Codebase list chemical-structures / cf6595c
gone further in the python3 migration Georges Khaznadar 4 years ago
3 changed file(s) with 816 addition(s) and 532 deletion(s). Raw diff Collapse all Expand all
+727
-532
debian/patches/build-xyz-files.patch less more
00 lines added to build .xyz files from the original data
1 --- a/src/alcohols/CMakeLists.txt
2 +++ b/src/alcohols/CMakeLists.txt
3 @@ -43,6 +43,13 @@
4 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
5 )
6 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
7 + # Generate xyz files
8 + set(xyz_FILE "${cml_WE}.xyz")
9 + add_custom_command(TARGET ${CHEM_GROUP}
10 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
11 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
12 + )
13 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
14 # Generate smi files
15 set(smi_FILE "${cml_WE}.smi")
16 add_custom_command(TARGET ${CHEM_GROUP}
17 --- a/src/water/CMakeLists.txt
18 +++ b/src/water/CMakeLists.txt
19 @@ -43,6 +43,13 @@
20 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
21 )
22 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
23 + # Generate xyz files
24 + set(xyz_FILE "${cml_WE}.xyz")
25 + add_custom_command(TARGET ${CHEM_GROUP}
26 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
27 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
28 + )
29 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
30 # Generate smi files
31 set(smi_FILE "${cml_WE}.smi")
32 add_custom_command(TARGET ${CHEM_GROUP}
33 --- a/src/acid_anhydrides/CMakeLists.txt
34 +++ b/src/acid_anhydrides/CMakeLists.txt
35 @@ -43,6 +43,13 @@
36 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
37 )
38 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
39 + # Generate xyz files
40 + set(xyz_FILE "${cml_WE}.xyz")
41 + add_custom_command(TARGET ${CHEM_GROUP}
42 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
43 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
44 + )
45 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
46 # Generate smi files
47 set(smi_FILE "${cml_WE}.smi")
48 add_custom_command(TARGET ${CHEM_GROUP}
49 --- a/src/aldehydes/CMakeLists.txt
50 +++ b/src/aldehydes/CMakeLists.txt
51 @@ -43,6 +43,13 @@
52 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
53 )
54 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
55 + # Generate xyz files
56 + set(xyz_FILE "${cml_WE}.xyz")
57 + add_custom_command(TARGET ${CHEM_GROUP}
58 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
59 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
60 + )
61 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
62 # Generate smi files
63 set(smi_FILE "${cml_WE}.smi")
64 add_custom_command(TARGET ${CHEM_GROUP}
65 --- a/src/alkanes/CMakeLists.txt
66 +++ b/src/alkanes/CMakeLists.txt
67 @@ -43,6 +43,13 @@
68 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
69 )
70 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
71 + # Generate xyz files
72 + set(xyz_FILE "${cml_WE}.xyz")
73 + add_custom_command(TARGET ${CHEM_GROUP}
74 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
75 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
76 + )
77 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
78 # Generate smi files
79 set(smi_FILE "${cml_WE}.smi")
80 add_custom_command(TARGET ${CHEM_GROUP}
81 --- a/src/alkenes/CMakeLists.txt
82 +++ b/src/alkenes/CMakeLists.txt
83 @@ -43,6 +43,13 @@
84 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
85 )
86 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
87 + # Generate xyz files
88 + set(xyz_FILE "${cml_WE}.xyz")
89 + add_custom_command(TARGET ${CHEM_GROUP}
90 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
91 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
92 + )
93 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
94 # Generate smi files
95 set(smi_FILE "${cml_WE}.smi")
96 add_custom_command(TARGET ${CHEM_GROUP}
97 --- a/src/alkynes/CMakeLists.txt
98 +++ b/src/alkynes/CMakeLists.txt
99 @@ -43,6 +43,13 @@
100 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
101 )
102 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
103 + # Generate xyz files
104 + set(xyz_FILE "${cml_WE}.xyz")
105 + add_custom_command(TARGET ${CHEM_GROUP}
106 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
107 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
108 + )
109 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
110 # Generate smi files
111 set(smi_FILE "${cml_WE}.smi")
112 add_custom_command(TARGET ${CHEM_GROUP}
113 --- a/src/amides/CMakeLists.txt
114 +++ b/src/amides/CMakeLists.txt
115 @@ -43,6 +43,13 @@
116 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
117 )
118 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
119 + # Generate xyz files
120 + set(xyz_FILE "${cml_WE}.xyz")
121 + add_custom_command(TARGET ${CHEM_GROUP}
122 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
123 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
124 + )
125 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
126 # Generate smi files
127 set(smi_FILE "${cml_WE}.smi")
128 add_custom_command(TARGET ${CHEM_GROUP}
129 --- a/src/amines/CMakeLists.txt
130 +++ b/src/amines/CMakeLists.txt
131 @@ -43,6 +43,13 @@
132 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
133 )
134 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
135 + # Generate xyz files
136 + set(xyz_FILE "${cml_WE}.xyz")
137 + add_custom_command(TARGET ${CHEM_GROUP}
138 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
139 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
140 + )
141 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
142 # Generate smi files
143 set(smi_FILE "${cml_WE}.smi")
144 add_custom_command(TARGET ${CHEM_GROUP}
145 --- a/src/amino_acids/CMakeLists.txt
146 +++ b/src/amino_acids/CMakeLists.txt
147 @@ -43,6 +43,13 @@
148 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
149 )
150 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
151 + # Generate xyz files
152 + set(xyz_FILE "${cml_WE}.xyz")
153 + add_custom_command(TARGET ${CHEM_GROUP}
154 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
155 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
156 + )
157 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
158 # Generate smi files
159 set(smi_FILE "${cml_WE}.smi")
160 add_custom_command(TARGET ${CHEM_GROUP}
161 --- a/src/aromatics/CMakeLists.txt
162 +++ b/src/aromatics/CMakeLists.txt
163 @@ -43,6 +43,13 @@
164 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
165 )
166 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
167 + # Generate xyz files
168 + set(xyz_FILE "${cml_WE}.xyz")
169 + add_custom_command(TARGET ${CHEM_GROUP}
170 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
171 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
172 + )
173 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
174 # Generate smi files
175 set(smi_FILE "${cml_WE}.smi")
176 add_custom_command(TARGET ${CHEM_GROUP}
177 --- a/src/carbamides/CMakeLists.txt
178 +++ b/src/carbamides/CMakeLists.txt
179 @@ -43,6 +43,13 @@
180 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
181 )
182 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
183 + # Generate xyz files
184 + set(xyz_FILE "${cml_WE}.xyz")
185 + add_custom_command(TARGET ${CHEM_GROUP}
186 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
187 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
188 + )
189 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
190 # Generate smi files
191 set(smi_FILE "${cml_WE}.smi")
192 add_custom_command(TARGET ${CHEM_GROUP}
193 --- a/src/carbohydrates/CMakeLists.txt
194 +++ b/src/carbohydrates/CMakeLists.txt
195 @@ -43,6 +43,13 @@
196 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
197 )
198 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
199 + # Generate xyz files
200 + set(xyz_FILE "${cml_WE}.xyz")
201 + add_custom_command(TARGET ${CHEM_GROUP}
202 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
203 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
204 + )
205 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
206 # Generate smi files
207 set(smi_FILE "${cml_WE}.smi")
208 add_custom_command(TARGET ${CHEM_GROUP}
209 --- a/src/carboxylic_acids/CMakeLists.txt
210 +++ b/src/carboxylic_acids/CMakeLists.txt
211 @@ -43,6 +43,13 @@
212 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
213 )
214 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
215 + # Generate xyz files
216 + set(xyz_FILE "${cml_WE}.xyz")
217 + add_custom_command(TARGET ${CHEM_GROUP}
218 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
219 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
220 + )
221 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
222 # Generate smi files
223 set(smi_FILE "${cml_WE}.smi")
224 add_custom_command(TARGET ${CHEM_GROUP}
225 --- a/src/drugs/CMakeLists.txt
226 +++ b/src/drugs/CMakeLists.txt
227 @@ -43,6 +43,13 @@
228 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
229 )
230 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
231 + # Generate xyz files
232 + set(xyz_FILE "${cml_WE}.xyz")
233 + add_custom_command(TARGET ${CHEM_GROUP}
234 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
235 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
236 + )
237 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
238 # Generate smi files
239 set(smi_FILE "${cml_WE}.smi")
240 add_custom_command(TARGET ${CHEM_GROUP}
241 --- a/src/esters/CMakeLists.txt
242 +++ b/src/esters/CMakeLists.txt
243 @@ -43,6 +43,13 @@
244 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
245 )
246 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
247 + # Generate xyz files
248 + set(xyz_FILE "${cml_WE}.xyz")
249 + add_custom_command(TARGET ${CHEM_GROUP}
250 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
251 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
252 + )
253 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
254 # Generate smi files
255 set(smi_FILE "${cml_WE}.smi")
256 add_custom_command(TARGET ${CHEM_GROUP}
257 --- a/src/ethers/CMakeLists.txt
258 +++ b/src/ethers/CMakeLists.txt
259 @@ -43,6 +43,13 @@
260 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
261 )
262 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
263 + # Generate xyz files
264 + set(xyz_FILE "${cml_WE}.xyz")
265 + add_custom_command(TARGET ${CHEM_GROUP}
266 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
267 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
268 + )
269 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
270 # Generate smi files
271 set(smi_FILE "${cml_WE}.smi")
272 add_custom_command(TARGET ${CHEM_GROUP}
273 --- a/src/fatty_acids/CMakeLists.txt
274 +++ b/src/fatty_acids/CMakeLists.txt
275 @@ -43,6 +43,13 @@
276 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
277 )
278 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
279 + # Generate xyz files
280 + set(xyz_FILE "${cml_WE}.xyz")
281 + add_custom_command(TARGET ${CHEM_GROUP}
282 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
283 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
284 + )
285 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
286 # Generate smi files
287 set(smi_FILE "${cml_WE}.smi")
288 add_custom_command(TARGET ${CHEM_GROUP}
289 --- a/src/haloalkanes/CMakeLists.txt
290 +++ b/src/haloalkanes/CMakeLists.txt
291 @@ -43,6 +43,13 @@
292 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
293 )
294 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
295 + # Generate xyz files
296 + set(xyz_FILE "${cml_WE}.xyz")
297 + add_custom_command(TARGET ${CHEM_GROUP}
298 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
299 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
300 + )
301 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
302 # Generate smi files
303 set(smi_FILE "${cml_WE}.smi")
304 add_custom_command(TARGET ${CHEM_GROUP}
305 --- a/src/heteroaromatics/CMakeLists.txt
306 +++ b/src/heteroaromatics/CMakeLists.txt
307 @@ -43,6 +43,13 @@
308 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
309 )
310 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
311 + # Generate xyz files
312 + set(xyz_FILE "${cml_WE}.xyz")
313 + add_custom_command(TARGET ${CHEM_GROUP}
314 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
315 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
316 + )
317 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
318 # Generate smi files
319 set(smi_FILE "${cml_WE}.smi")
320 add_custom_command(TARGET ${CHEM_GROUP}
321 --- a/src/ketones/CMakeLists.txt
322 +++ b/src/ketones/CMakeLists.txt
323 @@ -43,6 +43,13 @@
324 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
325 )
326 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
327 + # Generate xyz files
328 + set(xyz_FILE "${cml_WE}.xyz")
329 + add_custom_command(TARGET ${CHEM_GROUP}
330 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
331 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
332 + )
333 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
334 # Generate smi files
335 set(smi_FILE "${cml_WE}.smi")
336 add_custom_command(TARGET ${CHEM_GROUP}
337 --- a/src/macrocycles/CMakeLists.txt
338 +++ b/src/macrocycles/CMakeLists.txt
339 @@ -43,6 +43,13 @@
340 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
341 )
342 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
343 + # Generate xyz files
344 + set(xyz_FILE "${cml_WE}.xyz")
345 + add_custom_command(TARGET ${CHEM_GROUP}
346 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
347 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
348 + )
349 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
350 # Generate smi files
351 set(smi_FILE "${cml_WE}.smi")
352 add_custom_command(TARGET ${CHEM_GROUP}
353 --- a/src/natural_products/CMakeLists.txt
354 +++ b/src/natural_products/CMakeLists.txt
355 @@ -43,6 +43,13 @@
356 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
357 )
358 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
359 + # Generate xyz files
360 + set(xyz_FILE "${cml_WE}.xyz")
361 + add_custom_command(TARGET ${CHEM_GROUP}
362 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
363 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
364 + )
365 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
366 # Generate smi files
367 set(smi_FILE "${cml_WE}.smi")
368 add_custom_command(TARGET ${CHEM_GROUP}
369 --- a/src/nitriles/CMakeLists.txt
370 +++ b/src/nitriles/CMakeLists.txt
371 @@ -43,6 +43,13 @@
372 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
373 )
374 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
375 + # Generate xyz files
376 + set(xyz_FILE "${cml_WE}.xyz")
377 + add_custom_command(TARGET ${CHEM_GROUP}
378 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
379 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
380 + )
381 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
382 # Generate smi files
383 set(smi_FILE "${cml_WE}.smi")
384 add_custom_command(TARGET ${CHEM_GROUP}
385 --- a/src/nitroalkanes/CMakeLists.txt
386 +++ b/src/nitroalkanes/CMakeLists.txt
387 @@ -43,6 +43,13 @@
388 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
389 )
390 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
391 + # Generate xyz files
392 + set(xyz_FILE "${cml_WE}.xyz")
393 + add_custom_command(TARGET ${CHEM_GROUP}
394 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
395 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
396 + )
397 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
398 # Generate smi files
399 set(smi_FILE "${cml_WE}.smi")
400 add_custom_command(TARGET ${CHEM_GROUP}
401 --- a/src/nucleobases/CMakeLists.txt
402 +++ b/src/nucleobases/CMakeLists.txt
403 @@ -43,6 +43,13 @@
404 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
405 )
406 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
407 + # Generate xyz files
408 + set(xyz_FILE "${cml_WE}.xyz")
409 + add_custom_command(TARGET ${CHEM_GROUP}
410 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
411 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
412 + )
413 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
414 # Generate smi files
415 set(smi_FILE "${cml_WE}.smi")
416 add_custom_command(TARGET ${CHEM_GROUP}
417 --- a/src/peptides/CMakeLists.txt
418 +++ b/src/peptides/CMakeLists.txt
419 @@ -43,6 +43,13 @@
420 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
421 )
422 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
423 + # Generate xyz files
424 + set(xyz_FILE "${cml_WE}.xyz")
425 + add_custom_command(TARGET ${CHEM_GROUP}
426 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
427 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
428 + )
429 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
430 # Generate smi files
431 set(smi_FILE "${cml_WE}.smi")
432 add_custom_command(TARGET ${CHEM_GROUP}
433 --- a/src/polycyclic_alkanes/CMakeLists.txt
434 +++ b/src/polycyclic_alkanes/CMakeLists.txt
435 @@ -43,6 +43,13 @@
436 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
437 )
438 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
439 + # Generate xyz files
440 + set(xyz_FILE "${cml_WE}.xyz")
441 + add_custom_command(TARGET ${CHEM_GROUP}
442 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
443 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
444 + )
445 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
446 # Generate smi files
447 set(smi_FILE "${cml_WE}.smi")
448 add_custom_command(TARGET ${CHEM_GROUP}
449 --- a/src/polycyclic_aromatics/CMakeLists.txt
450 +++ b/src/polycyclic_aromatics/CMakeLists.txt
451 @@ -43,6 +43,13 @@
452 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
453 )
454 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
455 + # Generate xyz files
456 + set(xyz_FILE "${cml_WE}.xyz")
457 + add_custom_command(TARGET ${CHEM_GROUP}
458 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
459 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
460 + )
461 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
462 # Generate smi files
463 set(smi_FILE "${cml_WE}.smi")
464 add_custom_command(TARGET ${CHEM_GROUP}
465 --- a/src/sulfones/CMakeLists.txt
466 +++ b/src/sulfones/CMakeLists.txt
467 @@ -43,6 +43,13 @@
468 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
469 )
470 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
471 + # Generate xyz files
472 + set(xyz_FILE "${cml_WE}.xyz")
473 + add_custom_command(TARGET ${CHEM_GROUP}
474 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
475 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
476 + )
477 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
478 # Generate smi files
479 set(smi_FILE "${cml_WE}.smi")
480 add_custom_command(TARGET ${CHEM_GROUP}
481 --- a/src/sulfoxides/CMakeLists.txt
482 +++ b/src/sulfoxides/CMakeLists.txt
483 @@ -43,6 +43,13 @@
484 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
485 )
486 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
487 + # Generate xyz files
488 + set(xyz_FILE "${cml_WE}.xyz")
489 + add_custom_command(TARGET ${CHEM_GROUP}
490 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
491 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
492 + )
493 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
494 # Generate smi files
495 set(smi_FILE "${cml_WE}.smi")
496 add_custom_command(TARGET ${CHEM_GROUP}
497 --- a/src/thioethers/CMakeLists.txt
498 +++ b/src/thioethers/CMakeLists.txt
499 @@ -43,6 +43,13 @@
500 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
501 )
502 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
503 + # Generate xyz files
504 + set(xyz_FILE "${cml_WE}.xyz")
505 + add_custom_command(TARGET ${CHEM_GROUP}
506 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
507 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
508 + )
509 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
510 # Generate smi files
511 set(smi_FILE "${cml_WE}.smi")
512 add_custom_command(TARGET ${CHEM_GROUP}
513 --- a/src/thiols/CMakeLists.txt
514 +++ b/src/thiols/CMakeLists.txt
515 @@ -43,6 +43,13 @@
516 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
517 )
518 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
519 + # Generate xyz files
520 + set(xyz_FILE "${cml_WE}.xyz")
521 + add_custom_command(TARGET ${CHEM_GROUP}
522 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
523 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
524 + )
525 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
526 # Generate smi files
527 set(smi_FILE "${cml_WE}.smi")
528 add_custom_command(TARGET ${CHEM_GROUP}
529 --- a/tools/cmlwriter.py
530 +++ b/tools/cmlwriter.py
531 @@ -125,6 +125,7 @@
1 Index: chemical-structures/src/alcohols/CMakeLists.txt
2 ===================================================================
3 --- chemical-structures.orig/src/alcohols/CMakeLists.txt
4 +++ chemical-structures/src/alcohols/CMakeLists.txt
5 @@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
6 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
7 )
8 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
9 + # Generate xyz files
10 + set(xyz_FILE "${cml_WE}.xyz")
11 + add_custom_command(TARGET ${CHEM_GROUP}
12 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
13 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
14 + )
15 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
16 # Generate smi files
17 set(smi_FILE "${cml_WE}.smi")
18 add_custom_command(TARGET ${CHEM_GROUP}
19 Index: chemical-structures/src/water/CMakeLists.txt
20 ===================================================================
21 --- chemical-structures.orig/src/water/CMakeLists.txt
22 +++ chemical-structures/src/water/CMakeLists.txt
23 @@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
24 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
25 )
26 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
27 + # Generate xyz files
28 + set(xyz_FILE "${cml_WE}.xyz")
29 + add_custom_command(TARGET ${CHEM_GROUP}
30 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
31 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
32 + )
33 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
34 # Generate smi files
35 set(smi_FILE "${cml_WE}.smi")
36 add_custom_command(TARGET ${CHEM_GROUP}
37 Index: chemical-structures/src/acid_anhydrides/CMakeLists.txt
38 ===================================================================
39 --- chemical-structures.orig/src/acid_anhydrides/CMakeLists.txt
40 +++ chemical-structures/src/acid_anhydrides/CMakeLists.txt
41 @@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
42 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
43 )
44 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
45 + # Generate xyz files
46 + set(xyz_FILE "${cml_WE}.xyz")
47 + add_custom_command(TARGET ${CHEM_GROUP}
48 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
49 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
50 + )
51 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
52 # Generate smi files
53 set(smi_FILE "${cml_WE}.smi")
54 add_custom_command(TARGET ${CHEM_GROUP}
55 Index: chemical-structures/src/aldehydes/CMakeLists.txt
56 ===================================================================
57 --- chemical-structures.orig/src/aldehydes/CMakeLists.txt
58 +++ chemical-structures/src/aldehydes/CMakeLists.txt
59 @@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
60 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
61 )
62 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
63 + # Generate xyz files
64 + set(xyz_FILE "${cml_WE}.xyz")
65 + add_custom_command(TARGET ${CHEM_GROUP}
66 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
67 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
68 + )
69 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
70 # Generate smi files
71 set(smi_FILE "${cml_WE}.smi")
72 add_custom_command(TARGET ${CHEM_GROUP}
73 Index: chemical-structures/src/alkanes/CMakeLists.txt
74 ===================================================================
75 --- chemical-structures.orig/src/alkanes/CMakeLists.txt
76 +++ chemical-structures/src/alkanes/CMakeLists.txt
77 @@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
78 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
79 )
80 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
81 + # Generate xyz files
82 + set(xyz_FILE "${cml_WE}.xyz")
83 + add_custom_command(TARGET ${CHEM_GROUP}
84 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
85 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
86 + )
87 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
88 # Generate smi files
89 set(smi_FILE "${cml_WE}.smi")
90 add_custom_command(TARGET ${CHEM_GROUP}
91 Index: chemical-structures/src/alkenes/CMakeLists.txt
92 ===================================================================
93 --- chemical-structures.orig/src/alkenes/CMakeLists.txt
94 +++ chemical-structures/src/alkenes/CMakeLists.txt
95 @@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
96 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
97 )
98 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
99 + # Generate xyz files
100 + set(xyz_FILE "${cml_WE}.xyz")
101 + add_custom_command(TARGET ${CHEM_GROUP}
102 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
103 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
104 + )
105 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
106 # Generate smi files
107 set(smi_FILE "${cml_WE}.smi")
108 add_custom_command(TARGET ${CHEM_GROUP}
109 Index: chemical-structures/src/alkynes/CMakeLists.txt
110 ===================================================================
111 --- chemical-structures.orig/src/alkynes/CMakeLists.txt
112 +++ chemical-structures/src/alkynes/CMakeLists.txt
113 @@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
114 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
115 )
116 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
117 + # Generate xyz files
118 + set(xyz_FILE "${cml_WE}.xyz")
119 + add_custom_command(TARGET ${CHEM_GROUP}
120 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
121 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
122 + )
123 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
124 # Generate smi files
125 set(smi_FILE "${cml_WE}.smi")
126 add_custom_command(TARGET ${CHEM_GROUP}
127 Index: chemical-structures/src/amides/CMakeLists.txt
128 ===================================================================
129 --- chemical-structures.orig/src/amides/CMakeLists.txt
130 +++ chemical-structures/src/amides/CMakeLists.txt
131 @@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
132 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
133 )
134 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
135 + # Generate xyz files
136 + set(xyz_FILE "${cml_WE}.xyz")
137 + add_custom_command(TARGET ${CHEM_GROUP}
138 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
139 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
140 + )
141 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
142 # Generate smi files
143 set(smi_FILE "${cml_WE}.smi")
144 add_custom_command(TARGET ${CHEM_GROUP}
145 Index: chemical-structures/src/amines/CMakeLists.txt
146 ===================================================================
147 --- chemical-structures.orig/src/amines/CMakeLists.txt
148 +++ chemical-structures/src/amines/CMakeLists.txt
149 @@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
150 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
151 )
152 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
153 + # Generate xyz files
154 + set(xyz_FILE "${cml_WE}.xyz")
155 + add_custom_command(TARGET ${CHEM_GROUP}
156 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
157 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
158 + )
159 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
160 # Generate smi files
161 set(smi_FILE "${cml_WE}.smi")
162 add_custom_command(TARGET ${CHEM_GROUP}
163 Index: chemical-structures/src/amino_acids/CMakeLists.txt
164 ===================================================================
165 --- chemical-structures.orig/src/amino_acids/CMakeLists.txt
166 +++ chemical-structures/src/amino_acids/CMakeLists.txt
167 @@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
168 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
169 )
170 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
171 + # Generate xyz files
172 + set(xyz_FILE "${cml_WE}.xyz")
173 + add_custom_command(TARGET ${CHEM_GROUP}
174 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
175 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
176 + )
177 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
178 # Generate smi files
179 set(smi_FILE "${cml_WE}.smi")
180 add_custom_command(TARGET ${CHEM_GROUP}
181 Index: chemical-structures/src/aromatics/CMakeLists.txt
182 ===================================================================
183 --- chemical-structures.orig/src/aromatics/CMakeLists.txt
184 +++ chemical-structures/src/aromatics/CMakeLists.txt
185 @@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
186 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
187 )
188 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
189 + # Generate xyz files
190 + set(xyz_FILE "${cml_WE}.xyz")
191 + add_custom_command(TARGET ${CHEM_GROUP}
192 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
193 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
194 + )
195 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
196 # Generate smi files
197 set(smi_FILE "${cml_WE}.smi")
198 add_custom_command(TARGET ${CHEM_GROUP}
199 Index: chemical-structures/src/carbamides/CMakeLists.txt
200 ===================================================================
201 --- chemical-structures.orig/src/carbamides/CMakeLists.txt
202 +++ chemical-structures/src/carbamides/CMakeLists.txt
203 @@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
204 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
205 )
206 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
207 + # Generate xyz files
208 + set(xyz_FILE "${cml_WE}.xyz")
209 + add_custom_command(TARGET ${CHEM_GROUP}
210 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
211 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
212 + )
213 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
214 # Generate smi files
215 set(smi_FILE "${cml_WE}.smi")
216 add_custom_command(TARGET ${CHEM_GROUP}
217 Index: chemical-structures/src/carbohydrates/CMakeLists.txt
218 ===================================================================
219 --- chemical-structures.orig/src/carbohydrates/CMakeLists.txt
220 +++ chemical-structures/src/carbohydrates/CMakeLists.txt
221 @@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
222 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
223 )
224 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
225 + # Generate xyz files
226 + set(xyz_FILE "${cml_WE}.xyz")
227 + add_custom_command(TARGET ${CHEM_GROUP}
228 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
229 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
230 + )
231 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
232 # Generate smi files
233 set(smi_FILE "${cml_WE}.smi")
234 add_custom_command(TARGET ${CHEM_GROUP}
235 Index: chemical-structures/src/carboxylic_acids/CMakeLists.txt
236 ===================================================================
237 --- chemical-structures.orig/src/carboxylic_acids/CMakeLists.txt
238 +++ chemical-structures/src/carboxylic_acids/CMakeLists.txt
239 @@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
240 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
241 )
242 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
243 + # Generate xyz files
244 + set(xyz_FILE "${cml_WE}.xyz")
245 + add_custom_command(TARGET ${CHEM_GROUP}
246 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
247 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
248 + )
249 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
250 # Generate smi files
251 set(smi_FILE "${cml_WE}.smi")
252 add_custom_command(TARGET ${CHEM_GROUP}
253 Index: chemical-structures/src/drugs/CMakeLists.txt
254 ===================================================================
255 --- chemical-structures.orig/src/drugs/CMakeLists.txt
256 +++ chemical-structures/src/drugs/CMakeLists.txt
257 @@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
258 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
259 )
260 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
261 + # Generate xyz files
262 + set(xyz_FILE "${cml_WE}.xyz")
263 + add_custom_command(TARGET ${CHEM_GROUP}
264 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
265 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
266 + )
267 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
268 # Generate smi files
269 set(smi_FILE "${cml_WE}.smi")
270 add_custom_command(TARGET ${CHEM_GROUP}
271 Index: chemical-structures/src/esters/CMakeLists.txt
272 ===================================================================
273 --- chemical-structures.orig/src/esters/CMakeLists.txt
274 +++ chemical-structures/src/esters/CMakeLists.txt
275 @@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
276 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
277 )
278 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
279 + # Generate xyz files
280 + set(xyz_FILE "${cml_WE}.xyz")
281 + add_custom_command(TARGET ${CHEM_GROUP}
282 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
283 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
284 + )
285 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
286 # Generate smi files
287 set(smi_FILE "${cml_WE}.smi")
288 add_custom_command(TARGET ${CHEM_GROUP}
289 Index: chemical-structures/src/ethers/CMakeLists.txt
290 ===================================================================
291 --- chemical-structures.orig/src/ethers/CMakeLists.txt
292 +++ chemical-structures/src/ethers/CMakeLists.txt
293 @@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
294 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
295 )
296 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
297 + # Generate xyz files
298 + set(xyz_FILE "${cml_WE}.xyz")
299 + add_custom_command(TARGET ${CHEM_GROUP}
300 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
301 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
302 + )
303 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
304 # Generate smi files
305 set(smi_FILE "${cml_WE}.smi")
306 add_custom_command(TARGET ${CHEM_GROUP}
307 Index: chemical-structures/src/fatty_acids/CMakeLists.txt
308 ===================================================================
309 --- chemical-structures.orig/src/fatty_acids/CMakeLists.txt
310 +++ chemical-structures/src/fatty_acids/CMakeLists.txt
311 @@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
312 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
313 )
314 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
315 + # Generate xyz files
316 + set(xyz_FILE "${cml_WE}.xyz")
317 + add_custom_command(TARGET ${CHEM_GROUP}
318 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
319 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
320 + )
321 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
322 # Generate smi files
323 set(smi_FILE "${cml_WE}.smi")
324 add_custom_command(TARGET ${CHEM_GROUP}
325 Index: chemical-structures/src/haloalkanes/CMakeLists.txt
326 ===================================================================
327 --- chemical-structures.orig/src/haloalkanes/CMakeLists.txt
328 +++ chemical-structures/src/haloalkanes/CMakeLists.txt
329 @@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
330 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
331 )
332 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
333 + # Generate xyz files
334 + set(xyz_FILE "${cml_WE}.xyz")
335 + add_custom_command(TARGET ${CHEM_GROUP}
336 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
337 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
338 + )
339 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
340 # Generate smi files
341 set(smi_FILE "${cml_WE}.smi")
342 add_custom_command(TARGET ${CHEM_GROUP}
343 Index: chemical-structures/src/heteroaromatics/CMakeLists.txt
344 ===================================================================
345 --- chemical-structures.orig/src/heteroaromatics/CMakeLists.txt
346 +++ chemical-structures/src/heteroaromatics/CMakeLists.txt
347 @@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
348 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
349 )
350 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
351 + # Generate xyz files
352 + set(xyz_FILE "${cml_WE}.xyz")
353 + add_custom_command(TARGET ${CHEM_GROUP}
354 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
355 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
356 + )
357 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
358 # Generate smi files
359 set(smi_FILE "${cml_WE}.smi")
360 add_custom_command(TARGET ${CHEM_GROUP}
361 Index: chemical-structures/src/ketones/CMakeLists.txt
362 ===================================================================
363 --- chemical-structures.orig/src/ketones/CMakeLists.txt
364 +++ chemical-structures/src/ketones/CMakeLists.txt
365 @@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
366 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
367 )
368 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
369 + # Generate xyz files
370 + set(xyz_FILE "${cml_WE}.xyz")
371 + add_custom_command(TARGET ${CHEM_GROUP}
372 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
373 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
374 + )
375 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
376 # Generate smi files
377 set(smi_FILE "${cml_WE}.smi")
378 add_custom_command(TARGET ${CHEM_GROUP}
379 Index: chemical-structures/src/macrocycles/CMakeLists.txt
380 ===================================================================
381 --- chemical-structures.orig/src/macrocycles/CMakeLists.txt
382 +++ chemical-structures/src/macrocycles/CMakeLists.txt
383 @@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
384 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
385 )
386 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
387 + # Generate xyz files
388 + set(xyz_FILE "${cml_WE}.xyz")
389 + add_custom_command(TARGET ${CHEM_GROUP}
390 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
391 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
392 + )
393 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
394 # Generate smi files
395 set(smi_FILE "${cml_WE}.smi")
396 add_custom_command(TARGET ${CHEM_GROUP}
397 Index: chemical-structures/src/natural_products/CMakeLists.txt
398 ===================================================================
399 --- chemical-structures.orig/src/natural_products/CMakeLists.txt
400 +++ chemical-structures/src/natural_products/CMakeLists.txt
401 @@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
402 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
403 )
404 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
405 + # Generate xyz files
406 + set(xyz_FILE "${cml_WE}.xyz")
407 + add_custom_command(TARGET ${CHEM_GROUP}
408 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
409 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
410 + )
411 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
412 # Generate smi files
413 set(smi_FILE "${cml_WE}.smi")
414 add_custom_command(TARGET ${CHEM_GROUP}
415 Index: chemical-structures/src/nitriles/CMakeLists.txt
416 ===================================================================
417 --- chemical-structures.orig/src/nitriles/CMakeLists.txt
418 +++ chemical-structures/src/nitriles/CMakeLists.txt
419 @@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
420 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
421 )
422 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
423 + # Generate xyz files
424 + set(xyz_FILE "${cml_WE}.xyz")
425 + add_custom_command(TARGET ${CHEM_GROUP}
426 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
427 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
428 + )
429 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
430 # Generate smi files
431 set(smi_FILE "${cml_WE}.smi")
432 add_custom_command(TARGET ${CHEM_GROUP}
433 Index: chemical-structures/src/nitroalkanes/CMakeLists.txt
434 ===================================================================
435 --- chemical-structures.orig/src/nitroalkanes/CMakeLists.txt
436 +++ chemical-structures/src/nitroalkanes/CMakeLists.txt
437 @@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
438 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
439 )
440 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
441 + # Generate xyz files
442 + set(xyz_FILE "${cml_WE}.xyz")
443 + add_custom_command(TARGET ${CHEM_GROUP}
444 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
445 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
446 + )
447 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
448 # Generate smi files
449 set(smi_FILE "${cml_WE}.smi")
450 add_custom_command(TARGET ${CHEM_GROUP}
451 Index: chemical-structures/src/nucleobases/CMakeLists.txt
452 ===================================================================
453 --- chemical-structures.orig/src/nucleobases/CMakeLists.txt
454 +++ chemical-structures/src/nucleobases/CMakeLists.txt
455 @@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
456 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
457 )
458 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
459 + # Generate xyz files
460 + set(xyz_FILE "${cml_WE}.xyz")
461 + add_custom_command(TARGET ${CHEM_GROUP}
462 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
463 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
464 + )
465 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
466 # Generate smi files
467 set(smi_FILE "${cml_WE}.smi")
468 add_custom_command(TARGET ${CHEM_GROUP}
469 Index: chemical-structures/src/peptides/CMakeLists.txt
470 ===================================================================
471 --- chemical-structures.orig/src/peptides/CMakeLists.txt
472 +++ chemical-structures/src/peptides/CMakeLists.txt
473 @@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
474 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
475 )
476 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
477 + # Generate xyz files
478 + set(xyz_FILE "${cml_WE}.xyz")
479 + add_custom_command(TARGET ${CHEM_GROUP}
480 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
481 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
482 + )
483 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
484 # Generate smi files
485 set(smi_FILE "${cml_WE}.smi")
486 add_custom_command(TARGET ${CHEM_GROUP}
487 Index: chemical-structures/src/polycyclic_alkanes/CMakeLists.txt
488 ===================================================================
489 --- chemical-structures.orig/src/polycyclic_alkanes/CMakeLists.txt
490 +++ chemical-structures/src/polycyclic_alkanes/CMakeLists.txt
491 @@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
492 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
493 )
494 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
495 + # Generate xyz files
496 + set(xyz_FILE "${cml_WE}.xyz")
497 + add_custom_command(TARGET ${CHEM_GROUP}
498 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
499 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
500 + )
501 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
502 # Generate smi files
503 set(smi_FILE "${cml_WE}.smi")
504 add_custom_command(TARGET ${CHEM_GROUP}
505 Index: chemical-structures/src/polycyclic_aromatics/CMakeLists.txt
506 ===================================================================
507 --- chemical-structures.orig/src/polycyclic_aromatics/CMakeLists.txt
508 +++ chemical-structures/src/polycyclic_aromatics/CMakeLists.txt
509 @@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
510 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
511 )
512 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
513 + # Generate xyz files
514 + set(xyz_FILE "${cml_WE}.xyz")
515 + add_custom_command(TARGET ${CHEM_GROUP}
516 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
517 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
518 + )
519 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
520 # Generate smi files
521 set(smi_FILE "${cml_WE}.smi")
522 add_custom_command(TARGET ${CHEM_GROUP}
523 Index: chemical-structures/src/sulfones/CMakeLists.txt
524 ===================================================================
525 --- chemical-structures.orig/src/sulfones/CMakeLists.txt
526 +++ chemical-structures/src/sulfones/CMakeLists.txt
527 @@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
528 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
529 )
530 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
531 + # Generate xyz files
532 + set(xyz_FILE "${cml_WE}.xyz")
533 + add_custom_command(TARGET ${CHEM_GROUP}
534 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
535 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
536 + )
537 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
538 # Generate smi files
539 set(smi_FILE "${cml_WE}.smi")
540 add_custom_command(TARGET ${CHEM_GROUP}
541 Index: chemical-structures/src/sulfoxides/CMakeLists.txt
542 ===================================================================
543 --- chemical-structures.orig/src/sulfoxides/CMakeLists.txt
544 +++ chemical-structures/src/sulfoxides/CMakeLists.txt
545 @@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
546 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
547 )
548 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
549 + # Generate xyz files
550 + set(xyz_FILE "${cml_WE}.xyz")
551 + add_custom_command(TARGET ${CHEM_GROUP}
552 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
553 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
554 + )
555 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
556 # Generate smi files
557 set(smi_FILE "${cml_WE}.smi")
558 add_custom_command(TARGET ${CHEM_GROUP}
559 Index: chemical-structures/src/thioethers/CMakeLists.txt
560 ===================================================================
561 --- chemical-structures.orig/src/thioethers/CMakeLists.txt
562 +++ chemical-structures/src/thioethers/CMakeLists.txt
563 @@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
564 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
565 )
566 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
567 + # Generate xyz files
568 + set(xyz_FILE "${cml_WE}.xyz")
569 + add_custom_command(TARGET ${CHEM_GROUP}
570 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
571 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
572 + )
573 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
574 # Generate smi files
575 set(smi_FILE "${cml_WE}.smi")
576 add_custom_command(TARGET ${CHEM_GROUP}
577 Index: chemical-structures/src/thiols/CMakeLists.txt
578 ===================================================================
579 --- chemical-structures.orig/src/thiols/CMakeLists.txt
580 +++ chemical-structures/src/thiols/CMakeLists.txt
581 @@ -43,6 +43,13 @@ foreach(cml_SRC_FILE ${cml_SRCS})
582 WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
583 )
584 set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${mol_FILE}")
585 + # Generate xyz files
586 + set(xyz_FILE "${cml_WE}.xyz")
587 + add_custom_command(TARGET ${CHEM_GROUP}
588 + COMMAND ${OPENBABEL2_EXECUTABLE} -icml ${cml_FILE} -oxyz ${xyz_FILE}
589 + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
590 + )
591 + set(chemical_structure_files ${chemical_structure_files} "${CMAKE_CURRENT_BINARY_DIR}/${xyz_FILE}")
592 # Generate smi files
593 set(smi_FILE "${cml_WE}.smi")
594 add_custom_command(TARGET ${CHEM_GROUP}
595 Index: chemical-structures/tools/cmlwriter.py
596 ===================================================================
597 --- chemical-structures.orig/tools/cmlwriter.py
598 +++ chemical-structures/tools/cmlwriter.py
599 @@ -13,7 +13,7 @@ class CMLWriter:
600 """
601 def __init__(self, fout, cml_handler, l10n_handler):
602 """Creates an instance of the CMLWriter class.
603 - """
604 + """
605 self.fout = fout
606 self.cml = cml_handler
607 self.l10n = l10n_handler
608 @@ -100,7 +100,7 @@ class CMLWriter:
609
610 def parseFormula(self, raw_formula):
611 """Parse formula and return the HTML formula
612 - """
613 + """
614 formula = raw_formula.strip()
615 formula_ar = formula.split(" ")
616 formula = ""
617 @@ -111,7 +111,7 @@ class CMLWriter:
618 idx += 1
619 elif idx % 2: # we are in the multiple section"
620 formula += "<sub>" + i + "</sub>"
621 - idx += 1
622 + idx += 1
623 else: # we are in the element section
624 formula += i
625 idx += 1
626 @@ -125,6 +125,7 @@ class CMLWriter:
532627
533628 cml_file = entry_details.path + '.cml'
534629 mol_file = entry_details.path + '.mol'
536631 smi_file = entry_details.path + '.smi'
537632 smiles = ""
538633 if os.path.isfile(smi_file):
539 @@ -232,6 +233,8 @@
634 @@ -175,41 +176,41 @@ class CMLWriter:
635 else:
636 bpK = str(int(self.cml.bp) + 273)
637 xhtmlout.addBody(' <li>' + self.l10n.translate('Boiling point: ', lang) + self.cml.bp + ' &deg;C (' + bpK + ' K)</li>')
638 - #########################################################
639 - # Writing synonyms
640 - #
641 - # Write only if synonyms (localized or english) are
642 - # available
643 - #########################################################
644 - if entry_details.synDict.has_key(lang):
645 - if len(entry_details.synDict[lang]) == 1:
646 + #########################################################
647 + # Writing synonyms
648 + #
649 + # Write only if synonyms (localized or english) are
650 + # available
651 + #########################################################
652 + if entry_details.synDict.has_key(lang):
653 + if len(entry_details.synDict[lang]) == 1:
654 xhtmlout.addBody(' <li>' + self.l10n.translate('Synonym:', lang) )
655 - else:
656 + else:
657 xhtmlout.addBody(' <li>' + self.l10n.translate('Synonyms:', lang) )
658 xhtmlout.addBody(' <ul>')
659 for synonym in entry_details.synDict[lang]:
660 xhtmlout.addBody(' <li>' + synonym + '</li>')
661 xhtmlout.addBody(' </ul>')
662 xhtmlout.addBody(' </li>')
663 - elif entry_details.synDict.has_key('en'):
664 - if len(entry_details.synDict['en']) == 1:
665 + elif entry_details.synDict.has_key('en'):
666 + if len(entry_details.synDict['en']) == 1:
667 xhtmlout.addBody(' <li>' + self.l10n.translate('Synonym:', lang) )
668 - else:
669 + else:
670 xhtmlout.addBody(' <li>' + self.l10n.translate('Synonyms:', lang) )
671 xhtmlout.addBody(' <ul>')
672 for synonym in entry_details.synDict['en']:
673 xhtmlout.addBody(' <li>' + synonym + ' (<i>en</i>)</li>')
674 xhtmlout.addBody(' </ul>')
675 xhtmlout.addBody(' </li>')
676 - #########################################################
677 - # Writing abbreviations
678 - #
679 - # Write only if abbreviations are available
680 - #########################################################
681 - if len(entry_details.abbreviation):
682 - if len(entry_details.abbreviation) == 1:
683 + #########################################################
684 + # Writing abbreviations
685 + #
686 + # Write only if abbreviations are available
687 + #########################################################
688 + if len(entry_details.abbreviation):
689 + if len(entry_details.abbreviation) == 1:
690 xhtmlout.addBody(' <li>' + self.l10n.translate('Abbreviation:', lang) )
691 - else:
692 + else:
693 xhtmlout.addBody(' <li>' + self.l10n.translate('Abbreviations:', lang) )
694 xhtmlout.addBody(' <ul>')
695 for abbreviation in entry_details.abbreviation:
696 @@ -232,32 +233,34 @@ class CMLWriter:
540697 xhtmlout.addBody(' <li>' + self.l10n.translate('In CML format', lang) + '&nbsp;<a href="' + cml_file + '" title="CML"><img src="' + '../'*level + 'images/download.png" alt="Download cml file" /></a></li>')
541698 if os.path.isfile(mol_file):
542699 xhtmlout.addBody(' <li>' + self.l10n.translate('In MOL format', lang) + '&nbsp;<a href="' + mol_file + '" title="MOL"><img src="' + '../'*level + 'images/download.png" alt="Download mol file" /></a></li>')
545702 xhtmlout.addBody(' <li>' + self.l10n.translate('Other formats', lang) + '&nbsp;'+self.selection+'</li>')
546703 xhtmlout.addBody(' </ul>')
547704 xhtmlout.addBody(' </div>')
705 xhtmlout.addBody(' <div id="inchi">')
706 xhtmlout.addBody(' <h3>' + self.l10n.translate('InChI', lang) + '</h3>')
707 - if len(self.cml.inchi) > 80:
708 - htmlinchi = ""
709 - size = int(len(self.cml.inchi)/80)
710 - for i in range(0,size):
711 - htmlinchi += self.cml.inchi[i*80:(i+1)*80] + "<br />\n"
712 + if len(self.cml.inchi) > 80:
713 + htmlinchi = ""
714 + size = int(len(self.cml.inchi)/80)
715 + for i in range(0,size):
716 + htmlinchi += self.cml.inchi[i*80:(i+1)*80] + "<br />\n"
717 htmlinchi += self.cml.inchi[size*80:len(self.cml.inchi)]
718 - else:
719 - htmlinchi = self.cml.inchi
720 + else:
721 + htmlinchi = self.cml.inchi
722 xhtmlout.addBody(' <span class="inchi">' + htmlinchi + '</span>')
723 xhtmlout.addBody(' </div>')
724 if smiles:
725 xhtmlout.addBody(' <div id="smiles">')
726 xhtmlout.addBody(' <h3>' + self.l10n.translate('SMILES', lang) + '</h3>')
727 if len(smiles) > 80:
728 - htmlsmiles = ""
729 - size = int(len(smiles)/80)
730 - for i in range(0,size):
731 - htmlsmiles += smiles[i*80:(i+1)*80] + "<br />\n"
732 + htmlsmiles = ""
733 + size = int(len(smiles)/80)
734 + for i in range(0,size):
735 + htmlsmiles += smiles[i*80:(i+1)*80] + "<br />\n"
736 htmlsmiles += smiles[size*80:len(smiles)]
737 else:
738 - htmlsmiles = smiles
739 + htmlsmiles = smiles
740 xhtmlout.addBody(' <span class="smiles">' + htmlsmiles + '</span>')
741 xhtmlout.addBody(' </div>')
742 xhtmlout.addBody(' </div>')
+88
-0
debian/patches/python3-conformity.patch less more
0 Index: chemical-structures/tools/formulaindexwriter.py
1 ===================================================================
2 --- chemical-structures.orig/tools/formulaindexwriter.py
3 +++ chemical-structures/tools/formulaindexwriter.py
4 @@ -16,12 +16,12 @@ class DataIndexWriter:
5 continue
6 if idx % 2:
7 formula += "<sub>" + i
8 - subBool = True
9 + subBool = True
10 idx += 1
11 else:
12 if subBool:
13 formula += "</sub>"
14 - subBool = False
15 + subBool = False
16 formula += i
17 idx += 1
18 if subBool:
19 Index: chemical-structures/tools/indexwriter.py
20 ===================================================================
21 --- chemical-structures.orig/tools/indexwriter.py
22 +++ chemical-structures/tools/indexwriter.py
23 @@ -5,14 +5,14 @@ class IndexWriter:
24 """
25 def __init__(self, fout, index_handler, l10n_handler):
26 """Creates an instance of the class.
27 - """
28 + """
29 self.fout = fout
30 self.index = index_handler
31 self.l10n = l10n_handler
32
33 def WriteXHTML(self, index_title, lang, level):
34 """
35 - """
36 + """
37 xhtmlout = xhtmlwriter.XHTMLWriter()
38 xhtmlout.setOutput(self.fout)
39 if index_title.has_key(lang):
40 @@ -37,9 +37,9 @@ class IndexWriter:
41 xhtmlout.addBody(' </div>')
42 xhtmlout.addBody(' </div>')
43 xhtmlout.addBody(' <div id="main">')
44 - """
45 - Create a list of directories
46 - """
47 + """
48 + Create a list of directories
49 + """
50 if len(self.index.entryList["dir"]) > 0:
51 # Order the entry list by alphabetic order
52 entryDict = {}
53 @@ -61,9 +61,9 @@ class IndexWriter:
54 xhtmlout.addBody(' <li><a href="./' + entry.path + '/index_' + lang + '.html">' + entry.name['en'] + ' (<i>en</i>)</a></li>')
55 xhtmlout.addBody(' </ul>')
56 xhtmlout.addBody(' </div>')
57 - """
58 - Create list of files
59 - """
60 + """
61 + Create list of files
62 + """
63 if len(self.index.entryList["file"]) > 0:
64 # Order the entry list by alphabetic order
65 entryDict = {}
66 Index: chemical-structures/tools/make_index_files.py
67 ===================================================================
68 --- chemical-structures.orig/tools/make_index_files.py
69 +++ chemical-structures/tools/make_index_files.py
70 @@ -44,7 +44,7 @@ def formulaCmp(tuple1, tuple2):
71
72 sourceDir = sys.argv[1]
73 if not os.path.isdir(sourceDir):
74 - print "Error: "+ sourceDir + ": no such directory"
75 + print ("Error: "+ sourceDir + ": no such directory")
76 sys.exit(1)
77 indexFile = sys.argv[2]
78 level = int(sys.argv[3])
79 @@ -77,7 +77,7 @@ for dir in src_list:
80 index_parser.setFeature(xml.sax.handler.feature_external_ges, 0)
81 index_handler = indexhandler.IndexHandler()
82 index_parser.setContentHandler(index_handler)
83 - print os.path.realpath(os.path.curdir)
84 + print (os.path.realpath(os.path.curdir))
85 index_parser.parse("index.xml")
86 for entry in index_handler.entryList["file"]:
87 name_list.append( (entry.name["en"], "./" + dir +"/" + entry.path) )
+1
-0
debian/patches/series less more
88 build-xyz-files.patch
99 apache.conf.patch
1010 privacy.patch
11 python3-conformity.patch