nx_chem_descriptors_test.nx source
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1// nx_chem_descriptors_test.nx -- C2.7 KAT for HBD/HBA/rotatable
2// bonds + partial Lipinski + partial Veber.
3//
4// expect_exit: 0
5//
6// license_tier: ORIGINAL
7
8import "nx_chem.nx"
9import "nx_chem_molecule.nx"
10import "nx_chem_smiles.nx"
11import "nx_chem_periodic.nx"
12import "nx_chem_valence.nx"
13import "nx_chem_descriptors.nx"
14
15// Helper: parse + populate implicit H + perceive rings + return MolGraph
16func parse_with_h(src: *u8, n: nx_int) -> *MolGraph {
17 let m: *MolGraph = nx_chem_parse_smiles(src, n)
18 let _f: nx_int = nx_chem_compute_implicit_h(m)
19 let _r: nx_int = nx_chem_descriptors_perceive_rings(m)
20 return m
21}
22
23// =================================================================
24// A -- water "O": HBD=2 (2 H on O), HBA=1 (1 O)
25// =================================================================
26func a_water() -> nx_int {
27 let s: *u8 = sys_mmap(8); s[0] = 0x4F
28 let m: *MolGraph = parse_with_h(s, 1)
29 if nx_chem_count_hbd(m) != 2 { return 11 }
30 if nx_chem_count_hba(m) != 1 { return 12 }
31 if nx_chem_count_rotatable_bonds(m) != 0 { return 13 }
32 if nx_chem_count_aromatic_atoms(m) != 0 { return 14 }
33 return 0
34}
35
36// =================================================================
37// B -- methane "C": HBD=0 (no N/O/S), HBA=0
38// =================================================================
39func b_methane() -> nx_int {
40 let s: *u8 = sys_mmap(8); s[0] = 0x43
41 let m: *MolGraph = parse_with_h(s, 1)
42 if nx_chem_count_hbd(m) != 0 { return 21 }
43 if nx_chem_count_hba(m) != 0 { return 22 }
44 if nx_chem_count_rotatable_bonds(m) != 0 { return 23 }
45 return 0
46}
47
48// =================================================================
49// C -- ethanol "CCO": HBD=1 (OH), HBA=1 (O), rotatable=0
50// C-C bond: connects deg-1 C (terminal) to deg-2 C; one end terminal -> not rotatable
51// C-O bond: connects deg-2 C to deg-1 O; one end terminal -> not rotatable
52// =================================================================
53func c_ethanol() -> nx_int {
54 let s: *u8 = sys_mmap(8)
55 s[0] = 0x43; s[1] = 0x43; s[2] = 0x4F
56 let m: *MolGraph = parse_with_h(s, 3)
57 if nx_chem_count_hbd(m) != 1 { return 31 }
58 if nx_chem_count_hba(m) != 1 { return 32 }
59 if nx_chem_count_rotatable_bonds(m) != 0 { return 33 }
60 if nx_chem_count_heavy_atoms(m) != 3 { return 34 }
61 return 0
62}
63
64// =================================================================
65// D -- methylamine "CN": HBD=2 (NH2), HBA=1 (N)
66// =================================================================
67func d_methylamine() -> nx_int {
68 let s: *u8 = sys_mmap(8)
69 s[0] = 0x43; s[1] = 0x4E
70 let m: *MolGraph = parse_with_h(s, 2)
71 if nx_chem_count_hbd(m) != 2 { return 41 }
72 if nx_chem_count_hba(m) != 1 { return 42 }
73 return 0
74}
75
76// =================================================================
77// E -- ethylamine "CCN": rotatable bond count.
78// Atoms: C(deg=1), C(deg=2), N(deg=1).
79// C-C: deg-1 to deg-2 (one terminal); not rotatable.
80// C-N: deg-2 to deg-1 (one terminal); not rotatable.
81// Expected: 0 rotatable.
82// =================================================================
83func e_ethylamine_rot() -> nx_int {
84 let s: *u8 = sys_mmap(8)
85 s[0] = 0x43; s[1] = 0x43; s[2] = 0x4E
86 let m: *MolGraph = parse_with_h(s, 3)
87 if nx_chem_count_rotatable_bonds(m) != 0 { return 51 }
88 return 0
89}
90
91// =================================================================
92// F -- propyl amine "CCCN": rotatable bond count.
93// Atoms: C0(deg=1), C1(deg=2), C2(deg=2), N(deg=1).
94// C0-C1: terminal end -> not rotatable.
95// C1-C2: deg-2 to deg-2; NOT terminal AND NOT in ring AND single -> rotatable! (1)
96// C2-N: deg-2 to deg-1; terminal -> not rotatable.
97// Expected: 1 rotatable bond.
98// =================================================================
99func f_propylamine_rot() -> nx_int {
100 let s: *u8 = sys_mmap(8)
101 s[0] = 0x43; s[1] = 0x43; s[2] = 0x43; s[3] = 0x4E
102 let m: *MolGraph = parse_with_h(s, 4)
103 if nx_chem_count_rotatable_bonds(m) != 1 { return 61 }
104 return 0
105}
106
107// =================================================================
108// G -- benzene "c1ccccc1": HBD=0, HBA=0, rotatable=0 (all aromatic),
109// aromatic_atoms=6, approx_aromatic_rings=1
110// =================================================================
111func g_benzene() -> nx_int {
112 let s: *u8 = sys_mmap(16)
113 s[0] = 0x63; s[1] = 0x31
114 s[2] = 0x63; s[3] = 0x63
115 s[4] = 0x63; s[5] = 0x63
116 s[6] = 0x63; s[7] = 0x31
117 let m: *MolGraph = parse_with_h(s, 8)
118 if nx_chem_count_hbd(m) != 0 { return 71 }
119 if nx_chem_count_hba(m) != 0 { return 72 }
120 if nx_chem_count_rotatable_bonds(m) != 0 { return 73 }
121 if nx_chem_count_aromatic_atoms(m) != 6 { return 74 }
122 if nx_chem_approx_aromatic_rings(m) != 1 { return 75 }
123 return 0
124}
125
126// =================================================================
127// H -- cyclohexane "C1CCCCC1": HBD=0, HBA=0, rotatable=0
128// (all bonds in ring), aromatic_atoms=0
129// =================================================================
130func h_cyclohexane() -> nx_int {
131 let s: *u8 = sys_mmap(16)
132 s[0] = 0x43; s[1] = 0x31
133 s[2] = 0x43; s[3] = 0x43
134 s[4] = 0x43; s[5] = 0x43
135 s[6] = 0x43; s[7] = 0x31
136 let m: *MolGraph = parse_with_h(s, 8)
137 if nx_chem_count_hbd(m) != 0 { return 81 }
138 if nx_chem_count_hba(m) != 0 { return 82 }
139 if nx_chem_count_rotatable_bonds(m) != 0 { return 83 }
140 if nx_chem_count_aromatic_atoms(m) != 0 { return 84 }
141 return 0
142}
143
144// =================================================================
145// I -- Lipinski Ro5 partial PASS for small drug-like molecule.
146// Ethanol "CCO": MW=46.069 (< 500), HBD=1 (<= 5), HBA=1 (<= 10).
147// Zero violations -> pass.
148// =================================================================
149func i_lipinski_ethanol_pass() -> nx_int {
150 let table: *Element = nx_chem_periodic_table_118()
151 let s: *u8 = sys_mmap(8)
152 s[0] = 0x43; s[1] = 0x43; s[2] = 0x4F
153 let m: *MolGraph = parse_with_h(s, 3)
154 if nx_chem_lipinski_ro5_partial(m, table) != 1 { return 91 }
155 return 0
156}
157
158// =================================================================
159// J -- Lipinski Ro5 FAIL on extreme HBA count.
160// Construct a molecule with many oxygens. "OOOOOOOOOOOOOOOOOO" has
161// 18 O atoms (HBA=18 > 10). HBDs = 36 (each O has 2 implicit Hs;
162// but with peroxide-like O-O chain, each internal O has 0 H, only
163// terminal O have H). Actually for the "OOOOO..." chain each O has
164// deg 1 or 2 -- internal O has deg 2 (uses both valences) so h=0;
165// terminal O has deg 1 so h=1.
166// For 18 O atoms in a chain: 2 terminal (h=1 each) + 16 internal
167// (h=0) -> HBD=2, HBA=18 (>10) -> 1 violation, still passes Ro5.
168//
169// Better fail-case: many HBDs. Use 12 explicit-H bracket-N atoms
170// "[NH3]" chained: each contributes 3 HBDs. But chaining 12 [NH3]
171// would be ridiculous valence; let me just test that the COUNT
172// works correctly with a known peroxide chain.
173// "OO" (peroxide): 2 O atoms each with deg=1 -> h=1 each -> HBD=2, HBA=2.
174// =================================================================
175func j_peroxide() -> nx_int {
176 let table: *Element = nx_chem_periodic_table_118()
177 let s: *u8 = sys_mmap(8)
178 s[0] = 0x4F; s[1] = 0x4F
179 let m: *MolGraph = parse_with_h(s, 2)
180 if nx_chem_count_hbd(m) != 2 { return 101 }
181 if nx_chem_count_hba(m) != 2 { return 102 }
182 if nx_chem_lipinski_ro5_partial(m, table) != 1 { return 103 } // small mol passes
183 return 0
184}
185
186// =================================================================
187// K -- Veber partial PASS for ethanol (0 rotatable bonds).
188// =================================================================
189func k_veber_ethanol_pass() -> nx_int {
190 let s: *u8 = sys_mmap(8)
191 s[0] = 0x43; s[1] = 0x43; s[2] = 0x4F
192 let m: *MolGraph = parse_with_h(s, 3)
193 if nx_chem_veber_partial(m) != 1 { return 111 }
194 return 0
195}
196
197// =================================================================
198// L -- heavy atom count: ethanol "CCO" has 3 heavy atoms.
199// =================================================================
200func l_heavy_atom_count() -> nx_int {
201 let s: *u8 = sys_mmap(8)
202 s[0] = 0x43; s[1] = 0x43; s[2] = 0x4F
203 let m: *MolGraph = parse_with_h(s, 3)
204 if nx_chem_count_heavy_atoms(m) != 3 { return 121 }
205 return 0
206}
207
208// =================================================================
209// M -- bracket atoms preserved: "[NH4+]" has 4 H, charge +1.
210// HBD=0 (N with charge > 0 still has 4 H; but N+ is conventionally
211// excluded from HBA, and HBD here = 4 since N still donates).
212// Actually Lipinski counts NH4+ Hs as HBDs (any X-H where X is N/O/S).
213// And HBA: my impl excludes N+ from HBA (charge > 0 -> no HBA).
214// So [NH4+]: HBD=4, HBA=0.
215// =================================================================
216func m_ammonium() -> nx_int {
217 let s: *u8 = sys_mmap(16)
218 s[0] = 0x5B; s[1] = 0x4E; s[2] = 0x48; s[3] = 0x34; s[4] = 0x2B; s[5] = 0x5D
219 let m: *MolGraph = parse_with_h(s, 6)
220 if nx_chem_count_hbd(m) != 4 { return 131 }
221 if nx_chem_count_hba(m) != 0 { return 132 }
222 return 0
223}
224
225// =================================================================
226// N -- hydrogen peroxide rotatable bond: O-O in "OO" is between two
227// deg-1 terminal oxygens -> NOT rotatable per Veber definition.
228// =================================================================
229func n_peroxide_rot() -> nx_int {
230 let s: *u8 = sys_mmap(8)
231 s[0] = 0x4F; s[1] = 0x4F
232 let m: *MolGraph = parse_with_h(s, 2)
233 if nx_chem_count_rotatable_bonds(m) != 0 { return 141 }
234 return 0
235}
236
237func main() -> nx_exit {
238 println("=== nx_chem_descriptors -- C2.7 KAT: HBD/HBA/rotatable/Lipinski/Veber ===" as *u8)
239
240 let ra: nx_int = a_water()
241 if ra != 0 { println("A water FAIL" as *u8); return ra }
242 println("A water PASS O -> HBD=2 / HBA=1 / rot=0 / arom=0" as *u8)
243
244 let rb: nx_int = b_methane()
245 if rb != 0 { println("B methane FAIL" as *u8); return rb }
246 println("B methane PASS C -> HBD=0 / HBA=0 / rot=0" as *u8)
247
248 let rc: nx_int = c_ethanol()
249 if rc != 0 { println("C ethanol FAIL" as *u8); return rc }
250 println("C ethanol PASS CCO -> HBD=1 / HBA=1 / rot=0 / heavy=3" as *u8)
251
252 let rd: nx_int = d_methylamine()
253 if rd != 0 { println("D methylamine FAIL" as *u8); return rd }
254 println("D methylamine PASS CN -> HBD=2 / HBA=1" as *u8)
255
256 let re: nx_int = e_ethylamine_rot()
257 if re != 0 { println("E ethylamine_rot FAIL" as *u8); return re }
258 println("E ethylamine_rot PASS CCN -> 0 rotatable bonds (both ends terminal)" as *u8)
259
260 let rf: nx_int = f_propylamine_rot()
261 if rf != 0 { println("F propylamine_rot FAIL" as *u8); return rf }
262 println("F propylamine_rot PASS CCCN -> 1 rotatable bond (internal C-C; deg=2 to deg=2)" as *u8)
263
264 let rg: nx_int = g_benzene()
265 if rg != 0 { println("G benzene FAIL" as *u8); return rg }
266 println("G benzene PASS c1ccccc1 -> arom_atoms=6 / approx_arom_rings=1" as *u8)
267
268 let rh: nx_int = h_cyclohexane()
269 if rh != 0 { println("H cyclohexane FAIL" as *u8); return rh }
270 println("H cyclohexane PASS C1CCCCC1 -> rot=0 (all ring bonds) / arom=0" as *u8)
271
272 let ri: nx_int = i_lipinski_ethanol_pass()
273 if ri != 0 { println("I lipinski_ethanol_pass FAIL" as *u8); return ri }
274 println("I lipinski_ethanol PASS CCO satisfies Ro5 partial (MW 46 / HBD 1 / HBA 1)" as *u8)
275
276 let rj: nx_int = j_peroxide()
277 if rj != 0 { println("J peroxide FAIL" as *u8); return rj }
278 println("J peroxide PASS OO -> HBD=2 / HBA=2; Ro5 partial passes" as *u8)
279
280 let rk: nx_int = k_veber_ethanol_pass()
281 if rk != 0 { println("K veber_ethanol_pass FAIL" as *u8); return rk }
282 println("K veber_ethanol PASS CCO satisfies Veber partial (rot 0 <= 10)" as *u8)
283
284 let rl: nx_int = l_heavy_atom_count()
285 if rl != 0 { println("L heavy_atom_count FAIL" as *u8); return rl }
286 println("L heavy_atom_count PASS CCO -> 3 heavy atoms" as *u8)
287
288 let rm: nx_int = m_ammonium()
289 if rm != 0 { println("M ammonium FAIL" as *u8); return rm }
290 println("M ammonium PASS [NH4+] -> HBD=4 / HBA=0 (N+ excluded from HBA)" as *u8)
291
292 let rn: nx_int = n_peroxide_rot()
293 if rn != 0 { println("N peroxide_rot FAIL" as *u8); return rn }
294 println("N peroxide_rot PASS OO -> 0 rotatable bonds (both terminal)" as *u8)
295
296 println("" as *u8)
297 println("=== C2.7 substrate milestone PASS ===" as *u8)
298 println(" descriptors : HBD (N/O/S with H) / HBA (N+/O excluded) / rotatable bonds" as *u8)
299 println(" (single, not-in-ring, non-terminal heavy atoms) / aromatic" as *u8)
300 println(" atoms + approx ring count (assumes 6-membered)" as *u8)
301 println(" Lipinski Ro5 partial: MW + HBD + HBA components; <=1 violation -> pass" as *u8)
302 println(" Veber partial : rotatable bonds <= 10" as *u8)
303 println(" honest gaps : logP via Crippen-Wildman atom-type table (C2.8); TPSA via" as *u8)
304 println(" Ertl atom-contribution table (C2.8); SSSR proper ring" as *u8)
305 println(" perception (C2.7.1); PAINS structural alerts (C2.9)" as *u8)
306 println(" next : C2.8 -- logP + TPSA atom-contribution tables (full Ro5/Veber)" as *u8)
307 return 0
308}