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