Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ResiduePropertiesTest	35	1,464	12	1.0100%	Show methods

Class ResiduePropertiesTest

Class ResiduePropertiesTest	Line # 35	Total Statements 1,464	Complexity 12	TOTAL Coverage 1.0100%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	3838	2.02	1.01	1.0 1.0100%
testCodonTranslate() : void   testCodonTranslate() : void	4848	64.064	1.01	1.0 1.0100%
testCodonTranslate_ambiguityCodes() : void   testCodonTranslate_ambiguityCodes() : void	122122	55.055	1.01	1.0 1.0100%
testGetResidues_nucleotide() : void   testGetResidues_nucleotide() : void	209209	6.06	1.01	1.0 1.0100%
testGetResidues_peptide() : void   testGetResidues_peptide() : void	229229	6.06	1.01	1.0 1.0100%
testGetCanonicalAminoAcid() : void   testGetCanonicalAminoAcid() : void	252252	1302.01,302	1.01	1.0 1.0100%
testGetSingleCharacterCode() : void   testGetSingleCharacterCode() : void	15611561	6.06	1.01	1.0 1.0100%
testGetDssp3State() : void   testGetDssp3State() : void	15721572	5.05	1.01	1.0 1.0100%
testPhysicoChemicalProperties() : void   testPhysicoChemicalProperties() : void	15821582	10.010	1.01	1.0 1.0100%
checkProperty(String,String) : void   checkProperty(String,String) : void	16041604	8.08	3.03	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.88159674	jalview.schemes.ResiduePropertiesTest.testGetCanonicalAminoAcidjalview.schemes.ResiduePropertiesTest.testGetCanonicalAminoAcid	1PASS
	0.04397835	jalview.schemes.ResiduePropertiesTest.testCodonTranslatejalview.schemes.ResiduePropertiesTest.testCodonTranslate	1PASS
	0.03788904	jalview.schemes.ResiduePropertiesTest.testCodonTranslate_ambiguityCodesjalview.schemes.ResiduePropertiesTest.testCodonTranslate_ambiguityCodes	1PASS
	0.01623816	jalview.schemes.ResiduePropertiesTest.testPhysicoChemicalPropertiesjalview.schemes.ResiduePropertiesTest.testPhysicoChemicalProperties	1PASS
	0.00473613	jalview.schemes.ResiduePropertiesTest.testGetResidues_peptidejalview.schemes.ResiduePropertiesTest.testGetResidues_peptide	1PASS
	0.00473613	jalview.schemes.ResiduePropertiesTest.testGetResidues_nucleotidejalview.schemes.ResiduePropertiesTest.testGetResidues_nucleotide	1PASS
	0.00405954	jalview.schemes.ResiduePropertiesTest.testGetDssp3Statejalview.schemes.ResiduePropertiesTest.testGetDssp3State	1PASS
	0.00473613	jalview.schemes.ResiduePropertiesTest.testGetSingleCharacterCodejalview.schemes.ResiduePropertiesTest.testGetSingleCharacterCode	1PASS

 

Source view

1		/*
2		* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3		* Copyright (C) $$Year-Rel$$ The Jalview Authors
4		*
5		* This file is part of Jalview.
6		*
7		* Jalview is free software: you can redistribute it and/or
8		* modify it under the terms of the GNU General Public License
9		* as published by the Free Software Foundation, either version 3
10		* of the License, or (at your option) any later version.
11		*
12		* Jalview is distributed in the hope that it will be useful, but
13		* WITHOUT ANY WARRANTY; without even the implied warranty
14		* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15		* PURPOSE. See the GNU General Public License for more details.
16		*
17		* You should have received a copy of the GNU General Public License
18		* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19		* The Jalview Authors are detailed in the 'AUTHORS' file.
20		*/
21		package jalview.schemes;
22
23		import static org.testng.AssertJUnit.assertEquals;
24		import static org.testng.AssertJUnit.assertNull;
25
26		import java.util.Collections;
27		import java.util.List;
28		import java.util.Map;
29
30		import org.testng.annotations.BeforeClass;
31		import org.testng.annotations.Test;
32
33		import jalview.gui.JvOptionPane;
34
		100% Uncovered Elements: 0 (1,478) Complexity: 12 Complexity Density: 0.01
35		public class ResiduePropertiesTest
36		{
37
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
38	1	@BeforeClass(alwaysRun = true)...
39		public void setUpJvOptionPane()
40		{
41	1	JvOptionPane.setInteractiveMode(false);
42	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
43		}
44
45		/**
46		* Test 'standard' codon translations (no ambiguity codes)
47		*/
		100% Uncovered Elements: 0 (64) Complexity: 1 Complexity Density: 0.02 1PASS
48	1	@Test(groups = { "Functional" })...
49		public void testCodonTranslate()
50		{
51		// standard translation table order column 1/2/3/4
52	1	assertEquals("F", ResidueProperties.codonTranslate("TTT"));
53	1	assertEquals("F", ResidueProperties.codonTranslate("TTC"));
54	1	assertEquals("L", ResidueProperties.codonTranslate("TTA"));
55	1	assertEquals("L", ResidueProperties.codonTranslate("TTG"));
56	1	assertEquals("L", ResidueProperties.codonTranslate("CTT"));
57	1	assertEquals("L", ResidueProperties.codonTranslate("CTC"));
58	1	assertEquals("L", ResidueProperties.codonTranslate("CTA"));
59	1	assertEquals("L", ResidueProperties.codonTranslate("CTG"));
60	1	assertEquals("I", ResidueProperties.codonTranslate("ATT"));
61	1	assertEquals("I", ResidueProperties.codonTranslate("ATC"));
62	1	assertEquals("I", ResidueProperties.codonTranslate("ATA"));
63	1	assertEquals("M", ResidueProperties.codonTranslate("ATG"));
64	1	assertEquals("V", ResidueProperties.codonTranslate("GTT"));
65	1	assertEquals("V", ResidueProperties.codonTranslate("GTC"));
66	1	assertEquals("V", ResidueProperties.codonTranslate("GTA"));
67	1	assertEquals("V", ResidueProperties.codonTranslate("GTG"));
68	1	assertEquals("S", ResidueProperties.codonTranslate("TCT"));
69	1	assertEquals("S", ResidueProperties.codonTranslate("TCC"));
70	1	assertEquals("S", ResidueProperties.codonTranslate("TCA"));
71	1	assertEquals("S", ResidueProperties.codonTranslate("TCG"));
72	1	assertEquals("P", ResidueProperties.codonTranslate("CCT"));
73	1	assertEquals("P", ResidueProperties.codonTranslate("CCC"));
74	1	assertEquals("P", ResidueProperties.codonTranslate("CCA"));
75	1	assertEquals("P", ResidueProperties.codonTranslate("CCG"));
76	1	assertEquals("T", ResidueProperties.codonTranslate("ACT"));
77	1	assertEquals("T", ResidueProperties.codonTranslate("ACC"));
78	1	assertEquals("T", ResidueProperties.codonTranslate("ACA"));
79	1	assertEquals("T", ResidueProperties.codonTranslate("ACG"));
80	1	assertEquals("A", ResidueProperties.codonTranslate("GCT"));
81	1	assertEquals("A", ResidueProperties.codonTranslate("GCC"));
82	1	assertEquals("A", ResidueProperties.codonTranslate("GCA"));
83	1	assertEquals("A", ResidueProperties.codonTranslate("GCG"));
84	1	assertEquals("Y", ResidueProperties.codonTranslate("TAT"));
85	1	assertEquals("Y", ResidueProperties.codonTranslate("TAC"));
86	1	assertEquals("STOP", ResidueProperties.codonTranslate("TAA"));
87	1	assertEquals("STOP", ResidueProperties.codonTranslate("TAG"));
88	1	assertEquals("H", ResidueProperties.codonTranslate("CAT"));
89	1	assertEquals("H", ResidueProperties.codonTranslate("CAC"));
90	1	assertEquals("Q", ResidueProperties.codonTranslate("CAA"));
91	1	assertEquals("Q", ResidueProperties.codonTranslate("CAG"));
92	1	assertEquals("N", ResidueProperties.codonTranslate("AAT"));
93	1	assertEquals("N", ResidueProperties.codonTranslate("AAC"));
94	1	assertEquals("K", ResidueProperties.codonTranslate("AAA"));
95	1	assertEquals("K", ResidueProperties.codonTranslate("AAG"));
96	1	assertEquals("D", ResidueProperties.codonTranslate("GAT"));
97	1	assertEquals("D", ResidueProperties.codonTranslate("GAC"));
98	1	assertEquals("E", ResidueProperties.codonTranslate("GAA"));
99	1	assertEquals("E", ResidueProperties.codonTranslate("GAG"));
100	1	assertEquals("C", ResidueProperties.codonTranslate("TGT"));
101	1	assertEquals("C", ResidueProperties.codonTranslate("TGC"));
102	1	assertEquals("STOP", ResidueProperties.codonTranslate("TGA"));
103	1	assertEquals("W", ResidueProperties.codonTranslate("TGG"));
104	1	assertEquals("R", ResidueProperties.codonTranslate("CGT"));
105	1	assertEquals("R", ResidueProperties.codonTranslate("CGC"));
106	1	assertEquals("R", ResidueProperties.codonTranslate("CGA"));
107	1	assertEquals("R", ResidueProperties.codonTranslate("CGG"));
108	1	assertEquals("S", ResidueProperties.codonTranslate("AGT"));
109	1	assertEquals("S", ResidueProperties.codonTranslate("AGC"));
110	1	assertEquals("R", ResidueProperties.codonTranslate("AGA"));
111	1	assertEquals("R", ResidueProperties.codonTranslate("AGG"));
112	1	assertEquals("G", ResidueProperties.codonTranslate("GGT"));
113	1	assertEquals("G", ResidueProperties.codonTranslate("GGC"));
114	1	assertEquals("G", ResidueProperties.codonTranslate("GGA"));
115	1	assertEquals("G", ResidueProperties.codonTranslate("GGG"));
116		}
117
118		/**
119		* Test a sample of codon translations involving ambiguity codes. Should
120		* return a protein value where the ambiguity does not affect the translation.
121		*/
		100% Uncovered Elements: 0 (55) Complexity: 1 Complexity Density: 0.02 1PASS
122	1	@Test(groups = { "Functional" })...
123		public void testCodonTranslate_ambiguityCodes()
124		{
125		// Y is C or T
126	1	assertEquals("C", ResidueProperties.codonTranslate("TGY"));
127		// Phenylalanine first base variation
128	1	assertEquals("L", ResidueProperties.codonTranslate("YTA"));
129
130		// W is A or T
131	1	assertEquals("L", ResidueProperties.codonTranslate("CTW"));
132	1	assertNull(ResidueProperties.codonTranslate("TTW"));
133
134		// S is G or C
135	1	assertEquals("G", ResidueProperties.codonTranslate("GGS"));
136	1	assertNull(ResidueProperties.codonTranslate("ATS"));
137
138		// K is T or G
139	1	assertEquals("S", ResidueProperties.codonTranslate("TCK"));
140	1	assertNull(ResidueProperties.codonTranslate("ATK"));
141
142		// M is C or A
143	1	assertEquals("T", ResidueProperties.codonTranslate("ACM"));
144		// Arginine first base variation
145	1	assertEquals("R", ResidueProperties.codonTranslate("MGA"));
146	1	assertEquals("R", ResidueProperties.codonTranslate("MGG"));
147	1	assertNull(ResidueProperties.codonTranslate("TAM"));
148
149		// D is A, G or T
150	1	assertEquals("P", ResidueProperties.codonTranslate("CCD"));
151	1	assertNull(ResidueProperties.codonTranslate("AAD"));
152
153		// V is A, C or G
154	1	assertEquals("V", ResidueProperties.codonTranslate("GTV"));
155	1	assertNull(ResidueProperties.codonTranslate("TTV"));
156
157		// H is A, C or T
158	1	assertEquals("A", ResidueProperties.codonTranslate("GCH"));
159	1	assertEquals("I", ResidueProperties.codonTranslate("ATH"));
160	1	assertNull(ResidueProperties.codonTranslate("AGH"));
161
162		// B is C, G or T
163	1	assertEquals("P", ResidueProperties.codonTranslate("CCB"));
164	1	assertNull(ResidueProperties.codonTranslate("TAB"));
165
166		// R is A or G
167		// additional tests for JAL-1685 (resolved)
168	1	assertEquals("L", ResidueProperties.codonTranslate("CTR"));
169	1	assertEquals("V", ResidueProperties.codonTranslate("GTR"));
170	1	assertEquals("S", ResidueProperties.codonTranslate("TCR"));
171	1	assertEquals("P", ResidueProperties.codonTranslate("CCR"));
172	1	assertEquals("T", ResidueProperties.codonTranslate("ACR"));
173	1	assertEquals("A", ResidueProperties.codonTranslate("GCR"));
174	1	assertEquals("R", ResidueProperties.codonTranslate("CGR"));
175	1	assertEquals("G", ResidueProperties.codonTranslate("GGR"));
176	1	assertEquals("R", ResidueProperties.codonTranslate("AGR"));
177	1	assertEquals("E", ResidueProperties.codonTranslate("GAR"));
178	1	assertEquals("K", ResidueProperties.codonTranslate("AAR"));
179	1	assertEquals("L", ResidueProperties.codonTranslate("TTR"));
180	1	assertEquals("Q", ResidueProperties.codonTranslate("CAR"));
181	1	assertEquals("STOP", ResidueProperties.codonTranslate("TAR"));
182	1	assertEquals("STOP", ResidueProperties.codonTranslate("TRA"));
183		// Arginine first and third base ambiguity
184	1	assertEquals("R", ResidueProperties.codonTranslate("MGR"));
185	1	assertNull(ResidueProperties.codonTranslate("ATR"));
186
187		// N is any base; 8 proteins accept any base in 3rd position
188	1	assertEquals("L", ResidueProperties.codonTranslate("CTN"));
189	1	assertEquals("V", ResidueProperties.codonTranslate("GTN"));
190	1	assertEquals("S", ResidueProperties.codonTranslate("TCN"));
191	1	assertEquals("P", ResidueProperties.codonTranslate("CCN"));
192	1	assertEquals("T", ResidueProperties.codonTranslate("ACN"));
193	1	assertEquals("A", ResidueProperties.codonTranslate("GCN"));
194	1	assertEquals("R", ResidueProperties.codonTranslate("CGN"));
195	1	assertEquals("G", ResidueProperties.codonTranslate("GGN"));
196	1	assertNull(ResidueProperties.codonTranslate("ATN"));
197	1	assertNull(ResidueProperties.codonTranslate("ANT"));
198	1	assertNull(ResidueProperties.codonTranslate("NAT"));
199	1	assertNull(ResidueProperties.codonTranslate("ANN"));
200	1	assertNull(ResidueProperties.codonTranslate("NNA"));
201	1	assertNull(ResidueProperties.codonTranslate("NNN"));
202
203		// some random stuff
204	1	assertNull(ResidueProperties.codonTranslate("YWB"));
205	1	assertNull(ResidueProperties.codonTranslate("VHD"));
206	1	assertNull(ResidueProperties.codonTranslate("WSK"));
207		}
208
		100% Uncovered Elements: 0 (6) Complexity: 1 Complexity Density: 0.17 1PASS
209	1	@Test(groups = { "Functional" })...
210		public void testGetResidues_nucleotide()
211		{
212		/*
213		* Non-ambiguous only; we don't care about the order of the list, it is just
214		* sorted here to make assertions reliable
215		*/
216	1	List<String> residues = ResidueProperties.getResidues(true, false);
217	1	Collections.sort(residues);
218	1	assertEquals("[A, C, G, T, U]", residues.toString());
219
220		/*
221		* Including ambiguity codes I N R X Y
222		*/
223	1	residues = ResidueProperties.getResidues(true, true);
224	1	Collections.sort(residues);
225	1	assertEquals("[A, B, C, D, G, H, I, K, M, N, R, S, T, U, V, W, X, Y]",
226		residues.toString());
227		}
228
		100% Uncovered Elements: 0 (6) Complexity: 1 Complexity Density: 0.17 1PASS
229	1	@Test(groups = { "Functional" })...
230		public void testGetResidues_peptide()
231		{
232		/*
233		* Non-ambiguous only; we don't care about the order of the list, it is just
234		* sorted here to make assertions reliable
235		*/
236	1	List<String> residues = ResidueProperties.getResidues(false, false);
237	1	Collections.sort(residues);
238	1	assertEquals(
239		"[ALA, ARG, ASN, ASP, CYS, GLN, GLU, GLY, HIS, ILE, LEU, LYS, MET, PHE, PRO, SER, THR, TRP, TYR, VAL]",
240		residues.toString());
241
242		/*
243		* Including ambiguity codes ASX, GLX, XAA
244		*/
245	1	residues = ResidueProperties.getResidues(false, true);
246	1	Collections.sort(residues);
247	1	assertEquals(
248		"[ALA, ARG, ASN, ASP, ASX, CYS, GLN, GLU, GLX, GLY, HIS, ILE, LEU, LYS, MET, PHE, PRO, SER, THR, TRP, TYR, VAL, XAA]",
249		residues.toString());
250		}
251
		100% Uncovered Elements: 0 (1,302) Complexity: 1 Complexity Density: 0 1PASS
252	1	@Test(groups = { "Functional" })...
253		public void testGetCanonicalAminoAcid()
254		{
255	1	assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MET"));
256	1	assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MSE"));
257
258	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("00C"));
259	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("01W"));
260	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("02K"));
261	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("03Y"));
262	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("07O"));
263	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("08P"));
264	1	assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("0A0"));
265	1	assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("0A1"));
266	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("0A2"));
267	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("0A8"));
268	1	assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("0AA"));
269	1	assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("0AB"));
270	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("0AC"));
271	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("0AD"));
272	1	assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("0AF"));
273	1	assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("0AG"));
274	1	assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("0AH"));
275	1	assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("0AK"));
276	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("0AM"));
277	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("0AP"));
278	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("0AU"));
279	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("0AV"));
280	1	assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("0AZ"));
281	1	assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("0BN"));
282	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("0C "));
283	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("0CS"));
284	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("0DC"));
285	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("0DG"));
286	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("0DT"));
287	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("0FL"));
288	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("0G "));
289	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("0NC"));
290	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("0SP"));
291	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("0U "));
292	1	assertEquals("YG", ResidueProperties.getCanonicalAminoAcid("0YG"));
293	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("10C"));
294	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("125"));
295	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("126"));
296	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("127"));
297	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("128"));
298	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("12A"));
299	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("143"));
300	1	assertEquals("ASG", ResidueProperties.getCanonicalAminoAcid("175"));
301	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("193"));
302	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("1AP"));
303	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("1MA"));
304	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("1MG"));
305	1	assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("1PA"));
306	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("1PI"));
307	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("1PR"));
308	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("1SC"));
309	1	assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("1TQ"));
310	1	assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("1TY"));
311	1	assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("1X6"));
312	1	assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("200"));
313	1	assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("23F"));
314	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("23S"));
315	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("26B"));
316	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("2AD"));
317	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("2AG"));
318	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("2AO"));
319	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("2AR"));
320	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("2AS"));
321	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("2AT"));
322	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("2AU"));
323	1	assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("2BD"));
324	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("2BT"));
325	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("2BU"));
326	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("2CO"));
327	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("2DA"));
328	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("2DF"));
329	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("2DM"));
330	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("2DO"));
331	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("2DT"));
332	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("2EG"));
333	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("2FE"));
334	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("2FI"));
335	1	assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("2FM"));
336	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("2GT"));
337	1	assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("2HF"));
338	1	assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("2LU"));
339	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("2MA"));
340	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("2MG"));
341	1	assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("2ML"));
342	1	assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("2MR"));
343	1	assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("2MT"));
344	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("2MU"));
345	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("2NT"));
346	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("2OM"));
347	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("2OT"));
348	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("2PI"));
349	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("2PR"));
350	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("2SA"));
351	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("2SI"));
352	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("2ST"));
353	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("2TL"));
354	1	assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("2TY"));
355	1	assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("2VA"));
356	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("2XA"));
357	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("32S"));
358	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("32T"));
359	1	assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("3AH"));
360	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("3AR"));
361	1	assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("3CF"));
362	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("3DA"));
363	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("3DR"));
364	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("3GA"));
365	1	assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("3MD"));
366	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("3ME"));
367	1	assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("3NF"));
368	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("3QN"));
369	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("3TY"));
370	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("3XH"));
371	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("4AC"));
372	1	assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("4BF"));
373	1	assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("4CF"));
374	1	assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("4CY"));
375	1	assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("4DP"));
376	1	assertEquals("GYG", ResidueProperties.getCanonicalAminoAcid("4F3"));
377	1	assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("4FB"));
378	1	assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("4FW"));
379	1	assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("4HT"));
380	1	assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("4IN"));
381	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("4MF"));
382	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("4MM"));
383	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("4OC"));
384	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("4PC"));
385	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("4PD"));
386	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("4PE"));
387	1	assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("4PH"));
388	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("4SC"));
389	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("4SU"));
390	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("4TA"));
391	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("4U7"));
392	1	assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("56A"));
393	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("5AA"));
394	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("5AB"));
395	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("5AT"));
396	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("5BU"));
397	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("5CG"));
398	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("5CM"));
399	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("5CS"));
400	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("5FA"));
401	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("5FC"));
402	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("5FU"));
403	1	assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("5HP"));
404	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("5HT"));
405	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("5HU"));
406	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("5IC"));
407	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("5IT"));
408	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("5IU"));
409	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("5MC"));
410	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("5MD"));
411	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("5MU"));
412	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("5NC"));
413	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("5PC"));
414	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("5PY"));
415	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("5SE"));
416	1	assertEquals("TWG", ResidueProperties.getCanonicalAminoAcid("5ZA"));
417	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("64T"));
418	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("6CL"));
419	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("6CT"));
420	1	assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("6CW"));
421	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("6HA"));
422	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("6HC"));
423	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("6HG"));
424	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("6HN"));
425	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("6HT"));
426	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("6IA"));
427	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("6MA"));
428	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("6MC"));
429	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("6MI"));
430	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("6MT"));
431	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("6MZ"));
432	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("6OG"));
433	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("70U"));
434	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("7DA"));
435	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("7GU"));
436	1	assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("7JA"));
437	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("7MG"));
438	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("8AN"));
439	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("8FG"));
440	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("8MG"));
441	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("8OG"));
442	1	assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("9NE"));
443	1	assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("9NF"));
444	1	assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("9NR"));
445	1	assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("9NV"));
446	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A "));
447	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("A1P"));
448	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A23"));
449	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A2L"));
450	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A2M"));
451	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A34"));
452	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A35"));
453	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A38"));
454	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A39"));
455	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A3A"));
456	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A3P"));
457	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A40"));
458	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A43"));
459	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A44"));
460	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A47"));
461	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A5L"));
462	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("A5M"));
463	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("A5N"));
464	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A5O"));
465	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("A66"));
466	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AA3"));
467	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AA4"));
468	1	assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("AAR"));
469	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("AB7"));
470	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ABA"));
471	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ABR"));
472	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ABS"));
473	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("ABT"));
474	1	assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("ACB"));
475	1	assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("ACL"));
476	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AD2"));
477	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("ADD"));
478	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("ADX"));
479	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("AEA"));
480	1	assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("AEI"));
481	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AET"));
482	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("AFA"));
483	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("AFF"));
484	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("AFG"));
485	1	assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("AGM"));
486	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("AGT"));
487	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("AHB"));
488	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("AHH"));
489	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AHO"));
490	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AHP"));
491	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("AHS"));
492	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("AHT"));
493	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AIB"));
494	1	assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("AKL"));
495	1	assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("AKZ"));
496	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ALA"));
497	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ALC"));
498	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ALM"));
499	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ALN"));
500	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("ALO"));
501	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("ALQ"));
502	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ALS"));
503	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ALT"));
504	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ALV"));
505	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("ALY"));
506	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AN8"));
507	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AP7"));
508	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("APE"));
509	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("APH"));
510	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("API"));
511	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("APK"));
512	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("APM"));
513	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("APP"));
514	1	assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("AR2"));
515	1	assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("AR4"));
516	1	assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("AR7"));
517	1	assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("ARG"));
518	1	assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("ARM"));
519	1	assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("ARO"));
520	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("ARV"));
521	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AS "));
522	1	assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("AS2"));
523	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("AS9"));
524	1	assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("ASA"));
525	1	assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("ASB"));
526	1	assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("ASI"));
527	1	assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("ASK"));
528	1	assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("ASL"));
529	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("ASM"));
530	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("ASN"));
531	1	assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("ASP"));
532	1	assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("ASQ"));
533	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("ASU"));
534	1	assertEquals("ASX", ResidueProperties.getCanonicalAminoAcid("ASX"));
535	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("ATD"));
536	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("ATL"));
537	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("ATM"));
538	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AVC"));
539	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("AVN"));
540	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AYA"));
541	1	assertEquals("AYG", ResidueProperties.getCanonicalAminoAcid("AYG"));
542	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("AZK"));
543	1	assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("AZS"));
544	1	assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("AZY"));
545	1	assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("B1F"));
546	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("B1P"));
547	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("B2A"));
548	1	assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("B2F"));
549	1	assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("B2I"));
550	1	assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("B2V"));
551	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("B3A"));
552	1	assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("B3D"));
553	1	assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("B3E"));
554	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("B3K"));
555	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("B3L"));
556	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("B3M"));
557	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("B3Q"));
558	1	assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("B3S"));
559	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("B3T"));
560	1	assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("B3U"));
561	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("B3X"));
562	1	assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("B3Y"));
563	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("BB6"));
564	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("BB7"));
565	1	assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("BB8"));
566	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("BB9"));
567	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("BBC"));
568	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("BCS"));
569	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("BE2"));
570	1	assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("BFD"));
571	1	assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("BG1"));
572	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("BGM"));
573	1	assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("BH2"));
574	1	assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("BHD"));
575	1	assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("BIF"));
576	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("BIL"));
577	1	assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("BIU"));
578	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("BJH"));
579	1	assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("BLE"));
580	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("BLY"));
581	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("BMP"));
582	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("BMT"));
583	1	assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("BNN"));
584	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("BNO"));
585	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("BOE"));
586	1	assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("BOR"));
587	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("BPE"));
588	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("BRU"));
589	1	assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("BSE"));
590	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("BT5"));
591	1	assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("BTA"));
592	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("BTC"));
593	1	assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("BTR"));
594	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("BUC"));
595	1	assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("BUG"));
596	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("BVP"));
597	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("BZG"));
598	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C "));
599	1	assertEquals("TYG", ResidueProperties.getCanonicalAminoAcid("C12"));
600	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("C1X"));
601	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C25"));
602	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C2L"));
603	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C2S"));
604	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C31"));
605	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C32"));
606	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C34"));
607	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C36"));
608	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C37"));
609	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C38"));
610	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C3Y"));
611	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C42"));
612	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C43"));
613	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C45"));
614	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C46"));
615	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C49"));
616	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C4R"));
617	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C4S"));
618	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C5C"));
619	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("C66"));
620	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C6C"));
621	1	assertEquals("TFG", ResidueProperties.getCanonicalAminoAcid("C99"));
622	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CAF"));
623	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CAL"));
624	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CAR"));
625	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CAS"));
626	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CAV"));
627	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CAY"));
628	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CB2"));
629	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CBR"));
630	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CBV"));
631	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CCC"));
632	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("CCL"));
633	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CCS"));
634	1	assertEquals("CYG", ResidueProperties.getCanonicalAminoAcid("CCY"));
635	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CDE"));
636	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CDV"));
637	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CDW"));
638	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CEA"));
639	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CFL"));
640	1	assertEquals("FCYG", ResidueProperties.getCanonicalAminoAcid("CFY")); // check
641	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("CG1"));
642	1	assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("CGA"));
643	1	assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("CGU"));
644	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CH "));
645	1	assertEquals("MYG", ResidueProperties.getCanonicalAminoAcid("CH6"));
646	1	assertEquals("KYG", ResidueProperties.getCanonicalAminoAcid("CH7"));
647	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CHF"));
648	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CHG"));
649	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("CHP"));
650	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CHS"));
651	1	assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("CIR"));
652	1	assertEquals("GYG", ResidueProperties.getCanonicalAminoAcid("CJO"));
653	1	assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("CLE"));
654	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("CLG"));
655	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("CLH"));
656	1	assertEquals("AFG", ResidueProperties.getCanonicalAminoAcid("CLV"));
657	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("CM0"));
658	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CME"));
659	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CMH"));
660	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CML"));
661	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CMR"));
662	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CMT"));
663	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("CNU"));
664	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CP1"));
665	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CPC"));
666	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CPI"));
667	1	assertEquals("GYG", ResidueProperties.getCanonicalAminoAcid("CQR"));
668	1	assertEquals("TLG", ResidueProperties.getCanonicalAminoAcid("CR0"));
669	1	assertEquals("GYG", ResidueProperties.getCanonicalAminoAcid("CR2"));
670	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("CR5"));
671	1	assertEquals("KYG", ResidueProperties.getCanonicalAminoAcid("CR7"));
672	1	assertEquals("HYG", ResidueProperties.getCanonicalAminoAcid("CR8"));
673	1	assertEquals("TWG", ResidueProperties.getCanonicalAminoAcid("CRF"));
674	1	assertEquals("THG", ResidueProperties.getCanonicalAminoAcid("CRG"));
675	1	assertEquals("MYG", ResidueProperties.getCanonicalAminoAcid("CRK"));
676	1	assertEquals("GYG", ResidueProperties.getCanonicalAminoAcid("CRO"));
677	1	assertEquals("QYG", ResidueProperties.getCanonicalAminoAcid("CRQ"));
678	1	assertEquals("EYG", ResidueProperties.getCanonicalAminoAcid("CRU"));
679	1	assertEquals("ASG", ResidueProperties.getCanonicalAminoAcid("CRW"));
680	1	assertEquals("ASG", ResidueProperties.getCanonicalAminoAcid("CRX"));
681	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CS0"));
682	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CS1"));
683	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CS3"));
684	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CS4"));
685	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("CS8"));
686	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSA"));
687	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSB"));
688	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSD"));
689	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSE"));
690	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSF"));
691	1	assertEquals("SHG", ResidueProperties.getCanonicalAminoAcid("CSH"));
692	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("CSI"));
693	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSJ"));
694	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSL"));
695	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSO"));
696	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSP"));
697	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSR"));
698	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSS"));
699	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSU"));
700	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSW"));
701	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSX"));
702	1	assertEquals("SYG", ResidueProperties.getCanonicalAminoAcid("CSY"));
703	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSZ"));
704	1	assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("CTE"));
705	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("CTG"));
706	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("CTH"));
707	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CUC"));
708	1	assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("CWR"));
709	1	assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("CXM"));
710	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CY0"));
711	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CY1"));
712	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CY3"));
713	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CY4"));
714	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CYA"));
715	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CYD"));
716	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CYF"));
717	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CYG"));
718	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CYJ"));
719	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CYM"));
720	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CYQ"));
721	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CYR"));
722	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CYS"));
723	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CZ2"));
724	1	assertEquals("GYG", ResidueProperties.getCanonicalAminoAcid("CZO"));
725	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CZZ"));
726	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("D11"));
727	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("D1P"));
728	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("D3 "));
729	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("D33"));
730	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("D3P"));
731	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("D3T"));
732	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("D4M"));
733	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("D4P"));
734	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("DA "));
735	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("DA2"));
736	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("DAB"));
737	1	assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("DAH"));
738	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("DAL"));
739	1	assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("DAR"));
740	1	assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("DAS"));
741	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("DBB"));
742	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DBM"));
743	1	assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("DBS"));
744	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("DBU"));
745	1	assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("DBY"));
746	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("DBZ"));
747	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("DC "));
748	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("DC2"));
749	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("DCG"));
750	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("DCI"));
751	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("DCL"));
752	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("DCT"));
753	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("DCY"));
754	1	assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("DDE"));
755	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("DDG"));
756	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("DDN"));
757	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DDX"));
758	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("DFC"));
759	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("DFG"));
760	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("DFI"));
761	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("DFO"));
762	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DFT"));
763	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("DG "));
764	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("DGH"));
765	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("DGI"));
766	1	assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("DGL"));
767	1	assertEquals("GLN", ResidueProperties.getCanonicalAminoAcid("DGN"));
768	1	assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("DHA"));
769	1	assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("DHI"));
770	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("DHL"));
771	1	assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("DHN"));
772	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("DHP"));
773	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("DHU"));
774	1	assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("DHV"));
775	1	assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("DI "));
776	1	assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("DIL"));
777	1	assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("DIR"));
778	1	assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("DIV"));
779	1	assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("DLE"));
780	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("DLS"));
781	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("DLY"));
782	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("DM0"));
783	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DMH"));
784	1	assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("DMK"));
785	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("DMT"));
786	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DN "));
787	1	assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("DNE"));
788	1	assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("DNG"));
789	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("DNL"));
790	1	assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("DNM"));
791	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("DNP"));
792	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("DNR"));
793	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("DNS"));
794	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("DOA"));
795	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("DOC"));
796	1	assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("DOH"));
797	1	assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("DON"));
798	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("DPB"));
799	1	assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("DPH"));
800	1	assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("DPL"));
801	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("DPP"));
802	1	assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("DPQ"));
803	1	assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("DPR"));
804	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DPY"));
805	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("DRM"));
806	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DRP"));
807	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("DRT"));
808	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DRZ"));
809	1	assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("DSE"));
810	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DSG"));
811	1	assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("DSN"));
812	1	assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("DSP"));
813	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("DT "));
814	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("DTH"));
815	1	assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("DTR"));
816	1	assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("DTY"));
817	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("DU "));
818	1	assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("DVA"));
819	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DXD"));
820	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DXN"));
821	1	assertEquals("DYG", ResidueProperties.getCanonicalAminoAcid("DYG"));
822	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("DYS"));
823	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("DZM"));
824	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("E "));
825	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("E1X"));
826	1	assertEquals("GLN", ResidueProperties.getCanonicalAminoAcid("ECC"));
827	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("EDA"));
828	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("EFC"));
829	1	assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("EHP"));
830	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("EIT"));
831	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("ENP"));
832	1	assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("ESB"));
833	1	assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("ESC"));
834	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("EXB"));
835	1	assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("EXY"));
836	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("EY5"));
837	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("EYS"));
838	1	assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("F2F"));
839	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("FA2"));
840	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("FA5"));
841	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("FAG"));
842	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("FAI"));
843	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("FB5"));
844	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("FB6"));
845	1	assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("FCL"));
846	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("FFD"));
847	1	assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("FGA"));
848	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("FGL"));
849	1	assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("FGP"));
850	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("FHL"));
851	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("FHO"));
852	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("FHU"));
853	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("FLA"));
854	1	assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("FLE"));
855	1	assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("FLT"));
856	1	assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("FME"));
857	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("FMG"));
858	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("FMU"));
859	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("FOE"));
860	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("FOX"));
861	1	assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("FP9"));
862	1	assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("FPA"));
863	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("FRD"));
864	1	assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("FT6"));
865	1	assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("FTR"));
866	1	assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("FTY"));
867	1	assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("FVA"));
868	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("FZN"));
869	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G "));
870	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G25"));
871	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G2L"));
872	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G2S"));
873	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G31"));
874	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G32"));
875	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G33"));
876	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G36"));
877	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G38"));
878	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G42"));
879	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G46"));
880	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G47"));
881	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G48"));
882	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G49"));
883	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("G4P"));
884	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G7M"));
885	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GAO"));
886	1	assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("GAU"));
887	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("GCK"));
888	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("GCM"));
889	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GDP"));
890	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GDR"));
891	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GFL"));
892	1	assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("GGL"));
893	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GH3"));
894	1	assertEquals("GLN", ResidueProperties.getCanonicalAminoAcid("GHG"));
895	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GHP"));
896	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GL3"));
897	1	assertEquals("GLN", ResidueProperties.getCanonicalAminoAcid("GLH"));
898	1	assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("GLJ"));
899	1	assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("GLK"));
900	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("GLM"));
901	1	assertEquals("GLN", ResidueProperties.getCanonicalAminoAcid("GLN"));
902	1	assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("GLQ"));
903	1	assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("GLU"));
904	1	assertEquals("GLX", ResidueProperties.getCanonicalAminoAcid("GLX"));
905	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GLY"));
906	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GLZ"));
907	1	assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("GMA"));
908	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GMS"));
909	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("GMU"));
910	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GN7"));
911	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("GND"));
912	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("GNE"));
913	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GOM"));
914	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("GPL"));
915	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GS "));
916	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GSC"));
917	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GSR"));
918	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GSS"));
919	1	assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("GSU"));
920	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("GT9"));
921	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GTP"));
922	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("GVL"));
923	1	assertEquals("CYG", ResidueProperties.getCanonicalAminoAcid("GYC"));
924	1	assertEquals("SYG", ResidueProperties.getCanonicalAminoAcid("GYS"));
925	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("H2U"));
926	1	assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("H5M"));
927	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("HAC"));
928	1	assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("HAR"));
929	1	assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("HBN"));
930	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("HCS"));
931	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("HDP"));
932	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("HEU"));
933	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("HFA"));
934	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("HGL"));
935	1	assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("HHI"));
936	1	assertEquals("AK", ResidueProperties.getCanonicalAminoAcid("HHK")); // check
937	1	assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("HIA"));
938	1	assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("HIC"));
939	1	assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("HIP"));
940	1	assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("HIQ"));
941	1	assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("HIS"));
942	1	assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("HL2"));
943	1	assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("HLU"));
944	1	assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("HMR"));
945	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("HOL"));
946	1	assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("HPC"));
947	1	assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("HPE"));
948	1	assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("HPH"));
949	1	assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("HPQ"));
950	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("HQA"));
951	1	assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("HRG"));
952	1	assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("HRP"));
953	1	assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("HS8"));
954	1	assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("HS9"));
955	1	assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("HSE"));
956	1	assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("HSL"));
957	1	assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("HSO"));
958	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("HTI"));
959	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("HTN"));
960	1	assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("HTR"));
961	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("HV5"));
962	1	assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("HVA"));
963	1	assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("HY3"));
964	1	assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("HYP"));
965	1	assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("HZP"));
966	1	assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("I "));
967	1	assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("I2M"));
968	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("I58"));
969	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("I5C"));
970	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("IAM"));
971	1	assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("IAR"));
972	1	assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("IAS"));
973	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("IC "));
974	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("IEL"));
975	1	assertEquals("HYG", ResidueProperties.getCanonicalAminoAcid("IEY"));
976	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("IG "));
977	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("IGL"));
978	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("IGU"));
979	1	assertEquals("SHG", ResidueProperties.getCanonicalAminoAcid("IIC"));
980	1	assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("IIL"));
981	1	assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("ILE"));
982	1	assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("ILG"));
983	1	assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("ILX"));
984	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("IMC"));
985	1	assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("IML"));
986	1	assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("IOY"));
987	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("IPG"));
988	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("IPN"));
989	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("IRN"));
990	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("IT1"));
991	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("IU "));
992	1	assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("IYR"));
993	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("IYT"));
994	1	assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("IZO"));
995	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("JJJ"));
996	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("JJK"));
997	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("JJL"));
998	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("JW5"));
999	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("K1R"));
1000	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("KAG"));
1001	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("KCX"));
1002	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("KGC"));
1003	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("KNB"));
1004	1	assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("KOR"));
1005	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("KPI"));
1006	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("KST"));
1007	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("KYQ"));
1008	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("L2A"));
1009	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LA2"));
1010	1	assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("LAA"));
1011	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("LAL"));
1012	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LBY"));
1013	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("LC "));
1014	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("LCA"));
1015	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("LCC"));
1016	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("LCG"));
1017	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("LCH"));
1018	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LCK"));
1019	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LCX"));
1020	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LDH"));
1021	1	assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("LED"));
1022	1	assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("LEF"));
1023	1	assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("LEH"));
1024	1	assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("LEI"));
1025	1	assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("LEM"));
1026	1	assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("LEN"));
1027	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("LET"));
1028	1	assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("LEU"));
1029	1	assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("LEX"));
1030	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("LG "));
1031	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("LGP"));
1032	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("LHC"));
1033	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("LHU"));
1034	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("LKC"));
1035	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LLP"));
1036	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LLY"));
1037	1	assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("LME"));
1038	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LMF"));
1039	1	assertEquals("GLN", ResidueProperties.getCanonicalAminoAcid("LMQ"));
1040	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("LMS"));
1041	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LP6"));
1042	1	assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("LPD"));
1043	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("LPG"));
1044	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("LPL"));
1045	1	assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("LPS"));
1046	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("LSO"));
1047	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("LTA"));
1048	1	assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("LTR"));
1049	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("LVG"));
1050	1	assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("LVN"));
1051	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LYF"));
1052	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LYK"));
1053	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LYM"));
1054	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LYN"));
1055	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LYR"));
1056	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LYS"));
1057	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LYX"));
1058	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LYZ"));
1059	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("M0H"));
1060	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("M1G"));
1061	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("M2G"));
1062	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("M2L"));
1063	1	assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("M2S"));
1064	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("M30"));
1065	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("M3L"));
1066	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("M5M"));
1067	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("MA "));
1068	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("MA6"));
1069	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("MA7"));
1070	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("MAA"));
1071	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("MAD"));
1072	1	assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("MAI"));
1073	1	assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("MBQ"));
1074	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("MBZ"));
1075	1	assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("MC1"));
1076	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("MCG"));
1077	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("MCL"));
1078	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("MCS"));
1079	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("MCY"));
1080	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("MD3"));
1081	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("MD6"));
1082	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("MDH"));
1083	1	assertEquals("ASG", ResidueProperties.getCanonicalAminoAcid("MDO"));
1084	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("MDR"));
1085	1	assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("MEA"));
1086	1	assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MED"));
1087	1	assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("MEG"));
1088	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("MEN"));
1089	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("MEP"));
1090	1	assertEquals("GLN", ResidueProperties.getCanonicalAminoAcid("MEQ"));
1091	1	assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MET"));
1092	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("MEU"));
1093	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("MF3"));
1094	1	assertEquals("GYG", ResidueProperties.getCanonicalAminoAcid("MFC"));
1095	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("MG1"));
1096	1	assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("MGG"));
1097	1	assertEquals("GLN", ResidueProperties.getCanonicalAminoAcid("MGN"));
1098	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("MGQ"));
1099	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("MGV"));
1100	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("MGY"));
1101	1	assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("MHL"));
1102	1	assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MHO"));
1103	1	assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("MHS"));
1104	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("MIA"));
1105	1	assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("MIS"));
1106	1	assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("MK8"));
1107	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("ML3"));
1108	1	assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("MLE"));
1109	1	assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("MLL"));
1110	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("MLY"));
1111	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("MLZ"));
1112	1	assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MME"));
1113	1	assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("MMO"));
1114	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("MMT"));
1115	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("MND"));
1116	1	assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("MNL"));
1117	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("MNU"));
1118	1	assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("MNV"));
1119	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("MOD"));
1120	1	assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("MP8"));
1121	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("MPH"));
1122	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("MPJ"));
1123	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("MPQ"));
1124	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("MRG"));
1125	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("MSA"));
1126	1	assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MSE"));
1127	1	assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MSL"));
1128	1	assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MSO"));
1129	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("MSP"));
1130	1	assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MT2"));
1131	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("MTR"));
1132	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("MTU"));
1133	1	assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("MTY"));
1134	1	assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("MVA"));
1135	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("N "));
1136	1	assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("N10"));
1137	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("N2C"));
1138	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("N5I"));
1139	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("N5M"));
1140	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("N6G"));
1141	1	assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("N7P"));
1142	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("NA8"));
1143	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("NAL"));
1144	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("NAM"));
1145	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("NB8"));
1146	1	assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("NBQ"));
1147	1	assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("NC1"));
1148	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("NCB"));
1149	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("NCX"));
1150	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("NCY"));
1151	1	assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("NDF"));
1152	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("NDN"));
1153	1	assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("NEM"));
1154	1	assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("NEP"));
1155	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("NF2"));
1156	1	assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("NFA"));
1157	1	assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("NHL"));
1158	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("NIT"));
1159	1	assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("NIY"));
1160	1	assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("NLE"));
1161	1	assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("NLN"));
1162	1	assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("NLO"));
1163	1	assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("NLP"));
1164	1	assertEquals("GLN", ResidueProperties.getCanonicalAminoAcid("NLQ"));
1165	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("NMC"));
1166	1	assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("NMM"));
1167	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("NMS"));
1168	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("NMT"));
1169	1	assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("NNH"));
1170	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("NP3"));
1171	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("NPH"));
1172	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("NPI"));
1173	1	assertEquals("LYG", ResidueProperties.getCanonicalAminoAcid("NRP"));
1174	1	assertEquals("MYG", ResidueProperties.getCanonicalAminoAcid("NRQ"));
1175	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("NSK"));
1176	1	assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("NTY"));
1177	1	assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("NVA"));
1178	1	assertEquals("TWG", ResidueProperties.getCanonicalAminoAcid("NYC"));
1179	1	assertEquals("NYG", ResidueProperties.getCanonicalAminoAcid("NYG"));
1180	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("NYM"));
1181	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("NYS"));
1182	1	assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("NZH"));
1183	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("O12"));
1184	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("O2C"));
1185	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("O2G"));
1186	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("OAD"));
1187	1	assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("OAS"));
1188	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("OBF"));
1189	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("OBS"));
1190	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("OCS"));
1191	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("OCY"));
1192	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("ODP"));
1193	1	assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("OHI"));
1194	1	assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("OHS"));
1195	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("OIC"));
1196	1	assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("OIP"));
1197	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("OLE"));
1198	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("OLT"));
1199	1	assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("OLZ"));
1200	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("OMC"));
1201	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("OMG"));
1202	1	assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("OMT"));
1203	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("OMU"));
1204	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("ONE"));
1205	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ONH"));
1206	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("ONL"));
1207	1	assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("OPR"));
1208	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ORN"));
1209	1	assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("ORQ"));
1210	1	assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("OSE"));
1211	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("OTB"));
1212	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("OTH"));
1213	1	assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("OTY"));
1214	1	assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("OXX"));
1215	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("P "));
1216	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("P1L"));
1217	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("P1P"));
1218	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("P2T"));
1219	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("P2U"));
1220	1	assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("P2Y"));
1221	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("P5P"));
1222	1	assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("PAQ"));
1223	1	assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("PAS"));
1224	1	assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("PAT"));
1225	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("PAU"));
1226	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("PBB"));
1227	1	assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PBF"));
1228	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("PBT"));
1229	1	assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("PCA"));
1230	1	assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("PCC"));
1231	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("PCE"));
1232	1	assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PCS"));
1233	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("PDL"));
1234	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("PDU"));
1235	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("PEC"));
1236	1	assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PF5"));
1237	1	assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PFF"));
1238	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("PFX"));
1239	1	assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("PG1"));
1240	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("PG7"));
1241	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("PG9"));
1242	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("PGL"));
1243	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("PGN"));
1244	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("PGP"));
1245	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("PGY"));
1246	1	assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PHA"));
1247	1	assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("PHD"));
1248	1	assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PHE"));
1249	1	assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PHI"));
1250	1	assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PHL"));
1251	1	assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PHM"));
1252	1	assertEquals("AYG", ResidueProperties.getCanonicalAminoAcid("PIA"));
1253	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("PIV"));
1254	1	assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("PLE"));
1255	1	assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PM3"));
1256	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("PMT"));
1257	1	assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("POM"));
1258	1	assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PPN"));
1259	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("PPU"));
1260	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("PPW"));
1261	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("PQ1"));
1262	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("PR3"));
1263	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("PR5"));
1264	1	assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("PR9"));
1265	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("PRN"));
1266	1	assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("PRO"));
1267	1	assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("PRS"));
1268	1	assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PSA"));
1269	1	assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("PSH"));
1270	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("PST"));
1271	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("PSU"));
1272	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("PSW"));
1273	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("PTA"));
1274	1	assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("PTH"));
1275	1	assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("PTM"));
1276	1	assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("PTR"));
1277	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("PU "));
1278	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("PUY"));
1279	1	assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("PVH"));
1280	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("PVL"));
1281	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("PYA"));
1282	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("PYO"));
1283	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("PYX"));
1284	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("PYY"));
1285	1	assertEquals("QLG", ResidueProperties.getCanonicalAminoAcid("QLG"));
1286	1	assertEquals("GLN", ResidueProperties.getCanonicalAminoAcid("QMM"));
1287	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("QPA"));
1288	1	assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("QPH"));
1289	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("QUO"));
1290	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("R "));
1291	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("R1A"));
1292	1	assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("R4K"));
1293	1	assertEquals("HYG", ResidueProperties.getCanonicalAminoAcid("RC7"));
1294	1	assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("RE0"));
1295	1	assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("RE3"));
1296	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("RIA"));
1297	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("RMP"));
1298	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("RON"));
1299	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("RT "));
1300	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("RTP"));
1301	1	assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("S1H"));
1302	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("S2C"));
1303	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("S2D"));
1304	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("S2M"));
1305	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("S2P"));
1306	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("S4A"));
1307	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("S4C"));
1308	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("S4G"));
1309	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("S4U"));
1310	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("S6G"));
1311	1	assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SAC"));
1312	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SAH"));
1313	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("SAR"));
1314	1	assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SBL"));
1315	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SC "));
1316	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SCH"));
1317	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SCS"));
1318	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SCY"));
1319	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("SD2"));
1320	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("SDG"));
1321	1	assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SDP"));
1322	1	assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SEB"));
1323	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("SEC"));
1324	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("SEG"));
1325	1	assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SEL"));
1326	1	assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SEM"));
1327	1	assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SEN"));
1328	1	assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SEP"));
1329	1	assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SER"));
1330	1	assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SET"));
1331	1	assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SGB"));
1332	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SHC"));
1333	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("SHP"));
1334	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("SHR"));
1335	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SIB"));
1336	1	assertEquals("DC", ResidueProperties.getCanonicalAminoAcid("SIC")); // check
1337	1	assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("SLA"));
1338	1	assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("SLR"));
1339	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("SLZ"));
1340	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SMC"));
1341	1	assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("SME"));
1342	1	assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("SMF"));
1343	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("SMP"));
1344	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("SMT"));
1345	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SNC"));
1346	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("SNN"));
1347	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SOC"));
1348	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("SOS"));
1349	1	assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SOY"));
1350	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("SPT"));
1351	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("SRA"));
1352	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("SSU"));
1353	1	assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("STY"));
1354	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("SUB"));
1355	1	assertEquals("DG", ResidueProperties.getCanonicalAminoAcid("SUI"));
1356	1	assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SUN"));
1357	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("SUR"));
1358	1	assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SVA"));
1359	1	assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SVV"));
1360	1	assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SVW"));
1361	1	assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SVX"));
1362	1	assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SVY"));
1363	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("SVZ"));
1364	1	assertEquals("SWG", ResidueProperties.getCanonicalAminoAcid("SWG"));
1365	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SYS"));
1366	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T "));
1367	1	assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("T11"));
1368	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T23"));
1369	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T2S"));
1370	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("T2T"));
1371	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("T31"));
1372	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T32"));
1373	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T36"));
1374	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T37"));
1375	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T38"));
1376	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T39"));
1377	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T3P"));
1378	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T41"));
1379	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T48"));
1380	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T49"));
1381	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T4S"));
1382	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("T5O"));
1383	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T5S"));
1384	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("T66"));
1385	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("T6A"));
1386	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TA3"));
1387	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("TA4"));
1388	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TAF"));
1389	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("TAL"));
1390	1	assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("TAV"));
1391	1	assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("TBG"));
1392	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TBM"));
1393	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("TC1"));
1394	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TCP"));
1395	1	assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TCQ"));
1396	1	assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TCR"));
1397	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("TCY"));
1398	1	assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("TDD"));
1399	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TDY"));
1400	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TFE"));
1401	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("TFO"));
1402	1	assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("TFQ"));
1403	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TFT"));
1404	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("TGP"));
1405	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TH6"));
1406	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("THC"));
1407	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("THO"));
1408	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("THR"));
1409	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("THX"));
1410	1	assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("THZ"));
1411	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("TIH"));
1412	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("TLB"));
1413	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TLC"));
1414	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("TLN"));
1415	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TMB"));
1416	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TMD"));
1417	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("TNB"));
1418	1	assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("TNR"));
1419	1	assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TOX"));
1420	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TP1"));
1421	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("TPC"));
1422	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("TPG"));
1423	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("TPH"));
1424	1	assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TPL"));
1425	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TPO"));
1426	1	assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TPQ"));
1427	1	assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TQI"));
1428	1	assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TQQ"));
1429	1	assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TRF"));
1430	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("TRG"));
1431	1	assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TRN"));
1432	1	assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TRO"));
1433	1	assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TRP"));
1434	1	assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TRQ"));
1435	1	assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TRW"));
1436	1	assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TRX"));
1437	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("TS "));
1438	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("TST"));
1439	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("TT "));
1440	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TTD"));
1441	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("TTI"));
1442	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TTM"));
1443	1	assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TTQ"));
1444	1	assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TTS"));
1445	1	assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TY1"));
1446	1	assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TY2"));
1447	1	assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TY3"));
1448	1	assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TY5"));
1449	1	assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYB"));
1450	1	assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYI"));
1451	1	assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYJ"));
1452	1	assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYN"));
1453	1	assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYO"));
1454	1	assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYQ"));
1455	1	assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYR"));
1456	1	assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYS"));
1457	1	assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYT"));
1458	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("TYU"));
1459	1	assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYW"));
1460	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("TYX"));
1461	1	assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYY"));
1462	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("TZB"));
1463	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("TZO"));
1464	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U "));
1465	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U25"));
1466	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U2L"));
1467	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U2N"));
1468	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U2P"));
1469	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U31"));
1470	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U33"));
1471	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U34"));
1472	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U36"));
1473	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U37"));
1474	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U8U"));
1475	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("UAR"));
1476	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("UCL"));
1477	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("UD5"));
1478	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("UDP"));
1479	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("UFP"));
1480	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("UFR"));
1481	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("UFT"));
1482	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("UMA"));
1483	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("UMP"));
1484	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("UMS"));
1485	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("UN1"));
1486	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("UN2"));
1487	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("UNK"));
1488	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("UR3"));
1489	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("URD"));
1490	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("US1"));
1491	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("US2"));
1492	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("US3"));
1493	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("US5"));
1494	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("USM"));
1495	1	assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("VAD"));
1496	1	assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("VAF"));
1497	1	assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("VAL"));
1498	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("VB1"));
1499	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("VDL"));
1500	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("VLL"));
1501	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("VLM"));
1502	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("VMS"));
1503	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("VOL"));
1504	1	assertEquals("GYG", ResidueProperties.getCanonicalAminoAcid("WCR"));
1505	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("X "));
1506	1	assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("X2W"));
1507	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("X4A"));
1508	1	assertEquals("AFG", ResidueProperties.getCanonicalAminoAcid("X9Q"));
1509	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("XAD"));
1510	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("XAE"));
1511	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("XAL"));
1512	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("XAR"));
1513	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("XCL"));
1514	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("XCN"));
1515	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("XCP"));
1516	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("XCR"));
1517	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("XCS"));
1518	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("XCT"));
1519	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("XCY"));
1520	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("XGA"));
1521	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("XGL"));
1522	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("XGR"));
1523	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("XGU"));
1524	1	assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("XPR"));
1525	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("XSN"));
1526	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("XTH"));
1527	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("XTL"));
1528	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("XTR"));
1529	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("XTS"));
1530	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("XTY"));
1531	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("XUA"));
1532	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("XUG"));
1533	1	assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("XX1"));
1534	1	assertEquals("THG", ResidueProperties.getCanonicalAminoAcid("XXY"));
1535	1	assertEquals("DYG", ResidueProperties.getCanonicalAminoAcid("XYG"));
1536	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("Y "));
1537	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("YCM"));
1538	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("YG "));
1539	1	assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("YOF"));
1540	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("YRR"));
1541	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("YYG"));
1542	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("Z "));
1543	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("Z01"));
1544	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ZAD"));
1545	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ZAL"));
1546	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("ZBC"));
1547	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("ZBU"));
1548	1	assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("ZCL"));
1549	1	assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("ZCY"));
1550	1	assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("ZDU"));
1551	1	assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("ZFB"));
1552	1	assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("ZGU"));
1553	1	assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("ZHP"));
1554	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("ZTH"));
1555	1	assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("ZU0"));
1556	1	assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ZZJ"));
1557
1558	1	assertEquals(null, ResidueProperties.getCanonicalAminoAcid(null));
1559		}
1560
		100% Uncovered Elements: 0 (6) Complexity: 1 Complexity Density: 0.17 1PASS
1561	1	@Test(groups = { "Functional" })...
1562		public void testGetSingleCharacterCode()
1563		{
1564	1	assertEquals('0', ResidueProperties.getSingleCharacterCode(null));
1565	1	assertEquals('0', ResidueProperties.getSingleCharacterCode(null));
1566	1	assertEquals('0', ResidueProperties.getSingleCharacterCode(""));
1567	1	assertEquals('Q', ResidueProperties.getSingleCharacterCode("GLN"));
1568	1	assertEquals('Q', ResidueProperties.getSingleCharacterCode("Gln"));
1569	1	assertEquals('Q', ResidueProperties.getSingleCharacterCode("gln"));
1570		}
1571
		100% Uncovered Elements: 0 (5) Complexity: 1 Complexity Density: 0.2 1PASS
1572	1	@Test(groups = { "Functional" })...
1573		public void testGetDssp3State()
1574		{
1575	1	assertNull(ResidueProperties.getDssp3state(null));
1576	1	assertEquals("", ResidueProperties.getDssp3state(""));
1577	1	String foo = "0123 []<>abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ";
1578	1	String bar = " E E HHH ";
1579	1	assertEquals(bar, ResidueProperties.getDssp3state(foo));
1580		}
1581
		100% Uncovered Elements: 0 (10) Complexity: 1 Complexity Density: 0.1 1PASS
1582	1	@Test(groups = { "Functional" })...
1583		public void testPhysicoChemicalProperties()
1584		{
1585	1	checkProperty("aromatic", "FYWH-*");
1586	1	checkProperty("aliphatic", "IVL-*");
1587	1	checkProperty("tiny", "GAS-*");
1588	1	checkProperty("small", "VCTGACSDNP-*");
1589	1	checkProperty("charged", "HKRDE-*");
1590	1	checkProperty("negative", "DE-*");
1591	1	checkProperty("polar", "YWHRKTSNDEQ-*X");
1592	1	checkProperty("positive", "HKR-*");
1593	1	checkProperty("proline", "P-*");
1594	1	checkProperty("hydrophobic", "MILVFYWHKTGAC-*X");
1595		}
1596
1597		/**
1598		* Verify that the residues in the list have the named property, and other
1599		* residues do not
1600		*
1601		* @param property
1602		* @param residues
1603		*/
		100% Uncovered Elements: 0 (12) Complexity: 3 Complexity Density: 0.38
1604	10	void checkProperty(String property, String residues)...
1605		{
1606	10	Map<String, Integer> props = ResidueProperties.propHash.get(property);
1607
1608		/*
1609		* assert residues have the property (value 1 in lookup)
1610		*/
1611	10	for (char res : residues.toCharArray())
1612		{
1613	77	assertEquals(res + " should be " + property, 1,
1614		props.get(String.valueOf(res)).intValue());
1615		}
1616
1617		/*
1618		* assert other residues do not (value 0 in lookup)
1619		*/
1620	10	for (String res : ResidueProperties.aa)
1621		{
1622	280	if (!residues.contains(res))
1623		{
1624	214	Integer propValue = props.get(String.valueOf(res));
1625
1626	214	if (propValue != null)
1627		{
1628		/*
1629		* conservation calculation assigns unexpected symbols
1630		* the same value as '-'; here we just check those which
1631		* explicitly do not have the property
1632		*/
1633	146	assertEquals(res + " should not be " + property, 0,
1634		propValue.intValue());
1635		}
1636		}
1637		}
1638		}
1639		}