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