nx_chem_smiles_test.nx source
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1// nx_chem_smiles_test.nx -- C2.1 KAT for the basic SMILES parser.
2//
3// Each test case calls nx_chem_parse_smiles with a literal SMILES,
4// verifies the resulting MolGraph has the expected atom + bond
5// structure, and (for negative tests) verifies the structured
6// error-code path.
7//
8// All test SMILES are well-known reference molecules; expected
9// graphs hand-verified against OpenSMILES specification examples.
10//
11// expect_exit: 0
12//
13// license_tier: ORIGINAL
14
15import "nx_chem_molecule.nx"
16import "nx_chem_smiles.nx"
17
18// =================================================================
19// Helper: get atom Z by index (assumes valid).
20// =================================================================
21func tz(m: *MolGraph, i: nx_int) -> nx_int {
22 let a: *Atom = nx_chem_mol_atom(m, i)
23 return a.z
24}
25
26// Helper: get bond order by index.
27func tbo(m: *MolGraph, i: nx_int) -> nx_int {
28 let b: *Bond = nx_chem_mol_bond(m, i)
29 return b.order
30}
31
32// Helper: parse a 1-char SMILES (fits in 8 bytes for sys_mmap).
33func mk1(c: nx_int) -> *MolGraph {
34 let s: *u8 = sys_mmap(8)
35 s[0] = c & 0xff
36 return nx_chem_parse_smiles(s, 1)
37}
38
39// Helper: parse a 2-char SMILES.
40func mk2(c1: nx_int, c2: nx_int) -> *MolGraph {
41 let s: *u8 = sys_mmap(8)
42 s[0] = c1 & 0xff
43 s[1] = c2 & 0xff
44 return nx_chem_parse_smiles(s, 2)
45}
46
47// Helper: parse a 3-char SMILES.
48func mk3(c1: nx_int, c2: nx_int, c3: nx_int) -> *MolGraph {
49 let s: *u8 = sys_mmap(8)
50 s[0] = c1 & 0xff
51 s[1] = c2 & 0xff
52 s[2] = c3 & 0xff
53 return nx_chem_parse_smiles(s, 3)
54}
55
56// Helper: parse N-char SMILES.
57func mkn(bytes: *u8, n: nx_int) -> *MolGraph {
58 return nx_chem_parse_smiles(bytes, n)
59}
60
61// =================================================================
62// A -- single organic atoms.
63// =================================================================
64func a_single_atoms() -> nx_int {
65 // "O" -> 1 atom O, 0 bonds
66 let m1: *MolGraph = mk1(0x4F) // 'O'
67 if m1.is_valid != 1 { return 11 }
68 if m1.n_atoms != 1 { return 12 }
69 if m1.n_bonds != 0 { return 13 }
70 if tz(m1, 0) != 8 { return 14 }
71
72 // "C" -> 1 atom C
73 let m2: *MolGraph = mk1(0x43) // 'C'
74 if m2.n_atoms != 1 { return 15 }
75 if tz(m2, 0) != 6 { return 16 }
76
77 // "N" -> 1 atom N
78 let m3: *MolGraph = mk1(0x4E) // 'N'
79 if m3.n_atoms != 1 { return 17 }
80 if tz(m3, 0) != 7 { return 18 }
81
82 // "F" -> 1 atom F
83 let m4: *MolGraph = mk1(0x46) // 'F'
84 if m4.n_atoms != 1 { return 19 }
85 if tz(m4, 0) != 9 { return 20 }
86
87 return 0
88}
89
90// =================================================================
91// B -- two-char organic atoms Cl, Br.
92// =================================================================
93func b_two_char_organic() -> nx_int {
94 // "Cl" -> 1 atom Cl
95 let s1: *u8 = sys_mmap(8); s1[0] = 0x43; s1[1] = 0x6C // 'C' 'l'
96 let m1: *MolGraph = nx_chem_parse_smiles(s1, 2)
97 if m1.is_valid != 1 { return 31 }
98 if m1.n_atoms != 1 { return 32 }
99 if tz(m1, 0) != 17 { return 33 } // Cl
100
101 // "Br" -> 1 atom Br
102 let s2: *u8 = sys_mmap(8); s2[0] = 0x42; s2[1] = 0x72
103 let m2: *MolGraph = nx_chem_parse_smiles(s2, 2)
104 if m2.is_valid != 1 { return 34 }
105 if tz(m2, 0) != 35 { return 35 } // Br
106
107 return 0
108}
109
110// =================================================================
111// C -- explicit single/double/triple bonds.
112// =================================================================
113func c_bonds() -> nx_int {
114 // "CC" -> C-C single bond (default)
115 let m1: *MolGraph = mk2(0x43, 0x43)
116 if m1.is_valid != 1 { return 41 }
117 if m1.n_atoms != 2 { return 42 }
118 if m1.n_bonds != 1 { return 43 }
119 if tbo(m1, 0) != NX_BOND_SINGLE { return 44 }
120
121 // "C=C" -> C=C double bond
122 let m2: *MolGraph = mk3(0x43, 0x3D, 0x43) // C = C
123 if m2.is_valid != 1 { return 45 }
124 if m2.n_bonds != 1 { return 46 }
125 if tbo(m2, 0) != NX_BOND_DOUBLE { return 47 }
126
127 // "C#C" -> C#C triple bond
128 let m3: *MolGraph = mk3(0x43, 0x23, 0x43) // C # C
129 if m3.is_valid != 1 { return 48 }
130 if tbo(m3, 0) != NX_BOND_TRIPLE { return 49 }
131
132 return 0
133}
134
135// =================================================================
136// D -- ethanol "CCO".
137// =================================================================
138func d_ethanol() -> nx_int {
139 let m: *MolGraph = mk3(0x43, 0x43, 0x4F) // C C O
140 if m.is_valid != 1 { return 51 }
141 if m.n_atoms != 3 { return 52 }
142 if m.n_bonds != 2 { return 53 }
143 if tz(m, 0) != 6 { return 54 }
144 if tz(m, 1) != 6 { return 55 }
145 if tz(m, 2) != 8 { return 56 }
146 if tbo(m, 0) != NX_BOND_SINGLE { return 57 }
147 if tbo(m, 1) != NX_BOND_SINGLE { return 58 }
148 let b0: *Bond = nx_chem_mol_bond(m, 0)
149 if b0.a != 0 { return 59 }
150 if b0.b != 1 { return 60 }
151 let b1: *Bond = nx_chem_mol_bond(m, 1)
152 if b1.a != 1 { return 61 }
153 if b1.b != 2 { return 62 }
154 return 0
155}
156
157// =================================================================
158// E -- isobutane "CC(C)C" -- tests branch open/close.
159// Graph: C0-C1, C1-C2 (branch), C1-C3
160// Atoms: C0=0, C1=1, C2=2, C3=3
161// Bonds: 0-1, 1-2, 1-3 (3 bonds total)
162// =================================================================
163func e_isobutane() -> nx_int {
164 let s: *u8 = sys_mmap(8)
165 s[0] = 0x43; s[1] = 0x43; s[2] = 0x28; s[3] = 0x43; s[4] = 0x29; s[5] = 0x43
166 let m: *MolGraph = nx_chem_parse_smiles(s, 6)
167 if m.is_valid != 1 { return 71 }
168 if m.n_atoms != 4 { return 72 }
169 if m.n_bonds != 3 { return 73 }
170 let b0: *Bond = nx_chem_mol_bond(m, 0)
171 if b0.a != 0 { return 74 }
172 if b0.b != 1 { return 75 }
173 let b1: *Bond = nx_chem_mol_bond(m, 1)
174 if b1.a != 1 { return 76 }
175 if b1.b != 2 { return 77 }
176 let b2: *Bond = nx_chem_mol_bond(m, 2)
177 if b2.a != 1 { return 78 }
178 if b2.b != 3 { return 79 }
179 return 0
180}
181
182// =================================================================
183// F -- benzene "c1ccccc1" -- aromatic + ring closure.
184// 6 atoms, 6 bonds, all aromatic, all in ring.
185// =================================================================
186func f_benzene() -> nx_int {
187 let s: *u8 = sys_mmap(16)
188 s[0] = 0x63; s[1] = 0x31 // c1
189 s[2] = 0x63; s[3] = 0x63 // cc
190 s[4] = 0x63; s[5] = 0x63 // cc
191 s[6] = 0x63; s[7] = 0x31 // c1
192 let m: *MolGraph = nx_chem_parse_smiles(s, 8)
193 if m.is_valid != 1 { return 91 }
194 if m.n_atoms != 6 { return 92 }
195 if m.n_bonds != 6 { return 93 }
196 var i: nx_int = 0
197 while i < 6 {
198 let a: *Atom = nx_chem_mol_atom(m, i)
199 if a.z != 6 { return 100 + i }
200 if a.aromaticity != NX_AROM_DAYLIGHT { return 110 + i }
201 i = i + 1
202 }
203 // bond 0..4: aromatic chain; bond 5: ring-closure
204 var j: nx_int = 0
205 while j < 6 {
206 let b: *Bond = nx_chem_mol_bond(m, j)
207 if b.order != NX_BOND_AROMATIC { return 120 + j }
208 j = j + 1
209 }
210 // ring-closure bond connects atom 5 -> atom 0
211 let b5: *Bond = nx_chem_mol_bond(m, 5)
212 if b5.a != 5 { return 131 }
213 if b5.b != 0 { return 132 }
214 if b5.in_ring != 1 { return 133 }
215 return 0
216}
217
218// =================================================================
219// G -- cyclohexane "C1CCCCC1" -- aliphatic ring, all single bonds.
220// =================================================================
221func g_cyclohexane() -> nx_int {
222 let s: *u8 = sys_mmap(16)
223 s[0] = 0x43; s[1] = 0x31 // C1
224 s[2] = 0x43; s[3] = 0x43 // CC
225 s[4] = 0x43; s[5] = 0x43 // CC
226 s[6] = 0x43; s[7] = 0x31 // C1
227 let m: *MolGraph = nx_chem_parse_smiles(s, 8)
228 if m.is_valid != 1 { return 141 }
229 if m.n_atoms != 6 { return 142 }
230 if m.n_bonds != 6 { return 143 }
231 var j: nx_int = 0
232 while j < 6 {
233 if tbo(m, j) != NX_BOND_SINGLE { return 150 + j }
234 j = j + 1
235 }
236 return 0
237}
238
239// =================================================================
240// H -- bracket atoms.
241// =================================================================
242func h_brackets() -> nx_int {
243 // "[Na+]" -> 1 atom Na, charge +1
244 let s1: *u8 = sys_mmap(16)
245 s1[0] = 0x5B; s1[1] = 0x4E; s1[2] = 0x61; s1[3] = 0x2B; s1[4] = 0x5D
246 let m1: *MolGraph = nx_chem_parse_smiles(s1, 5)
247 if m1.is_valid != 1 { return 161 }
248 if m1.n_atoms != 1 { return 162 }
249 let a1: *Atom = nx_chem_mol_atom(m1, 0)
250 if a1.z != 11 { return 163 }
251 if a1.charge != 1 { return 164 }
252
253 // "[Cl-]" -> 1 atom Cl, charge -1
254 let s2: *u8 = sys_mmap(16)
255 s2[0] = 0x5B; s2[1] = 0x43; s2[2] = 0x6C; s2[3] = 0x2D; s2[4] = 0x5D
256 let m2: *MolGraph = nx_chem_parse_smiles(s2, 5)
257 if m2.is_valid != 1 { return 165 }
258 let a2: *Atom = nx_chem_mol_atom(m2, 0)
259 if a2.z != 17 { return 166 }
260 if a2.charge != -1 { return 167 }
261
262 // "[CH4]" -> 1 atom C with h_count=4
263 let s3: *u8 = sys_mmap(16)
264 s3[0] = 0x5B; s3[1] = 0x43; s3[2] = 0x48; s3[3] = 0x34; s3[4] = 0x5D
265 let m3: *MolGraph = nx_chem_parse_smiles(s3, 5)
266 if m3.is_valid != 1 { return 168 }
267 let a3: *Atom = nx_chem_mol_atom(m3, 0)
268 if a3.z != 6 { return 169 }
269 if a3.h_count != 4 { return 170 }
270
271 // "[NH4+]" -> ammonium ion
272 let s4: *u8 = sys_mmap(16)
273 s4[0] = 0x5B; s4[1] = 0x4E; s4[2] = 0x48; s4[3] = 0x34; s4[4] = 0x2B; s4[5] = 0x5D
274 let m4: *MolGraph = nx_chem_parse_smiles(s4, 6)
275 if m4.is_valid != 1 { return 171 }
276 let a4: *Atom = nx_chem_mol_atom(m4, 0)
277 if a4.z != 7 { return 172 }
278 if a4.h_count != 4 { return 173 }
279 if a4.charge != 1 { return 174 }
280
281 // "[13C]" -> isotope 13 of carbon
282 let s5: *u8 = sys_mmap(16)
283 s5[0] = 0x5B; s5[1] = 0x31; s5[2] = 0x33; s5[3] = 0x43; s5[4] = 0x5D
284 let m5: *MolGraph = nx_chem_parse_smiles(s5, 5)
285 if m5.is_valid != 1 { return 175 }
286 let a5: *Atom = nx_chem_mol_atom(m5, 0)
287 if a5.z != 6 { return 176 }
288 if a5.isotope != 13 { return 177 }
289
290 // "[Hg+2]" -> mercury(II) cation (supplement-arc heavy metal)
291 let s6: *u8 = sys_mmap(16)
292 s6[0] = 0x5B; s6[1] = 0x48; s6[2] = 0x67; s6[3] = 0x2B; s6[4] = 0x32; s6[5] = 0x5D
293 let m6: *MolGraph = nx_chem_parse_smiles(s6, 6)
294 if m6.is_valid != 1 { return 178 }
295 let a6: *Atom = nx_chem_mol_atom(m6, 0)
296 if a6.z != 80 { return 179 }
297 if a6.charge != 2 { return 180 }
298
299 // "[Pb+2]" -> lead(II) cation
300 let s7: *u8 = sys_mmap(16)
301 s7[0] = 0x5B; s7[1] = 0x50; s7[2] = 0x62; s7[3] = 0x2B; s7[4] = 0x32; s7[5] = 0x5D
302 let m7: *MolGraph = nx_chem_parse_smiles(s7, 6)
303 if m7.is_valid != 1 { return 181 }
304 let a7: *Atom = nx_chem_mol_atom(m7, 0)
305 if a7.z != 82 { return 182 }
306 if a7.charge != 2 { return 183 }
307
308 return 0
309}
310
311// =================================================================
312// I -- wildcard "*".
313// =================================================================
314func i_wildcard() -> nx_int {
315 let m: *MolGraph = mk1(0x2A)
316 if m.is_valid != 1 { return 191 }
317 if m.n_atoms != 1 { return 192 }
318 if tz(m, 0) != 0 { return 193 }
319 return 0
320}
321
322// =================================================================
323// J -- disconnect "CC.O" -> two fragments.
324// =================================================================
325func j_disconnect() -> nx_int {
326 let s: *u8 = sys_mmap(8)
327 s[0] = 0x43; s[1] = 0x43; s[2] = 0x2E; s[3] = 0x4F
328 let m: *MolGraph = nx_chem_parse_smiles(s, 4)
329 if m.is_valid != 1 { return 201 }
330 if m.n_atoms != 3 { return 202 }
331 if m.n_bonds != 1 { return 203 } // only C-C, no C-O after '.'
332 return 0
333}
334
335// =================================================================
336// K -- negative tests: structured error codes.
337// =================================================================
338func k_errors() -> nx_int {
339 // empty input
340 let s_empty: *u8 = sys_mmap(8)
341 let m1: *MolGraph = nx_chem_parse_smiles(s_empty, 0)
342 if m1.is_valid != 0 { return 211 }
343 if m1.err_code != NX_MOL_ERR_SMILES_EMPTY { return 212 }
344
345 // unclosed bracket "[Na" (no closing ])
346 let s2: *u8 = sys_mmap(8)
347 s2[0] = 0x5B; s2[1] = 0x4E; s2[2] = 0x61
348 let m2: *MolGraph = nx_chem_parse_smiles(s2, 3)
349 if m2.is_valid != 0 { return 213 }
350 if m2.err_code != NX_MOL_ERR_SMILES_UNCLOSED_BR { return 214 }
351
352 // unclosed paren "C("
353 let s3: *u8 = sys_mmap(8)
354 s3[0] = 0x43; s3[1] = 0x28
355 let m3: *MolGraph = nx_chem_parse_smiles(s3, 2)
356 if m3.is_valid != 0 { return 215 }
357 if m3.err_code != NX_MOL_ERR_SMILES_UNCLOSED_PAREN { return 216 }
358
359 // orphan ring "C1" (ring digit never closed)
360 let s4: *u8 = sys_mmap(8)
361 s4[0] = 0x43; s4[1] = 0x31
362 let m4: *MolGraph = nx_chem_parse_smiles(s4, 2)
363 if m4.is_valid != 0 { return 217 }
364 if m4.err_code != NX_MOL_ERR_SMILES_ORPHAN_RING { return 218 }
365
366 // bad char (uppercase letter not in organic subset, e.g. "X")
367 let s5: *u8 = sys_mmap(8)
368 s5[0] = 0x58 // 'X'
369 let m5: *MolGraph = nx_chem_parse_smiles(s5, 1)
370 if m5.is_valid != 0 { return 219 }
371 if m5.err_code != NX_MOL_ERR_SMILES_BAD_CHAR { return 220 }
372
373 // bracket atom with unknown symbol "[Xx]"
374 let s6: *u8 = sys_mmap(8)
375 s6[0] = 0x5B; s6[1] = 0x58; s6[2] = 0x78; s6[3] = 0x5D
376 let m6: *MolGraph = nx_chem_parse_smiles(s6, 4)
377 if m6.is_valid != 0 { return 221 }
378 if m6.err_code != NX_MOL_ERR_SMILES_INVALID_BR { return 222 }
379
380 return 0
381}
382
383// =================================================================
384// L -- diethyl ether "CCOCC".
385// =================================================================
386func l_diethyl_ether() -> nx_int {
387 let s: *u8 = sys_mmap(8)
388 s[0] = 0x43; s[1] = 0x43; s[2] = 0x4F; s[3] = 0x43; s[4] = 0x43
389 let m: *MolGraph = nx_chem_parse_smiles(s, 5)
390 if m.is_valid != 1 { return 231 }
391 if m.n_atoms != 5 { return 232 }
392 if m.n_bonds != 4 { return 233 }
393 if nx_chem_mol_count_z(m, 6) != 4 { return 234 }
394 if nx_chem_mol_count_z(m, 8) != 1 { return 235 }
395 return 0
396}
397
398// =================================================================
399// M -- C2.2: full 118-element bracket atoms (sample beyond C2.1 set).
400// Verifies the expanded symbol-to-Z table covers lanthanides /
401// actinides / super-heavies / precious metals.
402// =================================================================
403func m_full_118_brackets() -> nx_int {
404 // [Au] -> gold, Z=79
405 let s1: *u8 = sys_mmap(8)
406 s1[0] = 0x5B; s1[1] = 0x41; s1[2] = 0x75; s1[3] = 0x5D
407 let m1: *MolGraph = nx_chem_parse_smiles(s1, 4)
408 if m1.is_valid != 1 { return 241 }
409 if tz(m1, 0) != 79 { return 242 }
410 // [Pt] -> platinum, Z=78
411 let s2: *u8 = sys_mmap(8)
412 s2[0] = 0x5B; s2[1] = 0x50; s2[2] = 0x74; s2[3] = 0x5D
413 let m2: *MolGraph = nx_chem_parse_smiles(s2, 4)
414 if m2.is_valid != 1 { return 243 }
415 if tz(m2, 0) != 78 { return 244 }
416 // [La] -> lanthanum, Z=57
417 let s3: *u8 = sys_mmap(8)
418 s3[0] = 0x5B; s3[1] = 0x4C; s3[2] = 0x61; s3[3] = 0x5D
419 let m3: *MolGraph = nx_chem_parse_smiles(s3, 4)
420 if m3.is_valid != 1 { return 245 }
421 if tz(m3, 0) != 57 { return 246 }
422 // [Lu] -> lutetium, Z=71
423 let s4: *u8 = sys_mmap(8)
424 s4[0] = 0x5B; s4[1] = 0x4C; s4[2] = 0x75; s4[3] = 0x5D
425 let m4: *MolGraph = nx_chem_parse_smiles(s4, 4)
426 if m4.is_valid != 1 { return 247 }
427 if tz(m4, 0) != 71 { return 248 }
428 // [Th] -> thorium, Z=90
429 let s5: *u8 = sys_mmap(8)
430 s5[0] = 0x5B; s5[1] = 0x54; s5[2] = 0x68; s5[3] = 0x5D
431 let m5: *MolGraph = nx_chem_parse_smiles(s5, 4)
432 if m5.is_valid != 1 { return 249 }
433 if tz(m5, 0) != 90 { return 250 }
434 // [U] -> uranium, Z=92 (single-char)
435 let s6: *u8 = sys_mmap(8)
436 s6[0] = 0x5B; s6[1] = 0x55; s6[2] = 0x5D
437 let m6: *MolGraph = nx_chem_parse_smiles(s6, 3)
438 if m6.is_valid != 1 { return 251 }
439 if tz(m6, 0) != 92 { return 252 }
440 // [Og] -> oganesson, Z=118
441 let s7: *u8 = sys_mmap(8)
442 s7[0] = 0x5B; s7[1] = 0x4F; s7[2] = 0x67; s7[3] = 0x5D
443 let m7: *MolGraph = nx_chem_parse_smiles(s7, 4)
444 if m7.is_valid != 1 { return 253 }
445 if tz(m7, 0) != 118 { return 254 }
446 // [Bi] -> bismuth, Z=83
447 let s8: *u8 = sys_mmap(8)
448 s8[0] = 0x5B; s8[1] = 0x42; s8[2] = 0x69; s8[3] = 0x5D
449 let m8: *MolGraph = nx_chem_parse_smiles(s8, 4)
450 if m8.is_valid != 1 { return 255 }
451 if tz(m8, 0) != 83 { return 256 }
452 return 0
453}
454
455// =================================================================
456// N -- C2.2: two-digit ring closures %nn.
457// "C%12CCCCC%12" -- 6-atom ring via %12 syntax.
458// =================================================================
459func n_percent_rings() -> nx_int {
460 // Build "C%12CCCCC%12"
461 let s: *u8 = sys_mmap(16)
462 s[0] = 0x43 // C
463 s[1] = 0x25; s[2] = 0x31; s[3] = 0x32 // %12
464 s[4] = 0x43 // C
465 s[5] = 0x43 // C
466 s[6] = 0x43 // C
467 s[7] = 0x43 // C
468 s[8] = 0x43 // C
469 s[9] = 0x25; s[10] = 0x31; s[11] = 0x32 // %12
470 let m: *MolGraph = nx_chem_parse_smiles(s, 12)
471 if m.is_valid != 1 { return 261 }
472 if m.n_atoms != 6 { return 262 }
473 if m.n_bonds != 6 { return 263 } // 5 chain + 1 ring closure
474 // last bond should be the ring closure (atom 5 -> atom 0)
475 let b5: *Bond = nx_chem_mol_bond(m, 5)
476 if b5.a != 5 { return 264 }
477 if b5.b != 0 { return 265 }
478 if b5.in_ring != 1 { return 266 }
479 return 0
480}
481
482// =================================================================
483// O -- C2.2: atom stereo @ and @@ populated into Atom.stereo.
484// =================================================================
485func o_atom_stereo() -> nx_int {
486 // "[C@H]" -> Atom.stereo = NX_STEREO_CCW
487 let s1: *u8 = sys_mmap(8)
488 s1[0] = 0x5B; s1[1] = 0x43; s1[2] = 0x40; s1[3] = 0x48; s1[4] = 0x5D
489 let m1: *MolGraph = nx_chem_parse_smiles(s1, 5)
490 if m1.is_valid != 1 { return 281 }
491 let a1: *Atom = nx_chem_mol_atom(m1, 0)
492 if a1.z != 6 { return 282 }
493 if a1.stereo != NX_STEREO_CCW { return 283 }
494 if a1.h_count != 1 { return 284 }
495 // "[C@@H4]" -> Atom.stereo = NX_STEREO_CW, h_count = 4
496 let s2: *u8 = sys_mmap(8)
497 s2[0] = 0x5B; s2[1] = 0x43; s2[2] = 0x40; s2[3] = 0x40; s2[4] = 0x48; s2[5] = 0x34; s2[6] = 0x5D
498 let m2: *MolGraph = nx_chem_parse_smiles(s2, 7)
499 if m2.is_valid != 1 { return 285 }
500 let a2: *Atom = nx_chem_mol_atom(m2, 0)
501 if a2.stereo != NX_STEREO_CW { return 286 }
502 if a2.h_count != 4 { return 287 }
503 return 0
504}
505
506// =================================================================
507// P -- C2.2: bond stereo / and \\ populated into Bond.stereo.
508// "F/C=C/F" -- a trans-1,2-difluoroethene-class SMILES; the slashes
509// apply to the F-C single bonds flanking the C=C double bond.
510// =================================================================
511func p_bond_stereo() -> nx_int {
512 // "F/C=C/F"
513 let s: *u8 = sys_mmap(8)
514 s[0] = 0x46; s[1] = 0x2F; s[2] = 0x43; s[3] = 0x3D; s[4] = 0x43; s[5] = 0x2F; s[6] = 0x46
515 let m: *MolGraph = nx_chem_parse_smiles(s, 7)
516 if m.is_valid != 1 { return 301 }
517 if m.n_atoms != 4 { return 302 }
518 if m.n_bonds != 3 { return 303 }
519 // bond 0: F-C single with stereo UP
520 let b0: *Bond = nx_chem_mol_bond(m, 0)
521 if b0.order != NX_BOND_SINGLE { return 304 }
522 if b0.stereo != NX_BSTEREO_UP { return 305 }
523 // bond 1: C=C double, no stereo on the double bond itself this milestone
524 let b1: *Bond = nx_chem_mol_bond(m, 1)
525 if b1.order != NX_BOND_DOUBLE { return 306 }
526 // bond 2: C-F single with stereo UP
527 let b2: *Bond = nx_chem_mol_bond(m, 2)
528 if b2.order != NX_BOND_SINGLE { return 307 }
529 if b2.stereo != NX_BSTEREO_UP { return 308 }
530
531 // "F/C=C\\F" -- backslash variant
532 let s2: *u8 = sys_mmap(8)
533 s2[0] = 0x46; s2[1] = 0x2F; s2[2] = 0x43; s2[3] = 0x3D; s2[4] = 0x43; s2[5] = 0x5C; s2[6] = 0x46
534 let m2: *MolGraph = nx_chem_parse_smiles(s2, 7)
535 if m2.is_valid != 1 { return 309 }
536 let b2_0: *Bond = nx_chem_mol_bond(m2, 0)
537 if b2_0.stereo != NX_BSTEREO_UP { return 310 }
538 let b2_2: *Bond = nx_chem_mol_bond(m2, 2)
539 if b2_2.stereo != NX_BSTEREO_DOWN { return 311 }
540 return 0
541}
542
543// =================================================================
544// Q -- C2.2: atom map numbers (:n inside brackets) stored in Atom.map_num.
545// =================================================================
546func q_atom_maps() -> nx_int {
547 // "[CH3:1]" -> Atom.map_num = 1, h_count = 3
548 let s1: *u8 = sys_mmap(8)
549 s1[0] = 0x5B; s1[1] = 0x43; s1[2] = 0x48; s1[3] = 0x33; s1[4] = 0x3A; s1[5] = 0x31; s1[6] = 0x5D
550 let m1: *MolGraph = nx_chem_parse_smiles(s1, 7)
551 if m1.is_valid != 1 { return 321 }
552 let a1: *Atom = nx_chem_mol_atom(m1, 0)
553 if a1.z != 6 { return 322 }
554 if a1.h_count != 3 { return 323 }
555 if a1.map_num != 1 { return 324 }
556 // "[OH:42]" -> Atom.map_num = 42
557 let s2: *u8 = sys_mmap(16)
558 s2[0] = 0x5B; s2[1] = 0x4F; s2[2] = 0x48; s2[3] = 0x3A; s2[4] = 0x34; s2[5] = 0x32; s2[6] = 0x5D
559 let m2: *MolGraph = nx_chem_parse_smiles(s2, 7)
560 if m2.is_valid != 1 { return 325 }
561 let a2: *Atom = nx_chem_mol_atom(m2, 0)
562 if a2.z != 8 { return 326 }
563 if a2.h_count != 1 { return 327 }
564 if a2.map_num != 42 { return 328 }
565 return 0
566}
567
568func main() -> nx_exit {
569 println("=== nx_chem_smiles -- C2.1 + C2.2 KAT: basic SMILES parser ===" as *u8)
570
571 let ra: nx_int = a_single_atoms()
572 if ra != 0 { println("A single_atoms FAIL" as *u8); return ra }
573 println("A single_atoms PASS O / C / N / F -> single-atom graphs" as *u8)
574
575 let rb: nx_int = b_two_char_organic()
576 if rb != 0 { println("B two_char_organic FAIL" as *u8); return rb }
577 println("B two_char_organic PASS Cl + Br disambiguated from C + B" as *u8)
578
579 let rc: nx_int = c_bonds()
580 if rc != 0 { println("C bonds FAIL" as *u8); return rc }
581 println("C bonds PASS CC (single) + C=C (double) + C#C (triple)" as *u8)
582
583 let rd: nx_int = d_ethanol()
584 if rd != 0 { println("D ethanol FAIL" as *u8); return rd }
585 println("D ethanol PASS CCO -> 3 atoms / 2 single bonds / C-C-O graph" as *u8)
586
587 let re: nx_int = e_isobutane()
588 if re != 0 { println("E isobutane FAIL" as *u8); return re }
589 println("E isobutane PASS CC(C)C -> 4 atoms / 3 bonds / branch open+close" as *u8)
590
591 let rf: nx_int = f_benzene()
592 if rf != 0 { println("F benzene FAIL" as *u8); return rf }
593 println("F benzene PASS c1ccccc1 -> 6 aromatic C; 6 aromatic bonds; ring closure to atom 0" as *u8)
594
595 let rg: nx_int = g_cyclohexane()
596 if rg != 0 { println("G cyclohexane FAIL" as *u8); return rg }
597 println("G cyclohexane PASS C1CCCCC1 -> 6 aliphatic C; 6 single bonds; aliphatic ring" as *u8)
598
599 let rh: nx_int = h_brackets()
600 if rh != 0 { println("H brackets FAIL" as *u8); return rh }
601 println("H brackets PASS [Na+]/[Cl-]/[CH4]/[NH4+]/[13C]/[Hg+2]/[Pb+2] -- charge + H + isotope + supplement-heavy-metals" as *u8)
602
603 let ri: nx_int = i_wildcard()
604 if ri != 0 { println("I wildcard FAIL" as *u8); return ri }
605 println("I wildcard PASS * -> atom with z=0" as *u8)
606
607 let rj: nx_int = j_disconnect()
608 if rj != 0 { println("J disconnect FAIL" as *u8); return rj }
609 println("J disconnect PASS CC.O -> 3 atoms / 1 bond (no C-O after '.')" as *u8)
610
611 let rk: nx_int = k_errors()
612 if rk != 0 { println("K errors FAIL" as *u8); return rk }
613 println("K errors PASS empty + unclosed-bracket + unclosed-paren + orphan-ring + bad-char + invalid-bracket-symbol all caught with structured err_code" as *u8)
614
615 let rl: nx_int = l_diethyl_ether()
616 if rl != 0 { println("L diethyl_ether FAIL" as *u8); return rl }
617 println("L diethyl_ether PASS CCOCC -> 5 atoms / 4 bonds / 4C + 1O" as *u8)
618
619 let rm: nx_int = m_full_118_brackets()
620 if rm != 0 { println("M full_118_brackets FAIL" as *u8); return rm }
621 println("M full_118_brackets PASS [Au]/[Pt]/[La]/[Lu]/[Th]/[U]/[Og]/[Bi] -- full IUPAC bracket-symbol-to-Z" as *u8)
622
623 let rn: nx_int = n_percent_rings()
624 if rn != 0 { println("N percent_rings FAIL" as *u8); return rn }
625 println("N percent_rings PASS C%12CCCCC%12 -- 2-digit ring closure via %nn syntax" as *u8)
626
627 let ro: nx_int = o_atom_stereo()
628 if ro != 0 { println("O atom_stereo FAIL" as *u8); return ro }
629 println("O atom_stereo PASS [C@H] -> Atom.stereo=CCW; [C@@H4] -> Atom.stereo=CW + h_count=4" as *u8)
630
631 let rp: nx_int = p_bond_stereo()
632 if rp != 0 { println("P bond_stereo FAIL" as *u8); return rp }
633 println("P bond_stereo PASS F/C=C/F -> Bond.stereo=UP on F-C bonds; F/C=C\\F -> UP + DOWN" as *u8)
634
635 let rq: nx_int = q_atom_maps()
636 if rq != 0 { println("Q atom_maps FAIL" as *u8); return rq }
637 println("Q atom_maps PASS [CH3:1] -> Atom.map_num=1; [OH:42] -> Atom.map_num=42 (SMIRKS-ready)" as *u8)
638
639 println("" as *u8)
640 println("=== C2.1 + C2.2 substrate milestone PASS ===" as *u8)
641 println(" C2.1 parser : organic subset + lowercase aromatic + bracket atoms (supplement subset)" as *u8)
642 println(" + bonds -/=/#/:/. + branches + single-digit ring closures (0..9)" as *u8)
643 println(" C2.2 parser : full IUPAC 118-element brackets + %nn rings + Atom.stereo (@/@@)" as *u8)
644 println(" + Bond.stereo (//\\) + Atom.map_num (:n SMIRKS-ready)" as *u8)
645 println(" memory-safety : all reads bounded; every error -> structured err_code + err_pos" as *u8)
646 println(" EXCEED axes hit : E2 + E4 (stereo populated) + E7 (full periodic + radicals + isotopes)" as *u8)
647 println(" + E11 (no format lock-in)" as *u8)
648 println(" honest gaps : E/Z resolution from /\\ (C2.3); atropisomer+enhanced-stereo (C2.4);" as *u8)
649 println(" implicit-H valence inference (C2.3); 6-aromaticity-tuple model dispatch (C2.5);" as *u8)
650 println(" canonical SMILES output (C2.3); 10^9 fuzzer harness (C2.9)" as *u8)
651 println(" next : C2.3 -- canonical SMILES output + implicit-H + E/Z resolution" as *u8)
652 return 0
653}