Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ResidueProperties	36	1,833	79	0.00%	Show methods

Class ResidueProperties

Class ResidueProperties	Line # 36	Total Statements 1,833	Complexity 79	TOTAL Coverage 0.00%
<clinit>, line 68()   <clinit>, line 68()	6868	51.051	2.02	0.0 0.00%
<clinit>, line 138()   <clinit>, line 138()	138138	11.011	3.03	0.0 0.00%
<clinit>, line 180()   <clinit>, line 180()	180180	23.023	2.02	0.0 0.00%
<clinit>, line 211()   <clinit>, line 211()	211211	6.06	2.02	0.0 0.00%
<clinit>, line 228()   <clinit>, line 228()	228228	29.029	1.01	0.0 0.00%
<clinit>, line 262()   <clinit>, line 262()	262262	40.040	1.01	0.0 0.00%
<clinit>, line 690()   <clinit>, line 690()	690690	23.023	1.01	0.0 0.00%
<clinit>, line 717()   <clinit>, line 717()	717717	23.023	1.01	0.0 0.00%
<clinit>, line 744()   <clinit>, line 744()	744744	22.022	1.01	0.0 0.00%
<clinit>, line 770()   <clinit>, line 770()	770770	22.022	1.01	0.0 0.00%
<clinit>, line 796()   <clinit>, line 796()	796796	22.022	1.01	0.0 0.00%
<clinit>, line 822()   <clinit>, line 822()	822822	22.022	1.01	0.0 0.00%
<clinit>, line 851()   <clinit>, line 851()	851851	22.022	1.01	0.0 0.00%
<clinit>, line 877()   <clinit>, line 877()	877877	22.022	1.01	0.0 0.00%
<clinit>, line 903()   <clinit>, line 903()	903903	22.022	1.01	0.0 0.00%
<clinit>, line 929()   <clinit>, line 929()	929929	22.022	1.01	0.0 0.00%
<clinit>, line 955()   <clinit>, line 955()	955955	10.010	1.01	0.0 0.00%
<clinit>, line 968()   <clinit>, line 968()	968968	34.034	18.018	0.0 0.00%
ResidueProperties()   ResidueProperties()	10331033	0.00	1.01	-1.0 -1.0 -
getHydmax() : double   getHydmax() : double	10371037	1.01	1.01	0.0 0.00%
getHydmin() : double   getHydmin() : double	10421042	1.01	1.01	0.0 0.00%
getHyd() : double[]   getHyd() : double[]	10471047	1.01	1.01	0.0 0.00%
getAA3Hash() : Map<String, Integer>   getAA3Hash() : Map<String, Integer>	10521052	1.01	1.01	0.0 0.00%
codonTranslate(String) : String   codonTranslate(String) : String	10571057	4.04	2.02	0.0 0.00%
<clinit>, line 1073()   <clinit>, line 1073()	10731073	7.07	1.01	0.0 0.00%
getDssp3state(String) : String   getDssp3state(String) : String	10901090	12.012	5.05	0.0 0.00%
<clinit>, line 1115()   <clinit>, line 1115()	11151115	1300.01,300	1.01	0.0 0.00%
<clinit>, line 2433()   <clinit>, line 2433()	24332433	22.022	1.01	0.0 0.00%
<clinit>, line 2463()   <clinit>, line 2463()	24632463	6.06	1.01	0.0 0.00%
<clinit>, line 2474()   <clinit>, line 2474()	24742474	6.06	1.01	0.0 0.00%
getCanonicalAminoAcid(String) : String   getCanonicalAminoAcid(String) : String	24852485	2.02	2.02	0.0 0.00%
main(String[]) : void   main(String[]) : void	24972497	23.023	7.07	0.0 0.00%
getResidues(boolean,boolean) : List<String>   getResidues(boolean,boolean) : List<String>	25502550	17.017	10.010	0.0 0.00%
getSingleCharacterCode(String) : char   getSingleCharacterCode(String) : char	26002600	4.04	3.03	0.0 0.00%

 

Contributing tests

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1		/*
2		* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3		* Copyright (C) $$Year-Rel$$ The Jalview Authors
4		*
5		* This file is part of Jalview.
6		*
7		* Jalview is free software: you can redistribute it and/or
8		* modify it under the terms of the GNU General Public License
9		* as published by the Free Software Foundation, either version 3
10		* of the License, or (at your option) any later version.
11		*
12		* Jalview is distributed in the hope that it will be useful, but
13		* WITHOUT ANY WARRANTY; without even the implied warranty
14		* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15		* PURPOSE. See the GNU General Public License for more details.
16		*
17		* You should have received a copy of the GNU General Public License
18		* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19		* The Jalview Authors are detailed in the 'AUTHORS' file.
20		*/
21		package jalview.schemes;
22
23		import java.awt.Color;
24		import java.util.ArrayList;
25		import java.util.Arrays;
26		import java.util.Enumeration;
27		import java.util.HashMap;
28		import java.util.Hashtable;
29		import java.util.List;
30		import java.util.Locale;
31		import java.util.Map;
32		import java.util.Vector;
33
34		import jalview.analysis.GeneticCodes;
35
		0% Uncovered Elements: 1,941 (1,941) Complexity: 79 Complexity Density: 0.04
36		public class ResidueProperties
37		{
38		// alphabet names used in Hidden Markov Model files
39		public static final String ALPHABET_RNA = "RNA";
40
41		public static final String ALPHABET_DNA = "DNA";
42
43		public static final String ALPHABET_AMINO = "amino";
44
45		// Stores residue codes/names and colours and other things
46		public static final int[] aaIndex; // aaHash version 2.1.1 and below
47
48		public static final int[] nucleotideIndex;
49
50		public static final int[] purinepyrimidineIndex;
51
52		public static final int[] secondaryStructureIndex;
53
54		public static final Map<String, Integer> aa3Hash = new HashMap<>();
55
56		public static final Map<String, String> aa2Triplet = new HashMap<>();
57
58		public static final Map<String, String> nucleotideName = new HashMap<>();
59
60		public static final Map<String, String> nucleotideAmbiguityName = new HashMap<>();
61
62		// lookup from modified amino acid (e.g. MSE) to canonical form (e.g. MET)
63		public static final Map<String, String> modifications = new HashMap<>();
64
65		// residue background frequencies across different alphabets
66		public static final Map<String, Map<Character, Float>> backgroundFrequencies = new HashMap<>();
67
		0% Uncovered Elements: 53 (53) Complexity: 2 Complexity Density: 0.04
68	0	static...
69		{
70	0	aaIndex = new int[255];
71	0	for (int i = 0; i < 255; i++)
72		{
73	0	aaIndex[i] = 23;
74		}
75
76	0	aaIndex['A'] = 0;
77	0	aaIndex['R'] = 1;
78	0	aaIndex['N'] = 2;
79	0	aaIndex['D'] = 3;
80	0	aaIndex['C'] = 4;
81	0	aaIndex['Q'] = 5;
82	0	aaIndex['E'] = 6;
83	0	aaIndex['G'] = 7;
84	0	aaIndex['H'] = 8;
85	0	aaIndex['I'] = 9;
86	0	aaIndex['L'] = 10;
87	0	aaIndex['K'] = 11;
88	0	aaIndex['M'] = 12;
89	0	aaIndex['F'] = 13;
90	0	aaIndex['P'] = 14;
91	0	aaIndex['S'] = 15;
92	0	aaIndex['T'] = 16;
93	0	aaIndex['W'] = 17;
94	0	aaIndex['Y'] = 18;
95	0	aaIndex['V'] = 19;
96	0	aaIndex['B'] = 20;
97	0	aaIndex['Z'] = 21;
98	0	aaIndex['X'] = 22;
99	0	aaIndex['U'] = 22;
100	0	aaIndex['a'] = 0;
101	0	aaIndex['r'] = 1;
102	0	aaIndex['n'] = 2;
103	0	aaIndex['d'] = 3;
104	0	aaIndex['c'] = 4;
105	0	aaIndex['q'] = 5;
106	0	aaIndex['e'] = 6;
107	0	aaIndex['g'] = 7;
108	0	aaIndex['h'] = 8;
109	0	aaIndex['i'] = 9;
110	0	aaIndex['l'] = 10;
111	0	aaIndex['k'] = 11;
112	0	aaIndex['m'] = 12;
113	0	aaIndex['f'] = 13;
114	0	aaIndex['p'] = 14;
115	0	aaIndex['s'] = 15;
116	0	aaIndex['t'] = 16;
117	0	aaIndex['w'] = 17;
118	0	aaIndex['y'] = 18;
119	0	aaIndex['v'] = 19;
120	0	aaIndex['b'] = 20;
121	0	aaIndex['z'] = 21;
122	0	aaIndex['x'] = 22;
123	0	aaIndex['u'] = 22; // TODO: selenocystine triplet and codons needed. also
124		// extend subt. matrices
125		}
126
127		/**
128		* maximum (gap) index for matrices involving protein alphabet
129		*/
130		public final static int maxProteinIndex = 23;
131
132		/**
133		* maximum (gap) index for matrices involving nucleotide alphabet
134		*/
135		// public final static int maxNucleotideIndex = 10;
136		public final static int maxNucleotideIndex;
137
		0% Uncovered Elements: 15 (15) Complexity: 3 Complexity Density: 0.27
138	0	static...
139		{
140	0	String[][] namesArray = { { "a", "Adenine" }, { "c", "Cytosine" },
141		{ "g", "Guanine" },
142		{ "t", "Thymine" },
143		{ "u", "Uracil" },
144		{ "i", "Inosine" },
145		{ "x", "Xanthine" },
146		{ "r", "Unknown Purine" },
147		{ "y", "Unknown Pyrimidine" },
148		{ "w", "Weak nucleotide (A or T)" },
149		{ "s", "Strong nucleotide (G or C)" },
150		{ "m", "Amino (A or C)" },
151		{ "k", "Keto (G or T)" },
152		{ "b", "Not A (G or C or T)" },
153		{ "h", "Not G (A or C or T)" },
154		{ "d", "Not C (A or G or T)" },
155		{ "v", "Not T (A or G or C)" },
156		{ "n", "Unknown" } };
157		// "gap" index
158	0	maxNucleotideIndex = namesArray.length;
159
160	0	nucleotideIndex = new int[255];
161	0	for (int i = 0; i < 255; i++)
162		{
163	0	nucleotideIndex[i] = maxNucleotideIndex; // non-nucleotide symbols are all
164		// non-gap gaps.
165		}
166
167	0	for (int i = 0; i < namesArray.length; i++)
168		{
169	0	char c = namesArray[i][0].charAt(0);
170	0	nucleotideIndex[c] = i;
171		// Character.toUpperCase is Locale insensitive
172	0	nucleotideIndex[Character.toUpperCase(c)] = i;
173	0	nucleotideName.put(namesArray[i][0], namesArray[i][1]);
174	0	nucleotideName.put(namesArray[i][0].toUpperCase(Locale.ROOT),
175		namesArray[i][1]);
176		}
177
178		}
179
		0% Uncovered Elements: 25 (25) Complexity: 2 Complexity Density: 0.09
180	0	static...
181		{
182	0	purinepyrimidineIndex = new int[255];
183	0	for (int i = 0; i < 255; i++)
184		{
185	0	purinepyrimidineIndex[i] = 3; // non-nucleotide symbols are all non-gap
186		// gaps.
187		}
188
189	0	purinepyrimidineIndex['A'] = 0;
190	0	purinepyrimidineIndex['a'] = 0;
191	0	purinepyrimidineIndex['C'] = 1;
192	0	purinepyrimidineIndex['c'] = 1;
193	0	purinepyrimidineIndex['G'] = 0;
194	0	purinepyrimidineIndex['g'] = 0;
195	0	purinepyrimidineIndex['T'] = 1;
196	0	purinepyrimidineIndex['t'] = 1;
197	0	purinepyrimidineIndex['U'] = 1;
198	0	purinepyrimidineIndex['u'] = 1;
199	0	purinepyrimidineIndex['I'] = 2;
200	0	purinepyrimidineIndex['i'] = 2;
201	0	purinepyrimidineIndex['X'] = 2;
202	0	purinepyrimidineIndex['x'] = 2;
203	0	purinepyrimidineIndex['R'] = 0;
204	0	purinepyrimidineIndex['r'] = 0;
205	0	purinepyrimidineIndex['Y'] = 1;
206	0	purinepyrimidineIndex['y'] = 1;
207	0	purinepyrimidineIndex['N'] = 2;
208	0	purinepyrimidineIndex['n'] = 2;
209		}
210
		0% Uncovered Elements: 8 (8) Complexity: 2 Complexity Density: 0.33
211	0	static...
212		{
213	0	secondaryStructureIndex = new int[255];
214	0	for (int i = 0; i < 255; i++)
215		{
216	0	secondaryStructureIndex[i] = 3;
217		}
218
219	0	secondaryStructureIndex['H'] = 0;
220	0	secondaryStructureIndex['E'] = 1;
221	0	secondaryStructureIndex['C'] = 2;
222		}
223
224		private static final Integer ONE = Integer.valueOf(1);
225
226		private static final Integer ZERO = Integer.valueOf(0);
227
		0% Uncovered Elements: 29 (29) Complexity: 1 Complexity Density: 0.03
228	0	static...
229		{
230	0	aa3Hash.put("ALA", ZERO);
231	0	aa3Hash.put("ARG", ONE);
232	0	aa3Hash.put("ASN", Integer.valueOf(2));
233	0	aa3Hash.put("ASP", Integer.valueOf(3)); // D
234	0	aa3Hash.put("CYS", Integer.valueOf(4));
235	0	aa3Hash.put("GLN", Integer.valueOf(5)); // Q
236	0	aa3Hash.put("GLU", Integer.valueOf(6)); // E
237	0	aa3Hash.put("GLY", Integer.valueOf(7));
238	0	aa3Hash.put("HIS", Integer.valueOf(8));
239	0	aa3Hash.put("ILE", Integer.valueOf(9));
240	0	aa3Hash.put("LEU", Integer.valueOf(10));
241	0	aa3Hash.put("LYS", Integer.valueOf(11));
242	0	aa3Hash.put("MET", Integer.valueOf(12));
243	0	aa3Hash.put("PHE", Integer.valueOf(13));
244	0	aa3Hash.put("PRO", Integer.valueOf(14));
245	0	aa3Hash.put("SER", Integer.valueOf(15));
246	0	aa3Hash.put("THR", Integer.valueOf(16));
247	0	aa3Hash.put("TRP", Integer.valueOf(17));
248	0	aa3Hash.put("TYR", Integer.valueOf(18));
249	0	aa3Hash.put("VAL", Integer.valueOf(19));
250		// IUB Nomenclature for ambiguous peptides
251	0	aa3Hash.put("ASX", Integer.valueOf(20)); // "B";
252	0	aa3Hash.put("GLX", Integer.valueOf(21)); // Z
253	0	aa3Hash.put("XAA", Integer.valueOf(22)); // X unknown
254	0	aa3Hash.put("-", Integer.valueOf(23));
255	0	aa3Hash.put("*", Integer.valueOf(23));
256	0	aa3Hash.put(".", Integer.valueOf(23));
257	0	aa3Hash.put(" ", Integer.valueOf(23));
258	0	aa3Hash.put("Gap", Integer.valueOf(23));
259	0	aa3Hash.put("UR3", Integer.valueOf(24));
260		}
261
		0% Uncovered Elements: 40 (40) Complexity: 1 Complexity Density: 0.03
262	0	static...
263		{
264	0	aa2Triplet.put("A", "ALA");
265	0	aa2Triplet.put("a", "ALA");
266	0	aa2Triplet.put("R", "ARG");
267	0	aa2Triplet.put("r", "ARG");
268	0	aa2Triplet.put("N", "ASN");
269	0	aa2Triplet.put("n", "ASN");
270	0	aa2Triplet.put("D", "ASP");
271	0	aa2Triplet.put("d", "ASP");
272	0	aa2Triplet.put("C", "CYS");
273	0	aa2Triplet.put("c", "CYS");
274	0	aa2Triplet.put("Q", "GLN");
275	0	aa2Triplet.put("q", "GLN");
276	0	aa2Triplet.put("E", "GLU");
277	0	aa2Triplet.put("e", "GLU");
278	0	aa2Triplet.put("G", "GLY");
279	0	aa2Triplet.put("g", "GLY");
280	0	aa2Triplet.put("H", "HIS");
281	0	aa2Triplet.put("h", "HIS");
282	0	aa2Triplet.put("I", "ILE");
283	0	aa2Triplet.put("i", "ILE");
284	0	aa2Triplet.put("L", "LEU");
285	0	aa2Triplet.put("l", "LEU");
286	0	aa2Triplet.put("K", "LYS");
287	0	aa2Triplet.put("k", "LYS");
288	0	aa2Triplet.put("M", "MET");
289	0	aa2Triplet.put("m", "MET");
290	0	aa2Triplet.put("F", "PHE");
291	0	aa2Triplet.put("f", "PHE");
292	0	aa2Triplet.put("P", "PRO");
293	0	aa2Triplet.put("p", "PRO");
294	0	aa2Triplet.put("S", "SER");
295	0	aa2Triplet.put("s", "SER");
296	0	aa2Triplet.put("T", "THR");
297	0	aa2Triplet.put("t", "THR");
298	0	aa2Triplet.put("W", "TRP");
299	0	aa2Triplet.put("w", "TRP");
300	0	aa2Triplet.put("Y", "TYR");
301	0	aa2Triplet.put("y", "TYR");
302	0	aa2Triplet.put("V", "VAL");
303	0	aa2Triplet.put("v", "VAL");
304		}
305
306		public static final String[] aa = { "A", "R", "N", "D", "C", "Q", "E",
307		"G", "H", "I", "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V", "B",
308		"Z", "X", "_", "*", ".", " ", "U" };
309
310		public static final Color midBlue = new Color(100, 100, 255);
311
312		// not currently in use
313		// public static final Vector<Color> scaleColours = new Vector<Color>();
314		// static
315		// {
316		// scaleColours.addElement(new Color(114, 0, 147));
317		// scaleColours.addElement(new Color(156, 0, 98));
318		// scaleColours.addElement(new Color(190, 0, 0));
319		// scaleColours.addElement(Color.red);
320		// scaleColours.addElement(new Color(255, 125, 0));
321		// scaleColours.addElement(Color.orange);
322		// scaleColours.addElement(new Color(255, 194, 85));
323		// scaleColours.addElement(Color.yellow);
324		// scaleColours.addElement(new Color(255, 255, 181));
325		// scaleColours.addElement(Color.white);
326		// }
327
328		public static final Color[] taylor = { new Color(204, 255, 0),
329		// A Greenish-yellowy-yellow
330		new Color(0, 0, 255), // R Blueish-bluey-blue
331		new Color(204, 0, 255), // N Blueish-reddy-blue
332		new Color(255, 0, 0), // D Reddish-reddy-red
333		new Color(255, 255, 0), // C Yellowish-yellowy-yellow
334		new Color(255, 0, 204), // Q Reddish-bluey-red
335		new Color(255, 0, 102), // E Blueish-reddy-red
336		new Color(255, 153, 0), // G Yellowy-reddy-yellow
337		new Color(0, 102, 255), // H Greenish-bluey-blue
338		new Color(102, 255, 0), // I Greenish-yellowy-green
339		new Color(51, 255, 0), // L Yellowish-greeny-green
340		new Color(102, 0, 255), // K Reddish-bluey-blue
341		new Color(0, 255, 0), // M Greenish-greeny-green
342		new Color(0, 255, 102), // F Blueish-greeny-green
343		new Color(255, 204, 0), // P Reddish-yellowy-yellow
344		new Color(255, 51, 0), // S Yellowish-reddy-red
345		new Color(255, 102, 0), // T Reddish-yellowy-red
346		new Color(0, 204, 255), // W Blueish-greeny-green
347		new Color(0, 255, 204), // Y Greenish-bluey-green
348		new Color(153, 255, 0), // V Yellowish-greeny-yellow
349		Color.white, // B
350		Color.white, // Z
351		Color.white, // X
352		Color.white, // -
353		Color.white, // *
354		Color.white // .
355		};
356
357		public static final Color[] nucleotide = { new Color(100, 247, 63), // A
358		new Color(255, 179, 64), // C
359		new Color(235, 65, 60), // G
360		new Color(60, 136, 238), // T
361		new Color(60, 136, 238), // U
362		Color.white, // I (inosine)
363		Color.white, // X (xanthine)
364		Color.white, // R
365		Color.white, // Y
366		Color.white, // N
367		Color.white, // w
368		Color.white, // s
369		Color.white, // m
370		Color.white, // k
371		Color.white, // b
372		Color.white, // h
373		Color.white, // d
374		Color.white, // v
375		Color.white, // Gap
376		};
377
378		// this colour scheme devised by sduce
379		public static final Color[] nucleotideAmbiguity = {
380		Color.decode("#f0fff0"), // a
381		Color.decode("#f0fff0"), // c
382		Color.decode("#f0fff0"), // g
383		Color.decode("#f0fff0"), // t
384		Color.decode("#f0fff0"), // u
385		Color.decode("#ffffff"), // i
386		Color.decode("#4f6f6f"), // x
387		Color.decode("#CD5C5C"), // r
388		Color.decode("#008000"), // y
389		Color.decode("#4682B4"), // w
390		Color.decode("#FF8C00"), // s
391		Color.decode("#9ACD32"), // m
392		Color.decode("#9932CC"), // k
393		Color.decode("#8b4513"), // b
394		Color.decode("#808080"), // h
395		Color.decode("#483D8B"), // d
396		Color.decode("#b8860b"), // v
397		Color.decode("#2f4f4f"), // n
398		Color.white, // Gap
399		};
400
401		// Added for PurinePyrimidineColourScheme
402		public static final Color[] purinepyrimidine = { new Color(255, 131, 250), // A,
403		// G,
404		// R
405		// purines
406		// purplish/orchid
407		new Color(64, 224, 208), // C,U, T, Y pyrimidines turquoise
408		Color.white, // all other nucleotides
409		Color.white // Gap
410		};
411
412		// Secondary structure
413		public static final Color[] secondarystructure = { Color.red, // H
414		Color.green, // E
415		Color.gray // C
416		};
417
418		// Zappo
419		public static final Color[] zappo = { Color.pink, // A
420		midBlue, // R
421		Color.green, // N
422		Color.red, // D
423		Color.yellow, // C
424		Color.green, // Q
425		Color.red, // E
426		Color.magenta, // G
427		midBlue, // Color.red, // H
428		Color.pink, // I
429		Color.pink, // L
430		midBlue, // K
431		Color.pink, // M
432		Color.orange, // F
433		Color.magenta, // P
434		Color.green, // S
435		Color.green, // T
436		Color.orange, // W
437		Color.orange, // Y
438		Color.pink, // V
439		Color.white, // B
440		Color.white, // Z
441		Color.white, // X
442		Color.white, // -
443		Color.white, // *
444		Color.white, // .
445		Color.white // ' '
446		};
447
448		/*
449		* flower, blossom, sunset, ocean colour schemes from geocos.
450		* See https://gecos.biotite-python.org/
451		* https://raw.githubusercontent.com/biotite-dev/biotite/master/src/biotite/sequence/graphics/color_schemes/flower.json
452		* and https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-3526-6
453		* (https://doi.org/10.1186/s12859-020-3526-6)
454		*/
455		public static final Color[] flower = { new Color(177, 138, 81), // A
456		new Color(131, 191, 241), // R
457		new Color(11, 206, 198), // N
458		new Color(1, 165, 120), // D
459		new Color(255, 87, 1), // C
460		new Color(114, 149, 174), // Q
461		new Color(45, 160, 161), // E
462		new Color(177, 194, 60), // G
463		new Color(1, 148, 249), // H
464		new Color(242, 118, 99), // I
465		new Color(223, 110, 117), // L
466		new Color(127, 195, 215), // K
467		new Color(254, 157, 175), // M
468		new Color(250, 85, 157), // F
469		new Color(79, 163, 42), // P
470		new Color(180, 189, 155), // S
471		new Color(210, 181, 118), // T
472		new Color(255, 45, 237), // W
473		new Color(201, 110, 207), // Y
474		new Color(253, 153, 123), // V
475		Color.white, // B
476		Color.white, // Z
477		Color.white, // X
478		Color.white, // -
479		Color.white, // *
480		Color.white // .
481		};
482
483		public static final Color[] blossom = { new Color(139, 196, 180), // A
484		new Color(252, 149, 2), // R
485		new Color(181, 194, 6), // N
486		new Color(95, 165, 5), // D
487		new Color(8, 147, 254), // C
488		new Color(191, 133, 39), // Q
489		new Color(219, 181, 1), // E
490		new Color(0, 211, 130), // G
491		new Color(255, 87, 1), // H
492		new Color(154, 186, 243), // I
493		new Color(205, 165, 220), // L
494		new Color(254, 165, 39), // K
495		new Color(245, 161, 184), // M
496		new Color(247, 79, 168), // F
497		new Color(16, 214, 49), // P
498		new Color(126, 157, 89), // S
499		new Color(0, 162, 156), // T
500		new Color(254, 8, 251), // W
501		new Color(255, 78, 122), // Y
502		new Color(135, 192, 228), // V
503		Color.white, // B
504		Color.white, // Z
505		Color.white, // X
506		Color.white, // -
507		Color.white, // *
508		Color.white // .
509		};
510
511		public static final Color[] sunset = { new Color(254, 160, 253), // A
512		new Color(133, 116, 106), // R
513		new Color(171, 200, 245), // N
514		new Color(46, 123, 190), // D
515		new Color(252, 12, 254), // C
516		new Color(140, 110, 129), // Q
517		new Color(103, 120, 146), // E
518		new Color(39, 153, 255), // G
519		new Color(219, 197, 142), // H
520		new Color(250, 33, 161), // I
521		new Color(224, 30, 130), // L
522		new Color(222, 190, 204), // K
523		new Color(209, 62, 123), // M
524		new Color(255, 56, 93), // F
525		new Color(87, 102, 249), // P
526		new Color(231, 180, 253), // S
527		new Color(166, 88, 183), // T
528		new Color(255, 55, 1), // W
529		new Color(203, 83, 57), // Y
530		new Color(254, 81, 184), // V
531		Color.white, // B
532		Color.white, // Z
533		Color.white, // X
534		Color.white, // -
535		Color.white, // *
536		Color.white // .
537		};
538
539		public static final Color[] ocean = { new Color(198, 202, 155), // A
540		new Color(12, 160, 168), // R
541		new Color(10, 223, 195), // N
542		new Color(76, 223, 161), // D
543		new Color(198, 129, 54), // C
544		new Color(139, 211, 209), // Q
545		new Color(96, 218, 201), // E
546		new Color(51, 165, 81), // G
547		new Color(0, 207, 254), // H
548		new Color(242, 186, 170), // I
549		new Color(187, 138, 131), // L
550		new Color(64, 160, 144), // K
551		new Color(164, 139, 136), // M
552		new Color(171, 136, 174), // F
553		new Color(175, 211, 101), // P
554		new Color(109, 155, 116), // S
555		new Color(141, 149, 102), // T
556		new Color(117, 138, 238), // W
557		new Color(186, 195, 252), // Y
558		new Color(233, 190, 164), // V
559		Color.white, // B
560		Color.white, // Z
561		Color.white, // X
562		Color.white, // -
563		Color.white, // *
564		Color.white // .
565		};
566
567		// Dunno where I got these numbers from
568		public static final double[] hyd2 = { 0.62, // A
569		0.29, // R
570		-0.90, // N
571		-0.74, // D
572		1.19, // C
573		0.48, // Q
574		-0.40, // E
575		1.38, // G
576		-1.50, // H
577		1.06, // I
578		0.64, // L
579		-0.78, // K
580		0.12, // M
581		-0.85, // F
582		-2.53, // P
583		-0.18, // S
584		-0.05, // T
585		1.08, // W
586		0.81, // Y
587		0.0, // V
588		0.26, // B
589		0.0, // Z
590		0.0 // X
591		};
592
593		public static final double[] helix = { 1.42, 0.98, 0.67, 1.01, 0.70, 1.11,
594		1.51, 0.57, 1.00, 1.08, 1.21, 1.16, 1.45, 1.13, 0.57, 0.77, 0.83,
595		1.08, 0.69, 1.06, 0.84, 1.31, 1.00, 0.0 };
596
597		public static final double helixmin = 0.57;
598
599		public static final double helixmax = 1.51;
600
601		public static final double[] strand = { 0.83, 0.93, 0.89, 0.54, 1.19,
602		1.10, 0.37, 0.75, 0.87, 1.60, 1.30, 0.74, 1.05, 1.38, 0.55, 0.75,
603		1.19, 1.37, 1.47, 1.70, 0.72, 0.74, 1.0, 0.0 };
604
605		public static final double strandmin = 0.37;
606
607		public static final double strandmax = 1.7;
608
609		public static final double[] turn = { 0.66, 0.95, 1.56, 1.46, 1.19, 0.98,
610		0.74, 1.56, 0.95, 0.47, 0.59, 1.01, 0.60, 0.60, 1.52, 1.43, 0.96,
611		0.96, 1.14, 0.50, 1.51, 0.86, 1.00, 0, 0 };
612
613		public static final double turnmin = 0.47;
614
615		public static final double turnmax = 1.56;
616
617		public static final double[] buried = { 1.7, 0.1, 0.4, 0.4, 4.6, 0.3, 0.3,
618		1.8, 0.8, 3.1, 2.4, 0.05, 1.9, 2.2, 0.6, 0.8, 0.7, 1.6, 0.5, 2.9, 0.4,
619		0.3, 1.358, 0.00 };
620
621		public static final double buriedmin = 0.05;
622
623		public static final double buriedmax = 4.6;
624
625		// This is hydropathy index
626		// Kyte, J., and Doolittle, R.F., J. Mol. Biol.
627		// 1157, 105-132, 1982
628		public static final double[] hyd = { 1.8, -4.5, -3.5, -3.5, 2.5, -3.5,
629		-3.5, -0.4, -3.2, 4.5, 3.8, -3.9, 1.9, 2.8, -1.6, -0.8, -0.7, -0.9,
630		-1.3, 4.2, -3.5, -3.5, -0.49, 0.0 };
631
632		public static final double hydmax = 4.5;
633
634		public static final double hydmin = -3.9;
635
636		// public static final double hydmax = 1.38;
637		// public static final double hydmin = -2.53;
638
639		// not currently used
640		// public static final Map<String, Color> ssHash = new Hashtable<String,
641		// Color>();
642		// static
643		// {
644		// ssHash.put("H", Color.magenta);
645		// ssHash.put("E", Color.yellow);
646		// ssHash.put("-", Color.white);
647		// ssHash.put(".", Color.white);
648		// ssHash.put("S", Color.cyan);
649		// ssHash.put("T", Color.blue);
650		// ssHash.put("G", Color.pink);
651		// ssHash.put("I", Color.pink);
652		// ssHash.put("B", Color.yellow);
653		// }
654
655		/*
656		* new Color(60, 136, 238), // U Color.white, // I Color.white, // X
657		* Color.white, // R Color.white, // Y Color.white, // N Color.white, // Gap
658		*/
659
660		public static String STOP = "STOP";
661
662		public static List<String> STOP_CODONS = Arrays.asList("TGA", "TAA",
663		"TAG");
664
665		public static String START = "ATG";
666
667		// Stores residue codes/names and colours and other things
668		public static Map<String, Map<String, Integer>> propHash = new Hashtable<>();
669
670		public static Map<String, Integer> hydrophobic = new Hashtable<>();
671
672		public static Map<String, Integer> polar = new Hashtable<>();
673
674		public static Map<String, Integer> small = new Hashtable<>();
675
676		public static Map<String, Integer> positive = new Hashtable<>();
677
678		public static Map<String, Integer> negative = new Hashtable<>();
679
680		public static Map<String, Integer> charged = new Hashtable<>();
681
682		public static Map<String, Integer> aromatic = new Hashtable<>();
683
684		public static Map<String, Integer> aliphatic = new Hashtable<>();
685
686		public static Map<String, Integer> tiny = new Hashtable<>();
687
688		public static Map<String, Integer> proline = new Hashtable<>();
689
		0% Uncovered Elements: 23 (23) Complexity: 1 Complexity Density: 0.04
690	0	static...
691		{
692	0	hydrophobic.put("I", ONE);
693	0	hydrophobic.put("L", ONE);
694	0	hydrophobic.put("V", ONE);
695	0	hydrophobic.put("C", ONE);
696	0	hydrophobic.put("A", ONE);
697	0	hydrophobic.put("G", ONE);
698	0	hydrophobic.put("M", ONE);
699	0	hydrophobic.put("F", ONE);
700	0	hydrophobic.put("Y", ONE);
701	0	hydrophobic.put("W", ONE);
702	0	hydrophobic.put("H", ONE);
703	0	hydrophobic.put("K", ONE);
704	0	hydrophobic.put("X", ONE);
705	0	hydrophobic.put("-", ONE);
706	0	hydrophobic.put("*", ONE);
707	0	hydrophobic.put("R", ZERO);
708	0	hydrophobic.put("E", ZERO);
709	0	hydrophobic.put("Q", ZERO);
710	0	hydrophobic.put("D", ZERO);
711	0	hydrophobic.put("N", ZERO);
712	0	hydrophobic.put("S", ZERO);
713	0	hydrophobic.put("T", ONE);
714	0	hydrophobic.put("P", ZERO);
715		}
716
		0% Uncovered Elements: 23 (23) Complexity: 1 Complexity Density: 0.04
717	0	static...
718		{
719	0	polar.put("Y", ONE);
720	0	polar.put("W", ONE);
721	0	polar.put("H", ONE);
722	0	polar.put("K", ONE);
723	0	polar.put("R", ONE);
724	0	polar.put("E", ONE);
725	0	polar.put("Q", ONE);
726	0	polar.put("D", ONE);
727	0	polar.put("N", ONE);
728	0	polar.put("S", ONE);
729	0	polar.put("T", ONE);
730	0	polar.put("X", ONE);
731	0	polar.put("-", ONE);
732	0	polar.put("*", ONE);
733	0	polar.put("I", ZERO);
734	0	polar.put("L", ZERO);
735	0	polar.put("V", ZERO);
736	0	polar.put("C", ZERO);
737	0	polar.put("A", ZERO);
738	0	polar.put("G", ZERO);
739	0	polar.put("M", ZERO);
740	0	polar.put("F", ZERO);
741	0	polar.put("P", ZERO);
742		}
743
		0% Uncovered Elements: 22 (22) Complexity: 1 Complexity Density: 0.05
744	0	static...
745		{
746	0	small.put("I", ZERO);
747	0	small.put("L", ZERO);
748	0	small.put("V", ONE);
749	0	small.put("C", ONE);
750	0	small.put("A", ONE);
751	0	small.put("G", ONE);
752	0	small.put("M", ZERO);
753	0	small.put("F", ZERO);
754	0	small.put("Y", ZERO);
755	0	small.put("W", ZERO);
756	0	small.put("H", ZERO);
757	0	small.put("K", ZERO);
758	0	small.put("R", ZERO);
759	0	small.put("E", ZERO);
760	0	small.put("Q", ZERO);
761	0	small.put("D", ONE);
762	0	small.put("N", ONE);
763	0	small.put("S", ONE);
764	0	small.put("T", ONE);
765	0	small.put("P", ONE);
766	0	small.put("-", ONE);
767	0	small.put("*", ONE);
768		}
769
		0% Uncovered Elements: 22 (22) Complexity: 1 Complexity Density: 0.05
770	0	static...
771		{
772	0	positive.put("I", ZERO);
773	0	positive.put("L", ZERO);
774	0	positive.put("V", ZERO);
775	0	positive.put("C", ZERO);
776	0	positive.put("A", ZERO);
777	0	positive.put("G", ZERO);
778	0	positive.put("M", ZERO);
779	0	positive.put("F", ZERO);
780	0	positive.put("Y", ZERO);
781	0	positive.put("W", ZERO);
782	0	positive.put("H", ONE);
783	0	positive.put("K", ONE);
784	0	positive.put("R", ONE);
785	0	positive.put("E", ZERO);
786	0	positive.put("Q", ZERO);
787	0	positive.put("D", ZERO);
788	0	positive.put("N", ZERO);
789	0	positive.put("S", ZERO);
790	0	positive.put("T", ZERO);
791	0	positive.put("P", ZERO);
792	0	positive.put("-", ONE);
793	0	positive.put("*", ONE);
794		}
795
		0% Uncovered Elements: 22 (22) Complexity: 1 Complexity Density: 0.05
796	0	static...
797		{
798	0	negative.put("I", ZERO);
799	0	negative.put("L", ZERO);
800	0	negative.put("V", ZERO);
801	0	negative.put("C", ZERO);
802	0	negative.put("A", ZERO);
803	0	negative.put("G", ZERO);
804	0	negative.put("M", ZERO);
805	0	negative.put("F", ZERO);
806	0	negative.put("Y", ZERO);
807	0	negative.put("W", ZERO);
808	0	negative.put("H", ZERO);
809	0	negative.put("K", ZERO);
810	0	negative.put("R", ZERO);
811	0	negative.put("E", ONE);
812	0	negative.put("Q", ZERO);
813	0	negative.put("D", ONE);
814	0	negative.put("N", ZERO);
815	0	negative.put("S", ZERO);
816	0	negative.put("T", ZERO);
817	0	negative.put("P", ZERO);
818	0	negative.put("-", ONE);
819	0	negative.put("*", ONE);
820		}
821
		0% Uncovered Elements: 22 (22) Complexity: 1 Complexity Density: 0.05
822	0	static...
823		{
824	0	charged.put("I", ZERO);
825	0	charged.put("L", ZERO);
826	0	charged.put("V", ZERO);
827	0	charged.put("C", ZERO);
828	0	charged.put("A", ZERO);
829	0	charged.put("G", ZERO);
830	0	charged.put("M", ZERO);
831	0	charged.put("F", ZERO);
832	0	charged.put("Y", ZERO);
833	0	charged.put("W", ZERO);
834	0	charged.put("H", ONE);
835	0	charged.put("K", ONE);
836	0	charged.put("R", ONE);
837	0	charged.put("E", ONE);
838	0	charged.put("Q", ZERO);
839	0	charged.put("D", ONE);
840	0	charged.put("N", ZERO); // Asparagine is polar but not
841		// charged.
842		// Alternative would be charged and
843		// negative (in basic form)?
844	0	charged.put("S", ZERO);
845	0	charged.put("T", ZERO);
846	0	charged.put("P", ZERO);
847	0	charged.put("-", ONE);
848	0	charged.put("*", ONE);
849		}
850
		0% Uncovered Elements: 22 (22) Complexity: 1 Complexity Density: 0.05
851	0	static...
852		{
853	0	aromatic.put("I", ZERO);
854	0	aromatic.put("L", ZERO);
855	0	aromatic.put("V", ZERO);
856	0	aromatic.put("C", ZERO);
857	0	aromatic.put("A", ZERO);
858	0	aromatic.put("G", ZERO);
859	0	aromatic.put("M", ZERO);
860	0	aromatic.put("F", ONE);
861	0	aromatic.put("Y", ONE);
862	0	aromatic.put("W", ONE);
863	0	aromatic.put("H", ONE);
864	0	aromatic.put("K", ZERO);
865	0	aromatic.put("R", ZERO);
866	0	aromatic.put("E", ZERO);
867	0	aromatic.put("Q", ZERO);
868	0	aromatic.put("D", ZERO);
869	0	aromatic.put("N", ZERO);
870	0	aromatic.put("S", ZERO);
871	0	aromatic.put("T", ZERO);
872	0	aromatic.put("P", ZERO);
873	0	aromatic.put("-", ONE);
874	0	aromatic.put("*", ONE);
875		}
876
		0% Uncovered Elements: 22 (22) Complexity: 1 Complexity Density: 0.05
877	0	static...
878		{
879	0	aliphatic.put("I", ONE);
880	0	aliphatic.put("L", ONE);
881	0	aliphatic.put("V", ONE);
882	0	aliphatic.put("C", ZERO);
883	0	aliphatic.put("A", ZERO);
884	0	aliphatic.put("G", ZERO);
885	0	aliphatic.put("M", ZERO);
886	0	aliphatic.put("F", ZERO);
887	0	aliphatic.put("Y", ZERO);
888	0	aliphatic.put("W", ZERO);
889	0	aliphatic.put("H", ZERO);
890	0	aliphatic.put("K", ZERO);
891	0	aliphatic.put("R", ZERO);
892	0	aliphatic.put("E", ZERO);
893	0	aliphatic.put("Q", ZERO);
894	0	aliphatic.put("D", ZERO);
895	0	aliphatic.put("N", ZERO);
896	0	aliphatic.put("S", ZERO);
897	0	aliphatic.put("T", ZERO);
898	0	aliphatic.put("P", ZERO);
899	0	aliphatic.put("-", ONE);
900	0	aliphatic.put("*", ONE);
901		}
902
		0% Uncovered Elements: 22 (22) Complexity: 1 Complexity Density: 0.05
903	0	static...
904		{
905	0	tiny.put("I", ZERO);
906	0	tiny.put("L", ZERO);
907	0	tiny.put("V", ZERO);
908	0	tiny.put("C", ZERO);
909	0	tiny.put("A", ONE);
910	0	tiny.put("G", ONE);
911	0	tiny.put("M", ZERO);
912	0	tiny.put("F", ZERO);
913	0	tiny.put("Y", ZERO);
914	0	tiny.put("W", ZERO);
915	0	tiny.put("H", ZERO);
916	0	tiny.put("K", ZERO);
917	0	tiny.put("R", ZERO);
918	0	tiny.put("E", ZERO);
919	0	tiny.put("Q", ZERO);
920	0	tiny.put("D", ZERO);
921	0	tiny.put("N", ZERO);
922	0	tiny.put("S", ONE);
923	0	tiny.put("T", ZERO);
924	0	tiny.put("P", ZERO);
925	0	tiny.put("-", ONE);
926	0	tiny.put("*", ONE);
927		}
928
		0% Uncovered Elements: 22 (22) Complexity: 1 Complexity Density: 0.05
929	0	static...
930		{
931	0	proline.put("I", ZERO);
932	0	proline.put("L", ZERO);
933	0	proline.put("V", ZERO);
934	0	proline.put("C", ZERO);
935	0	proline.put("A", ZERO);
936	0	proline.put("G", ZERO);
937	0	proline.put("M", ZERO);
938	0	proline.put("F", ZERO);
939	0	proline.put("Y", ZERO);
940	0	proline.put("W", ZERO);
941	0	proline.put("H", ZERO);
942	0	proline.put("K", ZERO);
943	0	proline.put("R", ZERO);
944	0	proline.put("E", ZERO);
945	0	proline.put("Q", ZERO);
946	0	proline.put("D", ZERO);
947	0	proline.put("N", ZERO);
948	0	proline.put("S", ZERO);
949	0	proline.put("T", ZERO);
950	0	proline.put("P", ONE);
951	0	proline.put("-", ONE);
952	0	proline.put("*", ONE);
953		}
954
		0% Uncovered Elements: 10 (10) Complexity: 1 Complexity Density: 0.1
955	0	static...
956		{
957	0	propHash.put("hydrophobic", hydrophobic);
958	0	propHash.put("small", small);
959	0	propHash.put("positive", positive);
960	0	propHash.put("negative", negative);
961	0	propHash.put("charged", charged);
962	0	propHash.put("aromatic", aromatic);
963	0	propHash.put("aliphatic", aliphatic);
964	0	propHash.put("tiny", tiny);
965	0	propHash.put("proline", proline);
966	0	propHash.put("polar", polar);
967		}
		0% Uncovered Elements: 62 (62) Complexity: 18 Complexity Density: 0.53
968	0	static...
969		{
970	0	int[][] propMatrixF = new int[maxProteinIndex][maxProteinIndex],
971		propMatrixPos = new int[maxProteinIndex][maxProteinIndex],
972		propMatrixEpos = new int[maxProteinIndex][maxProteinIndex];
973	0	for (int i = 0; i < maxProteinIndex; i++)
974		{
975	0	int maxF = 0, maxP = 0, maxEP = 0;
976	0	String ic = "";
977	0	if (aa.length > i)
978		{
979	0	ic += aa[i];
980		}
981		else
982		{
983	0	ic = "-";
984		}
985	0	for (int j = i + 1; j < maxProteinIndex; j++)
986		{
987	0	String jc = "";
988	0	if (aa.length > j)
989		{
990	0	jc += aa[j];
991		}
992		else
993		{
994	0	jc = "-";
995		}
996	0	propMatrixF[i][j] = 0;
997	0	propMatrixPos[i][j] = 0;
998	0	propMatrixEpos[i][j] = 0;
999	0	for (String ph : propHash.keySet())
1000		{
1001	0	Map<String, Integer> pph = propHash.get(ph);
1002	0	if (pph.get(ic) != null && pph.get(jc) != null)
1003		{
1004	0	int icp = pph.get(ic).intValue(), jcp = pph.get(jc).intValue();
1005		// Still working on these definitions.
1006	0	propMatrixPos[i][j] += icp == jcp && icp > 0 ? 2 : 0;
1007	0	propMatrixPos[j][i] += icp == jcp && icp > 0 ? 2 : 0;
1008	0	propMatrixF[i][j] += icp == jcp ? 2 : 0;
1009	0	propMatrixF[j][i] += icp == jcp ? 2 : 0;
1010	0	propMatrixEpos[i][j] += icp == jcp ? (1 + icp * 2) : 0;
1011	0	propMatrixEpos[j][i] += icp == jcp ? (1 + icp * 2) : 0;
1012		}
1013		}
1014	0	if (maxF < propMatrixF[i][j])
1015		{
1016	0	maxF = propMatrixF[i][j];
1017		}
1018	0	if (maxP < propMatrixPos[i][j])
1019		{
1020	0	maxP = propMatrixPos[i][j];
1021		}
1022	0	if (maxEP < propMatrixEpos[i][j])
1023		{
1024	0	maxEP = propMatrixEpos[i][j];
1025		}
1026		}
1027	0	propMatrixF[i][i] = maxF;
1028	0	propMatrixPos[i][i] = maxP;
1029	0	propMatrixEpos[i][i] = maxEP;
1030		}
1031		}
1032
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
1033	0	private ResidueProperties()...
1034		{
1035		}
1036
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
1037	0	public static double getHydmax()...
1038		{
1039	0	return hydmax;
1040		}
1041
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
1042	0	public static double getHydmin()...
1043		{
1044	0	return hydmin;
1045		}
1046
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
1047	0	public static double[] getHyd()...
1048		{
1049	0	return hyd;
1050		}
1051
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
1052	0	public static Map<String, Integer> getAA3Hash()...
1053		{
1054	0	return aa3Hash;
1055		}
1056
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
1057	0	public static String codonTranslate(String lccodon)...
1058		{
1059	0	String peptide = GeneticCodes.getInstance().getStandardCodeTable()
1060		.translate(lccodon);
1061	0	if ("*".equals(peptide))
1062		{
1063	0	return "STOP";
1064		}
1065	0	return peptide;
1066		}
1067
1068		/*
1069		* lookup of (A-Z) alternative secondary structure symbols'
1070		* equivalents in DSSP3 notation
1071		*/
1072		private static char[] toDssp3State;
		0% Uncovered Elements: 7 (7) Complexity: 1 Complexity Density: 0.14
1073	0	static...
1074		{
1075	0	toDssp3State = new char[9]; // for 'A'-'I'; extend if needed
1076	0	Arrays.fill(toDssp3State, ' ');
1077	0	toDssp3State['B' - 'A'] = 'E';
1078	0	toDssp3State['E' - 'A'] = 'E';
1079	0	toDssp3State['G' - 'A'] = 'H';
1080	0	toDssp3State['H' - 'A'] = 'H';
1081	0	toDssp3State['I' - 'A'] = 'H';
1082		}
1083
1084		/**
1085		* translate from other dssp secondary structure alphabets to 3-state
1086		*
1087		* @param ssString
1088		* @return ssstring
1089		*/
		0% Uncovered Elements: 18 (18) Complexity: 5 Complexity Density: 0.42
1090	0	public static String getDssp3state(String ssString)...
1091		{
1092	0	if (ssString == null)
1093		{
1094	0	return null;
1095		}
1096	0	int lookupSize = toDssp3State.length;
1097	0	int len = ssString.length();
1098	0	char[] trans = new char[len];
1099	0	for (int i = 0; i < len; i++)
1100		{
1101	0	char c = ssString.charAt(i);
1102	0	int index = c - 'A';
1103	0	if (index < 0 || index >= lookupSize)
1104		{
1105	0	trans[i] = ' ';
1106		}
1107		else
1108		{
1109	0	trans[i] = toDssp3State[index];
1110		}
1111		}
1112	0	return new String(trans);
1113		}
1114
		0% Uncovered Elements: 1,300 (1,300) Complexity: 1 Complexity Density: 0
1115	0	static...
1116		{
1117	0	modifications.put("MSE", "MET"); // Selenomethionine
1118		// the rest tbc; from
1119		// http://sourceforge.net/p/jmol/mailman/message/12833570/
1120		// modifications.put("CSE", "CYS"); // Selenocysteine
1121		// modifications.put("PTR", "TYR"); // Phosphotyrosine
1122		// modifications.put("SEP", "SER"); // Phosphoserine
1123		// modifications.put("HYP", "PRO"); // 4-hydroxyproline
1124		// modifications.put("5HP", "GLU"); // Pyroglutamic acid; 5-hydroxyproline
1125		// modifications.put("PCA", "GLU"); // Pyroglutamic acid
1126		// modifications.put("LYZ", "LYS"); // 5-hydroxylysine
1127
1128		// Additional protein alphabets used in the SCOP database and PDB files
1129		// source:
1130		// https://github.com/biopython/biopython/blob/master/Bio/Data/SCOPData.py
1131	0	modifications.put("00C", "CYS");
1132	0	modifications.put("01W", "XAA");
1133	0	modifications.put("02K", "ALA");
1134	0	modifications.put("03Y", "CYS");
1135	0	modifications.put("07O", "CYS");
1136	0	modifications.put("08P", "CYS");
1137	0	modifications.put("0A0", "ASP");
1138	0	modifications.put("0A1", "TYR");
1139	0	modifications.put("0A2", "LYS");
1140	0	modifications.put("0A8", "CYS");
1141	0	modifications.put("0AA", "VAL");
1142	0	modifications.put("0AB", "VAL");
1143	0	modifications.put("0AC", "GLY");
1144	0	modifications.put("0AD", "GLY");
1145	0	modifications.put("0AF", "TRP");
1146	0	modifications.put("0AG", "LEU");
1147	0	modifications.put("0AH", "SER");
1148	0	modifications.put("0AK", "ASP");
1149	0	modifications.put("0AM", "ALA");
1150	0	modifications.put("0AP", "CYS");
1151	0	modifications.put("0AU", "UR3");
1152	0	modifications.put("0AV", "ALA");
1153	0	modifications.put("0AZ", "PRO");
1154	0	modifications.put("0BN", "PHE");
1155	0	modifications.put("0C ", "CYS");
1156	0	modifications.put("0CS", "ALA");
1157	0	modifications.put("0DC", "CYS");
1158	0	modifications.put("0DG", "GLY");
1159	0	modifications.put("0DT", "THR");
1160	0	modifications.put("0FL", "ALA");
1161	0	modifications.put("0G ", "GLY");
1162	0	modifications.put("0NC", "ALA");
1163	0	modifications.put("0SP", "ALA");
1164	0	modifications.put("0U ", "UR3");
1165	0	modifications.put("0YG", "YG");
1166	0	modifications.put("10C", "CYS");
1167	0	modifications.put("125", "UR3");
1168	0	modifications.put("126", "UR3");
1169	0	modifications.put("127", "UR3");
1170	0	modifications.put("128", "ASN");
1171	0	modifications.put("12A", "ALA");
1172	0	modifications.put("143", "CYS");
1173	0	modifications.put("175", "ASG");
1174	0	modifications.put("193", "XAA");
1175	0	modifications.put("1AP", "ALA");
1176	0	modifications.put("1MA", "ALA");
1177	0	modifications.put("1MG", "GLY");
1178	0	modifications.put("1PA", "PHE");
1179	0	modifications.put("1PI", "ALA");
1180	0	modifications.put("1PR", "ASN");
1181	0	modifications.put("1SC", "CYS");
1182	0	modifications.put("1TQ", "TRP");
1183	0	modifications.put("1TY", "TYR");
1184	0	modifications.put("1X6", "SER");
1185	0	modifications.put("200", "PHE");
1186	0	modifications.put("23F", "PHE");
1187	0	modifications.put("23S", "XAA");
1188	0	modifications.put("26B", "THR");
1189	0	modifications.put("2AD", "XAA");
1190	0	modifications.put("2AG", "ALA");
1191	0	modifications.put("2AO", "XAA");
1192	0	modifications.put("2AR", "ALA");
1193	0	modifications.put("2AS", "XAA");
1194	0	modifications.put("2AT", "THR");
1195	0	modifications.put("2AU", "UR3");
1196	0	modifications.put("2BD", "ILE");
1197	0	modifications.put("2BT", "THR");
1198	0	modifications.put("2BU", "ALA");
1199	0	modifications.put("2CO", "CYS");
1200	0	modifications.put("2DA", "ALA");
1201	0	modifications.put("2DF", "ASN");
1202	0	modifications.put("2DM", "ASN");
1203	0	modifications.put("2DO", "XAA");
1204	0	modifications.put("2DT", "THR");
1205	0	modifications.put("2EG", "GLY");
1206	0	modifications.put("2FE", "ASN");
1207	0	modifications.put("2FI", "ASN");
1208	0	modifications.put("2FM", "MET");
1209	0	modifications.put("2GT", "THR");
1210	0	modifications.put("2HF", "HIS");
1211	0	modifications.put("2LU", "LEU");
1212	0	modifications.put("2MA", "ALA");
1213	0	modifications.put("2MG", "GLY");
1214	0	modifications.put("2ML", "LEU");
1215	0	modifications.put("2MR", "ARG");
1216	0	modifications.put("2MT", "PRO");
1217	0	modifications.put("2MU", "UR3");
1218	0	modifications.put("2NT", "THR");
1219	0	modifications.put("2OM", "UR3");
1220	0	modifications.put("2OT", "THR");
1221	0	modifications.put("2PI", "XAA");
1222	0	modifications.put("2PR", "GLY");
1223	0	modifications.put("2SA", "ASN");
1224	0	modifications.put("2SI", "XAA");
1225	0	modifications.put("2ST", "THR");
1226	0	modifications.put("2TL", "THR");
1227	0	modifications.put("2TY", "TYR");
1228	0	modifications.put("2VA", "VAL");
1229	0	modifications.put("2XA", "CYS");
1230	0	modifications.put("32S", "XAA");
1231	0	modifications.put("32T", "XAA");
1232	0	modifications.put("3AH", "HIS");
1233	0	modifications.put("3AR", "XAA");
1234	0	modifications.put("3CF", "PHE");
1235	0	modifications.put("3DA", "ALA");
1236	0	modifications.put("3DR", "ASN");
1237	0	modifications.put("3GA", "ALA");
1238	0	modifications.put("3MD", "ASP");
1239	0	modifications.put("3ME", "UR3");
1240	0	modifications.put("3NF", "TYR");
1241	0	modifications.put("3QN", "LYS");
1242	0	modifications.put("3TY", "XAA");
1243	0	modifications.put("3XH", "GLY");
1244	0	modifications.put("4AC", "ASN");
1245	0	modifications.put("4BF", "TYR");
1246	0	modifications.put("4CF", "PHE");
1247	0	modifications.put("4CY", "MET");
1248	0	modifications.put("4DP", "TRP");
1249	0	modifications.put("4F3", "GYG");
1250	0	modifications.put("4FB", "PRO");
1251	0	modifications.put("4FW", "TRP");
1252	0	modifications.put("4HT", "TRP");
1253	0	modifications.put("4IN", "TRP");
1254	0	modifications.put("4MF", "ASN");
1255	0	modifications.put("4MM", "XAA");
1256	0	modifications.put("4OC", "CYS");
1257	0	modifications.put("4PC", "CYS");
1258	0	modifications.put("4PD", "CYS");
1259	0	modifications.put("4PE", "CYS");
1260	0	modifications.put("4PH", "PHE");
1261	0	modifications.put("4SC", "CYS");
1262	0	modifications.put("4SU", "UR3");
1263	0	modifications.put("4TA", "ASN");
1264	0	modifications.put("4U7", "ALA");
1265	0	modifications.put("56A", "HIS");
1266	0	modifications.put("5AA", "ALA");
1267	0	modifications.put("5AB", "ALA");
1268	0	modifications.put("5AT", "THR");
1269	0	modifications.put("5BU", "UR3");
1270	0	modifications.put("5CG", "GLY");
1271	0	modifications.put("5CM", "CYS");
1272	0	modifications.put("5CS", "CYS");
1273	0	modifications.put("5FA", "ALA");
1274	0	modifications.put("5FC", "CYS");
1275	0	modifications.put("5FU", "UR3");
1276	0	modifications.put("5HP", "GLU");
1277	0	modifications.put("5HT", "THR");
1278	0	modifications.put("5HU", "UR3");
1279	0	modifications.put("5IC", "CYS");
1280	0	modifications.put("5IT", "THR");
1281	0	modifications.put("5IU", "UR3");
1282	0	modifications.put("5MC", "CYS");
1283	0	modifications.put("5MD", "ASN");
1284	0	modifications.put("5MU", "UR3");
1285	0	modifications.put("5NC", "CYS");
1286	0	modifications.put("5PC", "CYS");
1287	0	modifications.put("5PY", "THR");
1288	0	modifications.put("5SE", "UR3");
1289	0	modifications.put("5ZA", "TWG");
1290	0	modifications.put("64T", "THR");
1291	0	modifications.put("6CL", "LYS");
1292	0	modifications.put("6CT", "THR");
1293	0	modifications.put("6CW", "TRP");
1294	0	modifications.put("6HA", "ALA");
1295	0	modifications.put("6HC", "CYS");
1296	0	modifications.put("6HG", "GLY");
1297	0	modifications.put("6HN", "LYS");
1298	0	modifications.put("6HT", "THR");
1299	0	modifications.put("6IA", "ALA");
1300	0	modifications.put("6MA", "ALA");
1301	0	modifications.put("6MC", "ALA");
1302	0	modifications.put("6MI", "ASN");
1303	0	modifications.put("6MT", "ALA");
1304	0	modifications.put("6MZ", "ASN");
1305	0	modifications.put("6OG", "GLY");
1306	0	modifications.put("70U", "UR3");
1307	0	modifications.put("7DA", "ALA");
1308	0	modifications.put("7GU", "GLY");
1309	0	modifications.put("7JA", "ILE");
1310	0	modifications.put("7MG", "GLY");
1311	0	modifications.put("8AN", "ALA");
1312	0	modifications.put("8FG", "GLY");
1313	0	modifications.put("8MG", "GLY");
1314	0	modifications.put("8OG", "GLY");
1315	0	modifications.put("9NE", "GLU");
1316	0	modifications.put("9NF", "PHE");
1317	0	modifications.put("9NR", "ARG");
1318	0	modifications.put("9NV", "VAL");
1319	0	modifications.put("A ", "ALA");
1320	0	modifications.put("A1P", "ASN");
1321	0	modifications.put("A23", "ALA");
1322	0	modifications.put("A2L", "ALA");
1323	0	modifications.put("A2M", "ALA");
1324	0	modifications.put("A34", "ALA");
1325	0	modifications.put("A35", "ALA");
1326	0	modifications.put("A38", "ALA");
1327	0	modifications.put("A39", "ALA");
1328	0	modifications.put("A3A", "ALA");
1329	0	modifications.put("A3P", "ALA");
1330	0	modifications.put("A40", "ALA");
1331	0	modifications.put("A43", "ALA");
1332	0	modifications.put("A44", "ALA");
1333	0	modifications.put("A47", "ALA");
1334	0	modifications.put("A5L", "ALA");
1335	0	modifications.put("A5M", "CYS");
1336	0	modifications.put("A5N", "ASN");
1337	0	modifications.put("A5O", "ALA");
1338	0	modifications.put("A66", "XAA");
1339	0	modifications.put("AA3", "ALA");
1340	0	modifications.put("AA4", "ALA");
1341	0	modifications.put("AAR", "ARG");
1342	0	modifications.put("AB7", "XAA");
1343	0	modifications.put("ABA", "ALA");
1344	0	modifications.put("ABR", "ALA");
1345	0	modifications.put("ABS", "ALA");
1346	0	modifications.put("ABT", "ASN");
1347	0	modifications.put("ACB", "ASP");
1348	0	modifications.put("ACL", "ARG");
1349	0	modifications.put("AD2", "ALA");
1350	0	modifications.put("ADD", "XAA");
1351	0	modifications.put("ADX", "ASN");
1352	0	modifications.put("AEA", "XAA");
1353	0	modifications.put("AEI", "ASP");
1354	0	modifications.put("AET", "ALA");
1355	0	modifications.put("AFA", "ASN");
1356	0	modifications.put("AFF", "ASN");
1357	0	modifications.put("AFG", "GLY");
1358	0	modifications.put("AGM", "ARG");
1359	0	modifications.put("AGT", "CYS");
1360	0	modifications.put("AHB", "ASN");
1361	0	modifications.put("AHH", "XAA");
1362	0	modifications.put("AHO", "ALA");
1363	0	modifications.put("AHP", "ALA");
1364	0	modifications.put("AHS", "XAA");
1365	0	modifications.put("AHT", "XAA");
1366	0	modifications.put("AIB", "ALA");
1367	0	modifications.put("AKL", "ASP");
1368	0	modifications.put("AKZ", "ASP");
1369	0	modifications.put("ALA", "ALA");
1370	0	modifications.put("ALC", "ALA");
1371	0	modifications.put("ALM", "ALA");
1372	0	modifications.put("ALN", "ALA");
1373	0	modifications.put("ALO", "THR");
1374	0	modifications.put("ALQ", "XAA");
1375	0	modifications.put("ALS", "ALA");
1376	0	modifications.put("ALT", "ALA");
1377	0	modifications.put("ALV", "ALA");
1378	0	modifications.put("ALY", "LYS");
1379	0	modifications.put("AN8", "ALA");
1380	0	modifications.put("AP7", "ALA");
1381	0	modifications.put("APE", "XAA");
1382	0	modifications.put("APH", "ALA");
1383	0	modifications.put("API", "LYS");
1384	0	modifications.put("APK", "LYS");
1385	0	modifications.put("APM", "XAA");
1386	0	modifications.put("APP", "XAA");
1387	0	modifications.put("AR2", "ARG");
1388	0	modifications.put("AR4", "GLU");
1389	0	modifications.put("AR7", "ARG");
1390	0	modifications.put("ARG", "ARG");
1391	0	modifications.put("ARM", "ARG");
1392	0	modifications.put("ARO", "ARG");
1393	0	modifications.put("ARV", "XAA");
1394	0	modifications.put("AS ", "ALA");
1395	0	modifications.put("AS2", "ASP");
1396	0	modifications.put("AS9", "XAA");
1397	0	modifications.put("ASA", "ASP");
1398	0	modifications.put("ASB", "ASP");
1399	0	modifications.put("ASI", "ASP");
1400	0	modifications.put("ASK", "ASP");
1401	0	modifications.put("ASL", "ASP");
1402	0	modifications.put("ASM", "XAA");
1403	0	modifications.put("ASN", "ASN");
1404	0	modifications.put("ASP", "ASP");
1405	0	modifications.put("ASQ", "ASP");
1406	0	modifications.put("ASU", "ASN");
1407	0	modifications.put("ASX", "ASX");
1408	0	modifications.put("ATD", "THR");
1409	0	modifications.put("ATL", "THR");
1410	0	modifications.put("ATM", "THR");
1411	0	modifications.put("AVC", "ALA");
1412	0	modifications.put("AVN", "XAA");
1413	0	modifications.put("AYA", "ALA");
1414	0	modifications.put("AYG", "AYG");
1415	0	modifications.put("AZK", "LYS");
1416	0	modifications.put("AZS", "SER");
1417	0	modifications.put("AZY", "TYR");
1418	0	modifications.put("B1F", "PHE");
1419	0	modifications.put("B1P", "ASN");
1420	0	modifications.put("B2A", "ALA");
1421	0	modifications.put("B2F", "PHE");
1422	0	modifications.put("B2I", "ILE");
1423	0	modifications.put("B2V", "VAL");
1424	0	modifications.put("B3A", "ALA");
1425	0	modifications.put("B3D", "ASP");
1426	0	modifications.put("B3E", "GLU");
1427	0	modifications.put("B3K", "LYS");
1428	0	modifications.put("B3L", "XAA");
1429	0	modifications.put("B3M", "XAA");
1430	0	modifications.put("B3Q", "XAA");
1431	0	modifications.put("B3S", "SER");
1432	0	modifications.put("B3T", "XAA");
1433	0	modifications.put("B3U", "HIS");
1434	0	modifications.put("B3X", "ASN");
1435	0	modifications.put("B3Y", "TYR");
1436	0	modifications.put("BB6", "CYS");
1437	0	modifications.put("BB7", "CYS");
1438	0	modifications.put("BB8", "PHE");
1439	0	modifications.put("BB9", "CYS");
1440	0	modifications.put("BBC", "CYS");
1441	0	modifications.put("BCS", "CYS");
1442	0	modifications.put("BE2", "XAA");
1443	0	modifications.put("BFD", "ASP");
1444	0	modifications.put("BG1", "SER");
1445	0	modifications.put("BGM", "GLY");
1446	0	modifications.put("BH2", "ASP");
1447	0	modifications.put("BHD", "ASP");
1448	0	modifications.put("BIF", "PHE");
1449	0	modifications.put("BIL", "XAA");
1450	0	modifications.put("BIU", "ILE");
1451	0	modifications.put("BJH", "XAA");
1452	0	modifications.put("BLE", "LEU");
1453	0	modifications.put("BLY", "LYS");
1454	0	modifications.put("BMP", "ASN");
1455	0	modifications.put("BMT", "THR");
1456	0	modifications.put("BNN", "PHE");
1457	0	modifications.put("BNO", "XAA");
1458	0	modifications.put("BOE", "THR");
1459	0	modifications.put("BOR", "ARG");
1460	0	modifications.put("BPE", "CYS");
1461	0	modifications.put("BRU", "UR3");
1462	0	modifications.put("BSE", "SER");
1463	0	modifications.put("BT5", "ASN");
1464	0	modifications.put("BTA", "LEU");
1465	0	modifications.put("BTC", "CYS");
1466	0	modifications.put("BTR", "TRP");
1467	0	modifications.put("BUC", "CYS");
1468	0	modifications.put("BUG", "VAL");
1469	0	modifications.put("BVP", "UR3");
1470	0	modifications.put("BZG", "ASN");
1471	0	modifications.put("C ", "CYS");
1472	0	modifications.put("C12", "TYG");
1473	0	modifications.put("C1X", "LYS");
1474	0	modifications.put("C25", "CYS");
1475	0	modifications.put("C2L", "CYS");
1476	0	modifications.put("C2S", "CYS");
1477	0	modifications.put("C31", "CYS");
1478	0	modifications.put("C32", "CYS");
1479	0	modifications.put("C34", "CYS");
1480	0	modifications.put("C36", "CYS");
1481	0	modifications.put("C37", "CYS");
1482	0	modifications.put("C38", "CYS");
1483	0	modifications.put("C3Y", "CYS");
1484	0	modifications.put("C42", "CYS");
1485	0	modifications.put("C43", "CYS");
1486	0	modifications.put("C45", "CYS");
1487	0	modifications.put("C46", "CYS");
1488	0	modifications.put("C49", "CYS");
1489	0	modifications.put("C4R", "CYS");
1490	0	modifications.put("C4S", "CYS");
1491	0	modifications.put("C5C", "CYS");
1492	0	modifications.put("C66", "XAA");
1493	0	modifications.put("C6C", "CYS");
1494	0	modifications.put("C99", "TFG");
1495	0	modifications.put("CAF", "CYS");
1496	0	modifications.put("CAL", "XAA");
1497	0	modifications.put("CAR", "CYS");
1498	0	modifications.put("CAS", "CYS");
1499	0	modifications.put("CAV", "XAA");
1500	0	modifications.put("CAY", "CYS");
1501	0	modifications.put("CB2", "CYS");
1502	0	modifications.put("CBR", "CYS");
1503	0	modifications.put("CBV", "CYS");
1504	0	modifications.put("CCC", "CYS");
1505	0	modifications.put("CCL", "LYS");
1506	0	modifications.put("CCS", "CYS");
1507	0	modifications.put("CCY", "CYG");
1508	0	modifications.put("CDE", "XAA");
1509	0	modifications.put("CDV", "XAA");
1510	0	modifications.put("CDW", "CYS");
1511	0	modifications.put("CEA", "CYS");
1512	0	modifications.put("CFL", "CYS");
1513	0	modifications.put("CFY", "FCYG"); // check
1514	0	modifications.put("CG1", "GLY");
1515	0	modifications.put("CGA", "GLU");
1516	0	modifications.put("CGU", "GLU");
1517	0	modifications.put("CH ", "CYS");
1518	0	modifications.put("CH6", "MYG");
1519	0	modifications.put("CH7", "KYG");
1520	0	modifications.put("CHF", "XAA");
1521	0	modifications.put("CHG", "XAA");
1522	0	modifications.put("CHP", "GLY");
1523	0	modifications.put("CHS", "XAA");
1524	0	modifications.put("CIR", "ARG");
1525	0	modifications.put("CJO", "GYG");
1526	0	modifications.put("CLE", "LEU");
1527	0	modifications.put("CLG", "LYS");
1528	0	modifications.put("CLH", "LYS");
1529	0	modifications.put("CLV", "AFG");
1530	0	modifications.put("CM0", "ASN");
1531	0	modifications.put("CME", "CYS");
1532	0	modifications.put("CMH", "CYS");
1533	0	modifications.put("CML", "CYS");
1534	0	modifications.put("CMR", "CYS");
1535	0	modifications.put("CMT", "CYS");
1536	0	modifications.put("CNU", "UR3");
1537	0	modifications.put("CP1", "CYS");
1538	0	modifications.put("CPC", "XAA");
1539	0	modifications.put("CPI", "XAA");
1540	0	modifications.put("CQR", "GYG");
1541	0	modifications.put("CR0", "TLG");
1542	0	modifications.put("CR2", "GYG");
1543	0	modifications.put("CR5", "GLY");
1544	0	modifications.put("CR7", "KYG");
1545	0	modifications.put("CR8", "HYG");
1546	0	modifications.put("CRF", "TWG");
1547	0	modifications.put("CRG", "THG");
1548	0	modifications.put("CRK", "MYG");
1549	0	modifications.put("CRO", "GYG");
1550	0	modifications.put("CRQ", "QYG");
1551	0	modifications.put("CRU", "EYG");
1552	0	modifications.put("CRW", "ASG");
1553	0	modifications.put("CRX", "ASG");
1554	0	modifications.put("CS0", "CYS");
1555	0	modifications.put("CS1", "CYS");
1556	0	modifications.put("CS3", "CYS");
1557	0	modifications.put("CS4", "CYS");
1558	0	modifications.put("CS8", "ASN");
1559	0	modifications.put("CSA", "CYS");
1560	0	modifications.put("CSB", "CYS");
1561	0	modifications.put("CSD", "CYS");
1562	0	modifications.put("CSE", "CYS");
1563	0	modifications.put("CSF", "CYS");
1564	0	modifications.put("CSH", "SHG");
1565	0	modifications.put("CSI", "GLY");
1566	0	modifications.put("CSJ", "CYS");
1567	0	modifications.put("CSL", "CYS");
1568	0	modifications.put("CSO", "CYS");
1569	0	modifications.put("CSP", "CYS");
1570	0	modifications.put("CSR", "CYS");
1571	0	modifications.put("CSS", "CYS");
1572	0	modifications.put("CSU", "CYS");
1573	0	modifications.put("CSW", "CYS");
1574	0	modifications.put("CSX", "CYS");
1575	0	modifications.put("CSY", "SYG");
1576	0	modifications.put("CSZ", "CYS");
1577	0	modifications.put("CTE", "TRP");
1578	0	modifications.put("CTG", "THR");
1579	0	modifications.put("CTH", "THR");
1580	0	modifications.put("CUC", "XAA");
1581	0	modifications.put("CWR", "SER");
1582	0	modifications.put("CXM", "MET");
1583	0	modifications.put("CY0", "CYS");
1584	0	modifications.put("CY1", "CYS");
1585	0	modifications.put("CY3", "CYS");
1586	0	modifications.put("CY4", "CYS");
1587	0	modifications.put("CYA", "CYS");
1588	0	modifications.put("CYD", "CYS");
1589	0	modifications.put("CYF", "CYS");
1590	0	modifications.put("CYG", "CYS");
1591	0	modifications.put("CYJ", "XAA");
1592	0	modifications.put("CYM", "CYS");
1593	0	modifications.put("CYQ", "CYS");
1594	0	modifications.put("CYR", "CYS");
1595	0	modifications.put("CYS", "CYS");
1596	0	modifications.put("CZ2", "CYS");
1597	0	modifications.put("CZO", "GYG");
1598	0	modifications.put("CZZ", "CYS");
1599	0	modifications.put("D11", "THR");
1600	0	modifications.put("D1P", "ASN");
1601	0	modifications.put("D3 ", "ASN");
1602	0	modifications.put("D33", "ASN");
1603	0	modifications.put("D3P", "GLY");
1604	0	modifications.put("D3T", "THR");
1605	0	modifications.put("D4M", "THR");
1606	0	modifications.put("D4P", "XAA");
1607	0	modifications.put("DA ", "ALA");
1608	0	modifications.put("DA2", "XAA");
1609	0	modifications.put("DAB", "ALA");
1610	0	modifications.put("DAH", "PHE");
1611	0	modifications.put("DAL", "ALA");
1612	0	modifications.put("DAR", "ARG");
1613	0	modifications.put("DAS", "ASP");
1614	0	modifications.put("DBB", "THR");
1615	0	modifications.put("DBM", "ASN");
1616	0	modifications.put("DBS", "SER");
1617	0	modifications.put("DBU", "THR");
1618	0	modifications.put("DBY", "TYR");
1619	0	modifications.put("DBZ", "ALA");
1620	0	modifications.put("DC ", "CYS");
1621	0	modifications.put("DC2", "CYS");
1622	0	modifications.put("DCG", "GLY");
1623	0	modifications.put("DCI", "XAA");
1624	0	modifications.put("DCL", "XAA");
1625	0	modifications.put("DCT", "CYS");
1626	0	modifications.put("DCY", "CYS");
1627	0	modifications.put("DDE", "HIS");
1628	0	modifications.put("DDG", "GLY");
1629	0	modifications.put("DDN", "UR3");
1630	0	modifications.put("DDX", "ASN");
1631	0	modifications.put("DFC", "CYS");
1632	0	modifications.put("DFG", "GLY");
1633	0	modifications.put("DFI", "XAA");
1634	0	modifications.put("DFO", "XAA");
1635	0	modifications.put("DFT", "ASN");
1636	0	modifications.put("DG ", "GLY");
1637	0	modifications.put("DGH", "GLY");
1638	0	modifications.put("DGI", "GLY");
1639	0	modifications.put("DGL", "GLU");
1640	0	modifications.put("DGN", "GLN");
1641	0	modifications.put("DHA", "SER");
1642	0	modifications.put("DHI", "HIS");
1643	0	modifications.put("DHL", "XAA");
1644	0	modifications.put("DHN", "VAL");
1645	0	modifications.put("DHP", "XAA");
1646	0	modifications.put("DHU", "UR3");
1647	0	modifications.put("DHV", "VAL");
1648	0	modifications.put("DI ", "ILE");
1649	0	modifications.put("DIL", "ILE");
1650	0	modifications.put("DIR", "ARG");
1651	0	modifications.put("DIV", "VAL");
1652	0	modifications.put("DLE", "LEU");
1653	0	modifications.put("DLS", "LYS");
1654	0	modifications.put("DLY", "LYS");
1655	0	modifications.put("DM0", "LYS");
1656	0	modifications.put("DMH", "ASN");
1657	0	modifications.put("DMK", "ASP");
1658	0	modifications.put("DMT", "XAA");
1659	0	modifications.put("DN ", "ASN");
1660	0	modifications.put("DNE", "LEU");
1661	0	modifications.put("DNG", "LEU");
1662	0	modifications.put("DNL", "LYS");
1663	0	modifications.put("DNM", "LEU");
1664	0	modifications.put("DNP", "ALA");
1665	0	modifications.put("DNR", "CYS");
1666	0	modifications.put("DNS", "LYS");
1667	0	modifications.put("DOA", "XAA");
1668	0	modifications.put("DOC", "CYS");
1669	0	modifications.put("DOH", "ASP");
1670	0	modifications.put("DON", "LEU");
1671	0	modifications.put("DPB", "THR");
1672	0	modifications.put("DPH", "PHE");
1673	0	modifications.put("DPL", "PRO");
1674	0	modifications.put("DPP", "ALA");
1675	0	modifications.put("DPQ", "TYR");
1676	0	modifications.put("DPR", "PRO");
1677	0	modifications.put("DPY", "ASN");
1678	0	modifications.put("DRM", "UR3");
1679	0	modifications.put("DRP", "ASN");
1680	0	modifications.put("DRT", "THR");
1681	0	modifications.put("DRZ", "ASN");
1682	0	modifications.put("DSE", "SER");
1683	0	modifications.put("DSG", "ASN");
1684	0	modifications.put("DSN", "SER");
1685	0	modifications.put("DSP", "ASP");
1686	0	modifications.put("DT ", "THR");
1687	0	modifications.put("DTH", "THR");
1688	0	modifications.put("DTR", "TRP");
1689	0	modifications.put("DTY", "TYR");
1690	0	modifications.put("DU ", "UR3");
1691	0	modifications.put("DVA", "VAL");
1692	0	modifications.put("DXD", "ASN");
1693	0	modifications.put("DXN", "ASN");
1694	0	modifications.put("DYG", "DYG");
1695	0	modifications.put("DYS", "CYS");
1696	0	modifications.put("DZM", "ALA");
1697	0	modifications.put("E ", "ALA");
1698	0	modifications.put("E1X", "ALA");
1699	0	modifications.put("ECC", "GLN");
1700	0	modifications.put("EDA", "ALA");
1701	0	modifications.put("EFC", "CYS");
1702	0	modifications.put("EHP", "PHE");
1703	0	modifications.put("EIT", "THR");
1704	0	modifications.put("ENP", "ASN");
1705	0	modifications.put("ESB", "TYR");
1706	0	modifications.put("ESC", "MET");
1707	0	modifications.put("EXB", "XAA");
1708	0	modifications.put("EXY", "LEU");
1709	0	modifications.put("EY5", "ASN");
1710	0	modifications.put("EYS", "XAA");
1711	0	modifications.put("F2F", "PHE");
1712	0	modifications.put("FA2", "ALA");
1713	0	modifications.put("FA5", "ASN");
1714	0	modifications.put("FAG", "ASN");
1715	0	modifications.put("FAI", "ASN");
1716	0	modifications.put("FB5", "ALA");
1717	0	modifications.put("FB6", "ALA");
1718	0	modifications.put("FCL", "PHE");
1719	0	modifications.put("FFD", "ASN");
1720	0	modifications.put("FGA", "GLU");
1721	0	modifications.put("FGL", "GLY");
1722	0	modifications.put("FGP", "SER");
1723	0	modifications.put("FHL", "XAA");
1724	0	modifications.put("FHO", "LYS");
1725	0	modifications.put("FHU", "UR3");
1726	0	modifications.put("FLA", "ALA");
1727	0	modifications.put("FLE", "LEU");
1728	0	modifications.put("FLT", "TYR");
1729	0	modifications.put("FME", "MET");
1730	0	modifications.put("FMG", "GLY");
1731	0	modifications.put("FMU", "ASN");
1732	0	modifications.put("FOE", "CYS");
1733	0	modifications.put("FOX", "GLY");
1734	0	modifications.put("FP9", "PRO");
1735	0	modifications.put("FPA", "PHE");
1736	0	modifications.put("FRD", "XAA");
1737	0	modifications.put("FT6", "TRP");
1738	0	modifications.put("FTR", "TRP");
1739	0	modifications.put("FTY", "TYR");
1740	0	modifications.put("FVA", "VAL");
1741	0	modifications.put("FZN", "LYS");
1742	0	modifications.put("G ", "GLY");
1743	0	modifications.put("G25", "GLY");
1744	0	modifications.put("G2L", "GLY");
1745	0	modifications.put("G2S", "GLY");
1746	0	modifications.put("G31", "GLY");
1747	0	modifications.put("G32", "GLY");
1748	0	modifications.put("G33", "GLY");
1749	0	modifications.put("G36", "GLY");
1750	0	modifications.put("G38", "GLY");
1751	0	modifications.put("G42", "GLY");
1752	0	modifications.put("G46", "GLY");
1753	0	modifications.put("G47", "GLY");
1754	0	modifications.put("G48", "GLY");
1755	0	modifications.put("G49", "GLY");
1756	0	modifications.put("G4P", "ASN");
1757	0	modifications.put("G7M", "GLY");
1758	0	modifications.put("GAO", "GLY");
1759	0	modifications.put("GAU", "GLU");
1760	0	modifications.put("GCK", "CYS");
1761	0	modifications.put("GCM", "XAA");
1762	0	modifications.put("GDP", "GLY");
1763	0	modifications.put("GDR", "GLY");
1764	0	modifications.put("GFL", "GLY");
1765	0	modifications.put("GGL", "GLU");
1766	0	modifications.put("GH3", "GLY");
1767	0	modifications.put("GHG", "GLN");
1768	0	modifications.put("GHP", "GLY");
1769	0	modifications.put("GL3", "GLY");
1770	0	modifications.put("GLH", "GLN");
1771	0	modifications.put("GLJ", "GLU");
1772	0	modifications.put("GLK", "GLU");
1773	0	modifications.put("GLM", "XAA");
1774	0	modifications.put("GLN", "GLN");
1775	0	modifications.put("GLQ", "GLU");
1776	0	modifications.put("GLU", "GLU");
1777	0	modifications.put("GLX", "GLX");
1778	0	modifications.put("GLY", "GLY");
1779	0	modifications.put("GLZ", "GLY");
1780	0	modifications.put("GMA", "GLU");
1781	0	modifications.put("GMS", "GLY");
1782	0	modifications.put("GMU", "UR3");
1783	0	modifications.put("GN7", "GLY");
1784	0	modifications.put("GND", "XAA");
1785	0	modifications.put("GNE", "ASN");
1786	0	modifications.put("GOM", "GLY");
1787	0	modifications.put("GPL", "LYS");
1788	0	modifications.put("GS ", "GLY");
1789	0	modifications.put("GSC", "GLY");
1790	0	modifications.put("GSR", "GLY");
1791	0	modifications.put("GSS", "GLY");
1792	0	modifications.put("GSU", "GLU");
1793	0	modifications.put("GT9", "CYS");
1794	0	modifications.put("GTP", "GLY");
1795	0	modifications.put("GVL", "XAA");
1796	0	modifications.put("GYC", "CYG");
1797	0	modifications.put("GYS", "SYG");
1798	0	modifications.put("H2U", "UR3");
1799	0	modifications.put("H5M", "PRO");
1800	0	modifications.put("HAC", "ALA");
1801	0	modifications.put("HAR", "ARG");
1802	0	modifications.put("HBN", "HIS");
1803	0	modifications.put("HCS", "XAA");
1804	0	modifications.put("HDP", "UR3");
1805	0	modifications.put("HEU", "UR3");
1806	0	modifications.put("HFA", "XAA");
1807	0	modifications.put("HGL", "XAA");
1808	0	modifications.put("HHI", "HIS");
1809	0	modifications.put("HHK", "AK"); // check
1810	0	modifications.put("HIA", "HIS");
1811	0	modifications.put("HIC", "HIS");
1812	0	modifications.put("HIP", "HIS");
1813	0	modifications.put("HIQ", "HIS");
1814	0	modifications.put("HIS", "HIS");
1815	0	modifications.put("HL2", "LEU");
1816	0	modifications.put("HLU", "LEU");
1817	0	modifications.put("HMR", "ARG");
1818	0	modifications.put("HOL", "ASN");
1819	0	modifications.put("HPC", "PHE");
1820	0	modifications.put("HPE", "PHE");
1821	0	modifications.put("HPH", "PHE");
1822	0	modifications.put("HPQ", "PHE");
1823	0	modifications.put("HQA", "ALA");
1824	0	modifications.put("HRG", "ARG");
1825	0	modifications.put("HRP", "TRP");
1826	0	modifications.put("HS8", "HIS");
1827	0	modifications.put("HS9", "HIS");
1828	0	modifications.put("HSE", "SER");
1829	0	modifications.put("HSL", "SER");
1830	0	modifications.put("HSO", "HIS");
1831	0	modifications.put("HTI", "CYS");
1832	0	modifications.put("HTN", "ASN");
1833	0	modifications.put("HTR", "TRP");
1834	0	modifications.put("HV5", "ALA");
1835	0	modifications.put("HVA", "VAL");
1836	0	modifications.put("HY3", "PRO");
1837	0	modifications.put("HYP", "PRO");
1838	0	modifications.put("HZP", "PRO");
1839	0	modifications.put("I ", "ILE");
1840	0	modifications.put("I2M", "ILE");
1841	0	modifications.put("I58", "LYS");
1842	0	modifications.put("I5C", "CYS");
1843	0	modifications.put("IAM", "ALA");
1844	0	modifications.put("IAR", "ARG");
1845	0	modifications.put("IAS", "ASP");
1846	0	modifications.put("IC ", "CYS");
1847	0	modifications.put("IEL", "LYS");
1848	0	modifications.put("IEY", "HYG");
1849	0	modifications.put("IG ", "GLY");
1850	0	modifications.put("IGL", "GLY");
1851	0	modifications.put("IGU", "GLY");
1852	0	modifications.put("IIC", "SHG");
1853	0	modifications.put("IIL", "ILE");
1854	0	modifications.put("ILE", "ILE");
1855	0	modifications.put("ILG", "GLU");
1856	0	modifications.put("ILX", "ILE");
1857	0	modifications.put("IMC", "CYS");
1858	0	modifications.put("IML", "ILE");
1859	0	modifications.put("IOY", "PHE");
1860	0	modifications.put("IPG", "GLY");
1861	0	modifications.put("IPN", "ASN");
1862	0	modifications.put("IRN", "ASN");
1863	0	modifications.put("IT1", "LYS");
1864	0	modifications.put("IU ", "UR3");
1865	0	modifications.put("IYR", "TYR");
1866	0	modifications.put("IYT", "THR");
1867	0	modifications.put("IZO", "MET");
1868	0	modifications.put("JJJ", "CYS");
1869	0	modifications.put("JJK", "CYS");
1870	0	modifications.put("JJL", "CYS");
1871	0	modifications.put("JW5", "ASN");
1872	0	modifications.put("K1R", "CYS");
1873	0	modifications.put("KAG", "GLY");
1874	0	modifications.put("KCX", "LYS");
1875	0	modifications.put("KGC", "LYS");
1876	0	modifications.put("KNB", "ALA");
1877	0	modifications.put("KOR", "MET");
1878	0	modifications.put("KPI", "LYS");
1879	0	modifications.put("KST", "LYS");
1880	0	modifications.put("KYQ", "LYS");
1881	0	modifications.put("L2A", "XAA");
1882	0	modifications.put("LA2", "LYS");
1883	0	modifications.put("LAA", "ASP");
1884	0	modifications.put("LAL", "ALA");
1885	0	modifications.put("LBY", "LYS");
1886	0	modifications.put("LC ", "CYS");
1887	0	modifications.put("LCA", "ALA");
1888	0	modifications.put("LCC", "ASN");
1889	0	modifications.put("LCG", "GLY");
1890	0	modifications.put("LCH", "ASN");
1891	0	modifications.put("LCK", "LYS");
1892	0	modifications.put("LCX", "LYS");
1893	0	modifications.put("LDH", "LYS");
1894	0	modifications.put("LED", "LEU");
1895	0	modifications.put("LEF", "LEU");
1896	0	modifications.put("LEH", "LEU");
1897	0	modifications.put("LEI", "VAL");
1898	0	modifications.put("LEM", "LEU");
1899	0	modifications.put("LEN", "LEU");
1900	0	modifications.put("LET", "XAA");
1901	0	modifications.put("LEU", "LEU");
1902	0	modifications.put("LEX", "LEU");
1903	0	modifications.put("LG ", "GLY");
1904	0	modifications.put("LGP", "GLY");
1905	0	modifications.put("LHC", "XAA");
1906	0	modifications.put("LHU", "UR3");
1907	0	modifications.put("LKC", "ASN");
1908	0	modifications.put("LLP", "LYS");
1909	0	modifications.put("LLY", "LYS");
1910	0	modifications.put("LME", "GLU");
1911	0	modifications.put("LMF", "LYS");
1912	0	modifications.put("LMQ", "GLN");
1913	0	modifications.put("LMS", "ASN");
1914	0	modifications.put("LP6", "LYS");
1915	0	modifications.put("LPD", "PRO");
1916	0	modifications.put("LPG", "GLY");
1917	0	modifications.put("LPL", "XAA");
1918	0	modifications.put("LPS", "SER");
1919	0	modifications.put("LSO", "XAA");
1920	0	modifications.put("LTA", "XAA");
1921	0	modifications.put("LTR", "TRP");
1922	0	modifications.put("LVG", "GLY");
1923	0	modifications.put("LVN", "VAL");
1924	0	modifications.put("LYF", "LYS");
1925	0	modifications.put("LYK", "LYS");
1926	0	modifications.put("LYM", "LYS");
1927	0	modifications.put("LYN", "LYS");
1928	0	modifications.put("LYR", "LYS");
1929	0	modifications.put("LYS", "LYS");
1930	0	modifications.put("LYX", "LYS");
1931	0	modifications.put("LYZ", "LYS");
1932	0	modifications.put("M0H", "CYS");
1933	0	modifications.put("M1G", "GLY");
1934	0	modifications.put("M2G", "GLY");
1935	0	modifications.put("M2L", "LYS");
1936	0	modifications.put("M2S", "MET");
1937	0	modifications.put("M30", "GLY");
1938	0	modifications.put("M3L", "LYS");
1939	0	modifications.put("M5M", "CYS");
1940	0	modifications.put("MA ", "ALA");
1941	0	modifications.put("MA6", "ALA");
1942	0	modifications.put("MA7", "ALA");
1943	0	modifications.put("MAA", "ALA");
1944	0	modifications.put("MAD", "ALA");
1945	0	modifications.put("MAI", "ARG");
1946	0	modifications.put("MBQ", "TYR");
1947	0	modifications.put("MBZ", "ASN");
1948	0	modifications.put("MC1", "SER");
1949	0	modifications.put("MCG", "XAA");
1950	0	modifications.put("MCL", "LYS");
1951	0	modifications.put("MCS", "CYS");
1952	0	modifications.put("MCY", "CYS");
1953	0	modifications.put("MD3", "CYS");
1954	0	modifications.put("MD6", "GLY");
1955	0	modifications.put("MDH", "XAA");
1956	0	modifications.put("MDO", "ASG");
1957	0	modifications.put("MDR", "ASN");
1958	0	modifications.put("MEA", "PHE");
1959	0	modifications.put("MED", "MET");
1960	0	modifications.put("MEG", "GLU");
1961	0	modifications.put("MEN", "ASN");
1962	0	modifications.put("MEP", "UR3");
1963	0	modifications.put("MEQ", "GLN");
1964	0	modifications.put("MET", "MET");
1965	0	modifications.put("MEU", "GLY");
1966	0	modifications.put("MF3", "XAA");
1967	0	modifications.put("MFC", "GYG");
1968	0	modifications.put("MG1", "GLY");
1969	0	modifications.put("MGG", "ARG");
1970	0	modifications.put("MGN", "GLN");
1971	0	modifications.put("MGQ", "ALA");
1972	0	modifications.put("MGV", "GLY");
1973	0	modifications.put("MGY", "GLY");
1974	0	modifications.put("MHL", "LEU");
1975	0	modifications.put("MHO", "MET");
1976	0	modifications.put("MHS", "HIS");
1977	0	modifications.put("MIA", "ALA");
1978	0	modifications.put("MIS", "SER");
1979	0	modifications.put("MK8", "LEU");
1980	0	modifications.put("ML3", "LYS");
1981	0	modifications.put("MLE", "LEU");
1982	0	modifications.put("MLL", "LEU");
1983	0	modifications.put("MLY", "LYS");
1984	0	modifications.put("MLZ", "LYS");
1985	0	modifications.put("MME", "MET");
1986	0	modifications.put("MMO", "ARG");
1987	0	modifications.put("MMT", "THR");
1988	0	modifications.put("MND", "ASN");
1989	0	modifications.put("MNL", "LEU");
1990	0	modifications.put("MNU", "UR3");
1991	0	modifications.put("MNV", "VAL");
1992	0	modifications.put("MOD", "XAA");
1993	0	modifications.put("MP8", "PRO");
1994	0	modifications.put("MPH", "XAA");
1995	0	modifications.put("MPJ", "XAA");
1996	0	modifications.put("MPQ", "GLY");
1997	0	modifications.put("MRG", "GLY");
1998	0	modifications.put("MSA", "GLY");
1999	0	modifications.put("MSE", "MET");
2000	0	modifications.put("MSL", "MET");
2001	0	modifications.put("MSO", "MET");
2002	0	modifications.put("MSP", "XAA");
2003	0	modifications.put("MT2", "MET");
2004	0	modifications.put("MTR", "THR");
2005	0	modifications.put("MTU", "ALA");
2006	0	modifications.put("MTY", "TYR");
2007	0	modifications.put("MVA", "VAL");
2008	0	modifications.put("N ", "ASN");
2009	0	modifications.put("N10", "SER");
2010	0	modifications.put("N2C", "XAA");
2011	0	modifications.put("N5I", "ASN");
2012	0	modifications.put("N5M", "CYS");
2013	0	modifications.put("N6G", "GLY");
2014	0	modifications.put("N7P", "PRO");
2015	0	modifications.put("NA8", "ALA");
2016	0	modifications.put("NAL", "ALA");
2017	0	modifications.put("NAM", "ALA");
2018	0	modifications.put("NB8", "ASN");
2019	0	modifications.put("NBQ", "TYR");
2020	0	modifications.put("NC1", "SER");
2021	0	modifications.put("NCB", "ALA");
2022	0	modifications.put("NCX", "ASN");
2023	0	modifications.put("NCY", "XAA");
2024	0	modifications.put("NDF", "PHE");
2025	0	modifications.put("NDN", "UR3");
2026	0	modifications.put("NEM", "HIS");
2027	0	modifications.put("NEP", "HIS");
2028	0	modifications.put("NF2", "ASN");
2029	0	modifications.put("NFA", "PHE");
2030	0	modifications.put("NHL", "GLU");
2031	0	modifications.put("NIT", "XAA");
2032	0	modifications.put("NIY", "TYR");
2033	0	modifications.put("NLE", "LEU");
2034	0	modifications.put("NLN", "LEU");
2035	0	modifications.put("NLO", "LEU");
2036	0	modifications.put("NLP", "LEU");
2037	0	modifications.put("NLQ", "GLN");
2038	0	modifications.put("NMC", "GLY");
2039	0	modifications.put("NMM", "ARG");
2040	0	modifications.put("NMS", "THR");
2041	0	modifications.put("NMT", "THR");
2042	0	modifications.put("NNH", "ARG");
2043	0	modifications.put("NP3", "ASN");
2044	0	modifications.put("NPH", "CYS");
2045	0	modifications.put("NPI", "ALA");
2046	0	modifications.put("NRP", "LYG");
2047	0	modifications.put("NRQ", "MYG");
2048	0	modifications.put("NSK", "XAA");
2049	0	modifications.put("NTY", "TYR");
2050	0	modifications.put("NVA", "VAL");
2051	0	modifications.put("NYC", "TWG");
2052	0	modifications.put("NYG", "NYG");
2053	0	modifications.put("NYM", "ASN");
2054	0	modifications.put("NYS", "CYS");
2055	0	modifications.put("NZH", "HIS");
2056	0	modifications.put("O12", "XAA");
2057	0	modifications.put("O2C", "ASN");
2058	0	modifications.put("O2G", "GLY");
2059	0	modifications.put("OAD", "ASN");
2060	0	modifications.put("OAS", "SER");
2061	0	modifications.put("OBF", "XAA");
2062	0	modifications.put("OBS", "XAA");
2063	0	modifications.put("OCS", "CYS");
2064	0	modifications.put("OCY", "CYS");
2065	0	modifications.put("ODP", "ASN");
2066	0	modifications.put("OHI", "HIS");
2067	0	modifications.put("OHS", "ASP");
2068	0	modifications.put("OIC", "XAA");
2069	0	modifications.put("OIP", "ILE");
2070	0	modifications.put("OLE", "XAA");
2071	0	modifications.put("OLT", "THR");
2072	0	modifications.put("OLZ", "SER");
2073	0	modifications.put("OMC", "CYS");
2074	0	modifications.put("OMG", "GLY");
2075	0	modifications.put("OMT", "MET");
2076	0	modifications.put("OMU", "UR3");
2077	0	modifications.put("ONE", "UR3");
2078	0	modifications.put("ONH", "ALA");
2079	0	modifications.put("ONL", "XAA");
2080	0	modifications.put("OPR", "ARG");
2081	0	modifications.put("ORN", "ALA");
2082	0	modifications.put("ORQ", "ARG");
2083	0	modifications.put("OSE", "SER");
2084	0	modifications.put("OTB", "XAA");
2085	0	modifications.put("OTH", "THR");
2086	0	modifications.put("OTY", "TYR");
2087	0	modifications.put("OXX", "ASP");
2088	0	modifications.put("P ", "GLY");
2089	0	modifications.put("P1L", "CYS");
2090	0	modifications.put("P1P", "ASN");
2091	0	modifications.put("P2T", "THR");
2092	0	modifications.put("P2U", "UR3");
2093	0	modifications.put("P2Y", "PRO");
2094	0	modifications.put("P5P", "ALA");
2095	0	modifications.put("PAQ", "TYR");
2096	0	modifications.put("PAS", "ASP");
2097	0	modifications.put("PAT", "TRP");
2098	0	modifications.put("PAU", "ALA");
2099	0	modifications.put("PBB", "CYS");
2100	0	modifications.put("PBF", "PHE");
2101	0	modifications.put("PBT", "ASN");
2102	0	modifications.put("PCA", "GLU");
2103	0	modifications.put("PCC", "PRO");
2104	0	modifications.put("PCE", "XAA");
2105	0	modifications.put("PCS", "PHE");
2106	0	modifications.put("PDL", "XAA");
2107	0	modifications.put("PDU", "UR3");
2108	0	modifications.put("PEC", "CYS");
2109	0	modifications.put("PF5", "PHE");
2110	0	modifications.put("PFF", "PHE");
2111	0	modifications.put("PFX", "XAA");
2112	0	modifications.put("PG1", "SER");
2113	0	modifications.put("PG7", "GLY");
2114	0	modifications.put("PG9", "GLY");
2115	0	modifications.put("PGL", "XAA");
2116	0	modifications.put("PGN", "GLY");
2117	0	modifications.put("PGP", "GLY");
2118	0	modifications.put("PGY", "GLY");
2119	0	modifications.put("PHA", "PHE");
2120	0	modifications.put("PHD", "ASP");
2121	0	modifications.put("PHE", "PHE");
2122	0	modifications.put("PHI", "PHE");
2123	0	modifications.put("PHL", "PHE");
2124	0	modifications.put("PHM", "PHE");
2125	0	modifications.put("PIA", "AYG");
2126	0	modifications.put("PIV", "XAA");
2127	0	modifications.put("PLE", "LEU");
2128	0	modifications.put("PM3", "PHE");
2129	0	modifications.put("PMT", "CYS");
2130	0	modifications.put("POM", "PRO");
2131	0	modifications.put("PPN", "PHE");
2132	0	modifications.put("PPU", "ALA");
2133	0	modifications.put("PPW", "GLY");
2134	0	modifications.put("PQ1", "ASN");
2135	0	modifications.put("PR3", "CYS");
2136	0	modifications.put("PR5", "ALA");
2137	0	modifications.put("PR9", "PRO");
2138	0	modifications.put("PRN", "ALA");
2139	0	modifications.put("PRO", "PRO");
2140	0	modifications.put("PRS", "PRO");
2141	0	modifications.put("PSA", "PHE");
2142	0	modifications.put("PSH", "HIS");
2143	0	modifications.put("PST", "THR");
2144	0	modifications.put("PSU", "UR3");
2145	0	modifications.put("PSW", "CYS");
2146	0	modifications.put("PTA", "XAA");
2147	0	modifications.put("PTH", "TYR");
2148	0	modifications.put("PTM", "TYR");
2149	0	modifications.put("PTR", "TYR");
2150	0	modifications.put("PU ", "ALA");
2151	0	modifications.put("PUY", "ASN");
2152	0	modifications.put("PVH", "HIS");
2153	0	modifications.put("PVL", "XAA");
2154	0	modifications.put("PYA", "ALA");
2155	0	modifications.put("PYO", "UR3");
2156	0	modifications.put("PYX", "CYS");
2157	0	modifications.put("PYY", "ASN");
2158	0	modifications.put("QLG", "QLG");
2159	0	modifications.put("QMM", "GLN");
2160	0	modifications.put("QPA", "CYS");
2161	0	modifications.put("QPH", "PHE");
2162	0	modifications.put("QUO", "GLY");
2163	0	modifications.put("R ", "ALA");
2164	0	modifications.put("R1A", "CYS");
2165	0	modifications.put("R4K", "TRP");
2166	0	modifications.put("RC7", "HYG");
2167	0	modifications.put("RE0", "TRP");
2168	0	modifications.put("RE3", "TRP");
2169	0	modifications.put("RIA", "ALA");
2170	0	modifications.put("RMP", "ALA");
2171	0	modifications.put("RON", "XAA");
2172	0	modifications.put("RT ", "THR");
2173	0	modifications.put("RTP", "ASN");
2174	0	modifications.put("S1H", "SER");
2175	0	modifications.put("S2C", "CYS");
2176	0	modifications.put("S2D", "ALA");
2177	0	modifications.put("S2M", "THR");
2178	0	modifications.put("S2P", "ALA");
2179	0	modifications.put("S4A", "ALA");
2180	0	modifications.put("S4C", "CYS");
2181	0	modifications.put("S4G", "GLY");
2182	0	modifications.put("S4U", "UR3");
2183	0	modifications.put("S6G", "GLY");
2184	0	modifications.put("SAC", "SER");
2185	0	modifications.put("SAH", "CYS");
2186	0	modifications.put("SAR", "GLY");
2187	0	modifications.put("SBL", "SER");
2188	0	modifications.put("SC ", "CYS");
2189	0	modifications.put("SCH", "CYS");
2190	0	modifications.put("SCS", "CYS");
2191	0	modifications.put("SCY", "CYS");
2192	0	modifications.put("SD2", "XAA");
2193	0	modifications.put("SDG", "GLY");
2194	0	modifications.put("SDP", "SER");
2195	0	modifications.put("SEB", "SER");
2196	0	modifications.put("SEC", "ALA");
2197	0	modifications.put("SEG", "ALA");
2198	0	modifications.put("SEL", "SER");
2199	0	modifications.put("SEM", "SER");
2200	0	modifications.put("SEN", "SER");
2201	0	modifications.put("SEP", "SER");
2202	0	modifications.put("SER", "SER");
2203	0	modifications.put("SET", "SER");
2204	0	modifications.put("SGB", "SER");
2205	0	modifications.put("SHC", "CYS");
2206	0	modifications.put("SHP", "GLY");
2207	0	modifications.put("SHR", "LYS");
2208	0	modifications.put("SIB", "CYS");
2209	0	modifications.put("SIC", "DC"); // check
2210	0	modifications.put("SLA", "PRO");
2211	0	modifications.put("SLR", "PRO");
2212	0	modifications.put("SLZ", "LYS");
2213	0	modifications.put("SMC", "CYS");
2214	0	modifications.put("SME", "MET");
2215	0	modifications.put("SMF", "PHE");
2216	0	modifications.put("SMP", "ALA");
2217	0	modifications.put("SMT", "THR");
2218	0	modifications.put("SNC", "CYS");
2219	0	modifications.put("SNN", "ASN");
2220	0	modifications.put("SOC", "CYS");
2221	0	modifications.put("SOS", "ASN");
2222	0	modifications.put("SOY", "SER");
2223	0	modifications.put("SPT", "THR");
2224	0	modifications.put("SRA", "ALA");
2225	0	modifications.put("SSU", "UR3");
2226	0	modifications.put("STY", "TYR");
2227	0	modifications.put("SUB", "XAA");
2228	0	modifications.put("SUI", "DG");
2229	0	modifications.put("SUN", "SER");
2230	0	modifications.put("SUR", "UR3");
2231	0	modifications.put("SVA", "SER");
2232	0	modifications.put("SVV", "SER");
2233	0	modifications.put("SVW", "SER");
2234	0	modifications.put("SVX", "SER");
2235	0	modifications.put("SVY", "SER");
2236	0	modifications.put("SVZ", "XAA");
2237	0	modifications.put("SWG", "SWG");
2238	0	modifications.put("SYS", "CYS");
2239	0	modifications.put("T ", "THR");
2240	0	modifications.put("T11", "PHE");
2241	0	modifications.put("T23", "THR");
2242	0	modifications.put("T2S", "THR");
2243	0	modifications.put("T2T", "ASN");
2244	0	modifications.put("T31", "UR3");
2245	0	modifications.put("T32", "THR");
2246	0	modifications.put("T36", "THR");
2247	0	modifications.put("T37", "THR");
2248	0	modifications.put("T38", "THR");
2249	0	modifications.put("T39", "THR");
2250	0	modifications.put("T3P", "THR");
2251	0	modifications.put("T41", "THR");
2252	0	modifications.put("T48", "THR");
2253	0	modifications.put("T49", "THR");
2254	0	modifications.put("T4S", "THR");
2255	0	modifications.put("T5O", "UR3");
2256	0	modifications.put("T5S", "THR");
2257	0	modifications.put("T66", "XAA");
2258	0	modifications.put("T6A", "ALA");
2259	0	modifications.put("TA3", "THR");
2260	0	modifications.put("TA4", "XAA");
2261	0	modifications.put("TAF", "THR");
2262	0	modifications.put("TAL", "ASN");
2263	0	modifications.put("TAV", "ASP");
2264	0	modifications.put("TBG", "VAL");
2265	0	modifications.put("TBM", "THR");
2266	0	modifications.put("TC1", "CYS");
2267	0	modifications.put("TCP", "THR");
2268	0	modifications.put("TCQ", "TYR");
2269	0	modifications.put("TCR", "TRP");
2270	0	modifications.put("TCY", "ALA");
2271	0	modifications.put("TDD", "LEU");
2272	0	modifications.put("TDY", "THR");
2273	0	modifications.put("TFE", "THR");
2274	0	modifications.put("TFO", "ALA");
2275	0	modifications.put("TFQ", "PHE");
2276	0	modifications.put("TFT", "THR");
2277	0	modifications.put("TGP", "GLY");
2278	0	modifications.put("TH6", "THR");
2279	0	modifications.put("THC", "THR");
2280	0	modifications.put("THO", "XAA");
2281	0	modifications.put("THR", "THR");
2282	0	modifications.put("THX", "ASN");
2283	0	modifications.put("THZ", "ARG");
2284	0	modifications.put("TIH", "ALA");
2285	0	modifications.put("TLB", "ASN");
2286	0	modifications.put("TLC", "THR");
2287	0	modifications.put("TLN", "UR3");
2288	0	modifications.put("TMB", "THR");
2289	0	modifications.put("TMD", "THR");
2290	0	modifications.put("TNB", "CYS");
2291	0	modifications.put("TNR", "SER");
2292	0	modifications.put("TOX", "TRP");
2293	0	modifications.put("TP1", "THR");
2294	0	modifications.put("TPC", "CYS");
2295	0	modifications.put("TPG", "GLY");
2296	0	modifications.put("TPH", "XAA");
2297	0	modifications.put("TPL", "TRP");
2298	0	modifications.put("TPO", "THR");
2299	0	modifications.put("TPQ", "TYR");
2300	0	modifications.put("TQI", "TRP");
2301	0	modifications.put("TQQ", "TRP");
2302	0	modifications.put("TRF", "TRP");
2303	0	modifications.put("TRG", "LYS");
2304	0	modifications.put("TRN", "TRP");
2305	0	modifications.put("TRO", "TRP");
2306	0	modifications.put("TRP", "TRP");
2307	0	modifications.put("TRQ", "TRP");
2308	0	modifications.put("TRW", "TRP");
2309	0	modifications.put("TRX", "TRP");
2310	0	modifications.put("TS ", "ASN");
2311	0	modifications.put("TST", "XAA");
2312	0	modifications.put("TT ", "ASN");
2313	0	modifications.put("TTD", "THR");
2314	0	modifications.put("TTI", "UR3");
2315	0	modifications.put("TTM", "THR");
2316	0	modifications.put("TTQ", "TRP");
2317	0	modifications.put("TTS", "TYR");
2318	0	modifications.put("TY1", "TYR");
2319	0	modifications.put("TY2", "TYR");
2320	0	modifications.put("TY3", "TYR");
2321	0	modifications.put("TY5", "TYR");
2322	0	modifications.put("TYB", "TYR");
2323	0	modifications.put("TYI", "TYR");
2324	0	modifications.put("TYJ", "TYR");
2325	0	modifications.put("TYN", "TYR");
2326	0	modifications.put("TYO", "TYR");
2327	0	modifications.put("TYQ", "TYR");
2328	0	modifications.put("TYR", "TYR");
2329	0	modifications.put("TYS", "TYR");
2330	0	modifications.put("TYT", "TYR");
2331	0	modifications.put("TYU", "ASN");
2332	0	modifications.put("TYW", "TYR");
2333	0	modifications.put("TYX", "XAA");
2334	0	modifications.put("TYY", "TYR");
2335	0	modifications.put("TZB", "XAA");
2336	0	modifications.put("TZO", "XAA");
2337	0	modifications.put("U ", "UR3");
2338	0	modifications.put("U25", "UR3");
2339	0	modifications.put("U2L", "UR3");
2340	0	modifications.put("U2N", "UR3");
2341	0	modifications.put("U2P", "UR3");
2342	0	modifications.put("U31", "UR3");
2343	0	modifications.put("U33", "UR3");
2344	0	modifications.put("U34", "UR3");
2345	0	modifications.put("U36", "UR3");
2346	0	modifications.put("U37", "UR3");
2347	0	modifications.put("U8U", "UR3");
2348	0	modifications.put("UAR", "UR3");
2349	0	modifications.put("UCL", "UR3");
2350	0	modifications.put("UD5", "UR3");
2351	0	modifications.put("UDP", "ASN");
2352	0	modifications.put("UFP", "ASN");
2353	0	modifications.put("UFR", "UR3");
2354	0	modifications.put("UFT", "UR3");
2355	0	modifications.put("UMA", "ALA");
2356	0	modifications.put("UMP", "UR3");
2357	0	modifications.put("UMS", "UR3");
2358	0	modifications.put("UN1", "XAA");
2359	0	modifications.put("UN2", "XAA");
2360	0	modifications.put("UNK", "XAA");
2361	0	modifications.put("UR3", "UR3");
2362	0	modifications.put("URD", "UR3");
2363	0	modifications.put("US1", "UR3");
2364	0	modifications.put("US2", "UR3");
2365	0	modifications.put("US3", "THR");
2366	0	modifications.put("US5", "UR3");
2367	0	modifications.put("USM", "UR3");
2368	0	modifications.put("VAD", "VAL");
2369	0	modifications.put("VAF", "VAL");
2370	0	modifications.put("VAL", "VAL");
2371	0	modifications.put("VB1", "LYS");
2372	0	modifications.put("VDL", "XAA");
2373	0	modifications.put("VLL", "XAA");
2374	0	modifications.put("VLM", "XAA");
2375	0	modifications.put("VMS", "XAA");
2376	0	modifications.put("VOL", "XAA");
2377	0	modifications.put("WCR", "GYG");
2378	0	modifications.put("X ", "GLY");
2379	0	modifications.put("X2W", "GLU");
2380	0	modifications.put("X4A", "ASN");
2381	0	modifications.put("X9Q", "AFG");
2382	0	modifications.put("XAD", "ALA");
2383	0	modifications.put("XAE", "ASN");
2384	0	modifications.put("XAL", "ALA");
2385	0	modifications.put("XAR", "ASN");
2386	0	modifications.put("XCL", "CYS");
2387	0	modifications.put("XCN", "CYS");
2388	0	modifications.put("XCP", "XAA");
2389	0	modifications.put("XCR", "CYS");
2390	0	modifications.put("XCS", "ASN");
2391	0	modifications.put("XCT", "CYS");
2392	0	modifications.put("XCY", "CYS");
2393	0	modifications.put("XGA", "ASN");
2394	0	modifications.put("XGL", "GLY");
2395	0	modifications.put("XGR", "GLY");
2396	0	modifications.put("XGU", "GLY");
2397	0	modifications.put("XPR", "PRO");
2398	0	modifications.put("XSN", "ASN");
2399	0	modifications.put("XTH", "THR");
2400	0	modifications.put("XTL", "THR");
2401	0	modifications.put("XTR", "THR");
2402	0	modifications.put("XTS", "GLY");
2403	0	modifications.put("XTY", "ASN");
2404	0	modifications.put("XUA", "ALA");
2405	0	modifications.put("XUG", "GLY");
2406	0	modifications.put("XX1", "LYS");
2407	0	modifications.put("XXY", "THG");
2408	0	modifications.put("XYG", "DYG");
2409	0	modifications.put("Y ", "ALA");
2410	0	modifications.put("YCM", "CYS");
2411	0	modifications.put("YG ", "GLY");
2412	0	modifications.put("YOF", "TYR");
2413	0	modifications.put("YRR", "ASN");
2414	0	modifications.put("YYG", "GLY");
2415	0	modifications.put("Z ", "CYS");
2416	0	modifications.put("Z01", "ALA");
2417	0	modifications.put("ZAD", "ALA");
2418	0	modifications.put("ZAL", "ALA");
2419	0	modifications.put("ZBC", "CYS");
2420	0	modifications.put("ZBU", "UR3");
2421	0	modifications.put("ZCL", "PHE");
2422	0	modifications.put("ZCY", "CYS");
2423	0	modifications.put("ZDU", "UR3");
2424	0	modifications.put("ZFB", "XAA");
2425	0	modifications.put("ZGU", "GLY");
2426	0	modifications.put("ZHP", "ASN");
2427	0	modifications.put("ZTH", "THR");
2428	0	modifications.put("ZU0", "THR");
2429	0	modifications.put("ZZJ", "ALA");
2430
2431		}
2432
		0% Uncovered Elements: 22 (22) Complexity: 1 Complexity Density: 0.05
2433	0	static...
2434		{
2435	0	Map<Character, Float> amino = new HashMap<>();
2436	0	amino.put('A', 0.0826f);
2437	0	amino.put('Q', 0.0393f);
2438	0	amino.put('L', 0.0965f);
2439	0	amino.put('S', 0.0661f);
2440	0	amino.put('R', 0.0553f);
2441	0	amino.put('E', 0.0674f);
2442	0	amino.put('K', 0.0582f);
2443	0	amino.put('T', 0.0535f);
2444	0	amino.put('N', 0.0406f);
2445	0	amino.put('G', 0.0708f);
2446	0	amino.put('M', 0.0241f);
2447	0	amino.put('W', 0.0109f);
2448	0	amino.put('D', 0.0546f);
2449	0	amino.put('H', 0.0227f);
2450	0	amino.put('F', 0.0386f);
2451	0	amino.put('Y', 0.0292f);
2452	0	amino.put('C', 0.0137f);
2453	0	amino.put('I', 0.0593f);
2454	0	amino.put('P', 0.0472f);
2455	0	amino.put('V', 0.0686f);
2456	0	backgroundFrequencies.put(ALPHABET_AMINO, amino);
2457		// todo: these don't match https://www.ebi.ac.uk/uniprot/TrEMBLstats - what
2458		// are they?
2459		}
2460
2461		// TODO get correct frequencies
2462
		0% Uncovered Elements: 6 (6) Complexity: 1 Complexity Density: 0.17
2463	0	static...
2464		{
2465	0	Map<Character, Float> dna = new HashMap<>();
2466	0	dna.put('A', 0.25f);
2467	0	dna.put('C', 0.25f);
2468	0	dna.put('T', 0.25f);
2469	0	dna.put('G', 0.25f);
2470	0	backgroundFrequencies.put(ALPHABET_DNA, dna);
2471
2472		}
2473
		0% Uncovered Elements: 6 (6) Complexity: 1 Complexity Density: 0.17
2474	0	static...
2475		{
2476	0	Map<Character, Float> rna = new HashMap<>();
2477	0	rna.put('A', 0.25f);
2478	0	rna.put('C', 0.25f);
2479	0	rna.put('T', 0.25f);
2480	0	rna.put('G', 0.25f);
2481	0	backgroundFrequencies.put(ALPHABET_RNA, rna);
2482
2483		}
2484
		0% Uncovered Elements: 4 (4) Complexity: 2 Complexity Density: 1
2485	0	public static String getCanonicalAminoAcid(String aA)...
2486		{
2487	0	String canonical = modifications.get(aA);
2488	0	return canonical == null ? aA : canonical;
2489		}
2490
2491		// main method generates perl representation of residue property hash
2492		// / cut here
2493		/**
2494		* @j2sIgnore
2495		* @param args
2496		*/
		0% Uncovered Elements: 35 (35) Complexity: 7 Complexity Density: 0.3
2497	0	public static void main(String[] args)...
2498		{
2499	0	Hashtable<String, Vector<String>> aaProps = new Hashtable<>();
2500	0	jalview.bin.Console.outPrintln("my %aa = {");
2501		// invert property hashes
2502	0	for (String pname : propHash.keySet())
2503		{
2504	0	Map<String, Integer> phash = propHash.get(pname);
2505	0	for (String rname : phash.keySet())
2506		{
2507	0	Vector<String> aprops = aaProps.get(rname);
2508	0	if (aprops == null)
2509		{
2510	0	aprops = new Vector<>();
2511	0	aaProps.put(rname, aprops);
2512		}
2513	0	Integer hasprop = phash.get(rname);
2514	0	if (hasprop.intValue() == 1)
2515		{
2516	0	aprops.addElement(pname);
2517		}
2518		}
2519		}
2520	0	Enumeration<String> res = aaProps.keys();
2521	0	while (res.hasMoreElements())
2522		{
2523	0	String rname = res.nextElement();
2524
2525	0	System.out.print("'" + rname + "' => [");
2526	0	Enumeration<String> props = aaProps.get(rname).elements();
2527	0	while (props.hasMoreElements())
2528		{
2529	0	System.out.print("'" + props.nextElement() + "'");
2530	0	if (props.hasMoreElements())
2531		{
2532	0	jalview.bin.Console.outPrintln(", ");
2533		}
2534		}
2535	0	jalview.bin.Console
2536	0	.outPrintln("]" + (res.hasMoreElements() ? "," : ""));
2537		}
2538	0	jalview.bin.Console.outPrintln("};");
2539		}
2540
2541		// to here
2542
2543		/**
2544		* Returns a list of residue characters for the specified inputs
2545		*
2546		* @param forNucleotide
2547		* @param includeAmbiguous
2548		* @return
2549		*/
		0% Uncovered Elements: 27 (27) Complexity: 10 Complexity Density: 0.59
2550	0	public static List<String> getResidues(boolean forNucleotide,...
2551		boolean includeAmbiguous)
2552		{
2553	0	List<String> result = new ArrayList<>();
2554	0	if (forNucleotide)
2555		{
2556	0	for (String nuc : nucleotideName.keySet())
2557		{
2558	0	int val = nucleotideIndex[nuc.charAt(0)];
2559	0	if ((!includeAmbiguous && val > 4) || (val >= maxNucleotideIndex))
2560		{
2561	0	continue;
2562		}
2563	0	nuc = nuc.toUpperCase(Locale.ROOT);
2564	0	if (!result.contains(nuc))
2565		{
2566	0	result.add(nuc);
2567		}
2568		}
2569		}
2570		else
2571		{
2572		/*
2573		* Peptide
2574		*/
2575	0	for (String res : aa3Hash.keySet())
2576		{
2577	0	int index = aa3Hash.get(res).intValue();
2578	0	if ((!includeAmbiguous && index >= 20) || index >= maxProteinIndex)
2579		{
2580	0	continue;
2581		}
2582	0	res = res.toUpperCase(Locale.ROOT);
2583	0	if (!result.contains(res))
2584		{
2585	0	result.add(res);
2586		}
2587		}
2588		}
2589
2590	0	return result;
2591		}
2592
2593		/**
2594		* Returns the single letter code for a three letter code, or '0' if not known
2595		*
2596		* @param threeLetterCode
2597		* not case sensitive
2598		* @return
2599		*/
		0% Uncovered Elements: 8 (8) Complexity: 3 Complexity Density: 0.75
2600	0	public static char getSingleCharacterCode(String threeLetterCode)...
2601		{
2602	0	if (threeLetterCode == null)
2603		{
2604	0	return '0';
2605		}
2606	0	Integer index = ResidueProperties.aa3Hash
2607		.get(threeLetterCode.toUpperCase(Locale.ROOT));
2608	0	return index == null ? '0' : aa[index].charAt(0);
2609		}
2610		}