec\": \"null\", \"rl\": \"null\", \"configfile_input\": \"null\"}",
|
|
232 "tool_version": "1.0",
|
|
233 "type": "tool",
|
|
234 "user_outputs": []
|
|
235 },
|
|
236 "8": {
|
|
237 "annotation": "",
|
|
238 "id": 8,
|
|
239 "input_connections": {
|
|
240 "ini": {
|
|
241 "id": 7,
|
|
242 "output_name": "o"
|
|
243 },
|
|
244 "rec": {
|
|
245 "id": 4,
|
|
246 "output_name": "o"
|
|
247 },
|
|
248 "rl": {
|
|
249 "id": 2,
|
|
250 "output_name": "output"
|
|
251 }
|
|
252 },
|
|
253 "inputs": [],
|
|
254 "name": "GridBuilder",
|
|
255 "outputs": [
|
|
256 {
|
|
257 "name": "grd",
|
|
258 "type": "grd.gz"
|
|
259 }
|
|
260 ],
|
|
261 "position": {
|
|
262 "left": 982.5,
|
|
263 "top": 425
|
|
264 },
|
|
265 "tool_errors": null,
|
|
266 "tool_id": "gridbuilder",
|
|
267 "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"input1\": \"null\", \"configfile\": \"null\", \"ini\": \"null\", \"rl\": \"null\", \"rec\": \"null\"}",
|
|
268 "tool_version": "1.0",
|
|
269 "type": "tool",
|
|
270 "user_outputs": []
|
|
271 }
|
|
272 }
|
|
273 } |