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ResiduePropertiesTest | 35 | 1,464 | 12 |
1 | /* | |
2 | * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) | |
3 | * Copyright (C) $$Year-Rel$$ The Jalview Authors | |
4 | * | |
5 | * This file is part of Jalview. | |
6 | * | |
7 | * Jalview is free software: you can redistribute it and/or | |
8 | * modify it under the terms of the GNU General Public License | |
9 | * as published by the Free Software Foundation, either version 3 | |
10 | * of the License, or (at your option) any later version. | |
11 | * | |
12 | * Jalview is distributed in the hope that it will be useful, but | |
13 | * WITHOUT ANY WARRANTY; without even the implied warranty | |
14 | * of MERCHANTABILITY or FITNESS FOR A PARTICULAR | |
15 | * PURPOSE. See the GNU General Public License for more details. | |
16 | * | |
17 | * You should have received a copy of the GNU General Public License | |
18 | * along with Jalview. If not, see <http://www.gnu.org/licenses/>. | |
19 | * The Jalview Authors are detailed in the 'AUTHORS' file. | |
20 | */ | |
21 | package jalview.schemes; | |
22 | ||
23 | import static org.testng.AssertJUnit.assertEquals; | |
24 | import static org.testng.AssertJUnit.assertNull; | |
25 | ||
26 | import java.util.Collections; | |
27 | import java.util.List; | |
28 | import java.util.Map; | |
29 | ||
30 | import org.testng.annotations.BeforeClass; | |
31 | import org.testng.annotations.Test; | |
32 | ||
33 | import jalview.gui.JvOptionPane; | |
34 | ||
35 | public class ResiduePropertiesTest | |
36 | { | |
37 | ||
38 | 1 | @BeforeClass(alwaysRun = true) |
39 | public void setUpJvOptionPane() | |
40 | { | |
41 | 1 | JvOptionPane.setInteractiveMode(false); |
42 | 1 | JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); |
43 | } | |
44 | ||
45 | /** | |
46 | * Test 'standard' codon translations (no ambiguity codes) | |
47 | */ | |
48 | 1 | @Test(groups = { "Functional" }) |
49 | public void testCodonTranslate() | |
50 | { | |
51 | // standard translation table order column 1/2/3/4 | |
52 | 1 | assertEquals("F", ResidueProperties.codonTranslate("TTT")); |
53 | 1 | assertEquals("F", ResidueProperties.codonTranslate("TTC")); |
54 | 1 | assertEquals("L", ResidueProperties.codonTranslate("TTA")); |
55 | 1 | assertEquals("L", ResidueProperties.codonTranslate("TTG")); |
56 | 1 | assertEquals("L", ResidueProperties.codonTranslate("CTT")); |
57 | 1 | assertEquals("L", ResidueProperties.codonTranslate("CTC")); |
58 | 1 | assertEquals("L", ResidueProperties.codonTranslate("CTA")); |
59 | 1 | assertEquals("L", ResidueProperties.codonTranslate("CTG")); |
60 | 1 | assertEquals("I", ResidueProperties.codonTranslate("ATT")); |
61 | 1 | assertEquals("I", ResidueProperties.codonTranslate("ATC")); |
62 | 1 | assertEquals("I", ResidueProperties.codonTranslate("ATA")); |
63 | 1 | assertEquals("M", ResidueProperties.codonTranslate("ATG")); |
64 | 1 | assertEquals("V", ResidueProperties.codonTranslate("GTT")); |
65 | 1 | assertEquals("V", ResidueProperties.codonTranslate("GTC")); |
66 | 1 | assertEquals("V", ResidueProperties.codonTranslate("GTA")); |
67 | 1 | assertEquals("V", ResidueProperties.codonTranslate("GTG")); |
68 | 1 | assertEquals("S", ResidueProperties.codonTranslate("TCT")); |
69 | 1 | assertEquals("S", ResidueProperties.codonTranslate("TCC")); |
70 | 1 | assertEquals("S", ResidueProperties.codonTranslate("TCA")); |
71 | 1 | assertEquals("S", ResidueProperties.codonTranslate("TCG")); |
72 | 1 | assertEquals("P", ResidueProperties.codonTranslate("CCT")); |
73 | 1 | assertEquals("P", ResidueProperties.codonTranslate("CCC")); |
74 | 1 | assertEquals("P", ResidueProperties.codonTranslate("CCA")); |
75 | 1 | assertEquals("P", ResidueProperties.codonTranslate("CCG")); |
76 | 1 | assertEquals("T", ResidueProperties.codonTranslate("ACT")); |
77 | 1 | assertEquals("T", ResidueProperties.codonTranslate("ACC")); |
78 | 1 | assertEquals("T", ResidueProperties.codonTranslate("ACA")); |
79 | 1 | assertEquals("T", ResidueProperties.codonTranslate("ACG")); |
80 | 1 | assertEquals("A", ResidueProperties.codonTranslate("GCT")); |
81 | 1 | assertEquals("A", ResidueProperties.codonTranslate("GCC")); |
82 | 1 | assertEquals("A", ResidueProperties.codonTranslate("GCA")); |
83 | 1 | assertEquals("A", ResidueProperties.codonTranslate("GCG")); |
84 | 1 | assertEquals("Y", ResidueProperties.codonTranslate("TAT")); |
85 | 1 | assertEquals("Y", ResidueProperties.codonTranslate("TAC")); |
86 | 1 | assertEquals("STOP", ResidueProperties.codonTranslate("TAA")); |
87 | 1 | assertEquals("STOP", ResidueProperties.codonTranslate("TAG")); |
88 | 1 | assertEquals("H", ResidueProperties.codonTranslate("CAT")); |
89 | 1 | assertEquals("H", ResidueProperties.codonTranslate("CAC")); |
90 | 1 | assertEquals("Q", ResidueProperties.codonTranslate("CAA")); |
91 | 1 | assertEquals("Q", ResidueProperties.codonTranslate("CAG")); |
92 | 1 | assertEquals("N", ResidueProperties.codonTranslate("AAT")); |
93 | 1 | assertEquals("N", ResidueProperties.codonTranslate("AAC")); |
94 | 1 | assertEquals("K", ResidueProperties.codonTranslate("AAA")); |
95 | 1 | assertEquals("K", ResidueProperties.codonTranslate("AAG")); |
96 | 1 | assertEquals("D", ResidueProperties.codonTranslate("GAT")); |
97 | 1 | assertEquals("D", ResidueProperties.codonTranslate("GAC")); |
98 | 1 | assertEquals("E", ResidueProperties.codonTranslate("GAA")); |
99 | 1 | assertEquals("E", ResidueProperties.codonTranslate("GAG")); |
100 | 1 | assertEquals("C", ResidueProperties.codonTranslate("TGT")); |
101 | 1 | assertEquals("C", ResidueProperties.codonTranslate("TGC")); |
102 | 1 | assertEquals("STOP", ResidueProperties.codonTranslate("TGA")); |
103 | 1 | assertEquals("W", ResidueProperties.codonTranslate("TGG")); |
104 | 1 | assertEquals("R", ResidueProperties.codonTranslate("CGT")); |
105 | 1 | assertEquals("R", ResidueProperties.codonTranslate("CGC")); |
106 | 1 | assertEquals("R", ResidueProperties.codonTranslate("CGA")); |
107 | 1 | assertEquals("R", ResidueProperties.codonTranslate("CGG")); |
108 | 1 | assertEquals("S", ResidueProperties.codonTranslate("AGT")); |
109 | 1 | assertEquals("S", ResidueProperties.codonTranslate("AGC")); |
110 | 1 | assertEquals("R", ResidueProperties.codonTranslate("AGA")); |
111 | 1 | assertEquals("R", ResidueProperties.codonTranslate("AGG")); |
112 | 1 | assertEquals("G", ResidueProperties.codonTranslate("GGT")); |
113 | 1 | assertEquals("G", ResidueProperties.codonTranslate("GGC")); |
114 | 1 | assertEquals("G", ResidueProperties.codonTranslate("GGA")); |
115 | 1 | assertEquals("G", ResidueProperties.codonTranslate("GGG")); |
116 | } | |
117 | ||
118 | /** | |
119 | * Test a sample of codon translations involving ambiguity codes. Should | |
120 | * return a protein value where the ambiguity does not affect the translation. | |
121 | */ | |
122 | 1 | @Test(groups = { "Functional" }) |
123 | public void testCodonTranslate_ambiguityCodes() | |
124 | { | |
125 | // Y is C or T | |
126 | 1 | assertEquals("C", ResidueProperties.codonTranslate("TGY")); |
127 | // Phenylalanine first base variation | |
128 | 1 | assertEquals("L", ResidueProperties.codonTranslate("YTA")); |
129 | ||
130 | // W is A or T | |
131 | 1 | assertEquals("L", ResidueProperties.codonTranslate("CTW")); |
132 | 1 | assertNull(ResidueProperties.codonTranslate("TTW")); |
133 | ||
134 | // S is G or C | |
135 | 1 | assertEquals("G", ResidueProperties.codonTranslate("GGS")); |
136 | 1 | assertNull(ResidueProperties.codonTranslate("ATS")); |
137 | ||
138 | // K is T or G | |
139 | 1 | assertEquals("S", ResidueProperties.codonTranslate("TCK")); |
140 | 1 | assertNull(ResidueProperties.codonTranslate("ATK")); |
141 | ||
142 | // M is C or A | |
143 | 1 | assertEquals("T", ResidueProperties.codonTranslate("ACM")); |
144 | // Arginine first base variation | |
145 | 1 | assertEquals("R", ResidueProperties.codonTranslate("MGA")); |
146 | 1 | assertEquals("R", ResidueProperties.codonTranslate("MGG")); |
147 | 1 | assertNull(ResidueProperties.codonTranslate("TAM")); |
148 | ||
149 | // D is A, G or T | |
150 | 1 | assertEquals("P", ResidueProperties.codonTranslate("CCD")); |
151 | 1 | assertNull(ResidueProperties.codonTranslate("AAD")); |
152 | ||
153 | // V is A, C or G | |
154 | 1 | assertEquals("V", ResidueProperties.codonTranslate("GTV")); |
155 | 1 | assertNull(ResidueProperties.codonTranslate("TTV")); |
156 | ||
157 | // H is A, C or T | |
158 | 1 | assertEquals("A", ResidueProperties.codonTranslate("GCH")); |
159 | 1 | assertEquals("I", ResidueProperties.codonTranslate("ATH")); |
160 | 1 | assertNull(ResidueProperties.codonTranslate("AGH")); |
161 | ||
162 | // B is C, G or T | |
163 | 1 | assertEquals("P", ResidueProperties.codonTranslate("CCB")); |
164 | 1 | assertNull(ResidueProperties.codonTranslate("TAB")); |
165 | ||
166 | // R is A or G | |
167 | // additional tests for JAL-1685 (resolved) | |
168 | 1 | assertEquals("L", ResidueProperties.codonTranslate("CTR")); |
169 | 1 | assertEquals("V", ResidueProperties.codonTranslate("GTR")); |
170 | 1 | assertEquals("S", ResidueProperties.codonTranslate("TCR")); |
171 | 1 | assertEquals("P", ResidueProperties.codonTranslate("CCR")); |
172 | 1 | assertEquals("T", ResidueProperties.codonTranslate("ACR")); |
173 | 1 | assertEquals("A", ResidueProperties.codonTranslate("GCR")); |
174 | 1 | assertEquals("R", ResidueProperties.codonTranslate("CGR")); |
175 | 1 | assertEquals("G", ResidueProperties.codonTranslate("GGR")); |
176 | 1 | assertEquals("R", ResidueProperties.codonTranslate("AGR")); |
177 | 1 | assertEquals("E", ResidueProperties.codonTranslate("GAR")); |
178 | 1 | assertEquals("K", ResidueProperties.codonTranslate("AAR")); |
179 | 1 | assertEquals("L", ResidueProperties.codonTranslate("TTR")); |
180 | 1 | assertEquals("Q", ResidueProperties.codonTranslate("CAR")); |
181 | 1 | assertEquals("STOP", ResidueProperties.codonTranslate("TAR")); |
182 | 1 | assertEquals("STOP", ResidueProperties.codonTranslate("TRA")); |
183 | // Arginine first and third base ambiguity | |
184 | 1 | assertEquals("R", ResidueProperties.codonTranslate("MGR")); |
185 | 1 | assertNull(ResidueProperties.codonTranslate("ATR")); |
186 | ||
187 | // N is any base; 8 proteins accept any base in 3rd position | |
188 | 1 | assertEquals("L", ResidueProperties.codonTranslate("CTN")); |
189 | 1 | assertEquals("V", ResidueProperties.codonTranslate("GTN")); |
190 | 1 | assertEquals("S", ResidueProperties.codonTranslate("TCN")); |
191 | 1 | assertEquals("P", ResidueProperties.codonTranslate("CCN")); |
192 | 1 | assertEquals("T", ResidueProperties.codonTranslate("ACN")); |
193 | 1 | assertEquals("A", ResidueProperties.codonTranslate("GCN")); |
194 | 1 | assertEquals("R", ResidueProperties.codonTranslate("CGN")); |
195 | 1 | assertEquals("G", ResidueProperties.codonTranslate("GGN")); |
196 | 1 | assertNull(ResidueProperties.codonTranslate("ATN")); |
197 | 1 | assertNull(ResidueProperties.codonTranslate("ANT")); |
198 | 1 | assertNull(ResidueProperties.codonTranslate("NAT")); |
199 | 1 | assertNull(ResidueProperties.codonTranslate("ANN")); |
200 | 1 | assertNull(ResidueProperties.codonTranslate("NNA")); |
201 | 1 | assertNull(ResidueProperties.codonTranslate("NNN")); |
202 | ||
203 | // some random stuff | |
204 | 1 | assertNull(ResidueProperties.codonTranslate("YWB")); |
205 | 1 | assertNull(ResidueProperties.codonTranslate("VHD")); |
206 | 1 | assertNull(ResidueProperties.codonTranslate("WSK")); |
207 | } | |
208 | ||
209 | 1 | @Test(groups = { "Functional" }) |
210 | public void testGetResidues_nucleotide() | |
211 | { | |
212 | /* | |
213 | * Non-ambiguous only; we don't care about the order of the list, it is just | |
214 | * sorted here to make assertions reliable | |
215 | */ | |
216 | 1 | List<String> residues = ResidueProperties.getResidues(true, false); |
217 | 1 | Collections.sort(residues); |
218 | 1 | assertEquals("[A, C, G, T, U]", residues.toString()); |
219 | ||
220 | /* | |
221 | * Including ambiguity codes I N R X Y | |
222 | */ | |
223 | 1 | residues = ResidueProperties.getResidues(true, true); |
224 | 1 | Collections.sort(residues); |
225 | 1 | assertEquals("[A, B, C, D, G, H, I, K, M, N, R, S, T, U, V, W, X, Y]", |
226 | residues.toString()); | |
227 | } | |
228 | ||
229 | 1 | @Test(groups = { "Functional" }) |
230 | public void testGetResidues_peptide() | |
231 | { | |
232 | /* | |
233 | * Non-ambiguous only; we don't care about the order of the list, it is just | |
234 | * sorted here to make assertions reliable | |
235 | */ | |
236 | 1 | List<String> residues = ResidueProperties.getResidues(false, false); |
237 | 1 | Collections.sort(residues); |
238 | 1 | assertEquals( |
239 | "[ALA, ARG, ASN, ASP, CYS, GLN, GLU, GLY, HIS, ILE, LEU, LYS, MET, PHE, PRO, SER, THR, TRP, TYR, VAL]", | |
240 | residues.toString()); | |
241 | ||
242 | /* | |
243 | * Including ambiguity codes ASX, GLX, XAA | |
244 | */ | |
245 | 1 | residues = ResidueProperties.getResidues(false, true); |
246 | 1 | Collections.sort(residues); |
247 | 1 | assertEquals( |
248 | "[ALA, ARG, ASN, ASP, ASX, CYS, GLN, GLU, GLX, GLY, HIS, ILE, LEU, LYS, MET, PHE, PRO, SER, THR, TRP, TYR, VAL, XAA]", | |
249 | residues.toString()); | |
250 | } | |
251 | ||
252 | 1 | @Test(groups = { "Functional" }) |
253 | public void testGetCanonicalAminoAcid() | |
254 | { | |
255 | 1 | assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MET")); |
256 | 1 | assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MSE")); |
257 | ||
258 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("00C")); |
259 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("01W")); |
260 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("02K")); |
261 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("03Y")); |
262 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("07O")); |
263 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("08P")); |
264 | 1 | assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("0A0")); |
265 | 1 | assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("0A1")); |
266 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("0A2")); |
267 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("0A8")); |
268 | 1 | assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("0AA")); |
269 | 1 | assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("0AB")); |
270 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("0AC")); |
271 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("0AD")); |
272 | 1 | assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("0AF")); |
273 | 1 | assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("0AG")); |
274 | 1 | assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("0AH")); |
275 | 1 | assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("0AK")); |
276 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("0AM")); |
277 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("0AP")); |
278 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("0AU")); |
279 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("0AV")); |
280 | 1 | assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("0AZ")); |
281 | 1 | assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("0BN")); |
282 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("0C ")); |
283 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("0CS")); |
284 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("0DC")); |
285 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("0DG")); |
286 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("0DT")); |
287 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("0FL")); |
288 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("0G ")); |
289 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("0NC")); |
290 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("0SP")); |
291 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("0U ")); |
292 | 1 | assertEquals("YG", ResidueProperties.getCanonicalAminoAcid("0YG")); |
293 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("10C")); |
294 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("125")); |
295 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("126")); |
296 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("127")); |
297 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("128")); |
298 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("12A")); |
299 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("143")); |
300 | 1 | assertEquals("ASG", ResidueProperties.getCanonicalAminoAcid("175")); |
301 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("193")); |
302 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("1AP")); |
303 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("1MA")); |
304 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("1MG")); |
305 | 1 | assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("1PA")); |
306 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("1PI")); |
307 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("1PR")); |
308 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("1SC")); |
309 | 1 | assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("1TQ")); |
310 | 1 | assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("1TY")); |
311 | 1 | assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("1X6")); |
312 | 1 | assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("200")); |
313 | 1 | assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("23F")); |
314 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("23S")); |
315 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("26B")); |
316 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("2AD")); |
317 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("2AG")); |
318 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("2AO")); |
319 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("2AR")); |
320 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("2AS")); |
321 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("2AT")); |
322 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("2AU")); |
323 | 1 | assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("2BD")); |
324 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("2BT")); |
325 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("2BU")); |
326 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("2CO")); |
327 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("2DA")); |
328 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("2DF")); |
329 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("2DM")); |
330 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("2DO")); |
331 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("2DT")); |
332 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("2EG")); |
333 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("2FE")); |
334 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("2FI")); |
335 | 1 | assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("2FM")); |
336 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("2GT")); |
337 | 1 | assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("2HF")); |
338 | 1 | assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("2LU")); |
339 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("2MA")); |
340 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("2MG")); |
341 | 1 | assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("2ML")); |
342 | 1 | assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("2MR")); |
343 | 1 | assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("2MT")); |
344 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("2MU")); |
345 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("2NT")); |
346 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("2OM")); |
347 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("2OT")); |
348 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("2PI")); |
349 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("2PR")); |
350 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("2SA")); |
351 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("2SI")); |
352 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("2ST")); |
353 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("2TL")); |
354 | 1 | assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("2TY")); |
355 | 1 | assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("2VA")); |
356 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("2XA")); |
357 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("32S")); |
358 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("32T")); |
359 | 1 | assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("3AH")); |
360 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("3AR")); |
361 | 1 | assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("3CF")); |
362 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("3DA")); |
363 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("3DR")); |
364 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("3GA")); |
365 | 1 | assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("3MD")); |
366 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("3ME")); |
367 | 1 | assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("3NF")); |
368 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("3QN")); |
369 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("3TY")); |
370 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("3XH")); |
371 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("4AC")); |
372 | 1 | assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("4BF")); |
373 | 1 | assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("4CF")); |
374 | 1 | assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("4CY")); |
375 | 1 | assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("4DP")); |
376 | 1 | assertEquals("GYG", ResidueProperties.getCanonicalAminoAcid("4F3")); |
377 | 1 | assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("4FB")); |
378 | 1 | assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("4FW")); |
379 | 1 | assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("4HT")); |
380 | 1 | assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("4IN")); |
381 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("4MF")); |
382 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("4MM")); |
383 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("4OC")); |
384 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("4PC")); |
385 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("4PD")); |
386 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("4PE")); |
387 | 1 | assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("4PH")); |
388 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("4SC")); |
389 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("4SU")); |
390 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("4TA")); |
391 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("4U7")); |
392 | 1 | assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("56A")); |
393 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("5AA")); |
394 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("5AB")); |
395 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("5AT")); |
396 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("5BU")); |
397 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("5CG")); |
398 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("5CM")); |
399 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("5CS")); |
400 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("5FA")); |
401 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("5FC")); |
402 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("5FU")); |
403 | 1 | assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("5HP")); |
404 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("5HT")); |
405 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("5HU")); |
406 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("5IC")); |
407 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("5IT")); |
408 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("5IU")); |
409 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("5MC")); |
410 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("5MD")); |
411 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("5MU")); |
412 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("5NC")); |
413 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("5PC")); |
414 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("5PY")); |
415 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("5SE")); |
416 | 1 | assertEquals("TWG", ResidueProperties.getCanonicalAminoAcid("5ZA")); |
417 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("64T")); |
418 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("6CL")); |
419 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("6CT")); |
420 | 1 | assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("6CW")); |
421 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("6HA")); |
422 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("6HC")); |
423 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("6HG")); |
424 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("6HN")); |
425 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("6HT")); |
426 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("6IA")); |
427 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("6MA")); |
428 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("6MC")); |
429 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("6MI")); |
430 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("6MT")); |
431 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("6MZ")); |
432 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("6OG")); |
433 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("70U")); |
434 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("7DA")); |
435 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("7GU")); |
436 | 1 | assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("7JA")); |
437 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("7MG")); |
438 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("8AN")); |
439 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("8FG")); |
440 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("8MG")); |
441 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("8OG")); |
442 | 1 | assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("9NE")); |
443 | 1 | assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("9NF")); |
444 | 1 | assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("9NR")); |
445 | 1 | assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("9NV")); |
446 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A ")); |
447 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("A1P")); |
448 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A23")); |
449 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A2L")); |
450 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A2M")); |
451 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A34")); |
452 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A35")); |
453 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A38")); |
454 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A39")); |
455 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A3A")); |
456 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A3P")); |
457 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A40")); |
458 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A43")); |
459 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A44")); |
460 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A47")); |
461 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A5L")); |
462 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("A5M")); |
463 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("A5N")); |
464 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A5O")); |
465 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("A66")); |
466 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AA3")); |
467 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AA4")); |
468 | 1 | assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("AAR")); |
469 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("AB7")); |
470 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ABA")); |
471 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ABR")); |
472 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ABS")); |
473 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("ABT")); |
474 | 1 | assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("ACB")); |
475 | 1 | assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("ACL")); |
476 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AD2")); |
477 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("ADD")); |
478 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("ADX")); |
479 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("AEA")); |
480 | 1 | assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("AEI")); |
481 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AET")); |
482 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("AFA")); |
483 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("AFF")); |
484 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("AFG")); |
485 | 1 | assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("AGM")); |
486 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("AGT")); |
487 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("AHB")); |
488 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("AHH")); |
489 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AHO")); |
490 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AHP")); |
491 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("AHS")); |
492 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("AHT")); |
493 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AIB")); |
494 | 1 | assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("AKL")); |
495 | 1 | assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("AKZ")); |
496 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ALA")); |
497 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ALC")); |
498 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ALM")); |
499 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ALN")); |
500 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("ALO")); |
501 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("ALQ")); |
502 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ALS")); |
503 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ALT")); |
504 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ALV")); |
505 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("ALY")); |
506 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AN8")); |
507 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AP7")); |
508 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("APE")); |
509 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("APH")); |
510 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("API")); |
511 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("APK")); |
512 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("APM")); |
513 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("APP")); |
514 | 1 | assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("AR2")); |
515 | 1 | assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("AR4")); |
516 | 1 | assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("AR7")); |
517 | 1 | assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("ARG")); |
518 | 1 | assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("ARM")); |
519 | 1 | assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("ARO")); |
520 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("ARV")); |
521 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AS ")); |
522 | 1 | assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("AS2")); |
523 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("AS9")); |
524 | 1 | assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("ASA")); |
525 | 1 | assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("ASB")); |
526 | 1 | assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("ASI")); |
527 | 1 | assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("ASK")); |
528 | 1 | assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("ASL")); |
529 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("ASM")); |
530 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("ASN")); |
531 | 1 | assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("ASP")); |
532 | 1 | assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("ASQ")); |
533 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("ASU")); |
534 | 1 | assertEquals("ASX", ResidueProperties.getCanonicalAminoAcid("ASX")); |
535 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("ATD")); |
536 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("ATL")); |
537 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("ATM")); |
538 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AVC")); |
539 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("AVN")); |
540 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AYA")); |
541 | 1 | assertEquals("AYG", ResidueProperties.getCanonicalAminoAcid("AYG")); |
542 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("AZK")); |
543 | 1 | assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("AZS")); |
544 | 1 | assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("AZY")); |
545 | 1 | assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("B1F")); |
546 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("B1P")); |
547 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("B2A")); |
548 | 1 | assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("B2F")); |
549 | 1 | assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("B2I")); |
550 | 1 | assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("B2V")); |
551 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("B3A")); |
552 | 1 | assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("B3D")); |
553 | 1 | assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("B3E")); |
554 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("B3K")); |
555 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("B3L")); |
556 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("B3M")); |
557 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("B3Q")); |
558 | 1 | assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("B3S")); |
559 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("B3T")); |
560 | 1 | assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("B3U")); |
561 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("B3X")); |
562 | 1 | assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("B3Y")); |
563 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("BB6")); |
564 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("BB7")); |
565 | 1 | assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("BB8")); |
566 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("BB9")); |
567 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("BBC")); |
568 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("BCS")); |
569 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("BE2")); |
570 | 1 | assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("BFD")); |
571 | 1 | assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("BG1")); |
572 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("BGM")); |
573 | 1 | assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("BH2")); |
574 | 1 | assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("BHD")); |
575 | 1 | assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("BIF")); |
576 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("BIL")); |
577 | 1 | assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("BIU")); |
578 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("BJH")); |
579 | 1 | assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("BLE")); |
580 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("BLY")); |
581 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("BMP")); |
582 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("BMT")); |
583 | 1 | assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("BNN")); |
584 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("BNO")); |
585 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("BOE")); |
586 | 1 | assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("BOR")); |
587 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("BPE")); |
588 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("BRU")); |
589 | 1 | assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("BSE")); |
590 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("BT5")); |
591 | 1 | assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("BTA")); |
592 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("BTC")); |
593 | 1 | assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("BTR")); |
594 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("BUC")); |
595 | 1 | assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("BUG")); |
596 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("BVP")); |
597 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("BZG")); |
598 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C ")); |
599 | 1 | assertEquals("TYG", ResidueProperties.getCanonicalAminoAcid("C12")); |
600 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("C1X")); |
601 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C25")); |
602 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C2L")); |
603 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C2S")); |
604 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C31")); |
605 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C32")); |
606 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C34")); |
607 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C36")); |
608 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C37")); |
609 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C38")); |
610 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C3Y")); |
611 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C42")); |
612 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C43")); |
613 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C45")); |
614 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C46")); |
615 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C49")); |
616 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C4R")); |
617 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C4S")); |
618 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C5C")); |
619 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("C66")); |
620 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C6C")); |
621 | 1 | assertEquals("TFG", ResidueProperties.getCanonicalAminoAcid("C99")); |
622 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CAF")); |
623 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CAL")); |
624 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CAR")); |
625 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CAS")); |
626 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CAV")); |
627 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CAY")); |
628 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CB2")); |
629 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CBR")); |
630 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CBV")); |
631 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CCC")); |
632 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("CCL")); |
633 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CCS")); |
634 | 1 | assertEquals("CYG", ResidueProperties.getCanonicalAminoAcid("CCY")); |
635 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CDE")); |
636 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CDV")); |
637 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CDW")); |
638 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CEA")); |
639 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CFL")); |
640 | 1 | assertEquals("FCYG", ResidueProperties.getCanonicalAminoAcid("CFY")); // check |
641 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("CG1")); |
642 | 1 | assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("CGA")); |
643 | 1 | assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("CGU")); |
644 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CH ")); |
645 | 1 | assertEquals("MYG", ResidueProperties.getCanonicalAminoAcid("CH6")); |
646 | 1 | assertEquals("KYG", ResidueProperties.getCanonicalAminoAcid("CH7")); |
647 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CHF")); |
648 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CHG")); |
649 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("CHP")); |
650 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CHS")); |
651 | 1 | assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("CIR")); |
652 | 1 | assertEquals("GYG", ResidueProperties.getCanonicalAminoAcid("CJO")); |
653 | 1 | assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("CLE")); |
654 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("CLG")); |
655 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("CLH")); |
656 | 1 | assertEquals("AFG", ResidueProperties.getCanonicalAminoAcid("CLV")); |
657 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("CM0")); |
658 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CME")); |
659 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CMH")); |
660 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CML")); |
661 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CMR")); |
662 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CMT")); |
663 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("CNU")); |
664 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CP1")); |
665 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CPC")); |
666 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CPI")); |
667 | 1 | assertEquals("GYG", ResidueProperties.getCanonicalAminoAcid("CQR")); |
668 | 1 | assertEquals("TLG", ResidueProperties.getCanonicalAminoAcid("CR0")); |
669 | 1 | assertEquals("GYG", ResidueProperties.getCanonicalAminoAcid("CR2")); |
670 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("CR5")); |
671 | 1 | assertEquals("KYG", ResidueProperties.getCanonicalAminoAcid("CR7")); |
672 | 1 | assertEquals("HYG", ResidueProperties.getCanonicalAminoAcid("CR8")); |
673 | 1 | assertEquals("TWG", ResidueProperties.getCanonicalAminoAcid("CRF")); |
674 | 1 | assertEquals("THG", ResidueProperties.getCanonicalAminoAcid("CRG")); |
675 | 1 | assertEquals("MYG", ResidueProperties.getCanonicalAminoAcid("CRK")); |
676 | 1 | assertEquals("GYG", ResidueProperties.getCanonicalAminoAcid("CRO")); |
677 | 1 | assertEquals("QYG", ResidueProperties.getCanonicalAminoAcid("CRQ")); |
678 | 1 | assertEquals("EYG", ResidueProperties.getCanonicalAminoAcid("CRU")); |
679 | 1 | assertEquals("ASG", ResidueProperties.getCanonicalAminoAcid("CRW")); |
680 | 1 | assertEquals("ASG", ResidueProperties.getCanonicalAminoAcid("CRX")); |
681 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CS0")); |
682 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CS1")); |
683 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CS3")); |
684 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CS4")); |
685 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("CS8")); |
686 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSA")); |
687 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSB")); |
688 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSD")); |
689 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSE")); |
690 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSF")); |
691 | 1 | assertEquals("SHG", ResidueProperties.getCanonicalAminoAcid("CSH")); |
692 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("CSI")); |
693 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSJ")); |
694 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSL")); |
695 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSO")); |
696 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSP")); |
697 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSR")); |
698 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSS")); |
699 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSU")); |
700 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSW")); |
701 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSX")); |
702 | 1 | assertEquals("SYG", ResidueProperties.getCanonicalAminoAcid("CSY")); |
703 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSZ")); |
704 | 1 | assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("CTE")); |
705 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("CTG")); |
706 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("CTH")); |
707 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CUC")); |
708 | 1 | assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("CWR")); |
709 | 1 | assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("CXM")); |
710 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CY0")); |
711 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CY1")); |
712 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CY3")); |
713 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CY4")); |
714 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CYA")); |
715 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CYD")); |
716 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CYF")); |
717 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CYG")); |
718 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CYJ")); |
719 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CYM")); |
720 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CYQ")); |
721 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CYR")); |
722 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CYS")); |
723 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CZ2")); |
724 | 1 | assertEquals("GYG", ResidueProperties.getCanonicalAminoAcid("CZO")); |
725 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CZZ")); |
726 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("D11")); |
727 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("D1P")); |
728 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("D3 ")); |
729 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("D33")); |
730 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("D3P")); |
731 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("D3T")); |
732 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("D4M")); |
733 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("D4P")); |
734 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("DA ")); |
735 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("DA2")); |
736 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("DAB")); |
737 | 1 | assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("DAH")); |
738 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("DAL")); |
739 | 1 | assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("DAR")); |
740 | 1 | assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("DAS")); |
741 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("DBB")); |
742 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DBM")); |
743 | 1 | assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("DBS")); |
744 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("DBU")); |
745 | 1 | assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("DBY")); |
746 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("DBZ")); |
747 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("DC ")); |
748 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("DC2")); |
749 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("DCG")); |
750 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("DCI")); |
751 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("DCL")); |
752 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("DCT")); |
753 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("DCY")); |
754 | 1 | assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("DDE")); |
755 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("DDG")); |
756 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("DDN")); |
757 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DDX")); |
758 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("DFC")); |
759 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("DFG")); |
760 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("DFI")); |
761 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("DFO")); |
762 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DFT")); |
763 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("DG ")); |
764 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("DGH")); |
765 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("DGI")); |
766 | 1 | assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("DGL")); |
767 | 1 | assertEquals("GLN", ResidueProperties.getCanonicalAminoAcid("DGN")); |
768 | 1 | assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("DHA")); |
769 | 1 | assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("DHI")); |
770 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("DHL")); |
771 | 1 | assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("DHN")); |
772 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("DHP")); |
773 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("DHU")); |
774 | 1 | assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("DHV")); |
775 | 1 | assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("DI ")); |
776 | 1 | assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("DIL")); |
777 | 1 | assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("DIR")); |
778 | 1 | assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("DIV")); |
779 | 1 | assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("DLE")); |
780 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("DLS")); |
781 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("DLY")); |
782 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("DM0")); |
783 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DMH")); |
784 | 1 | assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("DMK")); |
785 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("DMT")); |
786 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DN ")); |
787 | 1 | assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("DNE")); |
788 | 1 | assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("DNG")); |
789 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("DNL")); |
790 | 1 | assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("DNM")); |
791 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("DNP")); |
792 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("DNR")); |
793 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("DNS")); |
794 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("DOA")); |
795 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("DOC")); |
796 | 1 | assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("DOH")); |
797 | 1 | assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("DON")); |
798 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("DPB")); |
799 | 1 | assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("DPH")); |
800 | 1 | assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("DPL")); |
801 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("DPP")); |
802 | 1 | assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("DPQ")); |
803 | 1 | assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("DPR")); |
804 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DPY")); |
805 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("DRM")); |
806 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DRP")); |
807 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("DRT")); |
808 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DRZ")); |
809 | 1 | assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("DSE")); |
810 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DSG")); |
811 | 1 | assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("DSN")); |
812 | 1 | assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("DSP")); |
813 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("DT ")); |
814 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("DTH")); |
815 | 1 | assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("DTR")); |
816 | 1 | assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("DTY")); |
817 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("DU ")); |
818 | 1 | assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("DVA")); |
819 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DXD")); |
820 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DXN")); |
821 | 1 | assertEquals("DYG", ResidueProperties.getCanonicalAminoAcid("DYG")); |
822 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("DYS")); |
823 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("DZM")); |
824 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("E ")); |
825 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("E1X")); |
826 | 1 | assertEquals("GLN", ResidueProperties.getCanonicalAminoAcid("ECC")); |
827 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("EDA")); |
828 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("EFC")); |
829 | 1 | assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("EHP")); |
830 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("EIT")); |
831 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("ENP")); |
832 | 1 | assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("ESB")); |
833 | 1 | assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("ESC")); |
834 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("EXB")); |
835 | 1 | assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("EXY")); |
836 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("EY5")); |
837 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("EYS")); |
838 | 1 | assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("F2F")); |
839 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("FA2")); |
840 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("FA5")); |
841 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("FAG")); |
842 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("FAI")); |
843 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("FB5")); |
844 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("FB6")); |
845 | 1 | assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("FCL")); |
846 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("FFD")); |
847 | 1 | assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("FGA")); |
848 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("FGL")); |
849 | 1 | assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("FGP")); |
850 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("FHL")); |
851 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("FHO")); |
852 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("FHU")); |
853 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("FLA")); |
854 | 1 | assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("FLE")); |
855 | 1 | assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("FLT")); |
856 | 1 | assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("FME")); |
857 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("FMG")); |
858 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("FMU")); |
859 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("FOE")); |
860 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("FOX")); |
861 | 1 | assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("FP9")); |
862 | 1 | assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("FPA")); |
863 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("FRD")); |
864 | 1 | assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("FT6")); |
865 | 1 | assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("FTR")); |
866 | 1 | assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("FTY")); |
867 | 1 | assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("FVA")); |
868 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("FZN")); |
869 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G ")); |
870 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G25")); |
871 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G2L")); |
872 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G2S")); |
873 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G31")); |
874 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G32")); |
875 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G33")); |
876 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G36")); |
877 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G38")); |
878 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G42")); |
879 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G46")); |
880 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G47")); |
881 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G48")); |
882 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G49")); |
883 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("G4P")); |
884 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G7M")); |
885 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GAO")); |
886 | 1 | assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("GAU")); |
887 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("GCK")); |
888 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("GCM")); |
889 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GDP")); |
890 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GDR")); |
891 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GFL")); |
892 | 1 | assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("GGL")); |
893 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GH3")); |
894 | 1 | assertEquals("GLN", ResidueProperties.getCanonicalAminoAcid("GHG")); |
895 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GHP")); |
896 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GL3")); |
897 | 1 | assertEquals("GLN", ResidueProperties.getCanonicalAminoAcid("GLH")); |
898 | 1 | assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("GLJ")); |
899 | 1 | assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("GLK")); |
900 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("GLM")); |
901 | 1 | assertEquals("GLN", ResidueProperties.getCanonicalAminoAcid("GLN")); |
902 | 1 | assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("GLQ")); |
903 | 1 | assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("GLU")); |
904 | 1 | assertEquals("GLX", ResidueProperties.getCanonicalAminoAcid("GLX")); |
905 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GLY")); |
906 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GLZ")); |
907 | 1 | assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("GMA")); |
908 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GMS")); |
909 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("GMU")); |
910 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GN7")); |
911 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("GND")); |
912 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("GNE")); |
913 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GOM")); |
914 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("GPL")); |
915 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GS ")); |
916 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GSC")); |
917 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GSR")); |
918 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GSS")); |
919 | 1 | assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("GSU")); |
920 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("GT9")); |
921 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GTP")); |
922 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("GVL")); |
923 | 1 | assertEquals("CYG", ResidueProperties.getCanonicalAminoAcid("GYC")); |
924 | 1 | assertEquals("SYG", ResidueProperties.getCanonicalAminoAcid("GYS")); |
925 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("H2U")); |
926 | 1 | assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("H5M")); |
927 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("HAC")); |
928 | 1 | assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("HAR")); |
929 | 1 | assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("HBN")); |
930 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("HCS")); |
931 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("HDP")); |
932 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("HEU")); |
933 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("HFA")); |
934 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("HGL")); |
935 | 1 | assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("HHI")); |
936 | 1 | assertEquals("AK", ResidueProperties.getCanonicalAminoAcid("HHK")); // check |
937 | 1 | assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("HIA")); |
938 | 1 | assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("HIC")); |
939 | 1 | assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("HIP")); |
940 | 1 | assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("HIQ")); |
941 | 1 | assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("HIS")); |
942 | 1 | assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("HL2")); |
943 | 1 | assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("HLU")); |
944 | 1 | assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("HMR")); |
945 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("HOL")); |
946 | 1 | assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("HPC")); |
947 | 1 | assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("HPE")); |
948 | 1 | assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("HPH")); |
949 | 1 | assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("HPQ")); |
950 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("HQA")); |
951 | 1 | assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("HRG")); |
952 | 1 | assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("HRP")); |
953 | 1 | assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("HS8")); |
954 | 1 | assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("HS9")); |
955 | 1 | assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("HSE")); |
956 | 1 | assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("HSL")); |
957 | 1 | assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("HSO")); |
958 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("HTI")); |
959 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("HTN")); |
960 | 1 | assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("HTR")); |
961 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("HV5")); |
962 | 1 | assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("HVA")); |
963 | 1 | assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("HY3")); |
964 | 1 | assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("HYP")); |
965 | 1 | assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("HZP")); |
966 | 1 | assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("I ")); |
967 | 1 | assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("I2M")); |
968 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("I58")); |
969 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("I5C")); |
970 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("IAM")); |
971 | 1 | assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("IAR")); |
972 | 1 | assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("IAS")); |
973 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("IC ")); |
974 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("IEL")); |
975 | 1 | assertEquals("HYG", ResidueProperties.getCanonicalAminoAcid("IEY")); |
976 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("IG ")); |
977 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("IGL")); |
978 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("IGU")); |
979 | 1 | assertEquals("SHG", ResidueProperties.getCanonicalAminoAcid("IIC")); |
980 | 1 | assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("IIL")); |
981 | 1 | assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("ILE")); |
982 | 1 | assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("ILG")); |
983 | 1 | assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("ILX")); |
984 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("IMC")); |
985 | 1 | assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("IML")); |
986 | 1 | assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("IOY")); |
987 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("IPG")); |
988 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("IPN")); |
989 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("IRN")); |
990 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("IT1")); |
991 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("IU ")); |
992 | 1 | assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("IYR")); |
993 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("IYT")); |
994 | 1 | assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("IZO")); |
995 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("JJJ")); |
996 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("JJK")); |
997 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("JJL")); |
998 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("JW5")); |
999 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("K1R")); |
1000 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("KAG")); |
1001 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("KCX")); |
1002 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("KGC")); |
1003 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("KNB")); |
1004 | 1 | assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("KOR")); |
1005 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("KPI")); |
1006 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("KST")); |
1007 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("KYQ")); |
1008 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("L2A")); |
1009 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LA2")); |
1010 | 1 | assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("LAA")); |
1011 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("LAL")); |
1012 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LBY")); |
1013 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("LC ")); |
1014 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("LCA")); |
1015 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("LCC")); |
1016 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("LCG")); |
1017 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("LCH")); |
1018 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LCK")); |
1019 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LCX")); |
1020 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LDH")); |
1021 | 1 | assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("LED")); |
1022 | 1 | assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("LEF")); |
1023 | 1 | assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("LEH")); |
1024 | 1 | assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("LEI")); |
1025 | 1 | assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("LEM")); |
1026 | 1 | assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("LEN")); |
1027 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("LET")); |
1028 | 1 | assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("LEU")); |
1029 | 1 | assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("LEX")); |
1030 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("LG ")); |
1031 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("LGP")); |
1032 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("LHC")); |
1033 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("LHU")); |
1034 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("LKC")); |
1035 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LLP")); |
1036 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LLY")); |
1037 | 1 | assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("LME")); |
1038 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LMF")); |
1039 | 1 | assertEquals("GLN", ResidueProperties.getCanonicalAminoAcid("LMQ")); |
1040 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("LMS")); |
1041 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LP6")); |
1042 | 1 | assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("LPD")); |
1043 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("LPG")); |
1044 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("LPL")); |
1045 | 1 | assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("LPS")); |
1046 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("LSO")); |
1047 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("LTA")); |
1048 | 1 | assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("LTR")); |
1049 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("LVG")); |
1050 | 1 | assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("LVN")); |
1051 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LYF")); |
1052 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LYK")); |
1053 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LYM")); |
1054 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LYN")); |
1055 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LYR")); |
1056 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LYS")); |
1057 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LYX")); |
1058 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LYZ")); |
1059 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("M0H")); |
1060 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("M1G")); |
1061 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("M2G")); |
1062 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("M2L")); |
1063 | 1 | assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("M2S")); |
1064 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("M30")); |
1065 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("M3L")); |
1066 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("M5M")); |
1067 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("MA ")); |
1068 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("MA6")); |
1069 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("MA7")); |
1070 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("MAA")); |
1071 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("MAD")); |
1072 | 1 | assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("MAI")); |
1073 | 1 | assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("MBQ")); |
1074 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("MBZ")); |
1075 | 1 | assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("MC1")); |
1076 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("MCG")); |
1077 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("MCL")); |
1078 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("MCS")); |
1079 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("MCY")); |
1080 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("MD3")); |
1081 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("MD6")); |
1082 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("MDH")); |
1083 | 1 | assertEquals("ASG", ResidueProperties.getCanonicalAminoAcid("MDO")); |
1084 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("MDR")); |
1085 | 1 | assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("MEA")); |
1086 | 1 | assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MED")); |
1087 | 1 | assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("MEG")); |
1088 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("MEN")); |
1089 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("MEP")); |
1090 | 1 | assertEquals("GLN", ResidueProperties.getCanonicalAminoAcid("MEQ")); |
1091 | 1 | assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MET")); |
1092 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("MEU")); |
1093 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("MF3")); |
1094 | 1 | assertEquals("GYG", ResidueProperties.getCanonicalAminoAcid("MFC")); |
1095 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("MG1")); |
1096 | 1 | assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("MGG")); |
1097 | 1 | assertEquals("GLN", ResidueProperties.getCanonicalAminoAcid("MGN")); |
1098 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("MGQ")); |
1099 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("MGV")); |
1100 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("MGY")); |
1101 | 1 | assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("MHL")); |
1102 | 1 | assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MHO")); |
1103 | 1 | assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("MHS")); |
1104 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("MIA")); |
1105 | 1 | assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("MIS")); |
1106 | 1 | assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("MK8")); |
1107 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("ML3")); |
1108 | 1 | assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("MLE")); |
1109 | 1 | assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("MLL")); |
1110 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("MLY")); |
1111 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("MLZ")); |
1112 | 1 | assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MME")); |
1113 | 1 | assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("MMO")); |
1114 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("MMT")); |
1115 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("MND")); |
1116 | 1 | assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("MNL")); |
1117 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("MNU")); |
1118 | 1 | assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("MNV")); |
1119 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("MOD")); |
1120 | 1 | assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("MP8")); |
1121 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("MPH")); |
1122 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("MPJ")); |
1123 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("MPQ")); |
1124 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("MRG")); |
1125 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("MSA")); |
1126 | 1 | assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MSE")); |
1127 | 1 | assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MSL")); |
1128 | 1 | assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MSO")); |
1129 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("MSP")); |
1130 | 1 | assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MT2")); |
1131 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("MTR")); |
1132 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("MTU")); |
1133 | 1 | assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("MTY")); |
1134 | 1 | assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("MVA")); |
1135 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("N ")); |
1136 | 1 | assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("N10")); |
1137 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("N2C")); |
1138 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("N5I")); |
1139 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("N5M")); |
1140 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("N6G")); |
1141 | 1 | assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("N7P")); |
1142 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("NA8")); |
1143 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("NAL")); |
1144 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("NAM")); |
1145 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("NB8")); |
1146 | 1 | assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("NBQ")); |
1147 | 1 | assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("NC1")); |
1148 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("NCB")); |
1149 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("NCX")); |
1150 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("NCY")); |
1151 | 1 | assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("NDF")); |
1152 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("NDN")); |
1153 | 1 | assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("NEM")); |
1154 | 1 | assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("NEP")); |
1155 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("NF2")); |
1156 | 1 | assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("NFA")); |
1157 | 1 | assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("NHL")); |
1158 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("NIT")); |
1159 | 1 | assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("NIY")); |
1160 | 1 | assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("NLE")); |
1161 | 1 | assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("NLN")); |
1162 | 1 | assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("NLO")); |
1163 | 1 | assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("NLP")); |
1164 | 1 | assertEquals("GLN", ResidueProperties.getCanonicalAminoAcid("NLQ")); |
1165 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("NMC")); |
1166 | 1 | assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("NMM")); |
1167 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("NMS")); |
1168 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("NMT")); |
1169 | 1 | assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("NNH")); |
1170 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("NP3")); |
1171 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("NPH")); |
1172 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("NPI")); |
1173 | 1 | assertEquals("LYG", ResidueProperties.getCanonicalAminoAcid("NRP")); |
1174 | 1 | assertEquals("MYG", ResidueProperties.getCanonicalAminoAcid("NRQ")); |
1175 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("NSK")); |
1176 | 1 | assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("NTY")); |
1177 | 1 | assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("NVA")); |
1178 | 1 | assertEquals("TWG", ResidueProperties.getCanonicalAminoAcid("NYC")); |
1179 | 1 | assertEquals("NYG", ResidueProperties.getCanonicalAminoAcid("NYG")); |
1180 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("NYM")); |
1181 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("NYS")); |
1182 | 1 | assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("NZH")); |
1183 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("O12")); |
1184 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("O2C")); |
1185 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("O2G")); |
1186 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("OAD")); |
1187 | 1 | assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("OAS")); |
1188 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("OBF")); |
1189 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("OBS")); |
1190 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("OCS")); |
1191 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("OCY")); |
1192 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("ODP")); |
1193 | 1 | assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("OHI")); |
1194 | 1 | assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("OHS")); |
1195 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("OIC")); |
1196 | 1 | assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("OIP")); |
1197 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("OLE")); |
1198 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("OLT")); |
1199 | 1 | assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("OLZ")); |
1200 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("OMC")); |
1201 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("OMG")); |
1202 | 1 | assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("OMT")); |
1203 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("OMU")); |
1204 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("ONE")); |
1205 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ONH")); |
1206 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("ONL")); |
1207 | 1 | assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("OPR")); |
1208 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ORN")); |
1209 | 1 | assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("ORQ")); |
1210 | 1 | assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("OSE")); |
1211 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("OTB")); |
1212 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("OTH")); |
1213 | 1 | assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("OTY")); |
1214 | 1 | assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("OXX")); |
1215 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("P ")); |
1216 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("P1L")); |
1217 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("P1P")); |
1218 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("P2T")); |
1219 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("P2U")); |
1220 | 1 | assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("P2Y")); |
1221 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("P5P")); |
1222 | 1 | assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("PAQ")); |
1223 | 1 | assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("PAS")); |
1224 | 1 | assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("PAT")); |
1225 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("PAU")); |
1226 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("PBB")); |
1227 | 1 | assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PBF")); |
1228 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("PBT")); |
1229 | 1 | assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("PCA")); |
1230 | 1 | assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("PCC")); |
1231 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("PCE")); |
1232 | 1 | assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PCS")); |
1233 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("PDL")); |
1234 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("PDU")); |
1235 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("PEC")); |
1236 | 1 | assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PF5")); |
1237 | 1 | assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PFF")); |
1238 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("PFX")); |
1239 | 1 | assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("PG1")); |
1240 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("PG7")); |
1241 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("PG9")); |
1242 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("PGL")); |
1243 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("PGN")); |
1244 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("PGP")); |
1245 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("PGY")); |
1246 | 1 | assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PHA")); |
1247 | 1 | assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("PHD")); |
1248 | 1 | assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PHE")); |
1249 | 1 | assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PHI")); |
1250 | 1 | assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PHL")); |
1251 | 1 | assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PHM")); |
1252 | 1 | assertEquals("AYG", ResidueProperties.getCanonicalAminoAcid("PIA")); |
1253 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("PIV")); |
1254 | 1 | assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("PLE")); |
1255 | 1 | assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PM3")); |
1256 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("PMT")); |
1257 | 1 | assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("POM")); |
1258 | 1 | assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PPN")); |
1259 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("PPU")); |
1260 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("PPW")); |
1261 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("PQ1")); |
1262 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("PR3")); |
1263 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("PR5")); |
1264 | 1 | assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("PR9")); |
1265 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("PRN")); |
1266 | 1 | assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("PRO")); |
1267 | 1 | assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("PRS")); |
1268 | 1 | assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PSA")); |
1269 | 1 | assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("PSH")); |
1270 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("PST")); |
1271 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("PSU")); |
1272 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("PSW")); |
1273 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("PTA")); |
1274 | 1 | assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("PTH")); |
1275 | 1 | assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("PTM")); |
1276 | 1 | assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("PTR")); |
1277 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("PU ")); |
1278 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("PUY")); |
1279 | 1 | assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("PVH")); |
1280 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("PVL")); |
1281 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("PYA")); |
1282 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("PYO")); |
1283 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("PYX")); |
1284 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("PYY")); |
1285 | 1 | assertEquals("QLG", ResidueProperties.getCanonicalAminoAcid("QLG")); |
1286 | 1 | assertEquals("GLN", ResidueProperties.getCanonicalAminoAcid("QMM")); |
1287 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("QPA")); |
1288 | 1 | assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("QPH")); |
1289 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("QUO")); |
1290 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("R ")); |
1291 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("R1A")); |
1292 | 1 | assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("R4K")); |
1293 | 1 | assertEquals("HYG", ResidueProperties.getCanonicalAminoAcid("RC7")); |
1294 | 1 | assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("RE0")); |
1295 | 1 | assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("RE3")); |
1296 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("RIA")); |
1297 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("RMP")); |
1298 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("RON")); |
1299 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("RT ")); |
1300 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("RTP")); |
1301 | 1 | assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("S1H")); |
1302 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("S2C")); |
1303 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("S2D")); |
1304 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("S2M")); |
1305 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("S2P")); |
1306 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("S4A")); |
1307 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("S4C")); |
1308 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("S4G")); |
1309 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("S4U")); |
1310 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("S6G")); |
1311 | 1 | assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SAC")); |
1312 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SAH")); |
1313 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("SAR")); |
1314 | 1 | assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SBL")); |
1315 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SC ")); |
1316 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SCH")); |
1317 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SCS")); |
1318 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SCY")); |
1319 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("SD2")); |
1320 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("SDG")); |
1321 | 1 | assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SDP")); |
1322 | 1 | assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SEB")); |
1323 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("SEC")); |
1324 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("SEG")); |
1325 | 1 | assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SEL")); |
1326 | 1 | assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SEM")); |
1327 | 1 | assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SEN")); |
1328 | 1 | assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SEP")); |
1329 | 1 | assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SER")); |
1330 | 1 | assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SET")); |
1331 | 1 | assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SGB")); |
1332 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SHC")); |
1333 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("SHP")); |
1334 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("SHR")); |
1335 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SIB")); |
1336 | 1 | assertEquals("DC", ResidueProperties.getCanonicalAminoAcid("SIC")); // check |
1337 | 1 | assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("SLA")); |
1338 | 1 | assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("SLR")); |
1339 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("SLZ")); |
1340 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SMC")); |
1341 | 1 | assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("SME")); |
1342 | 1 | assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("SMF")); |
1343 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("SMP")); |
1344 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("SMT")); |
1345 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SNC")); |
1346 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("SNN")); |
1347 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SOC")); |
1348 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("SOS")); |
1349 | 1 | assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SOY")); |
1350 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("SPT")); |
1351 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("SRA")); |
1352 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("SSU")); |
1353 | 1 | assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("STY")); |
1354 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("SUB")); |
1355 | 1 | assertEquals("DG", ResidueProperties.getCanonicalAminoAcid("SUI")); |
1356 | 1 | assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SUN")); |
1357 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("SUR")); |
1358 | 1 | assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SVA")); |
1359 | 1 | assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SVV")); |
1360 | 1 | assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SVW")); |
1361 | 1 | assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SVX")); |
1362 | 1 | assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SVY")); |
1363 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("SVZ")); |
1364 | 1 | assertEquals("SWG", ResidueProperties.getCanonicalAminoAcid("SWG")); |
1365 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SYS")); |
1366 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T ")); |
1367 | 1 | assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("T11")); |
1368 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T23")); |
1369 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T2S")); |
1370 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("T2T")); |
1371 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("T31")); |
1372 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T32")); |
1373 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T36")); |
1374 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T37")); |
1375 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T38")); |
1376 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T39")); |
1377 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T3P")); |
1378 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T41")); |
1379 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T48")); |
1380 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T49")); |
1381 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T4S")); |
1382 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("T5O")); |
1383 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T5S")); |
1384 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("T66")); |
1385 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("T6A")); |
1386 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TA3")); |
1387 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("TA4")); |
1388 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TAF")); |
1389 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("TAL")); |
1390 | 1 | assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("TAV")); |
1391 | 1 | assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("TBG")); |
1392 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TBM")); |
1393 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("TC1")); |
1394 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TCP")); |
1395 | 1 | assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TCQ")); |
1396 | 1 | assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TCR")); |
1397 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("TCY")); |
1398 | 1 | assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("TDD")); |
1399 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TDY")); |
1400 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TFE")); |
1401 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("TFO")); |
1402 | 1 | assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("TFQ")); |
1403 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TFT")); |
1404 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("TGP")); |
1405 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TH6")); |
1406 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("THC")); |
1407 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("THO")); |
1408 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("THR")); |
1409 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("THX")); |
1410 | 1 | assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("THZ")); |
1411 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("TIH")); |
1412 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("TLB")); |
1413 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TLC")); |
1414 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("TLN")); |
1415 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TMB")); |
1416 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TMD")); |
1417 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("TNB")); |
1418 | 1 | assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("TNR")); |
1419 | 1 | assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TOX")); |
1420 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TP1")); |
1421 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("TPC")); |
1422 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("TPG")); |
1423 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("TPH")); |
1424 | 1 | assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TPL")); |
1425 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TPO")); |
1426 | 1 | assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TPQ")); |
1427 | 1 | assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TQI")); |
1428 | 1 | assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TQQ")); |
1429 | 1 | assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TRF")); |
1430 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("TRG")); |
1431 | 1 | assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TRN")); |
1432 | 1 | assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TRO")); |
1433 | 1 | assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TRP")); |
1434 | 1 | assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TRQ")); |
1435 | 1 | assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TRW")); |
1436 | 1 | assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TRX")); |
1437 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("TS ")); |
1438 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("TST")); |
1439 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("TT ")); |
1440 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TTD")); |
1441 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("TTI")); |
1442 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TTM")); |
1443 | 1 | assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TTQ")); |
1444 | 1 | assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TTS")); |
1445 | 1 | assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TY1")); |
1446 | 1 | assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TY2")); |
1447 | 1 | assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TY3")); |
1448 | 1 | assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TY5")); |
1449 | 1 | assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYB")); |
1450 | 1 | assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYI")); |
1451 | 1 | assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYJ")); |
1452 | 1 | assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYN")); |
1453 | 1 | assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYO")); |
1454 | 1 | assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYQ")); |
1455 | 1 | assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYR")); |
1456 | 1 | assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYS")); |
1457 | 1 | assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYT")); |
1458 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("TYU")); |
1459 | 1 | assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYW")); |
1460 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("TYX")); |
1461 | 1 | assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYY")); |
1462 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("TZB")); |
1463 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("TZO")); |
1464 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U ")); |
1465 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U25")); |
1466 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U2L")); |
1467 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U2N")); |
1468 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U2P")); |
1469 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U31")); |
1470 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U33")); |
1471 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U34")); |
1472 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U36")); |
1473 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U37")); |
1474 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U8U")); |
1475 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("UAR")); |
1476 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("UCL")); |
1477 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("UD5")); |
1478 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("UDP")); |
1479 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("UFP")); |
1480 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("UFR")); |
1481 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("UFT")); |
1482 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("UMA")); |
1483 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("UMP")); |
1484 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("UMS")); |
1485 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("UN1")); |
1486 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("UN2")); |
1487 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("UNK")); |
1488 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("UR3")); |
1489 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("URD")); |
1490 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("US1")); |
1491 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("US2")); |
1492 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("US3")); |
1493 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("US5")); |
1494 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("USM")); |
1495 | 1 | assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("VAD")); |
1496 | 1 | assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("VAF")); |
1497 | 1 | assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("VAL")); |
1498 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("VB1")); |
1499 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("VDL")); |
1500 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("VLL")); |
1501 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("VLM")); |
1502 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("VMS")); |
1503 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("VOL")); |
1504 | 1 | assertEquals("GYG", ResidueProperties.getCanonicalAminoAcid("WCR")); |
1505 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("X ")); |
1506 | 1 | assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("X2W")); |
1507 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("X4A")); |
1508 | 1 | assertEquals("AFG", ResidueProperties.getCanonicalAminoAcid("X9Q")); |
1509 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("XAD")); |
1510 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("XAE")); |
1511 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("XAL")); |
1512 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("XAR")); |
1513 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("XCL")); |
1514 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("XCN")); |
1515 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("XCP")); |
1516 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("XCR")); |
1517 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("XCS")); |
1518 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("XCT")); |
1519 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("XCY")); |
1520 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("XGA")); |
1521 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("XGL")); |
1522 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("XGR")); |
1523 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("XGU")); |
1524 | 1 | assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("XPR")); |
1525 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("XSN")); |
1526 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("XTH")); |
1527 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("XTL")); |
1528 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("XTR")); |
1529 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("XTS")); |
1530 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("XTY")); |
1531 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("XUA")); |
1532 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("XUG")); |
1533 | 1 | assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("XX1")); |
1534 | 1 | assertEquals("THG", ResidueProperties.getCanonicalAminoAcid("XXY")); |
1535 | 1 | assertEquals("DYG", ResidueProperties.getCanonicalAminoAcid("XYG")); |
1536 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("Y ")); |
1537 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("YCM")); |
1538 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("YG ")); |
1539 | 1 | assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("YOF")); |
1540 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("YRR")); |
1541 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("YYG")); |
1542 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("Z ")); |
1543 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("Z01")); |
1544 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ZAD")); |
1545 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ZAL")); |
1546 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("ZBC")); |
1547 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("ZBU")); |
1548 | 1 | assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("ZCL")); |
1549 | 1 | assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("ZCY")); |
1550 | 1 | assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("ZDU")); |
1551 | 1 | assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("ZFB")); |
1552 | 1 | assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("ZGU")); |
1553 | 1 | assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("ZHP")); |
1554 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("ZTH")); |
1555 | 1 | assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("ZU0")); |
1556 | 1 | assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ZZJ")); |
1557 | ||
1558 | 1 | assertEquals(null, ResidueProperties.getCanonicalAminoAcid(null)); |
1559 | } | |
1560 | ||
1561 | 1 | @Test(groups = { "Functional" }) |
1562 | public void testGetSingleCharacterCode() | |
1563 | { | |
1564 | 1 | assertEquals('0', ResidueProperties.getSingleCharacterCode(null)); |
1565 | 1 | assertEquals('0', ResidueProperties.getSingleCharacterCode(null)); |
1566 | 1 | assertEquals('0', ResidueProperties.getSingleCharacterCode("")); |
1567 | 1 | assertEquals('Q', ResidueProperties.getSingleCharacterCode("GLN")); |
1568 | 1 | assertEquals('Q', ResidueProperties.getSingleCharacterCode("Gln")); |
1569 | 1 | assertEquals('Q', ResidueProperties.getSingleCharacterCode("gln")); |
1570 | } | |
1571 | ||
1572 | 1 | @Test(groups = { "Functional" }) |
1573 | public void testGetDssp3State() | |
1574 | { | |
1575 | 1 | assertNull(ResidueProperties.getDssp3state(null)); |
1576 | 1 | assertEquals("", ResidueProperties.getDssp3state("")); |
1577 | 1 | String foo = "0123 []<>abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ"; |
1578 | 1 | String bar = " E E HHH "; |
1579 | 1 | assertEquals(bar, ResidueProperties.getDssp3state(foo)); |
1580 | } | |
1581 | ||
1582 | 1 | @Test(groups = { "Functional" }) |
1583 | public void testPhysicoChemicalProperties() | |
1584 | { | |
1585 | 1 | checkProperty("aromatic", "FYWH-*"); |
1586 | 1 | checkProperty("aliphatic", "IVL-*"); |
1587 | 1 | checkProperty("tiny", "GAS-*"); |
1588 | 1 | checkProperty("small", "VCTGACSDNP-*"); |
1589 | 1 | checkProperty("charged", "HKRDE-*"); |
1590 | 1 | checkProperty("negative", "DE-*"); |
1591 | 1 | checkProperty("polar", "YWHRKTSNDEQ-*X"); |
1592 | 1 | checkProperty("positive", "HKR-*"); |
1593 | 1 | checkProperty("proline", "P-*"); |
1594 | 1 | checkProperty("hydrophobic", "MILVFYWHKTGAC-*X"); |
1595 | } | |
1596 | ||
1597 | /** | |
1598 | * Verify that the residues in the list have the named property, and other | |
1599 | * residues do not | |
1600 | * | |
1601 | * @param property | |
1602 | * @param residues | |
1603 | */ | |
1604 | 10 | void checkProperty(String property, String residues) |
1605 | { | |
1606 | 10 | Map<String, Integer> props = ResidueProperties.propHash.get(property); |
1607 | ||
1608 | /* | |
1609 | * assert residues have the property (value 1 in lookup) | |
1610 | */ | |
1611 | 10 | for (char res : residues.toCharArray()) |
1612 | { | |
1613 | 77 | assertEquals(res + " should be " + property, 1, |
1614 | props.get(String.valueOf(res)).intValue()); | |
1615 | } | |
1616 | ||
1617 | /* | |
1618 | * assert other residues do not (value 0 in lookup) | |
1619 | */ | |
1620 | 10 | for (String res : ResidueProperties.aa) |
1621 | { | |
1622 | 280 | if (!residues.contains(res)) |
1623 | { | |
1624 | 214 | Integer propValue = props.get(String.valueOf(res)); |
1625 | ||
1626 | 214 | if (propValue != null) |
1627 | { | |
1628 | /* | |
1629 | * conservation calculation assigns unexpected symbols | |
1630 | * the same value as '-'; here we just check those which | |
1631 | * explicitly do not have the property | |
1632 | */ | |
1633 | 146 | assertEquals(res + " should not be " + property, 0, |
1634 | propValue.intValue()); | |
1635 | } | |
1636 | } | |
1637 | } | |
1638 | } | |
1639 | } |