X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fschemes%2FResiduePropertiesTest.java;h=28f39d858012fbd9df809ec33b54494c53c07628;hb=refs%2Fheads%2Fimprovement%2FJAL-3847_some_attempts_to_set_gradle_and_groovy_versions;hp=d7e0e0bcde36dbeea1996aa3a4ac8d900af001d2;hpb=c93b9ad2ebfab4cad4608a8890132918589576be;p=jalview.git
diff --git a/test/jalview/schemes/ResiduePropertiesTest.java b/test/jalview/schemes/ResiduePropertiesTest.java
index d7e0e0b..28f39d8 100644
--- a/test/jalview/schemes/ResiduePropertiesTest.java
+++ b/test/jalview/schemes/ResiduePropertiesTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.schemes;
import static org.testng.AssertJUnit.assertEquals;
@@ -5,16 +25,27 @@ import static org.testng.AssertJUnit.assertNull;
import java.util.Collections;
import java.util.List;
+import java.util.Map;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
+import jalview.gui.JvOptionPane;
+
public class ResiduePropertiesTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
/**
* Test 'standard' codon translations (no ambiguity codes)
*/
- @Test
+ @Test(groups = { "Functional" })
public void testCodonTranslate()
{
// standard translation table order column 1/2/3/4
@@ -88,7 +119,7 @@ public class ResiduePropertiesTest
* Test a sample of codon translations involving ambiguity codes. Should
* return a protein value where the ambiguity does not affect the translation.
*/
- @Test
+ @Test(groups = { "Functional" })
public void testCodonTranslate_ambiguityCodes()
{
// Y is C or T
@@ -175,7 +206,7 @@ public class ResiduePropertiesTest
assertNull(ResidueProperties.codonTranslate("WSK"));
}
- @Test
+ @Test(groups = { "Functional" })
public void testGetResidues_nucleotide()
{
/*
@@ -191,10 +222,11 @@ public class ResiduePropertiesTest
*/
residues = ResidueProperties.getResidues(true, true);
Collections.sort(residues);
- assertEquals("[A, C, G, I, N, R, T, U, X, Y]", residues.toString());
+ assertEquals("[A, B, C, D, G, H, I, K, M, N, R, S, T, U, V, W, X, Y]",
+ residues.toString());
}
- @Test
+ @Test(groups = { "Functional" })
public void testGetResidues_peptide()
{
/*
@@ -216,4 +248,1392 @@ public class ResiduePropertiesTest
"[ALA, ARG, ASN, ASP, ASX, CYS, GLN, GLU, GLX, GLY, HIS, ILE, LEU, LYS, MET, PHE, PRO, SER, THR, TRP, TYR, VAL, XAA]",
residues.toString());
}
+
+ @Test(groups = { "Functional" })
+ public void testGetCanonicalAminoAcid()
+ {
+ assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MET"));
+ assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MSE"));
+
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("00C"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("01W"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("02K"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("03Y"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("07O"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("08P"));
+ assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("0A0"));
+ assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("0A1"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("0A2"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("0A8"));
+ assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("0AA"));
+ assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("0AB"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("0AC"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("0AD"));
+ assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("0AF"));
+ assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("0AG"));
+ assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("0AH"));
+ assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("0AK"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("0AM"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("0AP"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("0AU"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("0AV"));
+ assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("0AZ"));
+ assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("0BN"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("0C "));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("0CS"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("0DC"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("0DG"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("0DT"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("0FL"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("0G "));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("0NC"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("0SP"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("0U "));
+ assertEquals("YG", ResidueProperties.getCanonicalAminoAcid("0YG"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("10C"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("125"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("126"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("127"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("128"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("12A"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("143"));
+ assertEquals("ASG", ResidueProperties.getCanonicalAminoAcid("175"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("193"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("1AP"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("1MA"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("1MG"));
+ assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("1PA"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("1PI"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("1PR"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("1SC"));
+ assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("1TQ"));
+ assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("1TY"));
+ assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("1X6"));
+ assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("200"));
+ assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("23F"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("23S"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("26B"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("2AD"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("2AG"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("2AO"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("2AR"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("2AS"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("2AT"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("2AU"));
+ assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("2BD"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("2BT"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("2BU"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("2CO"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("2DA"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("2DF"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("2DM"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("2DO"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("2DT"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("2EG"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("2FE"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("2FI"));
+ assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("2FM"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("2GT"));
+ assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("2HF"));
+ assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("2LU"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("2MA"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("2MG"));
+ assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("2ML"));
+ assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("2MR"));
+ assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("2MT"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("2MU"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("2NT"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("2OM"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("2OT"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("2PI"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("2PR"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("2SA"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("2SI"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("2ST"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("2TL"));
+ assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("2TY"));
+ assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("2VA"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("2XA"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("32S"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("32T"));
+ assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("3AH"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("3AR"));
+ assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("3CF"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("3DA"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("3DR"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("3GA"));
+ assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("3MD"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("3ME"));
+ assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("3NF"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("3QN"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("3TY"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("3XH"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("4AC"));
+ assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("4BF"));
+ assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("4CF"));
+ assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("4CY"));
+ assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("4DP"));
+ assertEquals("GYG", ResidueProperties.getCanonicalAminoAcid("4F3"));
+ assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("4FB"));
+ assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("4FW"));
+ assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("4HT"));
+ assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("4IN"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("4MF"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("4MM"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("4OC"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("4PC"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("4PD"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("4PE"));
+ assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("4PH"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("4SC"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("4SU"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("4TA"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("4U7"));
+ assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("56A"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("5AA"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("5AB"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("5AT"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("5BU"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("5CG"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("5CM"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("5CS"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("5FA"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("5FC"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("5FU"));
+ assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("5HP"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("5HT"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("5HU"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("5IC"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("5IT"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("5IU"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("5MC"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("5MD"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("5MU"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("5NC"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("5PC"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("5PY"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("5SE"));
+ assertEquals("TWG", ResidueProperties.getCanonicalAminoAcid("5ZA"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("64T"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("6CL"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("6CT"));
+ assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("6CW"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("6HA"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("6HC"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("6HG"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("6HN"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("6HT"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("6IA"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("6MA"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("6MC"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("6MI"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("6MT"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("6MZ"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("6OG"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("70U"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("7DA"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("7GU"));
+ assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("7JA"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("7MG"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("8AN"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("8FG"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("8MG"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("8OG"));
+ assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("9NE"));
+ assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("9NF"));
+ assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("9NR"));
+ assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("9NV"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A "));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("A1P"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A23"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A2L"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A2M"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A34"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A35"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A38"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A39"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A3A"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A3P"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A40"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A43"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A44"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A47"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A5L"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("A5M"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("A5N"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("A5O"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("A66"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AA3"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AA4"));
+ assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("AAR"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("AB7"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ABA"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ABR"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ABS"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("ABT"));
+ assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("ACB"));
+ assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("ACL"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AD2"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("ADD"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("ADX"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("AEA"));
+ assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("AEI"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AET"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("AFA"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("AFF"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("AFG"));
+ assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("AGM"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("AGT"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("AHB"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("AHH"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AHO"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AHP"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("AHS"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("AHT"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AIB"));
+ assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("AKL"));
+ assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("AKZ"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ALA"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ALC"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ALM"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ALN"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("ALO"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("ALQ"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ALS"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ALT"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ALV"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("ALY"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AN8"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AP7"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("APE"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("APH"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("API"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("APK"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("APM"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("APP"));
+ assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("AR2"));
+ assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("AR4"));
+ assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("AR7"));
+ assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("ARG"));
+ assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("ARM"));
+ assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("ARO"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("ARV"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AS "));
+ assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("AS2"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("AS9"));
+ assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("ASA"));
+ assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("ASB"));
+ assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("ASI"));
+ assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("ASK"));
+ assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("ASL"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("ASM"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("ASN"));
+ assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("ASP"));
+ assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("ASQ"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("ASU"));
+ assertEquals("ASX", ResidueProperties.getCanonicalAminoAcid("ASX"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("ATD"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("ATL"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("ATM"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AVC"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("AVN"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("AYA"));
+ assertEquals("AYG", ResidueProperties.getCanonicalAminoAcid("AYG"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("AZK"));
+ assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("AZS"));
+ assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("AZY"));
+ assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("B1F"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("B1P"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("B2A"));
+ assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("B2F"));
+ assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("B2I"));
+ assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("B2V"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("B3A"));
+ assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("B3D"));
+ assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("B3E"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("B3K"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("B3L"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("B3M"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("B3Q"));
+ assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("B3S"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("B3T"));
+ assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("B3U"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("B3X"));
+ assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("B3Y"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("BB6"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("BB7"));
+ assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("BB8"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("BB9"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("BBC"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("BCS"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("BE2"));
+ assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("BFD"));
+ assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("BG1"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("BGM"));
+ assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("BH2"));
+ assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("BHD"));
+ assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("BIF"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("BIL"));
+ assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("BIU"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("BJH"));
+ assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("BLE"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("BLY"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("BMP"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("BMT"));
+ assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("BNN"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("BNO"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("BOE"));
+ assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("BOR"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("BPE"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("BRU"));
+ assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("BSE"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("BT5"));
+ assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("BTA"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("BTC"));
+ assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("BTR"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("BUC"));
+ assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("BUG"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("BVP"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("BZG"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C "));
+ assertEquals("TYG", ResidueProperties.getCanonicalAminoAcid("C12"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("C1X"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C25"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C2L"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C2S"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C31"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C32"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C34"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C36"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C37"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C38"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C3Y"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C42"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C43"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C45"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C46"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C49"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C4R"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C4S"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C5C"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("C66"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("C6C"));
+ assertEquals("TFG", ResidueProperties.getCanonicalAminoAcid("C99"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CAF"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CAL"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CAR"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CAS"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CAV"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CAY"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CB2"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CBR"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CBV"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CCC"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("CCL"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CCS"));
+ assertEquals("CYG", ResidueProperties.getCanonicalAminoAcid("CCY"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CDE"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CDV"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CDW"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CEA"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CFL"));
+ assertEquals("FCYG", ResidueProperties.getCanonicalAminoAcid("CFY")); // check
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("CG1"));
+ assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("CGA"));
+ assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("CGU"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CH "));
+ assertEquals("MYG", ResidueProperties.getCanonicalAminoAcid("CH6"));
+ assertEquals("KYG", ResidueProperties.getCanonicalAminoAcid("CH7"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CHF"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CHG"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("CHP"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CHS"));
+ assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("CIR"));
+ assertEquals("GYG", ResidueProperties.getCanonicalAminoAcid("CJO"));
+ assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("CLE"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("CLG"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("CLH"));
+ assertEquals("AFG", ResidueProperties.getCanonicalAminoAcid("CLV"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("CM0"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CME"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CMH"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CML"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CMR"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CMT"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("CNU"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CP1"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CPC"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CPI"));
+ assertEquals("GYG", ResidueProperties.getCanonicalAminoAcid("CQR"));
+ assertEquals("TLG", ResidueProperties.getCanonicalAminoAcid("CR0"));
+ assertEquals("GYG", ResidueProperties.getCanonicalAminoAcid("CR2"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("CR5"));
+ assertEquals("KYG", ResidueProperties.getCanonicalAminoAcid("CR7"));
+ assertEquals("HYG", ResidueProperties.getCanonicalAminoAcid("CR8"));
+ assertEquals("TWG", ResidueProperties.getCanonicalAminoAcid("CRF"));
+ assertEquals("THG", ResidueProperties.getCanonicalAminoAcid("CRG"));
+ assertEquals("MYG", ResidueProperties.getCanonicalAminoAcid("CRK"));
+ assertEquals("GYG", ResidueProperties.getCanonicalAminoAcid("CRO"));
+ assertEquals("QYG", ResidueProperties.getCanonicalAminoAcid("CRQ"));
+ assertEquals("EYG", ResidueProperties.getCanonicalAminoAcid("CRU"));
+ assertEquals("ASG", ResidueProperties.getCanonicalAminoAcid("CRW"));
+ assertEquals("ASG", ResidueProperties.getCanonicalAminoAcid("CRX"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CS0"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CS1"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CS3"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CS4"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("CS8"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSA"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSB"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSD"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSE"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSF"));
+ assertEquals("SHG", ResidueProperties.getCanonicalAminoAcid("CSH"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("CSI"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSJ"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSL"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSO"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSP"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSR"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSS"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSU"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSW"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSX"));
+ assertEquals("SYG", ResidueProperties.getCanonicalAminoAcid("CSY"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CSZ"));
+ assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("CTE"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("CTG"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("CTH"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CUC"));
+ assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("CWR"));
+ assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("CXM"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CY0"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CY1"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CY3"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CY4"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CYA"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CYD"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CYF"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CYG"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("CYJ"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CYM"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CYQ"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CYR"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CYS"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CZ2"));
+ assertEquals("GYG", ResidueProperties.getCanonicalAminoAcid("CZO"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("CZZ"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("D11"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("D1P"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("D3 "));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("D33"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("D3P"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("D3T"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("D4M"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("D4P"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("DA "));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("DA2"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("DAB"));
+ assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("DAH"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("DAL"));
+ assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("DAR"));
+ assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("DAS"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("DBB"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DBM"));
+ assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("DBS"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("DBU"));
+ assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("DBY"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("DBZ"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("DC "));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("DC2"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("DCG"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("DCI"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("DCL"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("DCT"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("DCY"));
+ assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("DDE"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("DDG"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("DDN"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DDX"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("DFC"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("DFG"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("DFI"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("DFO"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DFT"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("DG "));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("DGH"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("DGI"));
+ assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("DGL"));
+ assertEquals("GLN", ResidueProperties.getCanonicalAminoAcid("DGN"));
+ assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("DHA"));
+ assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("DHI"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("DHL"));
+ assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("DHN"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("DHP"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("DHU"));
+ assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("DHV"));
+ assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("DI "));
+ assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("DIL"));
+ assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("DIR"));
+ assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("DIV"));
+ assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("DLE"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("DLS"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("DLY"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("DM0"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DMH"));
+ assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("DMK"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("DMT"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DN "));
+ assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("DNE"));
+ assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("DNG"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("DNL"));
+ assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("DNM"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("DNP"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("DNR"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("DNS"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("DOA"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("DOC"));
+ assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("DOH"));
+ assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("DON"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("DPB"));
+ assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("DPH"));
+ assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("DPL"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("DPP"));
+ assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("DPQ"));
+ assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("DPR"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DPY"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("DRM"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DRP"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("DRT"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DRZ"));
+ assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("DSE"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DSG"));
+ assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("DSN"));
+ assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("DSP"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("DT "));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("DTH"));
+ assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("DTR"));
+ assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("DTY"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("DU "));
+ assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("DVA"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DXD"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("DXN"));
+ assertEquals("DYG", ResidueProperties.getCanonicalAminoAcid("DYG"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("DYS"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("DZM"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("E "));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("E1X"));
+ assertEquals("GLN", ResidueProperties.getCanonicalAminoAcid("ECC"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("EDA"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("EFC"));
+ assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("EHP"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("EIT"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("ENP"));
+ assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("ESB"));
+ assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("ESC"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("EXB"));
+ assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("EXY"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("EY5"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("EYS"));
+ assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("F2F"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("FA2"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("FA5"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("FAG"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("FAI"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("FB5"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("FB6"));
+ assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("FCL"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("FFD"));
+ assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("FGA"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("FGL"));
+ assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("FGP"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("FHL"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("FHO"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("FHU"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("FLA"));
+ assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("FLE"));
+ assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("FLT"));
+ assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("FME"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("FMG"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("FMU"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("FOE"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("FOX"));
+ assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("FP9"));
+ assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("FPA"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("FRD"));
+ assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("FT6"));
+ assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("FTR"));
+ assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("FTY"));
+ assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("FVA"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("FZN"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G "));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G25"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G2L"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G2S"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G31"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G32"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G33"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G36"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G38"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G42"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G46"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G47"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G48"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G49"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("G4P"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("G7M"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GAO"));
+ assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("GAU"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("GCK"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("GCM"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GDP"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GDR"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GFL"));
+ assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("GGL"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GH3"));
+ assertEquals("GLN", ResidueProperties.getCanonicalAminoAcid("GHG"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GHP"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GL3"));
+ assertEquals("GLN", ResidueProperties.getCanonicalAminoAcid("GLH"));
+ assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("GLJ"));
+ assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("GLK"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("GLM"));
+ assertEquals("GLN", ResidueProperties.getCanonicalAminoAcid("GLN"));
+ assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("GLQ"));
+ assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("GLU"));
+ assertEquals("GLX", ResidueProperties.getCanonicalAminoAcid("GLX"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GLY"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GLZ"));
+ assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("GMA"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GMS"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("GMU"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GN7"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("GND"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("GNE"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GOM"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("GPL"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GS "));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GSC"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GSR"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GSS"));
+ assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("GSU"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("GT9"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("GTP"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("GVL"));
+ assertEquals("CYG", ResidueProperties.getCanonicalAminoAcid("GYC"));
+ assertEquals("SYG", ResidueProperties.getCanonicalAminoAcid("GYS"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("H2U"));
+ assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("H5M"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("HAC"));
+ assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("HAR"));
+ assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("HBN"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("HCS"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("HDP"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("HEU"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("HFA"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("HGL"));
+ assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("HHI"));
+ assertEquals("AK", ResidueProperties.getCanonicalAminoAcid("HHK")); // check
+ assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("HIA"));
+ assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("HIC"));
+ assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("HIP"));
+ assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("HIQ"));
+ assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("HIS"));
+ assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("HL2"));
+ assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("HLU"));
+ assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("HMR"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("HOL"));
+ assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("HPC"));
+ assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("HPE"));
+ assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("HPH"));
+ assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("HPQ"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("HQA"));
+ assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("HRG"));
+ assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("HRP"));
+ assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("HS8"));
+ assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("HS9"));
+ assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("HSE"));
+ assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("HSL"));
+ assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("HSO"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("HTI"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("HTN"));
+ assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("HTR"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("HV5"));
+ assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("HVA"));
+ assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("HY3"));
+ assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("HYP"));
+ assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("HZP"));
+ assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("I "));
+ assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("I2M"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("I58"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("I5C"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("IAM"));
+ assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("IAR"));
+ assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("IAS"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("IC "));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("IEL"));
+ assertEquals("HYG", ResidueProperties.getCanonicalAminoAcid("IEY"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("IG "));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("IGL"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("IGU"));
+ assertEquals("SHG", ResidueProperties.getCanonicalAminoAcid("IIC"));
+ assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("IIL"));
+ assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("ILE"));
+ assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("ILG"));
+ assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("ILX"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("IMC"));
+ assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("IML"));
+ assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("IOY"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("IPG"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("IPN"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("IRN"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("IT1"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("IU "));
+ assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("IYR"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("IYT"));
+ assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("IZO"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("JJJ"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("JJK"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("JJL"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("JW5"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("K1R"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("KAG"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("KCX"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("KGC"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("KNB"));
+ assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("KOR"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("KPI"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("KST"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("KYQ"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("L2A"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LA2"));
+ assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("LAA"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("LAL"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LBY"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("LC "));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("LCA"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("LCC"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("LCG"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("LCH"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LCK"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LCX"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LDH"));
+ assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("LED"));
+ assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("LEF"));
+ assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("LEH"));
+ assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("LEI"));
+ assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("LEM"));
+ assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("LEN"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("LET"));
+ assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("LEU"));
+ assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("LEX"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("LG "));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("LGP"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("LHC"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("LHU"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("LKC"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LLP"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LLY"));
+ assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("LME"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LMF"));
+ assertEquals("GLN", ResidueProperties.getCanonicalAminoAcid("LMQ"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("LMS"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LP6"));
+ assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("LPD"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("LPG"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("LPL"));
+ assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("LPS"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("LSO"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("LTA"));
+ assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("LTR"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("LVG"));
+ assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("LVN"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LYF"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LYK"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LYM"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LYN"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LYR"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LYS"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LYX"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("LYZ"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("M0H"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("M1G"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("M2G"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("M2L"));
+ assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("M2S"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("M30"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("M3L"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("M5M"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("MA "));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("MA6"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("MA7"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("MAA"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("MAD"));
+ assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("MAI"));
+ assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("MBQ"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("MBZ"));
+ assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("MC1"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("MCG"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("MCL"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("MCS"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("MCY"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("MD3"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("MD6"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("MDH"));
+ assertEquals("ASG", ResidueProperties.getCanonicalAminoAcid("MDO"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("MDR"));
+ assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("MEA"));
+ assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MED"));
+ assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("MEG"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("MEN"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("MEP"));
+ assertEquals("GLN", ResidueProperties.getCanonicalAminoAcid("MEQ"));
+ assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MET"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("MEU"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("MF3"));
+ assertEquals("GYG", ResidueProperties.getCanonicalAminoAcid("MFC"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("MG1"));
+ assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("MGG"));
+ assertEquals("GLN", ResidueProperties.getCanonicalAminoAcid("MGN"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("MGQ"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("MGV"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("MGY"));
+ assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("MHL"));
+ assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MHO"));
+ assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("MHS"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("MIA"));
+ assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("MIS"));
+ assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("MK8"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("ML3"));
+ assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("MLE"));
+ assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("MLL"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("MLY"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("MLZ"));
+ assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MME"));
+ assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("MMO"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("MMT"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("MND"));
+ assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("MNL"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("MNU"));
+ assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("MNV"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("MOD"));
+ assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("MP8"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("MPH"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("MPJ"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("MPQ"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("MRG"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("MSA"));
+ assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MSE"));
+ assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MSL"));
+ assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MSO"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("MSP"));
+ assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("MT2"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("MTR"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("MTU"));
+ assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("MTY"));
+ assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("MVA"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("N "));
+ assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("N10"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("N2C"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("N5I"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("N5M"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("N6G"));
+ assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("N7P"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("NA8"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("NAL"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("NAM"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("NB8"));
+ assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("NBQ"));
+ assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("NC1"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("NCB"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("NCX"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("NCY"));
+ assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("NDF"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("NDN"));
+ assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("NEM"));
+ assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("NEP"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("NF2"));
+ assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("NFA"));
+ assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("NHL"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("NIT"));
+ assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("NIY"));
+ assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("NLE"));
+ assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("NLN"));
+ assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("NLO"));
+ assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("NLP"));
+ assertEquals("GLN", ResidueProperties.getCanonicalAminoAcid("NLQ"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("NMC"));
+ assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("NMM"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("NMS"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("NMT"));
+ assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("NNH"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("NP3"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("NPH"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("NPI"));
+ assertEquals("LYG", ResidueProperties.getCanonicalAminoAcid("NRP"));
+ assertEquals("MYG", ResidueProperties.getCanonicalAminoAcid("NRQ"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("NSK"));
+ assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("NTY"));
+ assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("NVA"));
+ assertEquals("TWG", ResidueProperties.getCanonicalAminoAcid("NYC"));
+ assertEquals("NYG", ResidueProperties.getCanonicalAminoAcid("NYG"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("NYM"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("NYS"));
+ assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("NZH"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("O12"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("O2C"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("O2G"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("OAD"));
+ assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("OAS"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("OBF"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("OBS"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("OCS"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("OCY"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("ODP"));
+ assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("OHI"));
+ assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("OHS"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("OIC"));
+ assertEquals("ILE", ResidueProperties.getCanonicalAminoAcid("OIP"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("OLE"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("OLT"));
+ assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("OLZ"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("OMC"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("OMG"));
+ assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("OMT"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("OMU"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("ONE"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ONH"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("ONL"));
+ assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("OPR"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ORN"));
+ assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("ORQ"));
+ assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("OSE"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("OTB"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("OTH"));
+ assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("OTY"));
+ assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("OXX"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("P "));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("P1L"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("P1P"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("P2T"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("P2U"));
+ assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("P2Y"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("P5P"));
+ assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("PAQ"));
+ assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("PAS"));
+ assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("PAT"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("PAU"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("PBB"));
+ assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PBF"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("PBT"));
+ assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("PCA"));
+ assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("PCC"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("PCE"));
+ assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PCS"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("PDL"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("PDU"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("PEC"));
+ assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PF5"));
+ assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PFF"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("PFX"));
+ assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("PG1"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("PG7"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("PG9"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("PGL"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("PGN"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("PGP"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("PGY"));
+ assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PHA"));
+ assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("PHD"));
+ assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PHE"));
+ assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PHI"));
+ assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PHL"));
+ assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PHM"));
+ assertEquals("AYG", ResidueProperties.getCanonicalAminoAcid("PIA"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("PIV"));
+ assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("PLE"));
+ assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PM3"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("PMT"));
+ assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("POM"));
+ assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PPN"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("PPU"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("PPW"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("PQ1"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("PR3"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("PR5"));
+ assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("PR9"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("PRN"));
+ assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("PRO"));
+ assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("PRS"));
+ assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("PSA"));
+ assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("PSH"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("PST"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("PSU"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("PSW"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("PTA"));
+ assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("PTH"));
+ assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("PTM"));
+ assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("PTR"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("PU "));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("PUY"));
+ assertEquals("HIS", ResidueProperties.getCanonicalAminoAcid("PVH"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("PVL"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("PYA"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("PYO"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("PYX"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("PYY"));
+ assertEquals("QLG", ResidueProperties.getCanonicalAminoAcid("QLG"));
+ assertEquals("GLN", ResidueProperties.getCanonicalAminoAcid("QMM"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("QPA"));
+ assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("QPH"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("QUO"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("R "));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("R1A"));
+ assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("R4K"));
+ assertEquals("HYG", ResidueProperties.getCanonicalAminoAcid("RC7"));
+ assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("RE0"));
+ assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("RE3"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("RIA"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("RMP"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("RON"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("RT "));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("RTP"));
+ assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("S1H"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("S2C"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("S2D"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("S2M"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("S2P"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("S4A"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("S4C"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("S4G"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("S4U"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("S6G"));
+ assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SAC"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SAH"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("SAR"));
+ assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SBL"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SC "));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SCH"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SCS"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SCY"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("SD2"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("SDG"));
+ assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SDP"));
+ assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SEB"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("SEC"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("SEG"));
+ assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SEL"));
+ assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SEM"));
+ assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SEN"));
+ assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SEP"));
+ assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SER"));
+ assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SET"));
+ assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SGB"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SHC"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("SHP"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("SHR"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SIB"));
+ assertEquals("DC", ResidueProperties.getCanonicalAminoAcid("SIC")); // check
+ assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("SLA"));
+ assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("SLR"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("SLZ"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SMC"));
+ assertEquals("MET", ResidueProperties.getCanonicalAminoAcid("SME"));
+ assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("SMF"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("SMP"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("SMT"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SNC"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("SNN"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SOC"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("SOS"));
+ assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SOY"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("SPT"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("SRA"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("SSU"));
+ assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("STY"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("SUB"));
+ assertEquals("DG", ResidueProperties.getCanonicalAminoAcid("SUI"));
+ assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SUN"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("SUR"));
+ assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SVA"));
+ assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SVV"));
+ assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SVW"));
+ assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SVX"));
+ assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("SVY"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("SVZ"));
+ assertEquals("SWG", ResidueProperties.getCanonicalAminoAcid("SWG"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("SYS"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T "));
+ assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("T11"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T23"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T2S"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("T2T"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("T31"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T32"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T36"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T37"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T38"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T39"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T3P"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T41"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T48"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T49"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T4S"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("T5O"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("T5S"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("T66"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("T6A"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TA3"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("TA4"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TAF"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("TAL"));
+ assertEquals("ASP", ResidueProperties.getCanonicalAminoAcid("TAV"));
+ assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("TBG"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TBM"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("TC1"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TCP"));
+ assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TCQ"));
+ assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TCR"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("TCY"));
+ assertEquals("LEU", ResidueProperties.getCanonicalAminoAcid("TDD"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TDY"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TFE"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("TFO"));
+ assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("TFQ"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TFT"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("TGP"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TH6"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("THC"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("THO"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("THR"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("THX"));
+ assertEquals("ARG", ResidueProperties.getCanonicalAminoAcid("THZ"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("TIH"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("TLB"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TLC"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("TLN"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TMB"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TMD"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("TNB"));
+ assertEquals("SER", ResidueProperties.getCanonicalAminoAcid("TNR"));
+ assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TOX"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TP1"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("TPC"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("TPG"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("TPH"));
+ assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TPL"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TPO"));
+ assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TPQ"));
+ assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TQI"));
+ assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TQQ"));
+ assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TRF"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("TRG"));
+ assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TRN"));
+ assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TRO"));
+ assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TRP"));
+ assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TRQ"));
+ assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TRW"));
+ assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TRX"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("TS "));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("TST"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("TT "));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TTD"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("TTI"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("TTM"));
+ assertEquals("TRP", ResidueProperties.getCanonicalAminoAcid("TTQ"));
+ assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TTS"));
+ assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TY1"));
+ assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TY2"));
+ assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TY3"));
+ assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TY5"));
+ assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYB"));
+ assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYI"));
+ assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYJ"));
+ assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYN"));
+ assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYO"));
+ assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYQ"));
+ assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYR"));
+ assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYS"));
+ assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYT"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("TYU"));
+ assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYW"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("TYX"));
+ assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("TYY"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("TZB"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("TZO"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U "));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U25"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U2L"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U2N"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U2P"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U31"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U33"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U34"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U36"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U37"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("U8U"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("UAR"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("UCL"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("UD5"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("UDP"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("UFP"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("UFR"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("UFT"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("UMA"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("UMP"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("UMS"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("UN1"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("UN2"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("UNK"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("UR3"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("URD"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("US1"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("US2"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("US3"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("US5"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("USM"));
+ assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("VAD"));
+ assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("VAF"));
+ assertEquals("VAL", ResidueProperties.getCanonicalAminoAcid("VAL"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("VB1"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("VDL"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("VLL"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("VLM"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("VMS"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("VOL"));
+ assertEquals("GYG", ResidueProperties.getCanonicalAminoAcid("WCR"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("X "));
+ assertEquals("GLU", ResidueProperties.getCanonicalAminoAcid("X2W"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("X4A"));
+ assertEquals("AFG", ResidueProperties.getCanonicalAminoAcid("X9Q"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("XAD"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("XAE"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("XAL"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("XAR"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("XCL"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("XCN"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("XCP"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("XCR"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("XCS"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("XCT"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("XCY"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("XGA"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("XGL"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("XGR"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("XGU"));
+ assertEquals("PRO", ResidueProperties.getCanonicalAminoAcid("XPR"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("XSN"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("XTH"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("XTL"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("XTR"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("XTS"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("XTY"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("XUA"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("XUG"));
+ assertEquals("LYS", ResidueProperties.getCanonicalAminoAcid("XX1"));
+ assertEquals("THG", ResidueProperties.getCanonicalAminoAcid("XXY"));
+ assertEquals("DYG", ResidueProperties.getCanonicalAminoAcid("XYG"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("Y "));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("YCM"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("YG "));
+ assertEquals("TYR", ResidueProperties.getCanonicalAminoAcid("YOF"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("YRR"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("YYG"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("Z "));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("Z01"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ZAD"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ZAL"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("ZBC"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("ZBU"));
+ assertEquals("PHE", ResidueProperties.getCanonicalAminoAcid("ZCL"));
+ assertEquals("CYS", ResidueProperties.getCanonicalAminoAcid("ZCY"));
+ assertEquals("UR3", ResidueProperties.getCanonicalAminoAcid("ZDU"));
+ assertEquals("XAA", ResidueProperties.getCanonicalAminoAcid("ZFB"));
+ assertEquals("GLY", ResidueProperties.getCanonicalAminoAcid("ZGU"));
+ assertEquals("ASN", ResidueProperties.getCanonicalAminoAcid("ZHP"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("ZTH"));
+ assertEquals("THR", ResidueProperties.getCanonicalAminoAcid("ZU0"));
+ assertEquals("ALA", ResidueProperties.getCanonicalAminoAcid("ZZJ"));
+
+ assertEquals(null, ResidueProperties.getCanonicalAminoAcid(null));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testGetSingleCharacterCode()
+ {
+ assertEquals('0', ResidueProperties.getSingleCharacterCode(null));
+ assertEquals('0', ResidueProperties.getSingleCharacterCode(null));
+ assertEquals('0', ResidueProperties.getSingleCharacterCode(""));
+ assertEquals('Q', ResidueProperties.getSingleCharacterCode("GLN"));
+ assertEquals('Q', ResidueProperties.getSingleCharacterCode("Gln"));
+ assertEquals('Q', ResidueProperties.getSingleCharacterCode("gln"));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testGetDssp3State()
+ {
+ assertNull(ResidueProperties.getDssp3state(null));
+ assertEquals("", ResidueProperties.getDssp3state(""));
+ String foo = "0123 []<>abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ";
+ String bar = " E E HHH ";
+ assertEquals(bar, ResidueProperties.getDssp3state(foo));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testPhysicoChemicalProperties()
+ {
+ checkProperty("aromatic", "FYWH-*");
+ checkProperty("aliphatic", "IVL-*");
+ checkProperty("tiny", "GAS-*");
+ checkProperty("small", "VCTGACSDNP-*");
+ checkProperty("charged", "HKRDE-*");
+ checkProperty("negative", "DE-*");
+ checkProperty("polar", "YWHRKTSNDEQ-*X");
+ checkProperty("positive", "HKR-*");
+ checkProperty("proline", "P-*");
+ checkProperty("hydrophobic", "MILVFYWHKTGAC-*X");
+ }
+
+ /**
+ * Verify that the residues in the list have the named property, and other
+ * residues do not
+ *
+ * @param property
+ * @param residues
+ */
+ void checkProperty(String property, String residues)
+ {
+ Map props = ResidueProperties.propHash.get(property);
+
+ /*
+ * assert residues have the property (value 1 in lookup)
+ */
+ for (char res : residues.toCharArray())
+ {
+ assertEquals(res + " should be " + property, 1,
+ props.get(String.valueOf(res)).intValue());
+ }
+
+ /*
+ * assert other residues do not (value 0 in lookup)
+ */
+ for (String res : ResidueProperties.aa)
+ {
+ if (!residues.contains(res))
+ {
+ Integer propValue = props.get(String.valueOf(res));
+
+ if (propValue != null)
+ {
+ /*
+ * conservation calculation assigns unexpected symbols
+ * the same value as '-'; here we just check those which
+ * explicitly do not have the property
+ */
+ assertEquals(res + " should not be " + property, 0,
+ propValue.intValue());
+ }
+ }
+ }
+ }
}