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  1. Project Clover database Thu Nov 27 2025 17:21:41 GMT
  2. Package jalview.schemes

File ResidueProperties.java

Code metrics

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1,799
31
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2,548
2,303
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0.04
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2.45
Syntax error detected in source file:
/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1/src/jalview/schemes/ResidueProperties.java
Comparison method violates its general contract!
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 .
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  
36   public class ResidueProperties
37   {
38   // Stores residue codes/names and colours and other things
39   public static final int[] aaIndex; // aaHash version 2.1.1 and below
40  
41   public static final int[] nucleotideIndex;
42  
43   public static final int[] purinepyrimidineIndex;
44  
45   public static final int[] secondaryStructureIndex;
46  
47   public static final Map aa3Hash = new HashMap<>();
48  
49   public static final Map aa2Triplet = new HashMap<>();
50  
51   public static final Map nucleotideName = new HashMap<>();
52  
53   public static final Map nucleotideAmbiguityName = new HashMap<>();
54  
55   // lookup from modified amino acid (e.g. MSE) to canonical form (e.g. MET)
56   public static final Map modifications = new HashMap<>();
57  
58   static
59   {
60   aaIndex = new int[255];
61   for (int i = 0; i < 255; i++)
62   {
63   aaIndex[i] = 23;
64   }
65  
66   aaIndex['A'] = 0;
67   aaIndex['R'] = 1;
68   aaIndex['N'] = 2;
69   aaIndex['D'] = 3;
70   aaIndex['C'] = 4;
71   aaIndex['Q'] = 5;
72   aaIndex['E'] = 6;
73   aaIndex['G'] = 7;
74   aaIndex['H'] = 8;
75   aaIndex['I'] = 9;
76   aaIndex['L'] = 10;
77   aaIndex['K'] = 11;
78   aaIndex['M'] = 12;
79   aaIndex['F'] = 13;
80   aaIndex['P'] = 14;
81   aaIndex['S'] = 15;
82   aaIndex['T'] = 16;
83   aaIndex['W'] = 17;
84   aaIndex['Y'] = 18;
85   aaIndex['V'] = 19;
86   aaIndex['B'] = 20;
87   aaIndex['Z'] = 21;
88   aaIndex['X'] = 22;
89   aaIndex['U'] = 22;
90   aaIndex['a'] = 0;
91   aaIndex['r'] = 1;
92   aaIndex['n'] = 2;
93   aaIndex['d'] = 3;
94   aaIndex['c'] = 4;
95   aaIndex['q'] = 5;
96   aaIndex['e'] = 6;
97   aaIndex['g'] = 7;
98   aaIndex['h'] = 8;
99   aaIndex['i'] = 9;
100   aaIndex['l'] = 10;
101   aaIndex['k'] = 11;
102   aaIndex['m'] = 12;
103   aaIndex['f'] = 13;
104   aaIndex['p'] = 14;
105   aaIndex['s'] = 15;
106   aaIndex['t'] = 16;
107   aaIndex['w'] = 17;
108   aaIndex['y'] = 18;
109   aaIndex['v'] = 19;
110   aaIndex['b'] = 20;
111   aaIndex['z'] = 21;
112   aaIndex['x'] = 22;
113   aaIndex['u'] = 22; // TODO: selenocystine triplet and codons needed. also
114   // extend subt. matrices
115   }
116  
117   /**
118   * maximum (gap) index for matrices involving protein alphabet
119   */
120   public final static int maxProteinIndex = 23;
121  
122   /**
123   * maximum (gap) index for matrices involving nucleotide alphabet
124   */
125   // public final static int maxNucleotideIndex = 10;
126   public final static int maxNucleotideIndex;
127  
128   static
129   {
130   String[][] namesArray = { { "a", "Adenine" }, { "c", "Cytosine" },
131   { "g", "Guanine" },
132   { "t", "Thymine" },
133   { "u", "Uracil" },
134   { "i", "Inosine" },
135   { "x", "Xanthine" },
136   { "r", "Unknown Purine" },
137   { "y", "Unknown Pyrimidine" },
138   { "w", "Weak nucleotide (A or T)" },
139   { "s", "Strong nucleotide (G or C)" },
140   { "m", "Amino (A or C)" },
141   { "k", "Keto (G or T)" },
142   { "b", "Not A (G or C or T)" },
143   { "h", "Not G (A or C or T)" },
144   { "d", "Not C (A or G or T)" },
145   { "v", "Not T (A or G or C)" },
146   { "n", "Unknown" } };
147   // "gap" index
148   maxNucleotideIndex = namesArray.length;
149  
150   nucleotideIndex = new int[255];
151   for (int i = 0; i < 255; i++)
152   {
153   nucleotideIndex[i] = maxNucleotideIndex; // non-nucleotide symbols are all
154   // non-gap gaps.
155   }
156  
157   for (int i = 0; i < namesArray.length; i++)
158   {
159   char c = namesArray[i][0].charAt(0);
160   nucleotideIndex[c] = i;
161   // Character.toUpperCase is Locale insensitive
162   nucleotideIndex[Character.toUpperCase(c)] = i;
163   nucleotideName.put(namesArray[i][0], namesArray[i][1]);
164   nucleotideName.put(namesArray[i][0].toUpperCase(Locale.ROOT),
165   namesArray[i][1]);
166   }
167  
168   }
169  
170   static
171   {
172   purinepyrimidineIndex = new int[255];
173   for (int i = 0; i < 255; i++)
174   {
175   purinepyrimidineIndex[i] = 3; // non-nucleotide symbols are all non-gap
176   // gaps.
177   }
178  
179   purinepyrimidineIndex['A'] = 0;
180   purinepyrimidineIndex['a'] = 0;
181   purinepyrimidineIndex['C'] = 1;
182   purinepyrimidineIndex['c'] = 1;
183   purinepyrimidineIndex['G'] = 0;
184   purinepyrimidineIndex['g'] = 0;
185   purinepyrimidineIndex['T'] = 1;
186   purinepyrimidineIndex['t'] = 1;
187   purinepyrimidineIndex['U'] = 1;
188   purinepyrimidineIndex['u'] = 1;
189   purinepyrimidineIndex['I'] = 2;
190   purinepyrimidineIndex['i'] = 2;
191   purinepyrimidineIndex['X'] = 2;
192   purinepyrimidineIndex['x'] = 2;
193   purinepyrimidineIndex['R'] = 0;
194   purinepyrimidineIndex['r'] = 0;
195   purinepyrimidineIndex['Y'] = 1;
196   purinepyrimidineIndex['y'] = 1;
197   purinepyrimidineIndex['N'] = 2;
198   purinepyrimidineIndex['n'] = 2;
199   }
200  
201   static
202   {
203   secondaryStructureIndex = new int[255];
204   for (int i = 0; i < 255; i++)
205   {
206   secondaryStructureIndex[i] = 3;
207   }
208  
209   secondaryStructureIndex['H'] = 0;
210   secondaryStructureIndex['E'] = 1;
211   secondaryStructureIndex['C'] = 2;
212   }
213  
214   private static final Integer ONE = Integer.valueOf(1);
215  
216   private static final Integer ZERO = Integer.valueOf(0);
217  
218   static
219   {
220   aa3Hash.put("ALA", ZERO);
221   aa3Hash.put("ARG", ONE);
222   aa3Hash.put("ASN", Integer.valueOf(2));
223   aa3Hash.put("ASP", Integer.valueOf(3)); // D
224   aa3Hash.put("CYS", Integer.valueOf(4));
225   aa3Hash.put("GLN", Integer.valueOf(5)); // Q
226   aa3Hash.put("GLU", Integer.valueOf(6)); // E
227   aa3Hash.put("GLY", Integer.valueOf(7));
228   aa3Hash.put("HIS", Integer.valueOf(8));
229   aa3Hash.put("ILE", Integer.valueOf(9));
230   aa3Hash.put("LEU", Integer.valueOf(10));
231   aa3Hash.put("LYS", Integer.valueOf(11));
232   aa3Hash.put("MET", Integer.valueOf(12));
233   aa3Hash.put("PHE", Integer.valueOf(13));
234   aa3Hash.put("PRO", Integer.valueOf(14));
235   aa3Hash.put("SER", Integer.valueOf(15));
236   aa3Hash.put("THR", Integer.valueOf(16));
237   aa3Hash.put("TRP", Integer.valueOf(17));
238   aa3Hash.put("TYR", Integer.valueOf(18));
239   aa3Hash.put("VAL", Integer.valueOf(19));
240   // IUB Nomenclature for ambiguous peptides
241   aa3Hash.put("ASX", Integer.valueOf(20)); // "B";
242   aa3Hash.put("GLX", Integer.valueOf(21)); // Z
243   aa3Hash.put("XAA", Integer.valueOf(22)); // X unknown
244   aa3Hash.put("-", Integer.valueOf(23));
245   aa3Hash.put("*", Integer.valueOf(23));
246   aa3Hash.put(".", Integer.valueOf(23));
247   aa3Hash.put(" ", Integer.valueOf(23));
248   aa3Hash.put("Gap", Integer.valueOf(23));
249   aa3Hash.put("UR3", Integer.valueOf(24));
250   }
251  
252   static
253   {
254   aa2Triplet.put("A", "ALA");
255   aa2Triplet.put("a", "ALA");
256   aa2Triplet.put("R", "ARG");
257   aa2Triplet.put("r", "ARG");
258   aa2Triplet.put("N", "ASN");
259   aa2Triplet.put("n", "ASN");
260   aa2Triplet.put("D", "ASP");
261   aa2Triplet.put("d", "ASP");
262   aa2Triplet.put("C", "CYS");
263   aa2Triplet.put("c", "CYS");
264   aa2Triplet.put("Q", "GLN");
265   aa2Triplet.put("q", "GLN");
266   aa2Triplet.put("E", "GLU");
267   aa2Triplet.put("e", "GLU");
268   aa2Triplet.put("G", "GLY");
269   aa2Triplet.put("g", "GLY");
270   aa2Triplet.put("H", "HIS");
271   aa2Triplet.put("h", "HIS");
272   aa2Triplet.put("I", "ILE");
273   aa2Triplet.put("i", "ILE");
274   aa2Triplet.put("L", "LEU");
275   aa2Triplet.put("l", "LEU");
276   aa2Triplet.put("K", "LYS");
277   aa2Triplet.put("k", "LYS");
278   aa2Triplet.put("M", "MET");
279   aa2Triplet.put("m", "MET");
280   aa2Triplet.put("F", "PHE");
281   aa2Triplet.put("f", "PHE");
282   aa2Triplet.put("P", "PRO");
283   aa2Triplet.put("p", "PRO");
284   aa2Triplet.put("S", "SER");
285   aa2Triplet.put("s", "SER");
286   aa2Triplet.put("T", "THR");
287   aa2Triplet.put("t", "THR");
288   aa2Triplet.put("W", "TRP");
289   aa2Triplet.put("w", "TRP");
290   aa2Triplet.put("Y", "TYR");
291   aa2Triplet.put("y", "TYR");
292   aa2Triplet.put("V", "VAL");
293   aa2Triplet.put("v", "VAL");
294   }
295  
296   public static final String[] aa = { "A", "R", "N", "D", "C", "Q", "E",
297   "G", "H", "I", "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V", "B",
298   "Z", "X", "_", "*", ".", " ", "U" };
299  
300   public static final Color midBlue = new Color(100, 100, 255);
301  
302   // not currently in use
303   // public static final Vector scaleColours = new Vector();
304   // static
305   // {
306   // scaleColours.addElement(new Color(114, 0, 147));
307   // scaleColours.addElement(new Color(156, 0, 98));
308   // scaleColours.addElement(new Color(190, 0, 0));
309   // scaleColours.addElement(Color.red);
310   // scaleColours.addElement(new Color(255, 125, 0));
311   // scaleColours.addElement(Color.orange);
312   // scaleColours.addElement(new Color(255, 194, 85));
313   // scaleColours.addElement(Color.yellow);
314   // scaleColours.addElement(new Color(255, 255, 181));
315   // scaleColours.addElement(Color.white);
316   // }
317  
318   public static final Color[] taylor = { new Color(204, 255, 0),
319   // A Greenish-yellowy-yellow
320   new Color(0, 0, 255), // R Blueish-bluey-blue
321   new Color(204, 0, 255), // N Blueish-reddy-blue
322   new Color(255, 0, 0), // D Reddish-reddy-red
323   new Color(255, 255, 0), // C Yellowish-yellowy-yellow
324   new Color(255, 0, 204), // Q Reddish-bluey-red
325   new Color(255, 0, 102), // E Blueish-reddy-red
326   new Color(255, 153, 0), // G Yellowy-reddy-yellow
327   new Color(0, 102, 255), // H Greenish-bluey-blue
328   new Color(102, 255, 0), // I Greenish-yellowy-green
329   new Color(51, 255, 0), // L Yellowish-greeny-green
330   new Color(102, 0, 255), // K Reddish-bluey-blue
331   new Color(0, 255, 0), // M Greenish-greeny-green
332   new Color(0, 255, 102), // F Blueish-greeny-green
333   new Color(255, 204, 0), // P Reddish-yellowy-yellow
334   new Color(255, 51, 0), // S Yellowish-reddy-red
335   new Color(255, 102, 0), // T Reddish-yellowy-red
336   new Color(0, 204, 255), // W Blueish-greeny-green
337   new Color(0, 255, 204), // Y Greenish-bluey-green
338   new Color(153, 255, 0), // V Yellowish-greeny-yellow
339   Color.white, // B
340   Color.white, // Z
341   Color.white, // X
342   Color.white, // -
343   Color.white, // *
344   Color.white // .
345   };
346  
347   public static final Color[] nucleotide = { new Color(100, 247, 63), // A
348   new Color(255, 179, 64), // C
349   new Color(235, 65, 60), // G
350   new Color(60, 136, 238), // T
351   new Color(60, 136, 238), // U
352   Color.white, // I (inosine)
353   Color.white, // X (xanthine)
354   Color.white, // R
355   Color.white, // Y
356   Color.white, // N
357   Color.white, // w
358   Color.white, // s
359   Color.white, // m
360   Color.white, // k
361   Color.white, // b
362   Color.white, // h
363   Color.white, // d
364   Color.white, // v
365   Color.white, // Gap
366   };
367  
368   // this colour scheme devised by sduce
369   public static final Color[] nucleotideAmbiguity = {
370   Color.decode("#f0fff0"), // a
371   Color.decode("#f0fff0"), // c
372   Color.decode("#f0fff0"), // g
373   Color.decode("#f0fff0"), // t
374   Color.decode("#f0fff0"), // u
375   Color.decode("#ffffff"), // i
376   Color.decode("#4f6f6f"), // x
377   Color.decode("#CD5C5C"), // r
378   Color.decode("#008000"), // y
379   Color.decode("#4682B4"), // w
380   Color.decode("#FF8C00"), // s
381   Color.decode("#9ACD32"), // m
382   Color.decode("#9932CC"), // k
383   Color.decode("#8b4513"), // b
384   Color.decode("#808080"), // h
385   Color.decode("#483D8B"), // d
386   Color.decode("#b8860b"), // v
387   Color.decode("#2f4f4f"), // n
388   Color.white, // Gap
389   };
390  
391   // Added for PurinePyrimidineColourScheme
392   public static final Color[] purinepyrimidine = { new Color(255, 131, 250), // A,
393   // G,
394   // R
395   // purines
396   // purplish/orchid
397   new Color(64, 224, 208), // C,U, T, Y pyrimidines turquoise
398   Color.white, // all other nucleotides
399   Color.white // Gap
400   };
401  
402   // Secondary structure
403   public static final Color[] secondarystructure = { Color.red, // H
404   Color.green, // E
405   Color.gray // C
406   };
407  
408   // Zappo
409   public static final Color[] zappo = { Color.pink, // A
410   midBlue, // R
411   Color.green, // N
412   Color.red, // D
413   Color.yellow, // C
414   Color.green, // Q
415   Color.red, // E
416   Color.magenta, // G
417   midBlue, // Color.red, // H
418   Color.pink, // I
419   Color.pink, // L
420   midBlue, // K
421   Color.pink, // M
422   Color.orange, // F
423   Color.magenta, // P
424   Color.green, // S
425   Color.green, // T
426   Color.orange, // W
427   Color.orange, // Y
428   Color.pink, // V
429   Color.white, // B
430   Color.white, // Z
431   Color.white, // X
432   Color.white, // -
433   Color.white, // *
434   Color.white, // .
435   Color.white // ' '
436   };
437  
438   /*
439   * flower, blossom, sunset, ocean colour schemes from geocos.
440   * See https://gecos.biotite-python.org/
441   * https://raw.githubusercontent.com/biotite-dev/biotite/master/src/biotite/sequence/graphics/color_schemes/flower.json
442   * and https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-3526-6
443   * (https://doi.org/10.1186/s12859-020-3526-6)
444   */
445   public static final Color[] flower = { new Color(177, 138, 81), // A
446   new Color(131, 191, 241), // R
447   new Color(11, 206, 198), // N
448   new Color(1, 165, 120), // D
449   new Color(255, 87, 1), // C
450   new Color(114, 149, 174), // Q
451   new Color(45, 160, 161), // E
452   new Color(177, 194, 60), // G
453   new Color(1, 148, 249), // H
454   new Color(242, 118, 99), // I
455   new Color(223, 110, 117), // L
456   new Color(127, 195, 215), // K
457   new Color(254, 157, 175), // M
458   new Color(250, 85, 157), // F
459   new Color(79, 163, 42), // P
460   new Color(180, 189, 155), // S
461   new Color(210, 181, 118), // T
462   new Color(255, 45, 237), // W
463   new Color(201, 110, 207), // Y
464   new Color(253, 153, 123), // V
465   Color.white, // B
466   Color.white, // Z
467   Color.white, // X
468   Color.white, // -
469   Color.white, // *
470   Color.white // .
471   };
472  
473   public static final Color[] blossom = { new Color(139, 196, 180), // A
474   new Color(252, 149, 2), // R
475   new Color(181, 194, 6), // N
476   new Color(95, 165, 5), // D
477   new Color(8, 147, 254), // C
478   new Color(191, 133, 39), // Q
479   new Color(219, 181, 1), // E
480   new Color(0, 211, 130), // G
481   new Color(255, 87, 1), // H
482   new Color(154, 186, 243), // I
483   new Color(205, 165, 220), // L
484   new Color(254, 165, 39), // K
485   new Color(245, 161, 184), // M
486   new Color(247, 79, 168), // F
487   new Color(16, 214, 49), // P
488   new Color(126, 157, 89), // S
489   new Color(0, 162, 156), // T
490   new Color(254, 8, 251), // W
491   new Color(255, 78, 122), // Y
492   new Color(135, 192, 228), // V
493   Color.white, // B
494   Color.white, // Z
495   Color.white, // X
496   Color.white, // -
497   Color.white, // *
498   Color.white // .
499   };
500  
501   public static final Color[] sunset = { new Color(254, 160, 253), // A
502   new Color(133, 116, 106), // R
503   new Color(171, 200, 245), // N
504   new Color(46, 123, 190), // D
505   new Color(252, 12, 254), // C
506   new Color(140, 110, 129), // Q
507   new Color(103, 120, 146), // E
508   new Color(39, 153, 255), // G
509   new Color(219, 197, 142), // H
510   new Color(250, 33, 161), // I
511   new Color(224, 30, 130), // L
512   new Color(222, 190, 204), // K
513   new Color(209, 62, 123), // M
514   new Color(255, 56, 93), // F
515   new Color(87, 102, 249), // P
516   new Color(231, 180, 253), // S
517   new Color(166, 88, 183), // T
518   new Color(255, 55, 1), // W
519   new Color(203, 83, 57), // Y
520   new Color(254, 81, 184), // V
521   Color.white, // B
522   Color.white, // Z
523   Color.white, // X
524   Color.white, // -
525   Color.white, // *
526   Color.white // .
527   };
528  
529   public static final Color[] ocean = { new Color(198, 202, 155), // A
530   new Color(12, 160, 168), // R
531   new Color(10, 223, 195), // N
532   new Color(76, 223, 161), // D
533   new Color(198, 129, 54), // C
534   new Color(139, 211, 209), // Q
535   new Color(96, 218, 201), // E
536   new Color(51, 165, 81), // G
537   new Color(0, 207, 254), // H
538   new Color(242, 186, 170), // I
539   new Color(187, 138, 131), // L
540   new Color(64, 160, 144), // K
541   new Color(164, 139, 136), // M
542   new Color(171, 136, 174), // F
543   new Color(175, 211, 101), // P
544   new Color(109, 155, 116), // S
545   new Color(141, 149, 102), // T
546   new Color(117, 138, 238), // W
547   new Color(186, 195, 252), // Y
548   new Color(233, 190, 164), // V
549   Color.white, // B
550   Color.white, // Z
551   Color.white, // X
552   Color.white, // -
553   Color.white, // *
554   Color.white // .
555   };
556  
557   // Dunno where I got these numbers from
558   public static final double[] hyd2 = { 0.62, // A
559   0.29, // R
560   -0.90, // N
561   -0.74, // D
562   1.19, // C
563   0.48, // Q
564   -0.40, // E
565   1.38, // G
566   -1.50, // H
567   1.06, // I
568   0.64, // L
569   -0.78, // K
570   0.12, // M
571   -0.85, // F
572   -2.53, // P
573   -0.18, // S
574   -0.05, // T
575   1.08, // W
576   0.81, // Y
577   0.0, // V
578   0.26, // B
579   0.0, // Z
580   0.0 // X
581   };
582  
583   public static final double[] helix = { 1.42, 0.98, 0.67, 1.01, 0.70, 1.11,
584   1.51, 0.57, 1.00, 1.08, 1.21, 1.16, 1.45, 1.13, 0.57, 0.77, 0.83,
585   1.08, 0.69, 1.06, 0.84, 1.31, 1.00, 0.0 };
586  
587   public static final double helixmin = 0.57;
588  
589   public static final double helixmax = 1.51;
590  
591   public static final double[] strand = { 0.83, 0.93, 0.89, 0.54, 1.19,
592   1.10, 0.37, 0.75, 0.87, 1.60, 1.30, 0.74, 1.05, 1.38, 0.55, 0.75,
593   1.19, 1.37, 1.47, 1.70, 0.72, 0.74, 1.0, 0.0 };
594  
595   public static final double strandmin = 0.37;
596  
597   public static final double strandmax = 1.7;
598  
599   public static final double[] turn = { 0.66, 0.95, 1.56, 1.46, 1.19, 0.98,
600   0.74, 1.56, 0.95, 0.47, 0.59, 1.01, 0.60, 0.60, 1.52, 1.43, 0.96,
601   0.96, 1.14, 0.50, 1.51, 0.86, 1.00, 0, 0 };
602  
603   public static final double turnmin = 0.47;
604  
605   public static final double turnmax = 1.56;
606  
607   public static final double[] buried = { 1.7, 0.1, 0.4, 0.4, 4.6, 0.3, 0.3,
608   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,
609   0.3, 1.358, 0.00 };
610  
611   public static final double buriedmin = 0.05;
612  
613   public static final double buriedmax = 4.6;
614  
615   // This is hydropathy index
616   // Kyte, J., and Doolittle, R.F., J. Mol. Biol.
617   // 1157, 105-132, 1982
618   public static final double[] hyd = { 1.8, -4.5, -3.5, -3.5, 2.5, -3.5,
619   -3.5, -0.4, -3.2, 4.5, 3.8, -3.9, 1.9, 2.8, -1.6, -0.8, -0.7, -0.9,
620   -1.3, 4.2, -3.5, -3.5, -0.49, 0.0 };
621  
622   public static final double hydmax = 4.5;
623  
624   public static final double hydmin = -3.9;
625  
626   // public static final double hydmax = 1.38;
627   // public static final double hydmin = -2.53;
628  
629   // not currently used
630   // public static final Map ssHash = new Hashtable
631   // Color>();
632   // static
633   // {
634   // ssHash.put("H", Color.magenta);
635   // ssHash.put("E", Color.yellow);
636   // ssHash.put("-", Color.white);
637   // ssHash.put(".", Color.white);
638   // ssHash.put("S", Color.cyan);
639   // ssHash.put("T", Color.blue);
640   // ssHash.put("G", Color.pink);
641   // ssHash.put("I", Color.pink);
642   // ssHash.put("B", Color.yellow);
643   // }
644  
645   /*
646   * new Color(60, 136, 238), // U Color.white, // I Color.white, // X
647   * Color.white, // R Color.white, // Y Color.white, // N Color.white, // Gap
648   */
649  
650   public static String STOP = "STOP";
651  
652   public static List STOP_CODONS = Arrays.asList("TGA", "TAA",
653   "TAG");
654  
655   public static String START = "ATG";
656  
657   // Stores residue codes/names and colours and other things
658   public static Map> propHash = new Hashtable<>();
659  
660   public static Map hydrophobic = new Hashtable<>();
661  
662   public static Map polar = new Hashtable<>();
663  
664   public static Map small = new Hashtable<>();
665  
666   public static Map positive = new Hashtable<>();
667  
668   public static Map negative = new Hashtable<>();
669  
670   public static Map charged = new Hashtable<>();
671  
672   public static Map aromatic = new Hashtable<>();
673  
674   public static Map aliphatic = new Hashtable<>();
675  
676   public static Map tiny = new Hashtable<>();
677  
678   public static Map proline = new Hashtable<>();
679  
680   static
681   {
682   hydrophobic.put("I", ONE);
683   hydrophobic.put("L", ONE);
684   hydrophobic.put("V", ONE);
685   hydrophobic.put("C", ONE);
686   hydrophobic.put("A", ONE);
687   hydrophobic.put("G", ONE);
688   hydrophobic.put("M", ONE);
689   hydrophobic.put("F", ONE);
690   hydrophobic.put("Y", ONE);
691   hydrophobic.put("W", ONE);
692   hydrophobic.put("H", ONE);
693   hydrophobic.put("K", ONE);
694   hydrophobic.put("X", ONE);
695   hydrophobic.put("-", ONE);
696   hydrophobic.put("*", ONE);
697   hydrophobic.put("R", ZERO);
698   hydrophobic.put("E", ZERO);
699   hydrophobic.put("Q", ZERO);
700   hydrophobic.put("D", ZERO);
701   hydrophobic.put("N", ZERO);
702   hydrophobic.put("S", ZERO);
703   hydrophobic.put("T", ONE);
704   hydrophobic.put("P", ZERO);
705   }
706  
707   static
708   {
709   polar.put("Y", ONE);
710   polar.put("W", ONE);
711   polar.put("H", ONE);
712   polar.put("K", ONE);
713   polar.put("R", ONE);
714   polar.put("E", ONE);
715   polar.put("Q", ONE);
716   polar.put("D", ONE);
717   polar.put("N", ONE);
718   polar.put("S", ONE);
719   polar.put("T", ONE);
720   polar.put("X", ONE);
721   polar.put("-", ONE);
722   polar.put("*", ONE);
723   polar.put("I", ZERO);
724   polar.put("L", ZERO);
725   polar.put("V", ZERO);
726   polar.put("C", ZERO);
727   polar.put("A", ZERO);
728   polar.put("G", ZERO);
729   polar.put("M", ZERO);
730   polar.put("F", ZERO);
731   polar.put("P", ZERO);
732   }
733  
734   static
735   {
736   small.put("I", ZERO);
737   small.put("L", ZERO);
738   small.put("V", ONE);
739   small.put("C", ONE);
740   small.put("A", ONE);
741   small.put("G", ONE);
742   small.put("M", ZERO);
743   small.put("F", ZERO);
744   small.put("Y", ZERO);
745   small.put("W", ZERO);
746   small.put("H", ZERO);
747   small.put("K", ZERO);
748   small.put("R", ZERO);
749   small.put("E", ZERO);
750   small.put("Q", ZERO);
751   small.put("D", ONE);
752   small.put("N", ONE);
753   small.put("S", ONE);
754   small.put("T", ONE);
755   small.put("P", ONE);
756   small.put("-", ONE);
757   small.put("*", ONE);
758   }
759  
760   static
761   {
762   positive.put("I", ZERO);
763   positive.put("L", ZERO);
764   positive.put("V", ZERO);
765   positive.put("C", ZERO);
766   positive.put("A", ZERO);
767   positive.put("G", ZERO);
768   positive.put("M", ZERO);
769   positive.put("F", ZERO);
770   positive.put("Y", ZERO);
771   positive.put("W", ZERO);
772   positive.put("H", ONE);
773   positive.put("K", ONE);
774   positive.put("R", ONE);
775   positive.put("E", ZERO);
776   positive.put("Q", ZERO);
777   positive.put("D", ZERO);
778   positive.put("N", ZERO);
779   positive.put("S", ZERO);
780   positive.put("T", ZERO);
781   positive.put("P", ZERO);
782   positive.put("-", ONE);
783   positive.put("*", ONE);
784   }
785  
786   static
787   {
788   negative.put("I", ZERO);
789   negative.put("L", ZERO);
790   negative.put("V", ZERO);
791   negative.put("C", ZERO);
792   negative.put("A", ZERO);
793   negative.put("G", ZERO);
794   negative.put("M", ZERO);
795   negative.put("F", ZERO);
796   negative.put("Y", ZERO);
797   negative.put("W", ZERO);
798   negative.put("H", ZERO);
799   negative.put("K", ZERO);
800   negative.put("R", ZERO);
801   negative.put("E", ONE);
802   negative.put("Q", ZERO);
803   negative.put("D", ONE);
804   negative.put("N", ZERO);
805   negative.put("S", ZERO);
806   negative.put("T", ZERO);
807   negative.put("P", ZERO);
808   negative.put("-", ONE);
809   negative.put("*", ONE);
810   }
811  
812   static
813   {
814   charged.put("I", ZERO);
815   charged.put("L", ZERO);
816   charged.put("V", ZERO);
817   charged.put("C", ZERO);
818   charged.put("A", ZERO);
819   charged.put("G", ZERO);
820   charged.put("M", ZERO);
821   charged.put("F", ZERO);
822   charged.put("Y", ZERO);
823   charged.put("W", ZERO);
824   charged.put("H", ONE);
825   charged.put("K", ONE);
826   charged.put("R", ONE);
827   charged.put("E", ONE);
828   charged.put("Q", ZERO);
829   charged.put("D", ONE);
830   charged.put("N", ZERO); // Asparagine is polar but not
831   // charged.
832   // Alternative would be charged and
833   // negative (in basic form)?
834   charged.put("S", ZERO);
835   charged.put("T", ZERO);
836   charged.put("P", ZERO);
837   charged.put("-", ONE);
838   charged.put("*", ONE);
839   }
840  
841   static
842   {
843   aromatic.put("I", ZERO);
844   aromatic.put("L", ZERO);
845   aromatic.put("V", ZERO);
846   aromatic.put("C", ZERO);
847   aromatic.put("A", ZERO);
848   aromatic.put("G", ZERO);
849   aromatic.put("M", ZERO);
850   aromatic.put("F", ONE);
851   aromatic.put("Y", ONE);
852   aromatic.put("W", ONE);
853   aromatic.put("H", ONE);
854   aromatic.put("K", ZERO);
855   aromatic.put("R", ZERO);
856   aromatic.put("E", ZERO);
857   aromatic.put("Q", ZERO);
858   aromatic.put("D", ZERO);
859   aromatic.put("N", ZERO);
860   aromatic.put("S", ZERO);
861   aromatic.put("T", ZERO);
862   aromatic.put("P", ZERO);
863   aromatic.put("-", ONE);
864   aromatic.put("*", ONE);
865   }
866  
867   static
868   {
869   aliphatic.put("I", ONE);
870   aliphatic.put("L", ONE);
871   aliphatic.put("V", ONE);
872   aliphatic.put("C", ZERO);
873   aliphatic.put("A", ZERO);
874   aliphatic.put("G", ZERO);
875   aliphatic.put("M", ZERO);
876   aliphatic.put("F", ZERO);
877   aliphatic.put("Y", ZERO);
878   aliphatic.put("W", ZERO);
879   aliphatic.put("H", ZERO);
880   aliphatic.put("K", ZERO);
881   aliphatic.put("R", ZERO);
882   aliphatic.put("E", ZERO);
883   aliphatic.put("Q", ZERO);
884   aliphatic.put("D", ZERO);
885   aliphatic.put("N", ZERO);
886   aliphatic.put("S", ZERO);
887   aliphatic.put("T", ZERO);
888   aliphatic.put("P", ZERO);
889   aliphatic.put("-", ONE);
890   aliphatic.put("*", ONE);
891   }
892  
893   static
894   {
895   tiny.put("I", ZERO);
896   tiny.put("L", ZERO);
897   tiny.put("V", ZERO);
898   tiny.put("C", ZERO);
899   tiny.put("A", ONE);
900   tiny.put("G", ONE);
901   tiny.put("M", ZERO);
902   tiny.put("F", ZERO);
903   tiny.put("Y", ZERO);
904   tiny.put("W", ZERO);
905   tiny.put("H", ZERO);
906   tiny.put("K", ZERO);
907   tiny.put("R", ZERO);
908   tiny.put("E", ZERO);
909   tiny.put("Q", ZERO);
910   tiny.put("D", ZERO);
911   tiny.put("N", ZERO);
912   tiny.put("S", ONE);
913   tiny.put("T", ZERO);
914   tiny.put("P", ZERO);
915   tiny.put("-", ONE);
916   tiny.put("*", ONE);
917   }
918  
919   static
920   {
921   proline.put("I", ZERO);
922   proline.put("L", ZERO);
923   proline.put("V", ZERO);
924   proline.put("C", ZERO);
925   proline.put("A", ZERO);
926   proline.put("G", ZERO);
927   proline.put("M", ZERO);
928   proline.put("F", ZERO);
929   proline.put("Y", ZERO);
930   proline.put("W", ZERO);
931   proline.put("H", ZERO);
932   proline.put("K", ZERO);
933   proline.put("R", ZERO);
934   proline.put("E", ZERO);
935   proline.put("Q", ZERO);
936   proline.put("D", ZERO);
937   proline.put("N", ZERO);
938   proline.put("S", ZERO);
939   proline.put("T", ZERO);
940   proline.put("P", ONE);
941   proline.put("-", ONE);
942   proline.put("*", ONE);
943   }
944  
945   static
946   {
947   propHash.put("hydrophobic", hydrophobic);
948   propHash.put("small", small);
949   propHash.put("positive", positive);
950   propHash.put("negative", negative);
951   propHash.put("charged", charged);
952   propHash.put("aromatic", aromatic);
953   propHash.put("aliphatic", aliphatic);
954   propHash.put("tiny", tiny);
955   propHash.put("proline", proline);
956   propHash.put("polar", polar);
957   }
958   static
959   {
960   int[][] propMatrixF = new int[maxProteinIndex][maxProteinIndex],
961   propMatrixPos = new int[maxProteinIndex][maxProteinIndex],
962   propMatrixEpos = new int[maxProteinIndex][maxProteinIndex];
963   for (int i = 0; i < maxProteinIndex; i++)
964   {
965   int maxF = 0, maxP = 0, maxEP = 0;
966   String ic = "";
967   if (aa.length > i)
968   {
969   ic += aa[i];
970   }
971   else
972   {
973   ic = "-";
974   }
975   for (int j = i + 1; j < maxProteinIndex; j++)
976   {
977   String jc = "";
978   if (aa.length > j)
979   {
980   jc += aa[j];
981   }
982   else
983   {
984   jc = "-";
985   }
986   propMatrixF[i][j] = 0;
987   propMatrixPos[i][j] = 0;
988   propMatrixEpos[i][j] = 0;
989   for (String ph : propHash.keySet())
990   {
991   Map pph = propHash.get(ph);
992   if (pph.get(ic) != null && pph.get(jc) != null)
993   {
994   int icp = pph.get(ic).intValue(), jcp = pph.get(jc).intValue();
995   // Still working on these definitions.
996   propMatrixPos[i][j] += icp == jcp && icp > 0 ? 2 : 0;
997   propMatrixPos[j][i] += icp == jcp && icp > 0 ? 2 : 0;
998   propMatrixF[i][j] += icp == jcp ? 2 : 0;
999   propMatrixF[j][i] += icp == jcp ? 2 : 0;
1000   propMatrixEpos[i][j] += icp == jcp ? (1 + icp * 2) : 0;
1001   propMatrixEpos[j][i] += icp == jcp ? (1 + icp * 2) : 0;
1002   }
1003   }
1004   if (maxF < propMatrixF[i][j])
1005   {
1006   maxF = propMatrixF[i][j];
1007   }
1008   if (maxP < propMatrixPos[i][j])
1009   {
1010   maxP = propMatrixPos[i][j];
1011   }
1012   if (maxEP < propMatrixEpos[i][j])
1013   {
1014   maxEP = propMatrixEpos[i][j];
1015   }
1016   }
1017   propMatrixF[i][i] = maxF;
1018   propMatrixPos[i][i] = maxP;
1019   propMatrixEpos[i][i] = maxEP;
1020   }
1021   }
1022  
1023   private ResidueProperties()
1024   {
1025   }
1026  
1027   public static double getHydmax()
1028   {
1029   return hydmax;
1030   }
1031  
1032   public static double getHydmin()
1033   {
1034   return hydmin;
1035   }
1036  
1037   public static double[] getHyd()
1038   {
1039   return hyd;
1040   }
1041  
1042   public static Map getAA3Hash()
1043   {
1044   return aa3Hash;
1045   }
1046  
1047   public static String codonTranslate(String lccodon)
1048   {
1049   String peptide = GeneticCodes.getInstance().getStandardCodeTable()
1050   .translate(lccodon);
1051   if ("*".equals(peptide))
1052   {
1053   return "STOP";
1054   }
1055   return peptide;
1056   }
1057  
1058   /*
1059   * lookup of (A-Z) alternative secondary structure symbols'
1060   * equivalents in DSSP3 notation
1061   */
1062   private static char[] toDssp3State;
1063   static
1064   {
1065   toDssp3State = new char[9]; // for 'A'-'I'; extend if needed
1066   Arrays.fill(toDssp3State, ' ');
1067   toDssp3State['B' - 'A'] = 'E';
1068   toDssp3State['E' - 'A'] = 'E';
1069   toDssp3State['G' - 'A'] = 'H';
1070   toDssp3State['H' - 'A'] = 'H';
1071   toDssp3State['I' - 'A'] = 'H';
1072   }
1073  
1074   /**
1075   * translate from other dssp secondary structure alphabets to 3-state
1076   *
1077   * @param ssString
1078   * @return ssstring
1079   */
1080   public static String getDssp3state(String ssString)
1081   {
1082   if (ssString == null)
1083   {
1084   return null;
1085   }
1086   int lookupSize = toDssp3State.length;
1087   int len = ssString.length();
1088   char[] trans = new char[len];
1089   for (int i = 0; i < len; i++)
1090   {
1091   char c = ssString.charAt(i);
1092   int index = c - 'A';
1093   if (index < 0 || index >= lookupSize)
1094   {
1095   trans[i] = ' ';
1096   }
1097   else
1098   {
1099   trans[i] = toDssp3State[index];
1100   }
1101   }
1102   return new String(trans);
1103   }
1104  
1105   static
1106   {
1107   modifications.put("MSE", "MET"); // Selenomethionine
1108   // the rest tbc; from
1109   // http://sourceforge.net/p/jmol/mailman/message/12833570/
1110   // modifications.put("CSE", "CYS"); // Selenocysteine
1111   // modifications.put("PTR", "TYR"); // Phosphotyrosine
1112   // modifications.put("SEP", "SER"); // Phosphoserine
1113   // modifications.put("HYP", "PRO"); // 4-hydroxyproline
1114   // modifications.put("5HP", "GLU"); // Pyroglutamic acid; 5-hydroxyproline
1115   // modifications.put("PCA", "GLU"); // Pyroglutamic acid
1116   // modifications.put("LYZ", "LYS"); // 5-hydroxylysine
1117  
1118   // Additional protein alphabets used in the SCOP database and PDB files
1119   // source:
1120   // https://github.com/biopython/biopython/blob/master/Bio/Data/SCOPData.py
1121   modifications.put("00C", "CYS");
1122   modifications.put("01W", "XAA");
1123   modifications.put("02K", "ALA");
1124   modifications.put("03Y", "CYS");
1125   modifications.put("07O", "CYS");
1126   modifications.put("08P", "CYS");
1127   modifications.put("0A0", "ASP");
1128   modifications.put("0A1", "TYR");
1129   modifications.put("0A2", "LYS");
1130   modifications.put("0A8", "CYS");
1131   modifications.put("0AA", "VAL");
1132   modifications.put("0AB", "VAL");
1133   modifications.put("0AC", "GLY");
1134   modifications.put("0AD", "GLY");
1135   modifications.put("0AF", "TRP");
1136   modifications.put("0AG", "LEU");
1137   modifications.put("0AH", "SER");
1138   modifications.put("0AK", "ASP");
1139   modifications.put("0AM", "ALA");
1140   modifications.put("0AP", "CYS");
1141   modifications.put("0AU", "UR3");
1142   modifications.put("0AV", "ALA");
1143   modifications.put("0AZ", "PRO");
1144   modifications.put("0BN", "PHE");
1145   modifications.put("0C ", "CYS");
1146   modifications.put("0CS", "ALA");
1147   modifications.put("0DC", "CYS");
1148   modifications.put("0DG", "GLY");
1149   modifications.put("0DT", "THR");
1150   modifications.put("0FL", "ALA");
1151   modifications.put("0G ", "GLY");
1152   modifications.put("0NC", "ALA");
1153   modifications.put("0SP", "ALA");
1154   modifications.put("0U ", "UR3");
1155   modifications.put("0YG", "YG");
1156   modifications.put("10C", "CYS");
1157   modifications.put("125", "UR3");
1158   modifications.put("126", "UR3");
1159   modifications.put("127", "UR3");
1160   modifications.put("128", "ASN");
1161   modifications.put("12A", "ALA");
1162   modifications.put("143", "CYS");
1163   modifications.put("175", "ASG");
1164   modifications.put("193", "XAA");
1165   modifications.put("1AP", "ALA");
1166   modifications.put("1MA", "ALA");
1167   modifications.put("1MG", "GLY");
1168   modifications.put("1PA", "PHE");
1169   modifications.put("1PI", "ALA");
1170   modifications.put("1PR", "ASN");
1171   modifications.put("1SC", "CYS");
1172   modifications.put("1TQ", "TRP");
1173   modifications.put("1TY", "TYR");
1174   modifications.put("1X6", "SER");
1175   modifications.put("200", "PHE");
1176   modifications.put("23F", "PHE");
1177   modifications.put("23S", "XAA");
1178   modifications.put("26B", "THR");
1179   modifications.put("2AD", "XAA");
1180   modifications.put("2AG", "ALA");
1181   modifications.put("2AO", "XAA");
1182   modifications.put("2AR", "ALA");
1183   modifications.put("2AS", "XAA");
1184   modifications.put("2AT", "THR");
1185   modifications.put("2AU", "UR3");
1186   modifications.put("2BD", "ILE");
1187   modifications.put("2BT", "THR");
1188   modifications.put("2BU", "ALA");
1189   modifications.put("2CO", "CYS");
1190   modifications.put("2DA", "ALA");
1191   modifications.put("2DF", "ASN");
1192   modifications.put("2DM", "ASN");
1193   modifications.put("2DO", "XAA");
1194   modifications.put("2DT", "THR");
1195   modifications.put("2EG", "GLY");
1196   modifications.put("2FE", "ASN");
1197   modifications.put("2FI", "ASN");
1198   modifications.put("2FM", "MET");
1199   modifications.put("2GT", "THR");
1200   modifications.put("2HF", "HIS");
1201   modifications.put("2LU", "LEU");
1202   modifications.put("2MA", "ALA");
1203   modifications.put("2MG", "GLY");
1204   modifications.put("2ML", "LEU");
1205   modifications.put("2MR", "ARG");
1206   modifications.put("2MT", "PRO");
1207   modifications.put("2MU", "UR3");
1208   modifications.put("2NT", "THR");
1209   modifications.put("2OM", "UR3");
1210   modifications.put("2OT", "THR");
1211   modifications.put("2PI", "XAA");
1212   modifications.put("2PR", "GLY");
1213   modifications.put("2SA", "ASN");
1214   modifications.put("2SI", "XAA");
1215   modifications.put("2ST", "THR");
1216   modifications.put("2TL", "THR");
1217   modifications.put("2TY", "TYR");
1218   modifications.put("2VA", "VAL");
1219   modifications.put("2XA", "CYS");
1220   modifications.put("32S", "XAA");
1221   modifications.put("32T", "XAA");
1222   modifications.put("3AH", "HIS");
1223   modifications.put("3AR", "XAA");
1224   modifications.put("3CF", "PHE");
1225   modifications.put("3DA", "ALA");
1226   modifications.put("3DR", "ASN");
1227   modifications.put("3GA", "ALA");
1228   modifications.put("3MD", "ASP");
1229   modifications.put("3ME", "UR3");
1230   modifications.put("3NF", "TYR");
1231   modifications.put("3QN", "LYS");
1232   modifications.put("3TY", "XAA");
1233   modifications.put("3XH", "GLY");
1234   modifications.put("4AC", "ASN");
1235   modifications.put("4BF", "TYR");
1236   modifications.put("4CF", "PHE");
1237   modifications.put("4CY", "MET");
1238   modifications.put("4DP", "TRP");
1239   modifications.put("4F3", "GYG");
1240   modifications.put("4FB", "PRO");
1241   modifications.put("4FW", "TRP");
1242   modifications.put("4HT", "TRP");
1243   modifications.put("4IN", "TRP");
1244   modifications.put("4MF", "ASN");
1245   modifications.put("4MM", "XAA");
1246   modifications.put("4OC", "CYS");
1247   modifications.put("4PC", "CYS");
1248   modifications.put("4PD", "CYS");
1249   modifications.put("4PE", "CYS");
1250   modifications.put("4PH", "PHE");
1251   modifications.put("4SC", "CYS");
1252   modifications.put("4SU", "UR3");
1253   modifications.put("4TA", "ASN");
1254   modifications.put("4U7", "ALA");
1255   modifications.put("56A", "HIS");
1256   modifications.put("5AA", "ALA");
1257   modifications.put("5AB", "ALA");
1258   modifications.put("5AT", "THR");
1259   modifications.put("5BU", "UR3");
1260   modifications.put("5CG", "GLY");
1261   modifications.put("5CM", "CYS");
1262   modifications.put("5CS", "CYS");
1263   modifications.put("5FA", "ALA");
1264   modifications.put("5FC", "CYS");
1265   modifications.put("5FU", "UR3");
1266   modifications.put("5HP", "GLU");
1267   modifications.put("5HT", "THR");
1268   modifications.put("5HU", "UR3");
1269   modifications.put("5IC", "CYS");
1270   modifications.put("5IT", "THR");
1271   modifications.put("5IU", "UR3");
1272   modifications.put("5MC", "CYS");
1273   modifications.put("5MD", "ASN");
1274   modifications.put("5MU", "UR3");
1275   modifications.put("5NC", "CYS");
1276   modifications.put("5PC", "CYS");
1277   modifications.put("5PY", "THR");
1278   modifications.put("5SE", "UR3");
1279   modifications.put("5ZA", "TWG");
1280   modifications.put("64T", "THR");
1281   modifications.put("6CL", "LYS");
1282   modifications.put("6CT", "THR");
1283   modifications.put("6CW", "TRP");
1284   modifications.put("6HA", "ALA");
1285   modifications.put("6HC", "CYS");
1286   modifications.put("6HG", "GLY");
1287   modifications.put("6HN", "LYS");
1288   modifications.put("6HT", "THR");
1289   modifications.put("6IA", "ALA");
1290   modifications.put("6MA", "ALA");
1291   modifications.put("6MC", "ALA");
1292   modifications.put("6MI", "ASN");
1293   modifications.put("6MT", "ALA");
1294   modifications.put("6MZ", "ASN");
1295   modifications.put("6OG", "GLY");
1296   modifications.put("70U", "UR3");
1297   modifications.put("7DA", "ALA");
1298   modifications.put("7GU", "GLY");
1299   modifications.put("7JA", "ILE");
1300   modifications.put("7MG", "GLY");
1301   modifications.put("8AN", "ALA");
1302   modifications.put("8FG", "GLY");
1303   modifications.put("8MG", "GLY");
1304   modifications.put("8OG", "GLY");
1305   modifications.put("9NE", "GLU");
1306   modifications.put("9NF", "PHE");
1307   modifications.put("9NR", "ARG");
1308   modifications.put("9NV", "VAL");
1309   modifications.put("A ", "ALA");
1310   modifications.put("A1P", "ASN");
1311   modifications.put("A23", "ALA");
1312   modifications.put("A2L", "ALA");
1313   modifications.put("A2M", "ALA");
1314   modifications.put("A34", "ALA");
1315   modifications.put("A35", "ALA");
1316   modifications.put("A38", "ALA");
1317   modifications.put("A39", "ALA");
1318   modifications.put("A3A", "ALA");
1319   modifications.put("A3P", "ALA");
1320   modifications.put("A40", "ALA");
1321   modifications.put("A43", "ALA");
1322   modifications.put("A44", "ALA");
1323   modifications.put("A47", "ALA");
1324   modifications.put("A5L", "ALA");
1325   modifications.put("A5M", "CYS");
1326   modifications.put("A5N", "ASN");
1327   modifications.put("A5O", "ALA");
1328   modifications.put("A66", "XAA");
1329   modifications.put("AA3", "ALA");
1330   modifications.put("AA4", "ALA");
1331   modifications.put("AAR", "ARG");
1332   modifications.put("AB7", "XAA");
1333   modifications.put("ABA", "ALA");
1334   modifications.put("ABR", "ALA");
1335   modifications.put("ABS", "ALA");
1336   modifications.put("ABT", "ASN");
1337   modifications.put("ACB", "ASP");
1338   modifications.put("ACL", "ARG");
1339   modifications.put("AD2", "ALA");
1340   modifications.put("ADD", "XAA");
1341   modifications.put("ADX", "ASN");
1342   modifications.put("AEA", "XAA");
1343   modifications.put("AEI", "ASP");
1344   modifications.put("AET", "ALA");
1345   modifications.put("AFA", "ASN");
1346   modifications.put("AFF", "ASN");
1347   modifications.put("AFG", "GLY");
1348   modifications.put("AGM", "ARG");
1349   modifications.put("AGT", "CYS");
1350   modifications.put("AHB", "ASN");
1351   modifications.put("AHH", "XAA");
1352   modifications.put("AHO", "ALA");
1353   modifications.put("AHP", "ALA");
1354   modifications.put("AHS", "XAA");
1355   modifications.put("AHT", "XAA");
1356   modifications.put("AIB", "ALA");
1357   modifications.put("AKL", "ASP");
1358   modifications.put("AKZ", "ASP");
1359   modifications.put("ALA", "ALA");
1360   modifications.put("ALC", "ALA");
1361   modifications.put("ALM", "ALA");
1362   modifications.put("ALN", "ALA");
1363   modifications.put("ALO", "THR");
1364   modifications.put("ALQ", "XAA");
1365   modifications.put("ALS", "ALA");
1366   modifications.put("ALT", "ALA");
1367   modifications.put("ALV", "ALA");
1368   modifications.put("ALY", "LYS");
1369   modifications.put("AN8", "ALA");
1370   modifications.put("AP7", "ALA");
1371   modifications.put("APE", "XAA");
1372   modifications.put("APH", "ALA");
1373   modifications.put("API", "LYS");
1374   modifications.put("APK", "LYS");
1375   modifications.put("APM", "XAA");
1376   modifications.put("APP", "XAA");
1377   modifications.put("AR2", "ARG");
1378   modifications.put("AR4", "GLU");
1379   modifications.put("AR7", "ARG");
1380   modifications.put("ARG", "ARG");
1381   modifications.put("ARM", "ARG");
1382   modifications.put("ARO", "ARG");
1383   modifications.put("ARV", "XAA");
1384   modifications.put("AS ", "ALA");
1385   modifications.put("AS2", "ASP");
1386   modifications.put("AS9", "XAA");
1387   modifications.put("ASA", "ASP");
1388   modifications.put("ASB", "ASP");
1389   modifications.put("ASI", "ASP");
1390   modifications.put("ASK", "ASP");
1391   modifications.put("ASL", "ASP");
1392   modifications.put("ASM", "XAA");
1393   modifications.put("ASN", "ASN");
1394   modifications.put("ASP", "ASP");
1395   modifications.put("ASQ", "ASP");
1396   modifications.put("ASU", "ASN");
1397   modifications.put("ASX", "ASX");
1398   modifications.put("ATD", "THR");
1399   modifications.put("ATL", "THR");
1400   modifications.put("ATM", "THR");
1401   modifications.put("AVC", "ALA");
1402   modifications.put("AVN", "XAA");
1403   modifications.put("AYA", "ALA");
1404   modifications.put("AYG", "AYG");
1405   modifications.put("AZK", "LYS");
1406   modifications.put("AZS", "SER");
1407   modifications.put("AZY", "TYR");
1408   modifications.put("B1F", "PHE");
1409   modifications.put("B1P", "ASN");
1410   modifications.put("B2A", "ALA");
1411   modifications.put("B2F", "PHE");
1412   modifications.put("B2I", "ILE");
1413   modifications.put("B2V", "VAL");
1414   modifications.put("B3A", "ALA");
1415   modifications.put("B3D", "ASP");
1416   modifications.put("B3E", "GLU");
1417   modifications.put("B3K", "LYS");
1418   modifications.put("B3L", "XAA");
1419   modifications.put("B3M", "XAA");
1420   modifications.put("B3Q", "XAA");
1421   modifications.put("B3S", "SER");
1422   modifications.put("B3T", "XAA");
1423   modifications.put("B3U", "HIS");
1424   modifications.put("B3X", "ASN");
1425   modifications.put("B3Y", "TYR");
1426   modifications.put("BB6", "CYS");
1427   modifications.put("BB7", "CYS");
1428   modifications.put("BB8", "PHE");
1429   modifications.put("BB9", "CYS");
1430   modifications.put("BBC", "CYS");
1431   modifications.put("BCS", "CYS");
1432   modifications.put("BE2", "XAA");
1433   modifications.put("BFD", "ASP");
1434   modifications.put("BG1", "SER");
1435   modifications.put("BGM", "GLY");
1436   modifications.put("BH2", "ASP");
1437   modifications.put("BHD", "ASP");
1438   modifications.put("BIF", "PHE");
1439   modifications.put("BIL", "XAA");
1440   modifications.put("BIU", "ILE");
1441   modifications.put("BJH", "XAA");
1442   modifications.put("BLE", "LEU");
1443   modifications.put("BLY", "LYS");
1444   modifications.put("BMP", "ASN");
1445   modifications.put("BMT", "THR");
1446   modifications.put("BNN", "PHE");
1447   modifications.put("BNO", "XAA");
1448   modifications.put("BOE", "THR");
1449   modifications.put("BOR", "ARG");
1450   modifications.put("BPE", "CYS");
1451   modifications.put("BRU", "UR3");
1452   modifications.put("BSE", "SER");
1453   modifications.put("BT5", "ASN");
1454   modifications.put("BTA", "LEU");
1455   modifications.put("BTC", "CYS");
1456   modifications.put("BTR", "TRP");
1457   modifications.put("BUC", "CYS");
1458   modifications.put("BUG", "VAL");
1459   modifications.put("BVP", "UR3");
1460   modifications.put("BZG", "ASN");
1461   modifications.put("C ", "CYS");
1462   modifications.put("C12", "TYG");
1463   modifications.put("C1X", "LYS");
1464   modifications.put("C25", "CYS");
1465   modifications.put("C2L", "CYS");
1466   modifications.put("C2S", "CYS");
1467   modifications.put("C31", "CYS");
1468   modifications.put("C32", "CYS");
1469   modifications.put("C34", "CYS");
1470   modifications.put("C36", "CYS");
1471   modifications.put("C37", "CYS");
1472   modifications.put("C38", "CYS");
1473   modifications.put("C3Y", "CYS");
1474   modifications.put("C42", "CYS");
1475   modifications.put("C43", "CYS");
1476   modifications.put("C45", "CYS");
1477   modifications.put("C46", "CYS");
1478   modifications.put("C49", "CYS");
1479   modifications.put("C4R", "CYS");
1480   modifications.put("C4S", "CYS");
1481   modifications.put("C5C", "CYS");
1482   modifications.put("C66", "XAA");
1483   modifications.put("C6C", "CYS");
1484   modifications.put("C99", "TFG");
1485   modifications.put("CAF", "CYS");
1486   modifications.put("CAL", "XAA");
1487   modifications.put("CAR", "CYS");
1488   modifications.put("CAS", "CYS");
1489   modifications.put("CAV", "XAA");
1490   modifications.put("CAY", "CYS");
1491   modifications.put("CB2", "CYS");
1492   modifications.put("CBR", "CYS");
1493   modifications.put("CBV", "CYS");
1494   modifications.put("CCC", "CYS");
1495   modifications.put("CCL", "LYS");
1496   modifications.put("CCS", "CYS");
1497   modifications.put("CCY", "CYG");
1498   modifications.put("CDE", "XAA");
1499   modifications.put("CDV", "XAA");
1500   modifications.put("CDW", "CYS");
1501   modifications.put("CEA", "CYS");
1502   modifications.put("CFL", "CYS");
1503   modifications.put("CFY", "FCYG"); // check
1504   modifications.put("CG1", "GLY");
1505   modifications.put("CGA", "GLU");
1506   modifications.put("CGU", "GLU");
1507   modifications.put("CH ", "CYS");
1508   modifications.put("CH6", "MYG");
1509   modifications.put("CH7", "KYG");
1510   modifications.put("CHF", "XAA");
1511   modifications.put("CHG", "XAA");
1512   modifications.put("CHP", "GLY");
1513   modifications.put("CHS", "XAA");
1514   modifications.put("CIR", "ARG");
1515   modifications.put("CJO", "GYG");
1516   modifications.put("CLE", "LEU");
1517   modifications.put("CLG", "LYS");
1518   modifications.put("CLH", "LYS");
1519   modifications.put("CLV", "AFG");
1520   modifications.put("CM0", "ASN");
1521   modifications.put("CME", "CYS");
1522   modifications.put("CMH", "CYS");
1523   modifications.put("CML", "CYS");
1524   modifications.put("CMR", "CYS");
1525   modifications.put("CMT", "CYS");
1526   modifications.put("CNU", "UR3");
1527   modifications.put("CP1", "CYS");
1528   modifications.put("CPC", "XAA");
1529   modifications.put("CPI", "XAA");
1530   modifications.put("CQR", "GYG");
1531   modifications.put("CR0", "TLG");
1532   modifications.put("CR2", "GYG");
1533   modifications.put("CR5", "GLY");
1534   modifications.put("CR7", "KYG");
1535   modifications.put("CR8", "HYG");
1536   modifications.put("CRF", "TWG");
1537   modifications.put("CRG", "THG");
1538   modifications.put("CRK", "MYG");
1539   modifications.put("CRO", "GYG");
1540   modifications.put("CRQ", "QYG");
1541   modifications.put("CRU", "EYG");
1542   modifications.put("CRW", "ASG");
1543   modifications.put("CRX", "ASG");
1544   modifications.put("CS0", "CYS");
1545   modifications.put("CS1", "CYS");
1546   modifications.put("CS3", "CYS");
1547   modifications.put("CS4", "CYS");
1548   modifications.put("CS8", "ASN");
1549   modifications.put("CSA", "CYS");
1550   modifications.put("CSB", "CYS");
1551   modifications.put("CSD", "CYS");
1552   modifications.put("CSE", "CYS");
1553   modifications.put("CSF", "CYS");
1554   modifications.put("CSH", "SHG");
1555   modifications.put("CSI", "GLY");
1556   modifications.put("CSJ", "CYS");
1557   modifications.put("CSL", "CYS");
1558   modifications.put("CSO", "CYS");
1559   modifications.put("CSP", "CYS");
1560   modifications.put("CSR", "CYS");
1561   modifications.put("CSS", "CYS");
1562   modifications.put("CSU", "CYS");
1563   modifications.put("CSW", "CYS");
1564   modifications.put("CSX", "CYS");
1565   modifications.put("CSY", "SYG");
1566   modifications.put("CSZ", "CYS");
1567   modifications.put("CTE", "TRP");
1568   modifications.put("CTG", "THR");
1569   modifications.put("CTH", "THR");
1570   modifications.put("CUC", "XAA");
1571   modifications.put("CWR", "SER");
1572   modifications.put("CXM", "MET");
1573   modifications.put("CY0", "CYS");
1574   modifications.put("CY1", "CYS");
1575   modifications.put("CY3", "CYS");
1576   modifications.put("CY4", "CYS");
1577   modifications.put("CYA", "CYS");
1578   modifications.put("CYD", "CYS");
1579   modifications.put("CYF", "CYS");
1580   modifications.put("CYG", "CYS");
1581   modifications.put("CYJ", "XAA");
1582   modifications.put("CYM", "CYS");
1583   modifications.put("CYQ", "CYS");
1584   modifications.put("CYR", "CYS");
1585   modifications.put("CYS", "CYS");
1586   modifications.put("CZ2", "CYS");
1587   modifications.put("CZO", "GYG");
1588   modifications.put("CZZ", "CYS");
1589   modifications.put("D11", "THR");
1590   modifications.put("D1P", "ASN");
1591   modifications.put("D3 ", "ASN");
1592   modifications.put("D33", "ASN");
1593   modifications.put("D3P", "GLY");
1594   modifications.put("D3T", "THR");
1595   modifications.put("D4M", "THR");
1596   modifications.put("D4P", "XAA");
1597   modifications.put("DA ", "ALA");
1598   modifications.put("DA2", "XAA");
1599   modifications.put("DAB", "ALA");
1600   modifications.put("DAH", "PHE");
1601   modifications.put("DAL", "ALA");
1602   modifications.put("DAR", "ARG");
1603   modifications.put("DAS", "ASP");
1604   modifications.put("DBB", "THR");
1605   modifications.put("DBM", "ASN");
1606   modifications.put("DBS", "SER");
1607   modifications.put("DBU", "THR");
1608   modifications.put("DBY", "TYR");
1609   modifications.put("DBZ", "ALA");
1610   modifications.put("DC ", "CYS");
1611   modifications.put("DC2", "CYS");
1612   modifications.put("DCG", "GLY");
1613   modifications.put("DCI", "XAA");
1614   modifications.put("DCL", "XAA");
1615   modifications.put("DCT", "CYS");
1616   modifications.put("DCY", "CYS");
1617   modifications.put("DDE", "HIS");
1618   modifications.put("DDG", "GLY");
1619   modifications.put("DDN", "UR3");
1620   modifications.put("DDX", "ASN");
1621   modifications.put("DFC", "CYS");
1622   modifications.put("DFG", "GLY");
1623   modifications.put("DFI", "XAA");
1624   modifications.put("DFO", "XAA");
1625   modifications.put("DFT", "ASN");
1626   modifications.put("DG ", "GLY");
1627   modifications.put("DGH", "GLY");
1628   modifications.put("DGI", "GLY");
1629   modifications.put("DGL", "GLU");
1630   modifications.put("DGN", "GLN");
1631   modifications.put("DHA", "SER");
1632   modifications.put("DHI", "HIS");
1633   modifications.put("DHL", "XAA");
1634   modifications.put("DHN", "VAL");
1635   modifications.put("DHP", "XAA");
1636   modifications.put("DHU", "UR3");
1637   modifications.put("DHV", "VAL");
1638   modifications.put("DI ", "ILE");
1639   modifications.put("DIL", "ILE");
1640   modifications.put("DIR", "ARG");
1641   modifications.put("DIV", "VAL");
1642   modifications.put("DLE", "LEU");
1643   modifications.put("DLS", "LYS");
1644   modifications.put("DLY", "LYS");
1645   modifications.put("DM0", "LYS");
1646   modifications.put("DMH", "ASN");
1647   modifications.put("DMK", "ASP");
1648   modifications.put("DMT", "XAA");
1649   modifications.put("DN ", "ASN");
1650   modifications.put("DNE", "LEU");
1651   modifications.put("DNG", "LEU");
1652   modifications.put("DNL", "LYS");
1653   modifications.put("DNM", "LEU");
1654   modifications.put("DNP", "ALA");
1655   modifications.put("DNR", "CYS");
1656   modifications.put("DNS", "LYS");
1657   modifications.put("DOA", "XAA");
1658   modifications.put("DOC", "CYS");
1659   modifications.put("DOH", "ASP");
1660   modifications.put("DON", "LEU");
1661   modifications.put("DPB", "THR");
1662   modifications.put("DPH", "PHE");
1663   modifications.put("DPL", "PRO");
1664   modifications.put("DPP", "ALA");
1665   modifications.put("DPQ", "TYR");
1666   modifications.put("DPR", "PRO");
1667   modifications.put("DPY", "ASN");
1668   modifications.put("DRM", "UR3");
1669   modifications.put("DRP", "ASN");
1670   modifications.put("DRT", "THR");
1671   modifications.put("DRZ", "ASN");
1672   modifications.put("DSE", "SER");
1673   modifications.put("DSG", "ASN");
1674   modifications.put("DSN", "SER");
1675   modifications.put("DSP", "ASP");
1676   modifications.put("DT ", "THR");
1677   modifications.put("DTH", "THR");
1678   modifications.put("DTR", "TRP");
1679   modifications.put("DTY", "TYR");
1680   modifications.put("DU ", "UR3");
1681   modifications.put("DVA", "VAL");
1682   modifications.put("DXD", "ASN");
1683   modifications.put("DXN", "ASN");
1684   modifications.put("DYG", "DYG");
1685   modifications.put("DYS", "CYS");
1686   modifications.put("DZM", "ALA");
1687   modifications.put("E ", "ALA");
1688   modifications.put("E1X", "ALA");
1689   modifications.put("ECC", "GLN");
1690   modifications.put("EDA", "ALA");
1691   modifications.put("EFC", "CYS");
1692   modifications.put("EHP", "PHE");
1693   modifications.put("EIT", "THR");
1694   modifications.put("ENP", "ASN");
1695   modifications.put("ESB", "TYR");
1696   modifications.put("ESC", "MET");
1697   modifications.put("EXB", "XAA");
1698   modifications.put("EXY", "LEU");
1699   modifications.put("EY5", "ASN");
1700   modifications.put("EYS", "XAA");
1701   modifications.put("F2F", "PHE");
1702   modifications.put("FA2", "ALA");
1703   modifications.put("FA5", "ASN");
1704   modifications.put("FAG", "ASN");
1705   modifications.put("FAI", "ASN");
1706   modifications.put("FB5", "ALA");
1707   modifications.put("FB6", "ALA");
1708   modifications.put("FCL", "PHE");
1709   modifications.put("FFD", "ASN");
1710   modifications.put("FGA", "GLU");
1711   modifications.put("FGL", "GLY");
1712   modifications.put("FGP", "SER");
1713   modifications.put("FHL", "XAA");
1714   modifications.put("FHO", "LYS");
1715   modifications.put("FHU", "UR3");
1716   modifications.put("FLA", "ALA");
1717   modifications.put("FLE", "LEU");
1718   modifications.put("FLT", "TYR");
1719   modifications.put("FME", "MET");
1720   modifications.put("FMG", "GLY");
1721   modifications.put("FMU", "ASN");
1722   modifications.put("FOE", "CYS");
1723   modifications.put("FOX", "GLY");
1724   modifications.put("FP9", "PRO");
1725   modifications.put("FPA", "PHE");
1726   modifications.put("FRD", "XAA");
1727   modifications.put("FT6", "TRP");
1728   modifications.put("FTR", "TRP");
1729   modifications.put("FTY", "TYR");
1730   modifications.put("FVA", "VAL");
1731   modifications.put("FZN", "LYS");
1732   modifications.put("G ", "GLY");
1733   modifications.put("G25", "GLY");
1734   modifications.put("G2L", "GLY");
1735   modifications.put("G2S", "GLY");
1736   modifications.put("G31", "GLY");
1737   modifications.put("G32", "GLY");
1738   modifications.put("G33", "GLY");
1739   modifications.put("G36", "GLY");
1740   modifications.put("G38", "GLY");
1741   modifications.put("G42", "GLY");
1742   modifications.put("G46", "GLY");
1743   modifications.put("G47", "GLY");
1744   modifications.put("G48", "GLY");
1745   modifications.put("G49", "GLY");
1746   modifications.put("G4P", "ASN");
1747   modifications.put("G7M", "GLY");
1748   modifications.put("GAO", "GLY");
1749   modifications.put("GAU", "GLU");
1750   modifications.put("GCK", "CYS");
1751   modifications.put("GCM", "XAA");
1752   modifications.put("GDP", "GLY");
1753   modifications.put("GDR", "GLY");
1754   modifications.put("GFL", "GLY");
1755   modifications.put("GGL", "GLU");
1756   modifications.put("GH3", "GLY");
1757   modifications.put("GHG", "GLN");
1758   modifications.put("GHP", "GLY");
1759   modifications.put("GL3", "GLY");
1760   modifications.put("GLH", "GLN");
1761   modifications.put("GLJ", "GLU");
1762   modifications.put("GLK", "GLU");
1763   modifications.put("GLM", "XAA");
1764   modifications.put("GLN", "GLN");
1765   modifications.put("GLQ", "GLU");
1766   modifications.put("GLU", "GLU");
1767   modifications.put("GLX", "GLX");
1768   modifications.put("GLY", "GLY");
1769   modifications.put("GLZ", "GLY");
1770   modifications.put("GMA", "GLU");
1771   modifications.put("GMS", "GLY");
1772   modifications.put("GMU", "UR3");
1773   modifications.put("GN7", "GLY");
1774   modifications.put("GND", "XAA");
1775   modifications.put("GNE", "ASN");
1776   modifications.put("GOM", "GLY");
1777   modifications.put("GPL", "LYS");
1778   modifications.put("GS ", "GLY");
1779   modifications.put("GSC", "GLY");
1780   modifications.put("GSR", "GLY");
1781   modifications.put("GSS", "GLY");
1782   modifications.put("GSU", "GLU");
1783   modifications.put("GT9", "CYS");
1784   modifications.put("GTP", "GLY");
1785   modifications.put("GVL", "XAA");
1786   modifications.put("GYC", "CYG");
1787   modifications.put("GYS", "SYG");
1788   modifications.put("H2U", "UR3");
1789   modifications.put("H5M", "PRO");
1790   modifications.put("HAC", "ALA");
1791   modifications.put("HAR", "ARG");
1792   modifications.put("HBN", "HIS");
1793   modifications.put("HCS", "XAA");
1794   modifications.put("HDP", "UR3");
1795   modifications.put("HEU", "UR3");
1796   modifications.put("HFA", "XAA");
1797   modifications.put("HGL", "XAA");
1798   modifications.put("HHI", "HIS");
1799   modifications.put("HHK", "AK"); // check
1800   modifications.put("HIA", "HIS");
1801   modifications.put("HIC", "HIS");
1802   modifications.put("HIP", "HIS");
1803   modifications.put("HIQ", "HIS");
1804   modifications.put("HIS", "HIS");
1805   modifications.put("HL2", "LEU");
1806   modifications.put("HLU", "LEU");
1807   modifications.put("HMR", "ARG");
1808   modifications.put("HOL", "ASN");
1809   modifications.put("HPC", "PHE");
1810   modifications.put("HPE", "PHE");
1811   modifications.put("HPH", "PHE");
1812   modifications.put("HPQ", "PHE");
1813   modifications.put("HQA", "ALA");
1814   modifications.put("HRG", "ARG");
1815   modifications.put("HRP", "TRP");
1816   modifications.put("HS8", "HIS");
1817   modifications.put("HS9", "HIS");
1818   modifications.put("HSE", "SER");
1819   modifications.put("HSL", "SER");
1820   modifications.put("HSO", "HIS");
1821   modifications.put("HTI", "CYS");
1822   modifications.put("HTN", "ASN");
1823   modifications.put("HTR", "TRP");
1824   modifications.put("HV5", "ALA");
1825   modifications.put("HVA", "VAL");
1826   modifications.put("HY3", "PRO");
1827   modifications.put("HYP", "PRO");
1828   modifications.put("HZP", "PRO");
1829   modifications.put("I ", "ILE");
1830   modifications.put("I2M", "ILE");
1831   modifications.put("I58", "LYS");
1832   modifications.put("I5C", "CYS");
1833   modifications.put("IAM", "ALA");
1834   modifications.put("IAR", "ARG");
1835   modifications.put("IAS", "ASP");
1836   modifications.put("IC ", "CYS");
1837   modifications.put("IEL", "LYS");
1838   modifications.put("IEY", "HYG");
1839   modifications.put("IG ", "GLY");
1840   modifications.put("IGL", "GLY");
1841   modifications.put("IGU", "GLY");
1842   modifications.put("IIC", "SHG");
1843   modifications.put("IIL", "ILE");
1844   modifications.put("ILE", "ILE");
1845   modifications.put("ILG", "GLU");
1846   modifications.put("ILX", "ILE");
1847   modifications.put("IMC", "CYS");
1848   modifications.put("IML", "ILE");
1849   modifications.put("IOY", "PHE");
1850   modifications.put("IPG", "GLY");
1851   modifications.put("IPN", "ASN");
1852   modifications.put("IRN", "ASN");
1853   modifications.put("IT1", "LYS");
1854   modifications.put("IU ", "UR3");
1855   modifications.put("IYR", "TYR");
1856   modifications.put("IYT", "THR");
1857   modifications.put("IZO", "MET");
1858   modifications.put("JJJ", "CYS");
1859   modifications.put("JJK", "CYS");
1860   modifications.put("JJL", "CYS");
1861   modifications.put("JW5", "ASN");
1862   modifications.put("K1R", "CYS");
1863   modifications.put("KAG", "GLY");
1864   modifications.put("KCX", "LYS");
1865   modifications.put("KGC", "LYS");
1866   modifications.put("KNB", "ALA");
1867   modifications.put("KOR", "MET");
1868   modifications.put("KPI", "LYS");
1869   modifications.put("KST", "LYS");
1870   modifications.put("KYQ", "LYS");
1871   modifications.put("L2A", "XAA");
1872   modifications.put("LA2", "LYS");
1873   modifications.put("LAA", "ASP");
1874   modifications.put("LAL", "ALA");
1875   modifications.put("LBY", "LYS");
1876   modifications.put("LC ", "CYS");
1877   modifications.put("LCA", "ALA");
1878   modifications.put("LCC", "ASN");
1879   modifications.put("LCG", "GLY");
1880   modifications.put("LCH", "ASN");
1881   modifications.put("LCK", "LYS");
1882   modifications.put("LCX", "LYS");
1883   modifications.put("LDH", "LYS");
1884   modifications.put("LED", "LEU");
1885   modifications.put("LEF", "LEU");
1886   modifications.put("LEH", "LEU");
1887   modifications.put("LEI", "VAL");
1888   modifications.put("LEM", "LEU");
1889   modifications.put("LEN", "LEU");
1890   modifications.put("LET", "XAA");
1891   modifications.put("LEU", "LEU");
1892   modifications.put("LEX", "LEU");
1893   modifications.put("LG ", "GLY");
1894   modifications.put("LGP", "GLY");
1895   modifications.put("LHC", "XAA");
1896   modifications.put("LHU", "UR3");
1897   modifications.put("LKC", "ASN");
1898   modifications.put("LLP", "LYS");
1899   modifications.put("LLY", "LYS");
1900   modifications.put("LME", "GLU");
1901   modifications.put("LMF", "LYS");
1902   modifications.put("LMQ", "GLN");
1903   modifications.put("LMS", "ASN");
1904   modifications.put("LP6", "LYS");
1905   modifications.put("LPD", "PRO");
1906   modifications.put("LPG", "GLY");
1907   modifications.put("LPL", "XAA");
1908   modifications.put("LPS", "SER");
1909   modifications.put("LSO", "XAA");
1910   modifications.put("LTA", "XAA");
1911   modifications.put("LTR", "TRP");
1912   modifications.put("LVG", "GLY");
1913   modifications.put("LVN", "VAL");
1914   modifications.put("LYF", "LYS");
1915   modifications.put("LYK", "LYS");
1916   modifications.put("LYM", "LYS");
1917   modifications.put("LYN", "LYS");
1918   modifications.put("LYR", "LYS");
1919   modifications.put("LYS", "LYS");
1920   modifications.put("LYX", "LYS");
1921   modifications.put("LYZ", "LYS");
1922   modifications.put("M0H", "CYS");
1923   modifications.put("M1G", "GLY");
1924   modifications.put("M2G", "GLY");
1925   modifications.put("M2L", "LYS");
1926   modifications.put("M2S", "MET");
1927   modifications.put("M30", "GLY");
1928   modifications.put("M3L", "LYS");
1929   modifications.put("M5M", "CYS");
1930   modifications.put("MA ", "ALA");
1931   modifications.put("MA6", "ALA");
1932   modifications.put("MA7", "ALA");
1933   modifications.put("MAA", "ALA");
1934   modifications.put("MAD", "ALA");
1935   modifications.put("MAI", "ARG");
1936   modifications.put("MBQ", "TYR");
1937   modifications.put("MBZ", "ASN");
1938   modifications.put("MC1", "SER");
1939   modifications.put("MCG", "XAA");
1940   modifications.put("MCL", "LYS");
1941   modifications.put("MCS", "CYS");
1942   modifications.put("MCY", "CYS");
1943   modifications.put("MD3", "CYS");
1944   modifications.put("MD6", "GLY");
1945   modifications.put("MDH", "XAA");
1946   modifications.put("MDO", "ASG");
1947   modifications.put("MDR", "ASN");
1948   modifications.put("MEA", "PHE");
1949   modifications.put("MED", "MET");
1950   modifications.put("MEG", "GLU");
1951   modifications.put("MEN", "ASN");
1952   modifications.put("MEP", "UR3");
1953   modifications.put("MEQ", "GLN");
1954   modifications.put("MET", "MET");
1955   modifications.put("MEU", "GLY");
1956   modifications.put("MF3", "XAA");
1957   modifications.put("MFC", "GYG");
1958   modifications.put("MG1", "GLY");
1959   modifications.put("MGG", "ARG");
1960   modifications.put("MGN", "GLN");
1961   modifications.put("MGQ", "ALA");
1962   modifications.put("MGV", "GLY");
1963   modifications.put("MGY", "GLY");
1964   modifications.put("MHL", "LEU");
1965   modifications.put("MHO", "MET");
1966   modifications.put("MHS", "HIS");
1967   modifications.put("MIA", "ALA");
1968   modifications.put("MIS", "SER");
1969   modifications.put("MK8", "LEU");
1970   modifications.put("ML3", "LYS");
1971   modifications.put("MLE", "LEU");
1972   modifications.put("MLL", "LEU");
1973   modifications.put("MLY", "LYS");
1974   modifications.put("MLZ", "LYS");
1975   modifications.put("MME", "MET");
1976   modifications.put("MMO", "ARG");
1977   modifications.put("MMT", "THR");
1978   modifications.put("MND", "ASN");
1979   modifications.put("MNL", "LEU");
1980   modifications.put("MNU", "UR3");
1981   modifications.put("MNV", "VAL");
1982   modifications.put("MOD", "XAA");
1983   modifications.put("MP8", "PRO");
1984   modifications.put("MPH", "XAA");
1985   modifications.put("MPJ", "XAA");
1986   modifications.put("MPQ", "GLY");
1987   modifications.put("MRG", "GLY");
1988   modifications.put("MSA", "GLY");
1989   modifications.put("MSE", "MET");
1990   modifications.put("MSL", "MET");
1991   modifications.put("MSO", "MET");
1992   modifications.put("MSP", "XAA");
1993   modifications.put("MT2", "MET");
1994   modifications.put("MTR", "THR");
1995   modifications.put("MTU", "ALA");
1996   modifications.put("MTY", "TYR");
1997   modifications.put("MVA", "VAL");
1998   modifications.put("N ", "ASN");
1999   modifications.put("N10", "SER");
2000   modifications.put("N2C", "XAA");
2001   modifications.put("N5I", "ASN");
2002   modifications.put("N5M", "CYS");
2003   modifications.put("N6G", "GLY");
2004   modifications.put("N7P", "PRO");
2005   modifications.put("NA8", "ALA");
2006   modifications.put("NAL", "ALA");
2007   modifications.put("NAM", "ALA");
2008   modifications.put("NB8", "ASN");
2009   modifications.put("NBQ", "TYR");
2010   modifications.put("NC1", "SER");
2011   modifications.put("NCB", "ALA");
2012   modifications.put("NCX", "ASN");
2013   modifications.put("NCY", "XAA");
2014   modifications.put("NDF", "PHE");
2015   modifications.put("NDN", "UR3");
2016   modifications.put("NEM", "HIS");
2017   modifications.put("NEP", "HIS");
2018   modifications.put("NF2", "ASN");
2019   modifications.put("NFA", "PHE");
2020   modifications.put("NHL", "GLU");
2021   modifications.put("NIT", "XAA");
2022   modifications.put("NIY", "TYR");
2023   modifications.put("NLE", "LEU");
2024   modifications.put("NLN", "LEU");
2025   modifications.put("NLO", "LEU");
2026   modifications.put("NLP", "LEU");
2027   modifications.put("NLQ", "GLN");
2028   modifications.put("NMC", "GLY");
2029   modifications.put("NMM", "ARG");
2030   modifications.put("NMS", "THR");
2031   modifications.put("NMT", "THR");
2032   modifications.put("NNH", "ARG");
2033   modifications.put("NP3", "ASN");
2034   modifications.put("NPH", "CYS");
2035   modifications.put("NPI", "ALA");
2036   modifications.put("NRP", "LYG");
2037   modifications.put("NRQ", "MYG");
2038   modifications.put("NSK", "XAA");
2039   modifications.put("NTY", "TYR");
2040   modifications.put("NVA", "VAL");
2041   modifications.put("NYC", "TWG");
2042   modifications.put("NYG", "NYG");
2043   modifications.put("NYM", "ASN");
2044   modifications.put("NYS", "CYS");
2045   modifications.put("NZH", "HIS");
2046   modifications.put("O12", "XAA");
2047   modifications.put("O2C", "ASN");
2048   modifications.put("O2G", "GLY");
2049   modifications.put("OAD", "ASN");
2050   modifications.put("OAS", "SER");
2051   modifications.put("OBF", "XAA");
2052   modifications.put("OBS", "XAA");
2053   modifications.put("OCS", "CYS");
2054   modifications.put("OCY", "CYS");
2055   modifications.put("ODP", "ASN");
2056   modifications.put("OHI", "HIS");
2057   modifications.put("OHS", "ASP");
2058   modifications.put("OIC", "XAA");
2059   modifications.put("OIP", "ILE");
2060   modifications.put("OLE", "XAA");
2061   modifications.put("OLT", "THR");
2062   modifications.put("OLZ", "SER");
2063   modifications.put("OMC", "CYS");
2064   modifications.put("OMG", "GLY");
2065   modifications.put("OMT", "MET");
2066   modifications.put("OMU", "UR3");
2067   modifications.put("ONE", "UR3");
2068   modifications.put("ONH", "ALA");
2069   modifications.put("ONL", "XAA");
2070   modifications.put("OPR", "ARG");
2071   modifications.put("ORN", "ALA");
2072   modifications.put("ORQ", "ARG");
2073   modifications.put("OSE", "SER");
2074   modifications.put("OTB", "XAA");
2075   modifications.put("OTH", "THR");
2076   modifications.put("OTY", "TYR");
2077   modifications.put("OXX", "ASP");
2078   modifications.put("P ", "GLY");
2079   modifications.put("P1L", "CYS");
2080   modifications.put("P1P", "ASN");
2081   modifications.put("P2T", "THR");
2082   modifications.put("P2U", "UR3");
2083   modifications.put("P2Y", "PRO");
2084   modifications.put("P5P", "ALA");
2085   modifications.put("PAQ", "TYR");
2086   modifications.put("PAS", "ASP");
2087   modifications.put("PAT", "TRP");
2088   modifications.put("PAU", "ALA");
2089   modifications.put("PBB", "CYS");
2090   modifications.put("PBF", "PHE");
2091   modifications.put("PBT", "ASN");
2092   modifications.put("PCA", "GLU");
2093   modifications.put("PCC", "PRO");
2094   modifications.put("PCE", "XAA");
2095   modifications.put("PCS", "PHE");
2096   modifications.put("PDL", "XAA");
2097   modifications.put("PDU", "UR3");
2098   modifications.put("PEC", "CYS");
2099   modifications.put("PF5", "PHE");
2100   modifications.put("PFF", "PHE");
2101   modifications.put("PFX", "XAA");
2102   modifications.put("PG1", "SER");
2103   modifications.put("PG7", "GLY");
2104   modifications.put("PG9", "GLY");
2105   modifications.put("PGL", "XAA");
2106   modifications.put("PGN", "GLY");
2107   modifications.put("PGP", "GLY");
2108   modifications.put("PGY", "GLY");
2109   modifications.put("PHA", "PHE");
2110   modifications.put("PHD", "ASP");
2111   modifications.put("PHE", "PHE");
2112   modifications.put("PHI", "PHE");
2113   modifications.put("PHL", "PHE");
2114   modifications.put("PHM", "PHE");
2115   modifications.put("PIA", "AYG");
2116   modifications.put("PIV", "XAA");
2117   modifications.put("PLE", "LEU");
2118   modifications.put("PM3", "PHE");
2119   modifications.put("PMT", "CYS");
2120   modifications.put("POM", "PRO");
2121   modifications.put("PPN", "PHE");
2122   modifications.put("PPU", "ALA");
2123   modifications.put("PPW", "GLY");
2124   modifications.put("PQ1", "ASN");
2125   modifications.put("PR3", "CYS");
2126   modifications.put("PR5", "ALA");
2127   modifications.put("PR9", "PRO");
2128   modifications.put("PRN", "ALA");
2129   modifications.put("PRO", "PRO");
2130   modifications.put("PRS", "PRO");
2131   modifications.put("PSA", "PHE");
2132   modifications.put("PSH", "HIS");
2133   modifications.put("PST", "THR");
2134   modifications.put("PSU", "UR3");
2135   modifications.put("PSW", "CYS");
2136   modifications.put("PTA", "XAA");
2137   modifications.put("PTH", "TYR");
2138   modifications.put("PTM", "TYR");
2139   modifications.put("PTR", "TYR");
2140   modifications.put("PU ", "ALA");
2141   modifications.put("PUY", "ASN");
2142   modifications.put("PVH", "HIS");
2143   modifications.put("PVL", "XAA");
2144   modifications.put("PYA", "ALA");
2145   modifications.put("PYO", "UR3");
2146   modifications.put("PYX", "CYS");
2147   modifications.put("PYY", "ASN");
2148   modifications.put("QLG", "QLG");
2149   modifications.put("QMM", "GLN");
2150   modifications.put("QPA", "CYS");
2151   modifications.put("QPH", "PHE");
2152   modifications.put("QUO", "GLY");
2153   modifications.put("R ", "ALA");
2154   modifications.put("R1A", "CYS");
2155   modifications.put("R4K", "TRP");
2156   modifications.put("RC7", "HYG");
2157   modifications.put("RE0", "TRP");
2158   modifications.put("RE3", "TRP");
2159   modifications.put("RIA", "ALA");
2160   modifications.put("RMP", "ALA");
2161   modifications.put("RON", "XAA");
2162   modifications.put("RT ", "THR");
2163   modifications.put("RTP", "ASN");
2164   modifications.put("S1H", "SER");
2165   modifications.put("S2C", "CYS");
2166   modifications.put("S2D", "ALA");
2167   modifications.put("S2M", "THR");
2168   modifications.put("S2P", "ALA");
2169   modifications.put("S4A", "ALA");
2170   modifications.put("S4C", "CYS");
2171   modifications.put("S4G", "GLY");
2172   modifications.put("S4U", "UR3");
2173   modifications.put("S6G", "GLY");
2174   modifications.put("SAC", "SER");
2175   modifications.put("SAH", "CYS");
2176   modifications.put("SAR", "GLY");
2177   modifications.put("SBL", "SER");
2178   modifications.put("SC ", "CYS");
2179   modifications.put("SCH", "CYS");
2180   modifications.put("SCS", "CYS");
2181   modifications.put("SCY", "CYS");
2182   modifications.put("SD2", "XAA");
2183   modifications.put("SDG", "GLY");
2184   modifications.put("SDP", "SER");
2185   modifications.put("SEB", "SER");
2186   modifications.put("SEC", "ALA");
2187   modifications.put("SEG", "ALA");
2188   modifications.put("SEL", "SER");
2189   modifications.put("SEM", "SER");
2190   modifications.put("SEN", "SER");
2191   modifications.put("SEP", "SER");
2192   modifications.put("SER", "SER");
2193   modifications.put("SET", "SER");
2194   modifications.put("SGB", "SER");
2195   modifications.put("SHC", "CYS");
2196   modifications.put("SHP", "GLY");
2197   modifications.put("SHR", "LYS");
2198   modifications.put("SIB", "CYS");
2199   modifications.put("SIC", "DC"); // check
2200   modifications.put("SLA", "PRO");
2201   modifications.put("SLR", "PRO");
2202   modifications.put("SLZ", "LYS");
2203   modifications.put("SMC", "CYS");
2204   modifications.put("SME", "MET");
2205   modifications.put("SMF", "PHE");
2206   modifications.put("SMP", "ALA");
2207   modifications.put("SMT", "THR");
2208   modifications.put("SNC", "CYS");
2209   modifications.put("SNN", "ASN");
2210   modifications.put("SOC", "CYS");
2211   modifications.put("SOS", "ASN");
2212   modifications.put("SOY", "SER");
2213   modifications.put("SPT", "THR");
2214   modifications.put("SRA", "ALA");
2215   modifications.put("SSU", "UR3");
2216   modifications.put("STY", "TYR");
2217   modifications.put("SUB", "XAA");
2218   modifications.put("SUI", "DG");
2219   modifications.put("SUN", "SER");
2220   modifications.put("SUR", "UR3");
2221   modifications.put("SVA", "SER");
2222   modifications.put("SVV", "SER");
2223   modifications.put("SVW", "SER");
2224   modifications.put("SVX", "SER");
2225   modifications.put("SVY", "SER");
2226   modifications.put("SVZ", "XAA");
2227   modifications.put("SWG", "SWG");
2228   modifications.put("SYS", "CYS");
2229   modifications.put("T ", "THR");
2230   modifications.put("T11", "PHE");
2231   modifications.put("T23", "THR");
2232   modifications.put("T2S", "THR");
2233   modifications.put("T2T", "ASN");
2234   modifications.put("T31", "UR3");
2235   modifications.put("T32", "THR");
2236   modifications.put("T36", "THR");
2237   modifications.put("T37", "THR");
2238   modifications.put("T38", "THR");
2239   modifications.put("T39", "THR");
2240   modifications.put("T3P", "THR");
2241   modifications.put("T41", "THR");
2242   modifications.put("T48", "THR");
2243   modifications.put("T49", "THR");
2244   modifications.put("T4S", "THR");
2245   modifications.put("T5O", "UR3");
2246   modifications.put("T5S", "THR");
2247   modifications.put("T66", "XAA");
2248   modifications.put("T6A", "ALA");
2249   modifications.put("TA3", "THR");
2250   modifications.put("TA4", "XAA");
2251   modifications.put("TAF", "THR");
2252   modifications.put("TAL", "ASN");
2253   modifications.put("TAV", "ASP");
2254   modifications.put("TBG", "VAL");
2255   modifications.put("TBM", "THR");
2256   modifications.put("TC1", "CYS");
2257   modifications.put("TCP", "THR");
2258   modifications.put("TCQ", "TYR");
2259   modifications.put("TCR", "TRP");
2260   modifications.put("TCY", "ALA");
2261   modifications.put("TDD", "LEU");
2262   modifications.put("TDY", "THR");
2263   modifications.put("TFE", "THR");
2264   modifications.put("TFO", "ALA");
2265   modifications.put("TFQ", "PHE");
2266   modifications.put("TFT", "THR");
2267   modifications.put("TGP", "GLY");
2268   modifications.put("TH6", "THR");
2269   modifications.put("THC", "THR");
2270   modifications.put("THO", "XAA");
2271   modifications.put("THR", "THR");
2272   modifications.put("THX", "ASN");
2273   modifications.put("THZ", "ARG");
2274   modifications.put("TIH", "ALA");
2275   modifications.put("TLB", "ASN");
2276   modifications.put("TLC", "THR");
2277   modifications.put("TLN", "UR3");
2278   modifications.put("TMB", "THR");
2279   modifications.put("TMD", "THR");
2280   modifications.put("TNB", "CYS");
2281   modifications.put("TNR", "SER");
2282   modifications.put("TOX", "TRP");
2283   modifications.put("TP1", "THR");
2284   modifications.put("TPC", "CYS");
2285   modifications.put("TPG", "GLY");
2286   modifications.put("TPH", "XAA");
2287   modifications.put("TPL", "TRP");
2288   modifications.put("TPO", "THR");
2289   modifications.put("TPQ", "TYR");
2290   modifications.put("TQI", "TRP");
2291   modifications.put("TQQ", "TRP");
2292   modifications.put("TRF", "TRP");
2293   modifications.put("TRG", "LYS");
2294   modifications.put("TRN", "TRP");
2295   modifications.put("TRO", "TRP");
2296   modifications.put("TRP", "TRP");
2297   modifications.put("TRQ", "TRP");
2298   modifications.put("TRW", "TRP");
2299   modifications.put("TRX", "TRP");
2300   modifications.put("TS ", "ASN");
2301   modifications.put("TST", "XAA");
2302   modifications.put("TT ", "ASN");
2303   modifications.put("TTD", "THR");
2304   modifications.put("TTI", "UR3");
2305   modifications.put("TTM", "THR");
2306   modifications.put("TTQ", "TRP");
2307   modifications.put("TTS", "TYR");
2308   modifications.put("TY1", "TYR");
2309   modifications.put("TY2", "TYR");
2310   modifications.put("TY3", "TYR");
2311   modifications.put("TY5", "TYR");
2312   modifications.put("TYB", "TYR");
2313   modifications.put("TYI", "TYR");
2314   modifications.put("TYJ", "TYR");
2315   modifications.put("TYN", "TYR");
2316   modifications.put("TYO", "TYR");
2317   modifications.put("TYQ", "TYR");
2318   modifications.put("TYR", "TYR");
2319   modifications.put("TYS", "TYR");
2320   modifications.put("TYT", "TYR");
2321   modifications.put("TYU", "ASN");
2322   modifications.put("TYW", "TYR");
2323   modifications.put("TYX", "XAA");
2324   modifications.put("TYY", "TYR");
2325   modifications.put("TZB", "XAA");
2326   modifications.put("TZO", "XAA");
2327   modifications.put("U ", "UR3");
2328   modifications.put("U25", "UR3");
2329   modifications.put("U2L", "UR3");
2330   modifications.put("U2N", "UR3");
2331   modifications.put("U2P", "UR3");
2332   modifications.put("U31", "UR3");
2333   modifications.put("U33", "UR3");
2334   modifications.put("U34", "UR3");
2335   modifications.put("U36", "UR3");
2336   modifications.put("U37", "UR3");
2337   modifications.put("U8U", "UR3");
2338   modifications.put("UAR", "UR3");
2339   modifications.put("UCL", "UR3");
2340   modifications.put("UD5", "UR3");
2341   modifications.put("UDP", "ASN");
2342   modifications.put("UFP", "ASN");
2343   modifications.put("UFR", "UR3");
2344   modifications.put("UFT", "UR3");
2345   modifications.put("UMA", "ALA");
2346   modifications.put("UMP", "UR3");
2347   modifications.put("UMS", "UR3");
2348   modifications.put("UN1", "XAA");
2349   modifications.put("UN2", "XAA");
2350   modifications.put("UNK", "XAA");
2351   modifications.put("UR3", "UR3");
2352   modifications.put("URD", "UR3");
2353   modifications.put("US1", "UR3");
2354   modifications.put("US2", "UR3");
2355   modifications.put("US3", "THR");
2356   modifications.put("US5", "UR3");
2357   modifications.put("USM", "UR3");
2358   modifications.put("VAD", "VAL");
2359   modifications.put("VAF", "VAL");
2360   modifications.put("VAL", "VAL");
2361   modifications.put("VB1", "LYS");
2362   modifications.put("VDL", "XAA");
2363   modifications.put("VLL", "XAA");
2364   modifications.put("VLM", "XAA");
2365   modifications.put("VMS", "XAA");
2366   modifications.put("VOL", "XAA");
2367   modifications.put("WCR", "GYG");
2368   modifications.put("X ", "GLY");
2369   modifications.put("X2W", "GLU");
2370   modifications.put("X4A", "ASN");
2371   modifications.put("X9Q", "AFG");
2372   modifications.put("XAD", "ALA");
2373   modifications.put("XAE", "ASN");
2374   modifications.put("XAL", "ALA");
2375   modifications.put("XAR", "ASN");
2376   modifications.put("XCL", "CYS");
2377   modifications.put("XCN", "CYS");
2378   modifications.put("XCP", "XAA");
2379   modifications.put("XCR", "CYS");
2380   modifications.put("XCS", "ASN");
2381   modifications.put("XCT", "CYS");
2382   modifications.put("XCY", "CYS");
2383   modifications.put("XGA", "ASN");
2384   modifications.put("XGL", "GLY");
2385   modifications.put("XGR", "GLY");
2386   modifications.put("XGU", "GLY");
2387   modifications.put("XPR", "PRO");
2388   modifications.put("XSN", "ASN");
2389   modifications.put("XTH", "THR");
2390   modifications.put("XTL", "THR");
2391   modifications.put("XTR", "THR");
2392   modifications.put("XTS", "GLY");
2393   modifications.put("XTY", "ASN");
2394   modifications.put("XUA", "ALA");
2395   modifications.put("XUG", "GLY");
2396   modifications.put("XX1", "LYS");
2397   modifications.put("XXY", "THG");
2398   modifications.put("XYG", "DYG");
2399   modifications.put("Y ", "ALA");
2400   modifications.put("YCM", "CYS");
2401   modifications.put("YG ", "GLY");
2402   modifications.put("YOF", "TYR");
2403   modifications.put("YRR", "ASN");
2404   modifications.put("YYG", "GLY");
2405   modifications.put("Z ", "CYS");
2406   modifications.put("Z01", "ALA");
2407   modifications.put("ZAD", "ALA");
2408   modifications.put("ZAL", "ALA");
2409   modifications.put("ZBC", "CYS");
2410   modifications.put("ZBU", "UR3");
2411   modifications.put("ZCL", "PHE");
2412   modifications.put("ZCY", "CYS");
2413   modifications.put("ZDU", "UR3");
2414   modifications.put("ZFB", "XAA");
2415   modifications.put("ZGU", "GLY");
2416   modifications.put("ZHP", "ASN");
2417   modifications.put("ZTH", "THR");
2418   modifications.put("ZU0", "THR");
2419   modifications.put("ZZJ", "ALA");
2420  
2421   }
2422  
2423   public static String getCanonicalAminoAcid(String aA)
2424   {
2425   String canonical = modifications.get(aA);
2426   return canonical == null ? aA : canonical;
2427   }
2428  
2429   // main method generates perl representation of residue property hash
2430   // / cut here
2431   /**
2432   * @j2sIgnore
2433   * @param args
2434   */
2435   public static void main(String[] args)
2436   {
2437   Hashtable> aaProps = new Hashtable<>();
2438   jalview.bin.Console.outPrintln("my %aa = {");
2439   // invert property hashes
2440   for (String pname : propHash.keySet())
2441   {
2442   Map phash = propHash.get(pname);
2443   for (String rname : phash.keySet())
2444   {
2445   Vector aprops = aaProps.get(rname);
2446   if (aprops == null)
2447   {
2448   aprops = new Vector<>();
2449   aaProps.put(rname, aprops);
2450   }
2451   Integer hasprop = phash.get(rname);
2452   if (hasprop.intValue() == 1)
2453   {
2454   aprops.addElement(pname);
2455   }
2456   }
2457   }
2458   Enumeration res = aaProps.keys();
2459   while (res.hasMoreElements())
2460   {
2461   String rname = res.nextElement();
2462  
2463   System.out.print("'" + rname + "' => [");
2464   Enumeration props = aaProps.get(rname).elements();
2465   while (props.hasMoreElements())
2466   {
2467   System.out.print("'" + props.nextElement() + "'");
2468   if (props.hasMoreElements())
2469   {
2470   jalview.bin.Console.outPrintln(", ");
2471   }
2472   }
2473   jalview.bin.Console
2474   .outPrintln("]" + (res.hasMoreElements() ? "," : ""));
2475   }
2476   jalview.bin.Console.outPrintln("};");
2477   }
2478  
2479   // to here
2480  
2481   /**
2482   * Returns a list of residue characters for the specified inputs
2483   *
2484   * @param forNucleotide
2485   * @param includeAmbiguous
2486   * @return
2487   */
2488   public static List getResidues(boolean forNucleotide,
2489   boolean includeAmbiguous)
2490   {
2491   List result = new ArrayList<>();
2492   if (forNucleotide)
2493   {
2494   for (String nuc : nucleotideName.keySet())
2495   {
2496   int val = nucleotideIndex[nuc.charAt(0)];
2497   if ((!includeAmbiguous && val > 4) || (val >= maxNucleotideIndex))
2498   {
2499   continue;
2500   }
2501   nuc = nuc.toUpperCase(Locale.ROOT);
2502   if (!result.contains(nuc))
2503   {
2504   result.add(nuc);
2505   }
2506   }
2507   }
2508   else
2509   {
2510   /*
2511   * Peptide
2512   */
2513   for (String res : aa3Hash.keySet())
2514   {
2515   int index = aa3Hash.get(res).intValue();
2516   if ((!includeAmbiguous && index >= 20) || index >= maxProteinIndex)
2517   {
2518   continue;
2519   }
2520   res = res.toUpperCase(Locale.ROOT);
2521   if (!result.contains(res))
2522   {
2523   result.add(res);
2524   }
2525   }
2526   }
2527  
2528   return result;
2529   }
2530  
2531   /**
2532   * Returns the single letter code for a three letter code, or '0' if not known
2533   *
2534   * @param threeLetterCode
2535   * not case sensitive
2536   * @return
2537   */
2538   public static char getSingleCharacterCode(String threeLetterCode)
2539   {
2540   if (threeLetterCode == null)
2541   {
2542   return '0';
2543   }
2544   Integer index = ResidueProperties.aa3Hash
2545   .get(threeLetterCode.toUpperCase(Locale.ROOT));
2546   return index == null ? '0' : aa[index].charAt(0);
2547   }
2548   }
  • Report generated by OpenClover v 4.4.1 on Thu Nov 27 2025 17:31:18 GMT using coverage data from Thu Nov 27 2025 17:31:04 GMT.
  • OpenClover is free and open-source software.