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