Clover icon

Coverage Report

  1. Project Clover database Thu Aug 13 2020 12:04:21 BST
  2. Package jalview.schemes

File ResidueProperties.java

 

Coverage histogram

../../img/srcFileCovDistChart10.png
0% of files have more coverage

Code metrics

70
1,841
30
1
2,397
2,175
73
0.04
61.37
30
2.43

Classes

Class Line # Actions
ResidueProperties 35 1,841 73
0.9752704597.5%
 

Contributing tests

This file is covered by 53 tests. .

Source view

1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ The Jalview Authors
4    *
5    * This file is part of Jalview.
6    *
7    * Jalview is free software: you can redistribute it and/or
8    * modify it under the terms of the GNU General Public License
9    * as published by the Free Software Foundation, either version 3
10    * of the License, or (at your option) any later version.
11    *
12    * Jalview is distributed in the hope that it will be useful, but
13    * WITHOUT ANY WARRANTY; without even the implied warranty
14    * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15    * PURPOSE. See the GNU General Public License for more details.
16    *
17    * You should have received a copy of the GNU General Public License
18    * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19    * The Jalview Authors are detailed in the 'AUTHORS' file.
20    */
21    package jalview.schemes;
22   
23    import jalview.analysis.GeneticCodes;
24   
25    import java.awt.Color;
26    import java.util.ArrayList;
27    import java.util.Arrays;
28    import java.util.Enumeration;
29    import java.util.HashMap;
30    import java.util.Hashtable;
31    import java.util.List;
32    import java.util.Map;
33    import java.util.Vector;
34   
 
35    public class ResidueProperties
36    {
37    // Stores residue codes/names and colours and other things
38    public static final int[] aaIndex; // aaHash version 2.1.1 and below
39   
40    public static final int[] nucleotideIndex;
41   
42    public static final int[] purinepyrimidineIndex;
43   
44    public static final Map<String, Integer> aa3Hash = new HashMap<>();
45   
46    public static final Map<String, String> aa2Triplet = new HashMap<>();
47   
48    public static final Map<String, String> nucleotideName = new HashMap<>();
49   
50    // lookup from modified amino acid (e.g. MSE) to canonical form (e.g. MET)
51    public static final Map<String, String> modifications = new HashMap<>();
52   
 
53  18 toggle static
54    {
55  18 aaIndex = new int[255];
56  4608 for (int i = 0; i < 255; i++)
57    {
58  4590 aaIndex[i] = 23;
59    }
60   
61  18 aaIndex['A'] = 0;
62  18 aaIndex['R'] = 1;
63  18 aaIndex['N'] = 2;
64  18 aaIndex['D'] = 3;
65  18 aaIndex['C'] = 4;
66  18 aaIndex['Q'] = 5;
67  18 aaIndex['E'] = 6;
68  18 aaIndex['G'] = 7;
69  18 aaIndex['H'] = 8;
70  18 aaIndex['I'] = 9;
71  18 aaIndex['L'] = 10;
72  18 aaIndex['K'] = 11;
73  18 aaIndex['M'] = 12;
74  18 aaIndex['F'] = 13;
75  18 aaIndex['P'] = 14;
76  18 aaIndex['S'] = 15;
77  18 aaIndex['T'] = 16;
78  18 aaIndex['W'] = 17;
79  18 aaIndex['Y'] = 18;
80  18 aaIndex['V'] = 19;
81  18 aaIndex['B'] = 20;
82  18 aaIndex['Z'] = 21;
83  18 aaIndex['X'] = 22;
84  18 aaIndex['U'] = 22;
85  18 aaIndex['a'] = 0;
86  18 aaIndex['r'] = 1;
87  18 aaIndex['n'] = 2;
88  18 aaIndex['d'] = 3;
89  18 aaIndex['c'] = 4;
90  18 aaIndex['q'] = 5;
91  18 aaIndex['e'] = 6;
92  18 aaIndex['g'] = 7;
93  18 aaIndex['h'] = 8;
94  18 aaIndex['i'] = 9;
95  18 aaIndex['l'] = 10;
96  18 aaIndex['k'] = 11;
97  18 aaIndex['m'] = 12;
98  18 aaIndex['f'] = 13;
99  18 aaIndex['p'] = 14;
100  18 aaIndex['s'] = 15;
101  18 aaIndex['t'] = 16;
102  18 aaIndex['w'] = 17;
103  18 aaIndex['y'] = 18;
104  18 aaIndex['v'] = 19;
105  18 aaIndex['b'] = 20;
106  18 aaIndex['z'] = 21;
107  18 aaIndex['x'] = 22;
108  18 aaIndex['u'] = 22; // TODO: selenocystine triplet and codons needed. also
109    // extend subt. matrices
110    }
111   
112    /**
113    * maximum (gap) index for matrices involving protein alphabet
114    */
115    public final static int maxProteinIndex = 23;
116   
117    /**
118    * maximum (gap) index for matrices involving nucleotide alphabet
119    */
120    public final static int maxNucleotideIndex = 10;
121   
 
122  18 toggle static
123    {
124  18 nucleotideIndex = new int[255];
125  4608 for (int i = 0; i < 255; i++)
126    {
127  4590 nucleotideIndex[i] = 10; // non-nucleotide symbols are all non-gap gaps.
128    }
129   
130  18 nucleotideIndex['A'] = 0;
131  18 nucleotideIndex['a'] = 0;
132  18 nucleotideIndex['C'] = 1;
133  18 nucleotideIndex['c'] = 1;
134  18 nucleotideIndex['G'] = 2;
135  18 nucleotideIndex['g'] = 2;
136  18 nucleotideIndex['T'] = 3;
137  18 nucleotideIndex['t'] = 3;
138  18 nucleotideIndex['U'] = 4;
139  18 nucleotideIndex['u'] = 4;
140  18 nucleotideIndex['I'] = 5;
141  18 nucleotideIndex['i'] = 5;
142  18 nucleotideIndex['X'] = 6;
143  18 nucleotideIndex['x'] = 6;
144  18 nucleotideIndex['R'] = 7;
145  18 nucleotideIndex['r'] = 7;
146  18 nucleotideIndex['Y'] = 8;
147  18 nucleotideIndex['y'] = 8;
148  18 nucleotideIndex['N'] = 9;
149  18 nucleotideIndex['n'] = 9;
150   
151  18 nucleotideName.put("A", "Adenine");
152  18 nucleotideName.put("a", "Adenine");
153  18 nucleotideName.put("G", "Guanine");
154  18 nucleotideName.put("g", "Guanine");
155  18 nucleotideName.put("C", "Cytosine");
156  18 nucleotideName.put("c", "Cytosine");
157  18 nucleotideName.put("T", "Thymine");
158  18 nucleotideName.put("t", "Thymine");
159  18 nucleotideName.put("U", "Uracil");
160  18 nucleotideName.put("u", "Uracil");
161  18 nucleotideName.put("I", "Inosine");
162  18 nucleotideName.put("i", "Inosine");
163  18 nucleotideName.put("X", "Xanthine");
164  18 nucleotideName.put("x", "Xanthine");
165  18 nucleotideName.put("R", "Unknown Purine");
166  18 nucleotideName.put("r", "Unknown Purine");
167  18 nucleotideName.put("Y", "Unknown Pyrimidine");
168  18 nucleotideName.put("y", "Unknown Pyrimidine");
169  18 nucleotideName.put("N", "Unknown");
170  18 nucleotideName.put("n", "Unknown");
171  18 nucleotideName.put("W", "Weak nucleotide (A or T)");
172  18 nucleotideName.put("w", "Weak nucleotide (A or T)");
173  18 nucleotideName.put("S", "Strong nucleotide (G or C)");
174  18 nucleotideName.put("s", "Strong nucleotide (G or C)");
175  18 nucleotideName.put("M", "Amino (A or C)");
176  18 nucleotideName.put("m", "Amino (A or C)");
177  18 nucleotideName.put("K", "Keto (G or T)");
178  18 nucleotideName.put("k", "Keto (G or T)");
179  18 nucleotideName.put("B", "Not A (G or C or T)");
180  18 nucleotideName.put("b", "Not A (G or C or T)");
181  18 nucleotideName.put("H", "Not G (A or C or T)");
182  18 nucleotideName.put("h", "Not G (A or C or T)");
183  18 nucleotideName.put("D", "Not C (A or G or T)");
184  18 nucleotideName.put("d", "Not C (A or G or T)");
185  18 nucleotideName.put("V", "Not T (A or G or C");
186  18 nucleotideName.put("v", "Not T (A or G or C");
187   
188    }
189   
 
190  18 toggle static
191    {
192  18 purinepyrimidineIndex = new int[255];
193  4608 for (int i = 0; i < 255; i++)
194    {
195  4590 purinepyrimidineIndex[i] = 3; // non-nucleotide symbols are all non-gap
196    // gaps.
197    }
198   
199  18 purinepyrimidineIndex['A'] = 0;
200  18 purinepyrimidineIndex['a'] = 0;
201  18 purinepyrimidineIndex['C'] = 1;
202  18 purinepyrimidineIndex['c'] = 1;
203  18 purinepyrimidineIndex['G'] = 0;
204  18 purinepyrimidineIndex['g'] = 0;
205  18 purinepyrimidineIndex['T'] = 1;
206  18 purinepyrimidineIndex['t'] = 1;
207  18 purinepyrimidineIndex['U'] = 1;
208  18 purinepyrimidineIndex['u'] = 1;
209  18 purinepyrimidineIndex['I'] = 2;
210  18 purinepyrimidineIndex['i'] = 2;
211  18 purinepyrimidineIndex['X'] = 2;
212  18 purinepyrimidineIndex['x'] = 2;
213  18 purinepyrimidineIndex['R'] = 0;
214  18 purinepyrimidineIndex['r'] = 0;
215  18 purinepyrimidineIndex['Y'] = 1;
216  18 purinepyrimidineIndex['y'] = 1;
217  18 purinepyrimidineIndex['N'] = 2;
218  18 purinepyrimidineIndex['n'] = 2;
219    }
220   
221    private static final Integer ONE = Integer.valueOf(1);
222   
223    private static final Integer ZERO = Integer.valueOf(0);
224   
 
225  18 toggle static
226    {
227  18 aa3Hash.put("ALA", ZERO);
228  18 aa3Hash.put("ARG", ONE);
229  18 aa3Hash.put("ASN", Integer.valueOf(2));
230  18 aa3Hash.put("ASP", Integer.valueOf(3)); // D
231  18 aa3Hash.put("CYS", Integer.valueOf(4));
232  18 aa3Hash.put("GLN", Integer.valueOf(5)); // Q
233  18 aa3Hash.put("GLU", Integer.valueOf(6)); // E
234  18 aa3Hash.put("GLY", Integer.valueOf(7));
235  18 aa3Hash.put("HIS", Integer.valueOf(8));
236  18 aa3Hash.put("ILE", Integer.valueOf(9));
237  18 aa3Hash.put("LEU", Integer.valueOf(10));
238  18 aa3Hash.put("LYS", Integer.valueOf(11));
239  18 aa3Hash.put("MET", Integer.valueOf(12));
240  18 aa3Hash.put("PHE", Integer.valueOf(13));
241  18 aa3Hash.put("PRO", Integer.valueOf(14));
242  18 aa3Hash.put("SER", Integer.valueOf(15));
243  18 aa3Hash.put("THR", Integer.valueOf(16));
244  18 aa3Hash.put("TRP", Integer.valueOf(17));
245  18 aa3Hash.put("TYR", Integer.valueOf(18));
246  18 aa3Hash.put("VAL", Integer.valueOf(19));
247    // IUB Nomenclature for ambiguous peptides
248  18 aa3Hash.put("ASX", Integer.valueOf(20)); // "B";
249  18 aa3Hash.put("GLX", Integer.valueOf(21)); // Z
250  18 aa3Hash.put("XAA", Integer.valueOf(22)); // X unknown
251  18 aa3Hash.put("-", Integer.valueOf(23));
252  18 aa3Hash.put("*", Integer.valueOf(23));
253  18 aa3Hash.put(".", Integer.valueOf(23));
254  18 aa3Hash.put(" ", Integer.valueOf(23));
255  18 aa3Hash.put("Gap", Integer.valueOf(23));
256  18 aa3Hash.put("UR3", Integer.valueOf(24));
257    }
258   
 
259  18 toggle static
260    {
261  18 aa2Triplet.put("A", "ALA");
262  18 aa2Triplet.put("a", "ALA");
263  18 aa2Triplet.put("R", "ARG");
264  18 aa2Triplet.put("r", "ARG");
265  18 aa2Triplet.put("N", "ASN");
266  18 aa2Triplet.put("n", "ASN");
267  18 aa2Triplet.put("D", "ASP");
268  18 aa2Triplet.put("d", "ASP");
269  18 aa2Triplet.put("C", "CYS");
270  18 aa2Triplet.put("c", "CYS");
271  18 aa2Triplet.put("Q", "GLN");
272  18 aa2Triplet.put("q", "GLN");
273  18 aa2Triplet.put("E", "GLU");
274  18 aa2Triplet.put("e", "GLU");
275  18 aa2Triplet.put("G", "GLY");
276  18 aa2Triplet.put("g", "GLY");
277  18 aa2Triplet.put("H", "HIS");
278  18 aa2Triplet.put("h", "HIS");
279  18 aa2Triplet.put("I", "ILE");
280  18 aa2Triplet.put("i", "ILE");
281  18 aa2Triplet.put("L", "LEU");
282  18 aa2Triplet.put("l", "LEU");
283  18 aa2Triplet.put("K", "LYS");
284  18 aa2Triplet.put("k", "LYS");
285  18 aa2Triplet.put("M", "MET");
286  18 aa2Triplet.put("m", "MET");
287  18 aa2Triplet.put("F", "PHE");
288  18 aa2Triplet.put("f", "PHE");
289  18 aa2Triplet.put("P", "PRO");
290  18 aa2Triplet.put("p", "PRO");
291  18 aa2Triplet.put("S", "SER");
292  18 aa2Triplet.put("s", "SER");
293  18 aa2Triplet.put("T", "THR");
294  18 aa2Triplet.put("t", "THR");
295  18 aa2Triplet.put("W", "TRP");
296  18 aa2Triplet.put("w", "TRP");
297  18 aa2Triplet.put("Y", "TYR");
298  18 aa2Triplet.put("y", "TYR");
299  18 aa2Triplet.put("V", "VAL");
300  18 aa2Triplet.put("v", "VAL");
301    }
302   
303    public static final String[] aa = { "A", "R", "N", "D", "C", "Q", "E",
304    "G", "H", "I", "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V", "B",
305    "Z", "X", "_", "*", ".", " ", "U" };
306   
307    public static final Color midBlue = new Color(100, 100, 255);
308   
309    // not currently in use
310    // public static final Vector<Color> scaleColours = new Vector<Color>();
311    // static
312    // {
313    // scaleColours.addElement(new Color(114, 0, 147));
314    // scaleColours.addElement(new Color(156, 0, 98));
315    // scaleColours.addElement(new Color(190, 0, 0));
316    // scaleColours.addElement(Color.red);
317    // scaleColours.addElement(new Color(255, 125, 0));
318    // scaleColours.addElement(Color.orange);
319    // scaleColours.addElement(new Color(255, 194, 85));
320    // scaleColours.addElement(Color.yellow);
321    // scaleColours.addElement(new Color(255, 255, 181));
322    // scaleColours.addElement(Color.white);
323    // }
324   
325    public static final Color[] taylor = { new Color(204, 255, 0),
326    // A Greenish-yellowy-yellow
327    new Color(0, 0, 255), // R Blueish-bluey-blue
328    new Color(204, 0, 255), // N Blueish-reddy-blue
329    new Color(255, 0, 0), // D Reddish-reddy-red
330    new Color(255, 255, 0), // C Yellowish-yellowy-yellow
331    new Color(255, 0, 204), // Q Reddish-bluey-red
332    new Color(255, 0, 102), // E Blueish-reddy-red
333    new Color(255, 153, 0), // G Yellowy-reddy-yellow
334    new Color(0, 102, 255), // H Greenish-bluey-blue
335    new Color(102, 255, 0), // I Greenish-yellowy-green
336    new Color(51, 255, 0), // L Yellowish-greeny-green
337    new Color(102, 0, 255), // K Reddish-bluey-blue
338    new Color(0, 255, 0), // M Greenish-greeny-green
339    new Color(0, 255, 102), // F Blueish-greeny-green
340    new Color(255, 204, 0), // P Reddish-yellowy-yellow
341    new Color(255, 51, 0), // S Yellowish-reddy-red
342    new Color(255, 102, 0), // T Reddish-yellowy-red
343    new Color(0, 204, 255), // W Blueish-greeny-green
344    new Color(0, 255, 204), // Y Greenish-bluey-green
345    new Color(153, 255, 0), // V Yellowish-greeny-yellow
346    Color.white, // B
347    Color.white, // Z
348    Color.white, // X
349    Color.white, // -
350    Color.white, // *
351    Color.white // .
352    };
353   
354    public static final Color[] nucleotide = { new Color(100, 247, 63), // A
355    new Color(255, 179, 64), // C
356    new Color(235, 65, 60), // G
357    new Color(60, 136, 238), // T
358    new Color(60, 136, 238), // U
359    Color.white, // I (inosine)
360    Color.white, // X (xanthine)
361    Color.white, // R
362    Color.white, // Y
363    Color.white, // N
364    Color.white, // Gap
365    };
366   
367    // Added for PurinePyrimidineColourScheme
368    public static final Color[] purinepyrimidine = { new Color(255, 131, 250), // A,
369    // G,
370    // R
371    // purines
372    // purplish/orchid
373    new Color(64, 224, 208), // C,U, T, Y pyrimidines turquoise
374    Color.white, // all other nucleotides
375    Color.white // Gap
376    };
377   
378    // Zappo
379    public static final Color[] zappo = { Color.pink, // A
380    midBlue, // R
381    Color.green, // N
382    Color.red, // D
383    Color.yellow, // C
384    Color.green, // Q
385    Color.red, // E
386    Color.magenta, // G
387    midBlue, // Color.red, // H
388    Color.pink, // I
389    Color.pink, // L
390    midBlue, // K
391    Color.pink, // M
392    Color.orange, // F
393    Color.magenta, // P
394    Color.green, // S
395    Color.green, // T
396    Color.orange, // W
397    Color.orange, // Y
398    Color.pink, // V
399    Color.white, // B
400    Color.white, // Z
401    Color.white, // X
402    Color.white, // -
403    Color.white, // *
404    Color.white, // .
405    Color.white // ' '
406    };
407   
408    // Dunno where I got these numbers from
409    public static final double[] hyd2 = { 0.62, // A
410    0.29, // R
411    -0.90, // N
412    -0.74, // D
413    1.19, // C
414    0.48, // Q
415    -0.40, // E
416    1.38, // G
417    -1.50, // H
418    1.06, // I
419    0.64, // L
420    -0.78, // K
421    0.12, // M
422    -0.85, // F
423    -2.53, // P
424    -0.18, // S
425    -0.05, // T
426    1.08, // W
427    0.81, // Y
428    0.0, // V
429    0.26, // B
430    0.0, // Z
431    0.0 // X
432    };
433   
434    public static final double[] helix = { 1.42, 0.98, 0.67, 1.01, 0.70, 1.11,
435    1.51, 0.57, 1.00, 1.08, 1.21, 1.16, 1.45, 1.13, 0.57, 0.77, 0.83,
436    1.08, 0.69, 1.06, 0.84, 1.31, 1.00, 0.0 };
437   
438    public static final double helixmin = 0.57;
439   
440    public static final double helixmax = 1.51;
441   
442    public static final double[] strand = { 0.83, 0.93, 0.89, 0.54, 1.19,
443    1.10, 0.37, 0.75, 0.87, 1.60, 1.30, 0.74, 1.05, 1.38, 0.55, 0.75,
444    1.19, 1.37, 1.47, 1.70, 0.72, 0.74, 1.0, 0.0 };
445   
446    public static final double strandmin = 0.37;
447   
448    public static final double strandmax = 1.7;
449   
450    public static final double[] turn = { 0.66, 0.95, 1.56, 1.46, 1.19, 0.98,
451    0.74, 1.56, 0.95, 0.47, 0.59, 1.01, 0.60, 0.60, 1.52, 1.43, 0.96,
452    0.96, 1.14, 0.50, 1.51, 0.86, 1.00, 0, 0 };
453   
454    public static final double turnmin = 0.47;
455   
456    public static final double turnmax = 1.56;
457   
458    public static final double[] buried = { 1.7, 0.1, 0.4, 0.4, 4.6, 0.3, 0.3,
459    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,
460    0.3, 1.358, 0.00 };
461   
462    public static final double buriedmin = 0.05;
463   
464    public static final double buriedmax = 4.6;
465   
466    // This is hydropathy index
467    // Kyte, J., and Doolittle, R.F., J. Mol. Biol.
468    // 1157, 105-132, 1982
469    public static final double[] hyd = { 1.8, -4.5, -3.5, -3.5, 2.5, -3.5,
470    -3.5, -0.4, -3.2, 4.5, 3.8, -3.9, 1.9, 2.8, -1.6, -0.8, -0.7, -0.9,
471    -1.3, 4.2, -3.5, -3.5, -0.49, 0.0 };
472   
473    public static final double hydmax = 4.5;
474   
475    public static final double hydmin = -3.9;
476   
477    // public static final double hydmax = 1.38;
478    // public static final double hydmin = -2.53;
479   
480    // not currently used
481    // public static final Map<String, Color> ssHash = new Hashtable<String,
482    // Color>();
483    // static
484    // {
485    // ssHash.put("H", Color.magenta);
486    // ssHash.put("E", Color.yellow);
487    // ssHash.put("-", Color.white);
488    // ssHash.put(".", Color.white);
489    // ssHash.put("S", Color.cyan);
490    // ssHash.put("T", Color.blue);
491    // ssHash.put("G", Color.pink);
492    // ssHash.put("I", Color.pink);
493    // ssHash.put("B", Color.yellow);
494    // }
495   
496    /*
497    * new Color(60, 136, 238), // U Color.white, // I Color.white, // X
498    * Color.white, // R Color.white, // Y Color.white, // N Color.white, // Gap
499    */
500   
501    public static String STOP = "STOP";
502   
503    public static List<String> STOP_CODONS = Arrays.asList("TGA", "TAA", "TAG");
504   
505    public static String START = "ATG";
506   
507    // Stores residue codes/names and colours and other things
508    public static Map<String, Map<String, Integer>> propHash = new Hashtable<>();
509   
510    public static Map<String, Integer> hydrophobic = new Hashtable<>();
511   
512    public static Map<String, Integer> polar = new Hashtable<>();
513   
514    public static Map<String, Integer> small = new Hashtable<>();
515   
516    public static Map<String, Integer> positive = new Hashtable<>();
517   
518    public static Map<String, Integer> negative = new Hashtable<>();
519   
520    public static Map<String, Integer> charged = new Hashtable<>();
521   
522    public static Map<String, Integer> aromatic = new Hashtable<>();
523   
524    public static Map<String, Integer> aliphatic = new Hashtable<>();
525   
526    public static Map<String, Integer> tiny = new Hashtable<>();
527   
528    public static Map<String, Integer> proline = new Hashtable<>();
529   
 
530  18 toggle static
531    {
532  18 hydrophobic.put("I", ONE);
533  18 hydrophobic.put("L", ONE);
534  18 hydrophobic.put("V", ONE);
535  18 hydrophobic.put("C", ONE);
536  18 hydrophobic.put("A", ONE);
537  18 hydrophobic.put("G", ONE);
538  18 hydrophobic.put("M", ONE);
539  18 hydrophobic.put("F", ONE);
540  18 hydrophobic.put("Y", ONE);
541  18 hydrophobic.put("W", ONE);
542  18 hydrophobic.put("H", ONE);
543  18 hydrophobic.put("K", ONE);
544  18 hydrophobic.put("X", ONE);
545  18 hydrophobic.put("-", ONE);
546  18 hydrophobic.put("*", ONE);
547  18 hydrophobic.put("R", ZERO);
548  18 hydrophobic.put("E", ZERO);
549  18 hydrophobic.put("Q", ZERO);
550  18 hydrophobic.put("D", ZERO);
551  18 hydrophobic.put("N", ZERO);
552  18 hydrophobic.put("S", ZERO);
553  18 hydrophobic.put("T", ONE);
554  18 hydrophobic.put("P", ZERO);
555    }
556   
 
557  18 toggle static
558    {
559  18 polar.put("Y", ONE);
560  18 polar.put("W", ONE);
561  18 polar.put("H", ONE);
562  18 polar.put("K", ONE);
563  18 polar.put("R", ONE);
564  18 polar.put("E", ONE);
565  18 polar.put("Q", ONE);
566  18 polar.put("D", ONE);
567  18 polar.put("N", ONE);
568  18 polar.put("S", ONE);
569  18 polar.put("T", ONE);
570  18 polar.put("X", ONE);
571  18 polar.put("-", ONE);
572  18 polar.put("*", ONE);
573  18 polar.put("I", ZERO);
574  18 polar.put("L", ZERO);
575  18 polar.put("V", ZERO);
576  18 polar.put("C", ZERO);
577  18 polar.put("A", ZERO);
578  18 polar.put("G", ZERO);
579  18 polar.put("M", ZERO);
580  18 polar.put("F", ZERO);
581  18 polar.put("P", ZERO);
582    }
583   
 
584  18 toggle static
585    {
586  18 small.put("I", ZERO);
587  18 small.put("L", ZERO);
588  18 small.put("V", ONE);
589  18 small.put("C", ONE);
590  18 small.put("A", ONE);
591  18 small.put("G", ONE);
592  18 small.put("M", ZERO);
593  18 small.put("F", ZERO);
594  18 small.put("Y", ZERO);
595  18 small.put("W", ZERO);
596  18 small.put("H", ZERO);
597  18 small.put("K", ZERO);
598  18 small.put("R", ZERO);
599  18 small.put("E", ZERO);
600  18 small.put("Q", ZERO);
601  18 small.put("D", ONE);
602  18 small.put("N", ONE);
603  18 small.put("S", ONE);
604  18 small.put("T", ONE);
605  18 small.put("P", ONE);
606  18 small.put("-", ONE);
607  18 small.put("*", ONE);
608    }
609   
 
610  18 toggle static
611    {
612  18 positive.put("I", ZERO);
613  18 positive.put("L", ZERO);
614  18 positive.put("V", ZERO);
615  18 positive.put("C", ZERO);
616  18 positive.put("A", ZERO);
617  18 positive.put("G", ZERO);
618  18 positive.put("M", ZERO);
619  18 positive.put("F", ZERO);
620  18 positive.put("Y", ZERO);
621  18 positive.put("W", ZERO);
622  18 positive.put("H", ONE);
623  18 positive.put("K", ONE);
624  18 positive.put("R", ONE);
625  18 positive.put("E", ZERO);
626  18 positive.put("Q", ZERO);
627  18 positive.put("D", ZERO);
628  18 positive.put("N", ZERO);
629  18 positive.put("S", ZERO);
630  18 positive.put("T", ZERO);
631  18 positive.put("P", ZERO);
632  18 positive.put("-", ONE);
633  18 positive.put("*", ONE);
634    }
635   
 
636  18 toggle static
637    {
638  18 negative.put("I", ZERO);
639  18 negative.put("L", ZERO);
640  18 negative.put("V", ZERO);
641  18 negative.put("C", ZERO);
642  18 negative.put("A", ZERO);
643  18 negative.put("G", ZERO);
644  18 negative.put("M", ZERO);
645  18 negative.put("F", ZERO);
646  18 negative.put("Y", ZERO);
647  18 negative.put("W", ZERO);
648  18 negative.put("H", ZERO);
649  18 negative.put("K", ZERO);
650  18 negative.put("R", ZERO);
651  18 negative.put("E", ONE);
652  18 negative.put("Q", ZERO);
653  18 negative.put("D", ONE);
654  18 negative.put("N", ZERO);
655  18 negative.put("S", ZERO);
656  18 negative.put("T", ZERO);
657  18 negative.put("P", ZERO);
658  18 negative.put("-", ONE);
659  18 negative.put("*", ONE);
660    }
661   
 
662  18 toggle static
663    {
664  18 charged.put("I", ZERO);
665  18 charged.put("L", ZERO);
666  18 charged.put("V", ZERO);
667  18 charged.put("C", ZERO);
668  18 charged.put("A", ZERO);
669  18 charged.put("G", ZERO);
670  18 charged.put("M", ZERO);
671  18 charged.put("F", ZERO);
672  18 charged.put("Y", ZERO);
673  18 charged.put("W", ZERO);
674  18 charged.put("H", ONE);
675  18 charged.put("K", ONE);
676  18 charged.put("R", ONE);
677  18 charged.put("E", ONE);
678  18 charged.put("Q", ZERO);
679  18 charged.put("D", ONE);
680  18 charged.put("N", ZERO); // Asparagine is polar but not
681    // charged.
682    // Alternative would be charged and
683    // negative (in basic form)?
684  18 charged.put("S", ZERO);
685  18 charged.put("T", ZERO);
686  18 charged.put("P", ZERO);
687  18 charged.put("-", ONE);
688  18 charged.put("*", ONE);
689    }
690   
 
691  18 toggle static
692    {
693  18 aromatic.put("I", ZERO);
694  18 aromatic.put("L", ZERO);
695  18 aromatic.put("V", ZERO);
696  18 aromatic.put("C", ZERO);
697  18 aromatic.put("A", ZERO);
698  18 aromatic.put("G", ZERO);
699  18 aromatic.put("M", ZERO);
700  18 aromatic.put("F", ONE);
701  18 aromatic.put("Y", ONE);
702  18 aromatic.put("W", ONE);
703  18 aromatic.put("H", ONE);
704  18 aromatic.put("K", ZERO);
705  18 aromatic.put("R", ZERO);
706  18 aromatic.put("E", ZERO);
707  18 aromatic.put("Q", ZERO);
708  18 aromatic.put("D", ZERO);
709  18 aromatic.put("N", ZERO);
710  18 aromatic.put("S", ZERO);
711  18 aromatic.put("T", ZERO);
712  18 aromatic.put("P", ZERO);
713  18 aromatic.put("-", ONE);
714  18 aromatic.put("*", ONE);
715    }
716   
 
717  18 toggle static
718    {
719  18 aliphatic.put("I", ONE);
720  18 aliphatic.put("L", ONE);
721  18 aliphatic.put("V", ONE);
722  18 aliphatic.put("C", ZERO);
723  18 aliphatic.put("A", ZERO);
724  18 aliphatic.put("G", ZERO);
725  18 aliphatic.put("M", ZERO);
726  18 aliphatic.put("F", ZERO);
727  18 aliphatic.put("Y", ZERO);
728  18 aliphatic.put("W", ZERO);
729  18 aliphatic.put("H", ZERO);
730  18 aliphatic.put("K", ZERO);
731  18 aliphatic.put("R", ZERO);
732  18 aliphatic.put("E", ZERO);
733  18 aliphatic.put("Q", ZERO);
734  18 aliphatic.put("D", ZERO);
735  18 aliphatic.put("N", ZERO);
736  18 aliphatic.put("S", ZERO);
737  18 aliphatic.put("T", ZERO);
738  18 aliphatic.put("P", ZERO);
739  18 aliphatic.put("-", ONE);
740  18 aliphatic.put("*", ONE);
741    }
742   
 
743  18 toggle static
744    {
745  18 tiny.put("I", ZERO);
746  18 tiny.put("L", ZERO);
747  18 tiny.put("V", ZERO);
748  18 tiny.put("C", ZERO);
749  18 tiny.put("A", ONE);
750  18 tiny.put("G", ONE);
751  18 tiny.put("M", ZERO);
752  18 tiny.put("F", ZERO);
753  18 tiny.put("Y", ZERO);
754  18 tiny.put("W", ZERO);
755  18 tiny.put("H", ZERO);
756  18 tiny.put("K", ZERO);
757  18 tiny.put("R", ZERO);
758  18 tiny.put("E", ZERO);
759  18 tiny.put("Q", ZERO);
760  18 tiny.put("D", ZERO);
761  18 tiny.put("N", ZERO);
762  18 tiny.put("S", ONE);
763  18 tiny.put("T", ZERO);
764  18 tiny.put("P", ZERO);
765  18 tiny.put("-", ONE);
766  18 tiny.put("*", ONE);
767    }
768   
 
769  18 toggle static
770    {
771  18 proline.put("I", ZERO);
772  18 proline.put("L", ZERO);
773  18 proline.put("V", ZERO);
774  18 proline.put("C", ZERO);
775  18 proline.put("A", ZERO);
776  18 proline.put("G", ZERO);
777  18 proline.put("M", ZERO);
778  18 proline.put("F", ZERO);
779  18 proline.put("Y", ZERO);
780  18 proline.put("W", ZERO);
781  18 proline.put("H", ZERO);
782  18 proline.put("K", ZERO);
783  18 proline.put("R", ZERO);
784  18 proline.put("E", ZERO);
785  18 proline.put("Q", ZERO);
786  18 proline.put("D", ZERO);
787  18 proline.put("N", ZERO);
788  18 proline.put("S", ZERO);
789  18 proline.put("T", ZERO);
790  18 proline.put("P", ONE);
791  18 proline.put("-", ONE);
792  18 proline.put("*", ONE);
793    }
794   
 
795  18 toggle static
796    {
797  18 propHash.put("hydrophobic", hydrophobic);
798  18 propHash.put("small", small);
799  18 propHash.put("positive", positive);
800  18 propHash.put("negative", negative);
801  18 propHash.put("charged", charged);
802  18 propHash.put("aromatic", aromatic);
803  18 propHash.put("aliphatic", aliphatic);
804  18 propHash.put("tiny", tiny);
805  18 propHash.put("proline", proline);
806  18 propHash.put("polar", polar);
807    }
 
808  18 toggle static
809    {
810  18 int[][] propMatrixF = new int[maxProteinIndex][maxProteinIndex],
811    propMatrixPos = new int[maxProteinIndex][maxProteinIndex],
812    propMatrixEpos = new int[maxProteinIndex][maxProteinIndex];
813  432 for (int i = 0; i < maxProteinIndex; i++)
814    {
815  414 int maxF = 0, maxP = 0, maxEP = 0;
816  414 String ic = "";
817  414 if (aa.length > i)
818    {
819  414 ic += aa[i];
820    }
821    else
822    {
823  0 ic = "-";
824    }
825  4968 for (int j = i + 1; j < maxProteinIndex; j++)
826    {
827  4554 String jc = "";
828  4554 if (aa.length > j)
829    {
830  4554 jc += aa[j];
831    }
832    else
833    {
834  0 jc = "-";
835    }
836  4554 propMatrixF[i][j] = 0;
837  4554 propMatrixPos[i][j] = 0;
838  4554 propMatrixEpos[i][j] = 0;
839  4554 for (String ph : propHash.keySet())
840    {
841  45540 Map<String, Integer> pph = propHash.get(ph);
842  45540 if (pph.get(ic) != null && pph.get(jc) != null)
843    {
844  34920 int icp = pph.get(ic).intValue(), jcp = pph.get(jc).intValue();
845    // Still working on these definitions.
846  34920 propMatrixPos[i][j] += icp == jcp && icp > 0 ? 2 : 0;
847  34920 propMatrixPos[j][i] += icp == jcp && icp > 0 ? 2 : 0;
848  34920 propMatrixF[i][j] += icp == jcp ? 2 : 0;
849  34920 propMatrixF[j][i] += icp == jcp ? 2 : 0;
850  34920 propMatrixEpos[i][j] += icp == jcp ? (1 + icp * 2) : 0;
851  34920 propMatrixEpos[j][i] += icp == jcp ? (1 + icp * 2) : 0;
852    }
853    }
854  4554 if (maxF < propMatrixF[i][j])
855    {
856  666 maxF = propMatrixF[i][j];
857    }
858  4554 if (maxP < propMatrixPos[i][j])
859    {
860  558 maxP = propMatrixPos[i][j];
861    }
862  4554 if (maxEP < propMatrixEpos[i][j])
863    {
864  756 maxEP = propMatrixEpos[i][j];
865    }
866    }
867  414 propMatrixF[i][i] = maxF;
868  414 propMatrixPos[i][i] = maxP;
869  414 propMatrixEpos[i][i] = maxEP;
870    }
871    }
872   
 
873  0 toggle private ResidueProperties()
874    {
875    }
876   
 
877  0 toggle public static double getHydmax()
878    {
879  0 return hydmax;
880    }
881   
 
882  0 toggle public static double getHydmin()
883    {
884  0 return hydmin;
885    }
886   
 
887  0 toggle public static double[] getHyd()
888    {
889  0 return hyd;
890    }
891   
 
892  27382 toggle public static Map<String, Integer> getAA3Hash()
893    {
894  27382 return aa3Hash;
895    }
896   
 
897  260 toggle public static String codonTranslate(String lccodon)
898    {
899  260 String peptide = GeneticCodes.getInstance().getStandardCodeTable()
900    .translate(lccodon);
901  260 if ("*".equals(peptide))
902    {
903  19 return "STOP";
904    }
905  241 return peptide;
906    }
907   
908    /*
909    * lookup of (A-Z) alternative secondary structure symbols'
910    * equivalents in DSSP3 notation
911    */
912    private static char[] toDssp3State;
 
913  18 toggle static
914    {
915  18 toDssp3State = new char[9]; // for 'A'-'I'; extend if needed
916  18 Arrays.fill(toDssp3State, ' ');
917  18 toDssp3State['B' - 'A'] = 'E';
918  18 toDssp3State['E' - 'A'] = 'E';
919  18 toDssp3State['G' - 'A'] = 'H';
920  18 toDssp3State['H' - 'A'] = 'H';
921  18 toDssp3State['I' - 'A'] = 'H';
922    }
923   
924    /**
925    * translate from other dssp secondary structure alphabets to 3-state
926    *
927    * @param ssString
928    * @return ssstring
929    */
 
930  15047 toggle public static String getDssp3state(String ssString)
931    {
932  15047 if (ssString == null)
933    {
934  1 return null;
935    }
936  15046 int lookupSize = toDssp3State.length;
937  15046 int len = ssString.length();
938  15046 char[] trans = new char[len];
939  30151 for (int i = 0; i < len; i++)
940    {
941  15105 char c = ssString.charAt(i);
942  15105 int index = c - 'A';
943  15105 if (index < 0 || index >= lookupSize)
944    {
945  15096 trans[i] = ' ';
946    }
947    else
948    {
949  9 trans[i] = toDssp3State[index];
950    }
951    }
952  15046 return new String(trans);
953    }
954   
 
955  18 toggle static
956    {
957  18 modifications.put("MSE", "MET"); // Selenomethionine
958    // the rest tbc; from
959    // http://sourceforge.net/p/jmol/mailman/message/12833570/
960    // modifications.put("CSE", "CYS"); // Selenocysteine
961    // modifications.put("PTR", "TYR"); // Phosphotyrosine
962    // modifications.put("SEP", "SER"); // Phosphoserine
963    // modifications.put("HYP", "PRO"); // 4-hydroxyproline
964    // modifications.put("5HP", "GLU"); // Pyroglutamic acid; 5-hydroxyproline
965    // modifications.put("PCA", "GLU"); // Pyroglutamic acid
966    // modifications.put("LYZ", "LYS"); // 5-hydroxylysine
967   
968    // Additional protein alphabets used in the SCOP database and PDB files
969    // source:
970    // https://github.com/biopython/biopython/blob/master/Bio/Data/SCOPData.py
971  18 modifications.put("00C", "CYS");
972  18 modifications.put("01W", "XAA");
973  18 modifications.put("02K", "ALA");
974  18 modifications.put("03Y", "CYS");
975  18 modifications.put("07O", "CYS");
976  18 modifications.put("08P", "CYS");
977  18 modifications.put("0A0", "ASP");
978  18 modifications.put("0A1", "TYR");
979  18 modifications.put("0A2", "LYS");
980  18 modifications.put("0A8", "CYS");
981  18 modifications.put("0AA", "VAL");
982  18 modifications.put("0AB", "VAL");
983  18 modifications.put("0AC", "GLY");
984  18 modifications.put("0AD", "GLY");
985  18 modifications.put("0AF", "TRP");
986  18 modifications.put("0AG", "LEU");
987  18 modifications.put("0AH", "SER");
988  18 modifications.put("0AK", "ASP");
989  18 modifications.put("0AM", "ALA");
990  18 modifications.put("0AP", "CYS");
991  18 modifications.put("0AU", "UR3");
992  18 modifications.put("0AV", "ALA");
993  18 modifications.put("0AZ", "PRO");
994  18 modifications.put("0BN", "PHE");
995  18 modifications.put("0C ", "CYS");
996  18 modifications.put("0CS", "ALA");
997  18 modifications.put("0DC", "CYS");
998  18 modifications.put("0DG", "GLY");
999  18 modifications.put("0DT", "THR");
1000  18 modifications.put("0FL", "ALA");
1001  18 modifications.put("0G ", "GLY");
1002  18 modifications.put("0NC", "ALA");
1003  18 modifications.put("0SP", "ALA");
1004  18 modifications.put("0U ", "UR3");
1005  18 modifications.put("0YG", "YG");
1006  18 modifications.put("10C", "CYS");
1007  18 modifications.put("125", "UR3");
1008  18 modifications.put("126", "UR3");
1009  18 modifications.put("127", "UR3");
1010  18 modifications.put("128", "ASN");
1011  18 modifications.put("12A", "ALA");
1012  18 modifications.put("143", "CYS");
1013  18 modifications.put("175", "ASG");
1014  18 modifications.put("193", "XAA");
1015  18 modifications.put("1AP", "ALA");
1016  18 modifications.put("1MA", "ALA");
1017  18 modifications.put("1MG", "GLY");
1018  18 modifications.put("1PA", "PHE");
1019  18 modifications.put("1PI", "ALA");
1020  18 modifications.put("1PR", "ASN");
1021  18 modifications.put("1SC", "CYS");
1022  18 modifications.put("1TQ", "TRP");
1023  18 modifications.put("1TY", "TYR");
1024  18 modifications.put("1X6", "SER");
1025  18 modifications.put("200", "PHE");
1026  18 modifications.put("23F", "PHE");
1027  18 modifications.put("23S", "XAA");
1028  18 modifications.put("26B", "THR");
1029  18 modifications.put("2AD", "XAA");
1030  18 modifications.put("2AG", "ALA");
1031  18 modifications.put("2AO", "XAA");
1032  18 modifications.put("2AR", "ALA");
1033  18 modifications.put("2AS", "XAA");
1034  18 modifications.put("2AT", "THR");
1035  18 modifications.put("2AU", "UR3");
1036  18 modifications.put("2BD", "ILE");
1037  18 modifications.put("2BT", "THR");
1038  18 modifications.put("2BU", "ALA");
1039  18 modifications.put("2CO", "CYS");
1040  18 modifications.put("2DA", "ALA");
1041  18 modifications.put("2DF", "ASN");
1042  18 modifications.put("2DM", "ASN");
1043  18 modifications.put("2DO", "XAA");
1044  18 modifications.put("2DT", "THR");
1045  18 modifications.put("2EG", "GLY");
1046  18 modifications.put("2FE", "ASN");
1047  18 modifications.put("2FI", "ASN");
1048  18 modifications.put("2FM", "MET");
1049  18 modifications.put("2GT", "THR");
1050  18 modifications.put("2HF", "HIS");
1051  18 modifications.put("2LU", "LEU");
1052  18 modifications.put("2MA", "ALA");
1053  18 modifications.put("2MG", "GLY");
1054  18 modifications.put("2ML", "LEU");
1055  18 modifications.put("2MR", "ARG");
1056  18 modifications.put("2MT", "PRO");
1057  18 modifications.put("2MU", "UR3");
1058  18 modifications.put("2NT", "THR");
1059  18 modifications.put("2OM", "UR3");
1060  18 modifications.put("2OT", "THR");
1061  18 modifications.put("2PI", "XAA");
1062  18 modifications.put("2PR", "GLY");
1063  18 modifications.put("2SA", "ASN");
1064  18 modifications.put("2SI", "XAA");
1065  18 modifications.put("2ST", "THR");
1066  18 modifications.put("2TL", "THR");
1067  18 modifications.put("2TY", "TYR");
1068  18 modifications.put("2VA", "VAL");
1069  18 modifications.put("2XA", "CYS");
1070  18 modifications.put("32S", "XAA");
1071  18 modifications.put("32T", "XAA");
1072  18 modifications.put("3AH", "HIS");
1073  18 modifications.put("3AR", "XAA");
1074  18 modifications.put("3CF", "PHE");
1075  18 modifications.put("3DA", "ALA");
1076  18 modifications.put("3DR", "ASN");
1077  18 modifications.put("3GA", "ALA");
1078  18 modifications.put("3MD", "ASP");
1079  18 modifications.put("3ME", "UR3");
1080  18 modifications.put("3NF", "TYR");
1081  18 modifications.put("3QN", "LYS");
1082  18 modifications.put("3TY", "XAA");
1083  18 modifications.put("3XH", "GLY");
1084  18 modifications.put("4AC", "ASN");
1085  18 modifications.put("4BF", "TYR");
1086  18 modifications.put("4CF", "PHE");
1087  18 modifications.put("4CY", "MET");
1088  18 modifications.put("4DP", "TRP");
1089  18 modifications.put("4F3", "GYG");
1090  18 modifications.put("4FB", "PRO");
1091  18 modifications.put("4FW", "TRP");
1092  18 modifications.put("4HT", "TRP");
1093  18 modifications.put("4IN", "TRP");
1094  18 modifications.put("4MF", "ASN");
1095  18 modifications.put("4MM", "XAA");
1096  18 modifications.put("4OC", "CYS");
1097  18 modifications.put("4PC", "CYS");
1098  18 modifications.put("4PD", "CYS");
1099  18 modifications.put("4PE", "CYS");
1100  18 modifications.put("4PH", "PHE");
1101  18 modifications.put("4SC", "CYS");
1102  18 modifications.put("4SU", "UR3");
1103  18 modifications.put("4TA", "ASN");
1104  18 modifications.put("4U7", "ALA");
1105  18 modifications.put("56A", "HIS");
1106  18 modifications.put("5AA", "ALA");
1107  18 modifications.put("5AB", "ALA");
1108  18 modifications.put("5AT", "THR");
1109  18 modifications.put("5BU", "UR3");
1110  18 modifications.put("5CG", "GLY");
1111  18 modifications.put("5CM", "CYS");
1112  18 modifications.put("5CS", "CYS");
1113  18 modifications.put("5FA", "ALA");
1114  18 modifications.put("5FC", "CYS");
1115  18 modifications.put("5FU", "UR3");
1116  18 modifications.put("5HP", "GLU");
1117  18 modifications.put("5HT", "THR");
1118  18 modifications.put("5HU", "UR3");
1119  18 modifications.put("5IC", "CYS");
1120  18 modifications.put("5IT", "THR");
1121  18 modifications.put("5IU", "UR3");
1122  18 modifications.put("5MC", "CYS");
1123  18 modifications.put("5MD", "ASN");
1124  18 modifications.put("5MU", "UR3");
1125  18 modifications.put("5NC", "CYS");
1126  18 modifications.put("5PC", "CYS");
1127  18 modifications.put("5PY", "THR");
1128  18 modifications.put("5SE", "UR3");
1129  18 modifications.put("5ZA", "TWG");
1130  18 modifications.put("64T", "THR");
1131  18 modifications.put("6CL", "LYS");
1132  18 modifications.put("6CT", "THR");
1133  18 modifications.put("6CW", "TRP");
1134  18 modifications.put("6HA", "ALA");
1135  18 modifications.put("6HC", "CYS");
1136  18 modifications.put("6HG", "GLY");
1137  18 modifications.put("6HN", "LYS");
1138  18 modifications.put("6HT", "THR");
1139  18 modifications.put("6IA", "ALA");
1140  18 modifications.put("6MA", "ALA");
1141  18 modifications.put("6MC", "ALA");
1142  18 modifications.put("6MI", "ASN");
1143  18 modifications.put("6MT", "ALA");
1144  18 modifications.put("6MZ", "ASN");
1145  18 modifications.put("6OG", "GLY");
1146  18 modifications.put("70U", "UR3");
1147  18 modifications.put("7DA", "ALA");
1148  18 modifications.put("7GU", "GLY");
1149  18 modifications.put("7JA", "ILE");
1150  18 modifications.put("7MG", "GLY");
1151  18 modifications.put("8AN", "ALA");
1152  18 modifications.put("8FG", "GLY");
1153  18 modifications.put("8MG", "GLY");
1154  18 modifications.put("8OG", "GLY");
1155  18 modifications.put("9NE", "GLU");
1156  18 modifications.put("9NF", "PHE");
1157  18 modifications.put("9NR", "ARG");
1158  18 modifications.put("9NV", "VAL");
1159  18 modifications.put("A ", "ALA");
1160  18 modifications.put("A1P", "ASN");
1161  18 modifications.put("A23", "ALA");
1162  18 modifications.put("A2L", "ALA");
1163  18 modifications.put("A2M", "ALA");
1164  18 modifications.put("A34", "ALA");
1165  18 modifications.put("A35", "ALA");
1166  18 modifications.put("A38", "ALA");
1167  18 modifications.put("A39", "ALA");
1168  18 modifications.put("A3A", "ALA");
1169  18 modifications.put("A3P", "ALA");
1170  18 modifications.put("A40", "ALA");
1171  18 modifications.put("A43", "ALA");
1172  18 modifications.put("A44", "ALA");
1173  18 modifications.put("A47", "ALA");
1174  18 modifications.put("A5L", "ALA");
1175  18 modifications.put("A5M", "CYS");
1176  18 modifications.put("A5N", "ASN");
1177  18 modifications.put("A5O", "ALA");
1178  18 modifications.put("A66", "XAA");
1179  18 modifications.put("AA3", "ALA");
1180  18 modifications.put("AA4", "ALA");
1181  18 modifications.put("AAR", "ARG");
1182  18 modifications.put("AB7", "XAA");
1183  18 modifications.put("ABA", "ALA");
1184  18 modifications.put("ABR", "ALA");
1185  18 modifications.put("ABS", "ALA");
1186  18 modifications.put("ABT", "ASN");
1187  18 modifications.put("ACB", "ASP");
1188  18 modifications.put("ACL", "ARG");
1189  18 modifications.put("AD2", "ALA");
1190  18 modifications.put("ADD", "XAA");
1191  18 modifications.put("ADX", "ASN");
1192  18 modifications.put("AEA", "XAA");
1193  18 modifications.put("AEI", "ASP");
1194  18 modifications.put("AET", "ALA");
1195  18 modifications.put("AFA", "ASN");
1196  18 modifications.put("AFF", "ASN");
1197  18 modifications.put("AFG", "GLY");
1198  18 modifications.put("AGM", "ARG");
1199  18 modifications.put("AGT", "CYS");
1200  18 modifications.put("AHB", "ASN");
1201  18 modifications.put("AHH", "XAA");
1202  18 modifications.put("AHO", "ALA");
1203  18 modifications.put("AHP", "ALA");
1204  18 modifications.put("AHS", "XAA");
1205  18 modifications.put("AHT", "XAA");
1206  18 modifications.put("AIB", "ALA");
1207  18 modifications.put("AKL", "ASP");
1208  18 modifications.put("AKZ", "ASP");
1209  18 modifications.put("ALA", "ALA");
1210  18 modifications.put("ALC", "ALA");
1211  18 modifications.put("ALM", "ALA");
1212  18 modifications.put("ALN", "ALA");
1213  18 modifications.put("ALO", "THR");
1214  18 modifications.put("ALQ", "XAA");
1215  18 modifications.put("ALS", "ALA");
1216  18 modifications.put("ALT", "ALA");
1217  18 modifications.put("ALV", "ALA");
1218  18 modifications.put("ALY", "LYS");
1219  18 modifications.put("AN8", "ALA");
1220  18 modifications.put("AP7", "ALA");
1221  18 modifications.put("APE", "XAA");
1222  18 modifications.put("APH", "ALA");
1223  18 modifications.put("API", "LYS");
1224  18 modifications.put("APK", "LYS");
1225  18 modifications.put("APM", "XAA");
1226  18 modifications.put("APP", "XAA");
1227  18 modifications.put("AR2", "ARG");
1228  18 modifications.put("AR4", "GLU");
1229  18 modifications.put("AR7", "ARG");
1230  18 modifications.put("ARG", "ARG");
1231  18 modifications.put("ARM", "ARG");
1232  18 modifications.put("ARO", "ARG");
1233  18 modifications.put("ARV", "XAA");
1234  18 modifications.put("AS ", "ALA");
1235  18 modifications.put("AS2", "ASP");
1236  18 modifications.put("AS9", "XAA");
1237  18 modifications.put("ASA", "ASP");
1238  18 modifications.put("ASB", "ASP");
1239  18 modifications.put("ASI", "ASP");
1240  18 modifications.put("ASK", "ASP");
1241  18 modifications.put("ASL", "ASP");
1242  18 modifications.put("ASM", "XAA");
1243  18 modifications.put("ASN", "ASN");
1244  18 modifications.put("ASP", "ASP");
1245  18 modifications.put("ASQ", "ASP");
1246  18 modifications.put("ASU", "ASN");
1247  18 modifications.put("ASX", "ASX");
1248  18 modifications.put("ATD", "THR");
1249  18 modifications.put("ATL", "THR");
1250  18 modifications.put("ATM", "THR");
1251  18 modifications.put("AVC", "ALA");
1252  18 modifications.put("AVN", "XAA");
1253  18 modifications.put("AYA", "ALA");
1254  18 modifications.put("AYG", "AYG");
1255  18 modifications.put("AZK", "LYS");
1256  18 modifications.put("AZS", "SER");
1257  18 modifications.put("AZY", "TYR");
1258  18 modifications.put("B1F", "PHE");
1259  18 modifications.put("B1P", "ASN");
1260  18 modifications.put("B2A", "ALA");
1261  18 modifications.put("B2F", "PHE");
1262  18 modifications.put("B2I", "ILE");
1263  18 modifications.put("B2V", "VAL");
1264  18 modifications.put("B3A", "ALA");
1265  18 modifications.put("B3D", "ASP");
1266  18 modifications.put("B3E", "GLU");
1267  18 modifications.put("B3K", "LYS");
1268  18 modifications.put("B3L", "XAA");
1269  18 modifications.put("B3M", "XAA");
1270  18 modifications.put("B3Q", "XAA");
1271  18 modifications.put("B3S", "SER");
1272  18 modifications.put("B3T", "XAA");
1273  18 modifications.put("B3U", "HIS");
1274  18 modifications.put("B3X", "ASN");
1275  18 modifications.put("B3Y", "TYR");
1276  18 modifications.put("BB6", "CYS");
1277  18 modifications.put("BB7", "CYS");
1278  18 modifications.put("BB8", "PHE");
1279  18 modifications.put("BB9", "CYS");
1280  18 modifications.put("BBC", "CYS");
1281  18 modifications.put("BCS", "CYS");
1282  18 modifications.put("BE2", "XAA");
1283  18 modifications.put("BFD", "ASP");
1284  18 modifications.put("BG1", "SER");
1285  18 modifications.put("BGM", "GLY");
1286  18 modifications.put("BH2", "ASP");
1287  18 modifications.put("BHD", "ASP");
1288  18 modifications.put("BIF", "PHE");
1289  18 modifications.put("BIL", "XAA");
1290  18 modifications.put("BIU", "ILE");
1291  18 modifications.put("BJH", "XAA");
1292  18 modifications.put("BLE", "LEU");
1293  18 modifications.put("BLY", "LYS");
1294  18 modifications.put("BMP", "ASN");
1295  18 modifications.put("BMT", "THR");
1296  18 modifications.put("BNN", "PHE");
1297  18 modifications.put("BNO", "XAA");
1298  18 modifications.put("BOE", "THR");
1299  18 modifications.put("BOR", "ARG");
1300  18 modifications.put("BPE", "CYS");
1301  18 modifications.put("BRU", "UR3");
1302  18 modifications.put("BSE", "SER");
1303  18 modifications.put("BT5", "ASN");
1304  18 modifications.put("BTA", "LEU");
1305  18 modifications.put("BTC", "CYS");
1306  18 modifications.put("BTR", "TRP");
1307  18 modifications.put("BUC", "CYS");
1308  18 modifications.put("BUG", "VAL");
1309  18 modifications.put("BVP", "UR3");
1310  18 modifications.put("BZG", "ASN");
1311  18 modifications.put("C ", "CYS");
1312  18 modifications.put("C12", "TYG");
1313  18 modifications.put("C1X", "LYS");
1314  18 modifications.put("C25", "CYS");
1315  18 modifications.put("C2L", "CYS");
1316  18 modifications.put("C2S", "CYS");
1317  18 modifications.put("C31", "CYS");
1318  18 modifications.put("C32", "CYS");
1319  18 modifications.put("C34", "CYS");
1320  18 modifications.put("C36", "CYS");
1321  18 modifications.put("C37", "CYS");
1322  18 modifications.put("C38", "CYS");
1323  18 modifications.put("C3Y", "CYS");
1324  18 modifications.put("C42", "CYS");
1325  18 modifications.put("C43", "CYS");
1326  18 modifications.put("C45", "CYS");
1327  18 modifications.put("C46", "CYS");
1328  18 modifications.put("C49", "CYS");
1329  18 modifications.put("C4R", "CYS");
1330  18 modifications.put("C4S", "CYS");
1331  18 modifications.put("C5C", "CYS");
1332  18 modifications.put("C66", "XAA");
1333  18 modifications.put("C6C", "CYS");
1334  18 modifications.put("C99", "TFG");
1335  18 modifications.put("CAF", "CYS");
1336  18 modifications.put("CAL", "XAA");
1337  18 modifications.put("CAR", "CYS");
1338  18 modifications.put("CAS", "CYS");
1339  18 modifications.put("CAV", "XAA");
1340  18 modifications.put("CAY", "CYS");
1341  18 modifications.put("CB2", "CYS");
1342  18 modifications.put("CBR", "CYS");
1343  18 modifications.put("CBV", "CYS");
1344  18 modifications.put("CCC", "CYS");
1345  18 modifications.put("CCL", "LYS");
1346  18 modifications.put("CCS", "CYS");
1347  18 modifications.put("CCY", "CYG");
1348  18 modifications.put("CDE", "XAA");
1349  18 modifications.put("CDV", "XAA");
1350  18 modifications.put("CDW", "CYS");
1351  18 modifications.put("CEA", "CYS");
1352  18 modifications.put("CFL", "CYS");
1353  18 modifications.put("CFY", "FCYG"); // check
1354  18 modifications.put("CG1", "GLY");
1355  18 modifications.put("CGA", "GLU");
1356  18 modifications.put("CGU", "GLU");
1357  18 modifications.put("CH ", "CYS");
1358  18 modifications.put("CH6", "MYG");
1359  18 modifications.put("CH7", "KYG");
1360  18 modifications.put("CHF", "XAA");
1361  18 modifications.put("CHG", "XAA");
1362  18 modifications.put("CHP", "GLY");
1363  18 modifications.put("CHS", "XAA");
1364  18 modifications.put("CIR", "ARG");
1365  18 modifications.put("CJO", "GYG");
1366  18 modifications.put("CLE", "LEU");
1367  18 modifications.put("CLG", "LYS");
1368  18 modifications.put("CLH", "LYS");
1369  18 modifications.put("CLV", "AFG");
1370  18 modifications.put("CM0", "ASN");
1371  18 modifications.put("CME", "CYS");
1372  18 modifications.put("CMH", "CYS");
1373  18 modifications.put("CML", "CYS");
1374  18 modifications.put("CMR", "CYS");
1375  18 modifications.put("CMT", "CYS");
1376  18 modifications.put("CNU", "UR3");
1377  18 modifications.put("CP1", "CYS");
1378  18 modifications.put("CPC", "XAA");
1379  18 modifications.put("CPI", "XAA");
1380  18 modifications.put("CQR", "GYG");
1381  18 modifications.put("CR0", "TLG");
1382  18 modifications.put("CR2", "GYG");
1383  18 modifications.put("CR5", "GLY");
1384  18 modifications.put("CR7", "KYG");
1385  18 modifications.put("CR8", "HYG");
1386  18 modifications.put("CRF", "TWG");
1387  18 modifications.put("CRG", "THG");
1388  18 modifications.put("CRK", "MYG");
1389  18 modifications.put("CRO", "GYG");
1390  18 modifications.put("CRQ", "QYG");
1391  18 modifications.put("CRU", "EYG");
1392  18 modifications.put("CRW", "ASG");
1393  18 modifications.put("CRX", "ASG");
1394  18 modifications.put("CS0", "CYS");
1395  18 modifications.put("CS1", "CYS");
1396  18 modifications.put("CS3", "CYS");
1397  18 modifications.put("CS4", "CYS");
1398  18 modifications.put("CS8", "ASN");
1399  18 modifications.put("CSA", "CYS");
1400  18 modifications.put("CSB", "CYS");
1401  18 modifications.put("CSD", "CYS");
1402  18 modifications.put("CSE", "CYS");
1403  18 modifications.put("CSF", "CYS");
1404  18 modifications.put("CSH", "SHG");
1405  18 modifications.put("CSI", "GLY");
1406  18 modifications.put("CSJ", "CYS");
1407  18 modifications.put("CSL", "CYS");
1408  18 modifications.put("CSO", "CYS");
1409  18 modifications.put("CSP", "CYS");
1410  18 modifications.put("CSR", "CYS");
1411  18 modifications.put("CSS", "CYS");
1412  18 modifications.put("CSU", "CYS");
1413  18 modifications.put("CSW", "CYS");
1414  18 modifications.put("CSX", "CYS");
1415  18 modifications.put("CSY", "SYG");
1416  18 modifications.put("CSZ", "CYS");
1417  18 modifications.put("CTE", "TRP");
1418  18 modifications.put("CTG", "THR");
1419  18 modifications.put("CTH", "THR");
1420  18 modifications.put("CUC", "XAA");
1421  18 modifications.put("CWR", "SER");
1422  18 modifications.put("CXM", "MET");
1423  18 modifications.put("CY0", "CYS");
1424  18 modifications.put("CY1", "CYS");
1425  18 modifications.put("CY3", "CYS");
1426  18 modifications.put("CY4", "CYS");
1427  18 modifications.put("CYA", "CYS");
1428  18 modifications.put("CYD", "CYS");
1429  18 modifications.put("CYF", "CYS");
1430  18 modifications.put("CYG", "CYS");
1431  18 modifications.put("CYJ", "XAA");
1432  18 modifications.put("CYM", "CYS");
1433  18 modifications.put("CYQ", "CYS");
1434  18 modifications.put("CYR", "CYS");
1435  18 modifications.put("CYS", "CYS");
1436  18 modifications.put("CZ2", "CYS");
1437  18 modifications.put("CZO", "GYG");
1438  18 modifications.put("CZZ", "CYS");
1439  18 modifications.put("D11", "THR");
1440  18 modifications.put("D1P", "ASN");
1441  18 modifications.put("D3 ", "ASN");
1442  18 modifications.put("D33", "ASN");
1443  18 modifications.put("D3P", "GLY");
1444  18 modifications.put("D3T", "THR");
1445  18 modifications.put("D4M", "THR");
1446  18 modifications.put("D4P", "XAA");
1447  18 modifications.put("DA ", "ALA");
1448  18 modifications.put("DA2", "XAA");
1449  18 modifications.put("DAB", "ALA");
1450  18 modifications.put("DAH", "PHE");
1451  18 modifications.put("DAL", "ALA");
1452  18 modifications.put("DAR", "ARG");
1453  18 modifications.put("DAS", "ASP");
1454  18 modifications.put("DBB", "THR");
1455  18 modifications.put("DBM", "ASN");
1456  18 modifications.put("DBS", "SER");
1457  18 modifications.put("DBU", "THR");
1458  18 modifications.put("DBY", "TYR");
1459  18 modifications.put("DBZ", "ALA");
1460  18 modifications.put("DC ", "CYS");
1461  18 modifications.put("DC2", "CYS");
1462  18 modifications.put("DCG", "GLY");
1463  18 modifications.put("DCI", "XAA");
1464  18 modifications.put("DCL", "XAA");
1465  18 modifications.put("DCT", "CYS");
1466  18 modifications.put("DCY", "CYS");
1467  18 modifications.put("DDE", "HIS");
1468  18 modifications.put("DDG", "GLY");
1469  18 modifications.put("DDN", "UR3");
1470  18 modifications.put("DDX", "ASN");
1471  18 modifications.put("DFC", "CYS");
1472  18 modifications.put("DFG", "GLY");
1473  18 modifications.put("DFI", "XAA");
1474  18 modifications.put("DFO", "XAA");
1475  18 modifications.put("DFT", "ASN");
1476  18 modifications.put("DG ", "GLY");
1477  18 modifications.put("DGH", "GLY");
1478  18 modifications.put("DGI", "GLY");
1479  18 modifications.put("DGL", "GLU");
1480  18 modifications.put("DGN", "GLN");
1481  18 modifications.put("DHA", "SER");
1482  18 modifications.put("DHI", "HIS");
1483  18 modifications.put("DHL", "XAA");
1484  18 modifications.put("DHN", "VAL");
1485  18 modifications.put("DHP", "XAA");
1486  18 modifications.put("DHU", "UR3");
1487  18 modifications.put("DHV", "VAL");
1488  18 modifications.put("DI ", "ILE");
1489  18 modifications.put("DIL", "ILE");
1490  18 modifications.put("DIR", "ARG");
1491  18 modifications.put("DIV", "VAL");
1492  18 modifications.put("DLE", "LEU");
1493  18 modifications.put("DLS", "LYS");
1494  18 modifications.put("DLY", "LYS");
1495  18 modifications.put("DM0", "LYS");
1496  18 modifications.put("DMH", "ASN");
1497  18 modifications.put("DMK", "ASP");
1498  18 modifications.put("DMT", "XAA");
1499  18 modifications.put("DN ", "ASN");
1500  18 modifications.put("DNE", "LEU");
1501  18 modifications.put("DNG", "LEU");
1502  18 modifications.put("DNL", "LYS");
1503  18 modifications.put("DNM", "LEU");
1504  18 modifications.put("DNP", "ALA");
1505  18 modifications.put("DNR", "CYS");
1506  18 modifications.put("DNS", "LYS");
1507  18 modifications.put("DOA", "XAA");
1508  18 modifications.put("DOC", "CYS");
1509  18 modifications.put("DOH", "ASP");
1510  18 modifications.put("DON", "LEU");
1511  18 modifications.put("DPB", "THR");
1512  18 modifications.put("DPH", "PHE");
1513  18 modifications.put("DPL", "PRO");
1514  18 modifications.put("DPP", "ALA");
1515  18 modifications.put("DPQ", "TYR");
1516  18 modifications.put("DPR", "PRO");
1517  18 modifications.put("DPY", "ASN");
1518  18 modifications.put("DRM", "UR3");
1519  18 modifications.put("DRP", "ASN");
1520  18 modifications.put("DRT", "THR");
1521  18 modifications.put("DRZ", "ASN");
1522  18 modifications.put("DSE", "SER");
1523  18 modifications.put("DSG", "ASN");
1524  18 modifications.put("DSN", "SER");
1525  18 modifications.put("DSP", "ASP");
1526  18 modifications.put("DT ", "THR");
1527  18 modifications.put("DTH", "THR");
1528  18 modifications.put("DTR", "TRP");
1529  18 modifications.put("DTY", "TYR");
1530  18 modifications.put("DU ", "UR3");
1531  18 modifications.put("DVA", "VAL");
1532  18 modifications.put("DXD", "ASN");
1533  18 modifications.put("DXN", "ASN");
1534  18 modifications.put("DYG", "DYG");
1535  18 modifications.put("DYS", "CYS");
1536  18 modifications.put("DZM", "ALA");
1537  18 modifications.put("E ", "ALA");
1538  18 modifications.put("E1X", "ALA");
1539  18 modifications.put("ECC", "GLN");
1540  18 modifications.put("EDA", "ALA");
1541  18 modifications.put("EFC", "CYS");
1542  18 modifications.put("EHP", "PHE");
1543  18 modifications.put("EIT", "THR");
1544  18 modifications.put("ENP", "ASN");
1545  18 modifications.put("ESB", "TYR");
1546  18 modifications.put("ESC", "MET");
1547  18 modifications.put("EXB", "XAA");
1548  18 modifications.put("EXY", "LEU");
1549  18 modifications.put("EY5", "ASN");
1550  18 modifications.put("EYS", "XAA");
1551  18 modifications.put("F2F", "PHE");
1552  18 modifications.put("FA2", "ALA");
1553  18 modifications.put("FA5", "ASN");
1554  18 modifications.put("FAG", "ASN");
1555  18 modifications.put("FAI", "ASN");
1556  18 modifications.put("FB5", "ALA");
1557  18 modifications.put("FB6", "ALA");
1558  18 modifications.put("FCL", "PHE");
1559  18 modifications.put("FFD", "ASN");
1560  18 modifications.put("FGA", "GLU");
1561  18 modifications.put("FGL", "GLY");
1562  18 modifications.put("FGP", "SER");
1563  18 modifications.put("FHL", "XAA");
1564  18 modifications.put("FHO", "LYS");
1565  18 modifications.put("FHU", "UR3");
1566  18 modifications.put("FLA", "ALA");
1567  18 modifications.put("FLE", "LEU");
1568  18 modifications.put("FLT", "TYR");
1569  18 modifications.put("FME", "MET");
1570  18 modifications.put("FMG", "GLY");
1571  18 modifications.put("FMU", "ASN");
1572  18 modifications.put("FOE", "CYS");
1573  18 modifications.put("FOX", "GLY");
1574  18 modifications.put("FP9", "PRO");
1575  18 modifications.put("FPA", "PHE");
1576  18 modifications.put("FRD", "XAA");
1577  18 modifications.put("FT6", "TRP");
1578  18 modifications.put("FTR", "TRP");
1579  18 modifications.put("FTY", "TYR");
1580  18 modifications.put("FVA", "VAL");
1581  18 modifications.put("FZN", "LYS");
1582  18 modifications.put("G ", "GLY");
1583  18 modifications.put("G25", "GLY");
1584  18 modifications.put("G2L", "GLY");
1585  18 modifications.put("G2S", "GLY");
1586  18 modifications.put("G31", "GLY");
1587  18 modifications.put("G32", "GLY");
1588  18 modifications.put("G33", "GLY");
1589  18 modifications.put("G36", "GLY");
1590  18 modifications.put("G38", "GLY");
1591  18 modifications.put("G42", "GLY");
1592  18 modifications.put("G46", "GLY");
1593  18 modifications.put("G47", "GLY");
1594  18 modifications.put("G48", "GLY");
1595  18 modifications.put("G49", "GLY");
1596  18 modifications.put("G4P", "ASN");
1597  18 modifications.put("G7M", "GLY");
1598  18 modifications.put("GAO", "GLY");
1599  18 modifications.put("GAU", "GLU");
1600  18 modifications.put("GCK", "CYS");
1601  18 modifications.put("GCM", "XAA");
1602  18 modifications.put("GDP", "GLY");
1603  18 modifications.put("GDR", "GLY");
1604  18 modifications.put("GFL", "GLY");
1605  18 modifications.put("GGL", "GLU");
1606  18 modifications.put("GH3", "GLY");
1607  18 modifications.put("GHG", "GLN");
1608  18 modifications.put("GHP", "GLY");
1609  18 modifications.put("GL3", "GLY");
1610  18 modifications.put("GLH", "GLN");
1611  18 modifications.put("GLJ", "GLU");
1612  18 modifications.put("GLK", "GLU");
1613  18 modifications.put("GLM", "XAA");
1614  18 modifications.put("GLN", "GLN");
1615  18 modifications.put("GLQ", "GLU");
1616  18 modifications.put("GLU", "GLU");
1617  18 modifications.put("GLX", "GLX");
1618  18 modifications.put("GLY", "GLY");
1619  18 modifications.put("GLZ", "GLY");
1620  18 modifications.put("GMA", "GLU");
1621  18 modifications.put("GMS", "GLY");
1622  18 modifications.put("GMU", "UR3");
1623  18 modifications.put("GN7", "GLY");
1624  18 modifications.put("GND", "XAA");
1625  18 modifications.put("GNE", "ASN");
1626  18 modifications.put("GOM", "GLY");
1627  18 modifications.put("GPL", "LYS");
1628  18 modifications.put("GS ", "GLY");
1629  18 modifications.put("GSC", "GLY");
1630  18 modifications.put("GSR", "GLY");
1631  18 modifications.put("GSS", "GLY");
1632  18 modifications.put("GSU", "GLU");
1633  18 modifications.put("GT9", "CYS");
1634  18 modifications.put("GTP", "GLY");
1635  18 modifications.put("GVL", "XAA");
1636  18 modifications.put("GYC", "CYG");
1637  18 modifications.put("GYS", "SYG");
1638  18 modifications.put("H2U", "UR3");
1639  18 modifications.put("H5M", "PRO");
1640  18 modifications.put("HAC", "ALA");
1641  18 modifications.put("HAR", "ARG");
1642  18 modifications.put("HBN", "HIS");
1643  18 modifications.put("HCS", "XAA");
1644  18 modifications.put("HDP", "UR3");
1645  18 modifications.put("HEU", "UR3");
1646  18 modifications.put("HFA", "XAA");
1647  18 modifications.put("HGL", "XAA");
1648  18 modifications.put("HHI", "HIS");
1649  18 modifications.put("HHK", "AK"); // check
1650  18 modifications.put("HIA", "HIS");
1651  18 modifications.put("HIC", "HIS");
1652  18 modifications.put("HIP", "HIS");
1653  18 modifications.put("HIQ", "HIS");
1654  18 modifications.put("HIS", "HIS");
1655  18 modifications.put("HL2", "LEU");
1656  18 modifications.put("HLU", "LEU");
1657  18 modifications.put("HMR", "ARG");
1658  18 modifications.put("HOL", "ASN");
1659  18 modifications.put("HPC", "PHE");
1660  18 modifications.put("HPE", "PHE");
1661  18 modifications.put("HPH", "PHE");
1662  18 modifications.put("HPQ", "PHE");
1663  18 modifications.put("HQA", "ALA");
1664  18 modifications.put("HRG", "ARG");
1665  18 modifications.put("HRP", "TRP");
1666  18 modifications.put("HS8", "HIS");
1667  18 modifications.put("HS9", "HIS");
1668  18 modifications.put("HSE", "SER");
1669  18 modifications.put("HSL", "SER");
1670  18 modifications.put("HSO", "HIS");
1671  18 modifications.put("HTI", "CYS");
1672  18 modifications.put("HTN", "ASN");
1673  18 modifications.put("HTR", "TRP");
1674  18 modifications.put("HV5", "ALA");
1675  18 modifications.put("HVA", "VAL");
1676  18 modifications.put("HY3", "PRO");
1677  18 modifications.put("HYP", "PRO");
1678  18 modifications.put("HZP", "PRO");
1679  18 modifications.put("I ", "ILE");
1680  18 modifications.put("I2M", "ILE");
1681  18 modifications.put("I58", "LYS");
1682  18 modifications.put("I5C", "CYS");
1683  18 modifications.put("IAM", "ALA");
1684  18 modifications.put("IAR", "ARG");
1685  18 modifications.put("IAS", "ASP");
1686  18 modifications.put("IC ", "CYS");
1687  18 modifications.put("IEL", "LYS");
1688  18 modifications.put("IEY", "HYG");
1689  18 modifications.put("IG ", "GLY");
1690  18 modifications.put("IGL", "GLY");
1691  18 modifications.put("IGU", "GLY");
1692  18 modifications.put("IIC", "SHG");
1693  18 modifications.put("IIL", "ILE");
1694  18 modifications.put("ILE", "ILE");
1695  18 modifications.put("ILG", "GLU");
1696  18 modifications.put("ILX", "ILE");
1697  18 modifications.put("IMC", "CYS");
1698  18 modifications.put("IML", "ILE");
1699  18 modifications.put("IOY", "PHE");
1700  18 modifications.put("IPG", "GLY");
1701  18 modifications.put("IPN", "ASN");
1702  18 modifications.put("IRN", "ASN");
1703  18 modifications.put("IT1", "LYS");
1704  18 modifications.put("IU ", "UR3");
1705  18 modifications.put("IYR", "TYR");
1706  18 modifications.put("IYT", "THR");
1707  18 modifications.put("IZO", "MET");
1708  18 modifications.put("JJJ", "CYS");
1709  18 modifications.put("JJK", "CYS");
1710  18 modifications.put("JJL", "CYS");
1711  18 modifications.put("JW5", "ASN");
1712  18 modifications.put("K1R", "CYS");
1713  18 modifications.put("KAG", "GLY");
1714  18 modifications.put("KCX", "LYS");
1715  18 modifications.put("KGC", "LYS");
1716  18 modifications.put("KNB", "ALA");
1717  18 modifications.put("KOR", "MET");
1718  18 modifications.put("KPI", "LYS");
1719  18 modifications.put("KST", "LYS");
1720  18 modifications.put("KYQ", "LYS");
1721  18 modifications.put("L2A", "XAA");
1722  18 modifications.put("LA2", "LYS");
1723  18 modifications.put("LAA", "ASP");
1724  18 modifications.put("LAL", "ALA");
1725  18 modifications.put("LBY", "LYS");
1726  18 modifications.put("LC ", "CYS");
1727  18 modifications.put("LCA", "ALA");
1728  18 modifications.put("LCC", "ASN");
1729  18 modifications.put("LCG", "GLY");
1730  18 modifications.put("LCH", "ASN");
1731  18 modifications.put("LCK", "LYS");
1732  18 modifications.put("LCX", "LYS");
1733  18 modifications.put("LDH", "LYS");
1734  18 modifications.put("LED", "LEU");
1735  18 modifications.put("LEF", "LEU");
1736  18 modifications.put("LEH", "LEU");
1737  18 modifications.put("LEI", "VAL");
1738  18 modifications.put("LEM", "LEU");
1739  18 modifications.put("LEN", "LEU");
1740  18 modifications.put("LET", "XAA");
1741  18 modifications.put("LEU", "LEU");
1742  18 modifications.put("LEX", "LEU");
1743  18 modifications.put("LG ", "GLY");
1744  18 modifications.put("LGP", "GLY");
1745  18 modifications.put("LHC", "XAA");
1746  18 modifications.put("LHU", "UR3");
1747  18 modifications.put("LKC", "ASN");
1748  18 modifications.put("LLP", "LYS");
1749  18 modifications.put("LLY", "LYS");
1750  18 modifications.put("LME", "GLU");
1751  18 modifications.put("LMF", "LYS");
1752  18 modifications.put("LMQ", "GLN");
1753  18 modifications.put("LMS", "ASN");
1754  18 modifications.put("LP6", "LYS");
1755  18 modifications.put("LPD", "PRO");
1756  18 modifications.put("LPG", "GLY");
1757  18 modifications.put("LPL", "XAA");
1758  18 modifications.put("LPS", "SER");
1759  18 modifications.put("LSO", "XAA");
1760  18 modifications.put("LTA", "XAA");
1761  18 modifications.put("LTR", "TRP");
1762  18 modifications.put("LVG", "GLY");
1763  18 modifications.put("LVN", "VAL");
1764  18 modifications.put("LYF", "LYS");
1765  18 modifications.put("LYK", "LYS");
1766  18 modifications.put("LYM", "LYS");
1767  18 modifications.put("LYN", "LYS");
1768  18 modifications.put("LYR", "LYS");
1769  18 modifications.put("LYS", "LYS");
1770  18 modifications.put("LYX", "LYS");
1771  18 modifications.put("LYZ", "LYS");
1772  18 modifications.put("M0H", "CYS");
1773  18 modifications.put("M1G", "GLY");
1774  18 modifications.put("M2G", "GLY");
1775  18 modifications.put("M2L", "LYS");
1776  18 modifications.put("M2S", "MET");
1777  18 modifications.put("M30", "GLY");
1778  18 modifications.put("M3L", "LYS");
1779  18 modifications.put("M5M", "CYS");
1780  18 modifications.put("MA ", "ALA");
1781  18 modifications.put("MA6", "ALA");
1782  18 modifications.put("MA7", "ALA");
1783  18 modifications.put("MAA", "ALA");
1784  18 modifications.put("MAD", "ALA");
1785  18 modifications.put("MAI", "ARG");
1786  18 modifications.put("MBQ", "TYR");
1787  18 modifications.put("MBZ", "ASN");
1788  18 modifications.put("MC1", "SER");
1789  18 modifications.put("MCG", "XAA");
1790  18 modifications.put("MCL", "LYS");
1791  18 modifications.put("MCS", "CYS");
1792  18 modifications.put("MCY", "CYS");
1793  18 modifications.put("MD3", "CYS");
1794  18 modifications.put("MD6", "GLY");
1795  18 modifications.put("MDH", "XAA");
1796  18 modifications.put("MDO", "ASG");
1797  18 modifications.put("MDR", "ASN");
1798  18 modifications.put("MEA", "PHE");
1799  18 modifications.put("MED", "MET");
1800  18 modifications.put("MEG", "GLU");
1801  18 modifications.put("MEN", "ASN");
1802  18 modifications.put("MEP", "UR3");
1803  18 modifications.put("MEQ", "GLN");
1804  18 modifications.put("MET", "MET");
1805  18 modifications.put("MEU", "GLY");
1806  18 modifications.put("MF3", "XAA");
1807  18 modifications.put("MFC", "GYG");
1808  18 modifications.put("MG1", "GLY");
1809  18 modifications.put("MGG", "ARG");
1810  18 modifications.put("MGN", "GLN");
1811  18 modifications.put("MGQ", "ALA");
1812  18 modifications.put("MGV", "GLY");
1813  18 modifications.put("MGY", "GLY");
1814  18 modifications.put("MHL", "LEU");
1815  18 modifications.put("MHO", "MET");
1816  18 modifications.put("MHS", "HIS");
1817  18 modifications.put("MIA", "ALA");
1818  18 modifications.put("MIS", "SER");
1819  18 modifications.put("MK8", "LEU");
1820  18 modifications.put("ML3", "LYS");
1821  18 modifications.put("MLE", "LEU");
1822  18 modifications.put("MLL", "LEU");
1823  18 modifications.put("MLY", "LYS");
1824  18 modifications.put("MLZ", "LYS");
1825  18 modifications.put("MME", "MET");
1826  18 modifications.put("MMO", "ARG");
1827  18 modifications.put("MMT", "THR");
1828  18 modifications.put("MND", "ASN");
1829  18 modifications.put("MNL", "LEU");
1830  18 modifications.put("MNU", "UR3");
1831  18 modifications.put("MNV", "VAL");
1832  18 modifications.put("MOD", "XAA");
1833  18 modifications.put("MP8", "PRO");
1834  18 modifications.put("MPH", "XAA");
1835  18 modifications.put("MPJ", "XAA");
1836  18 modifications.put("MPQ", "GLY");
1837  18 modifications.put("MRG", "GLY");
1838  18 modifications.put("MSA", "GLY");
1839  18 modifications.put("MSE", "MET");
1840  18 modifications.put("MSL", "MET");
1841  18 modifications.put("MSO", "MET");
1842  18 modifications.put("MSP", "XAA");
1843  18 modifications.put("MT2", "MET");
1844  18 modifications.put("MTR", "THR");
1845  18 modifications.put("MTU", "ALA");
1846  18 modifications.put("MTY", "TYR");
1847  18 modifications.put("MVA", "VAL");
1848  18 modifications.put("N ", "ASN");
1849  18 modifications.put("N10", "SER");
1850  18 modifications.put("N2C", "XAA");
1851  18 modifications.put("N5I", "ASN");
1852  18 modifications.put("N5M", "CYS");
1853  18 modifications.put("N6G", "GLY");
1854  18 modifications.put("N7P", "PRO");
1855  18 modifications.put("NA8", "ALA");
1856  18 modifications.put("NAL", "ALA");
1857  18 modifications.put("NAM", "ALA");
1858  18 modifications.put("NB8", "ASN");
1859  18 modifications.put("NBQ", "TYR");
1860  18 modifications.put("NC1", "SER");
1861  18 modifications.put("NCB", "ALA");
1862  18 modifications.put("NCX", "ASN");
1863  18 modifications.put("NCY", "XAA");
1864  18 modifications.put("NDF", "PHE");
1865  18 modifications.put("NDN", "UR3");
1866  18 modifications.put("NEM", "HIS");
1867  18 modifications.put("NEP", "HIS");
1868  18 modifications.put("NF2", "ASN");
1869  18 modifications.put("NFA", "PHE");
1870  18 modifications.put("NHL", "GLU");
1871  18 modifications.put("NIT", "XAA");
1872  18 modifications.put("NIY", "TYR");
1873  18 modifications.put("NLE", "LEU");
1874  18 modifications.put("NLN", "LEU");
1875  18 modifications.put("NLO", "LEU");
1876  18 modifications.put("NLP", "LEU");
1877  18 modifications.put("NLQ", "GLN");
1878  18 modifications.put("NMC", "GLY");
1879  18 modifications.put("NMM", "ARG");
1880  18 modifications.put("NMS", "THR");
1881  18 modifications.put("NMT", "THR");
1882  18 modifications.put("NNH", "ARG");
1883  18 modifications.put("NP3", "ASN");
1884  18 modifications.put("NPH", "CYS");
1885  18 modifications.put("NPI", "ALA");
1886  18 modifications.put("NRP", "LYG");
1887  18 modifications.put("NRQ", "MYG");
1888  18 modifications.put("NSK", "XAA");
1889  18 modifications.put("NTY", "TYR");
1890  18 modifications.put("NVA", "VAL");
1891  18 modifications.put("NYC", "TWG");
1892  18 modifications.put("NYG", "NYG");
1893  18 modifications.put("NYM", "ASN");
1894  18 modifications.put("NYS", "CYS");
1895  18 modifications.put("NZH", "HIS");
1896  18 modifications.put("O12", "XAA");
1897  18 modifications.put("O2C", "ASN");
1898  18 modifications.put("O2G", "GLY");
1899  18 modifications.put("OAD", "ASN");
1900  18 modifications.put("OAS", "SER");
1901  18 modifications.put("OBF", "XAA");
1902  18 modifications.put("OBS", "XAA");
1903  18 modifications.put("OCS", "CYS");
1904  18 modifications.put("OCY", "CYS");
1905  18 modifications.put("ODP", "ASN");
1906  18 modifications.put("OHI", "HIS");
1907  18 modifications.put("OHS", "ASP");
1908  18 modifications.put("OIC", "XAA");
1909  18 modifications.put("OIP", "ILE");
1910  18 modifications.put("OLE", "XAA");
1911  18 modifications.put("OLT", "THR");
1912  18 modifications.put("OLZ", "SER");
1913  18 modifications.put("OMC", "CYS");
1914  18 modifications.put("OMG", "GLY");
1915  18 modifications.put("OMT", "MET");
1916  18 modifications.put("OMU", "UR3");
1917  18 modifications.put("ONE", "UR3");
1918  18 modifications.put("ONH", "ALA");
1919  18 modifications.put("ONL", "XAA");
1920  18 modifications.put("OPR", "ARG");
1921  18 modifications.put("ORN", "ALA");
1922  18 modifications.put("ORQ", "ARG");
1923  18 modifications.put("OSE", "SER");
1924  18 modifications.put("OTB", "XAA");
1925  18 modifications.put("OTH", "THR");
1926  18 modifications.put("OTY", "TYR");
1927  18 modifications.put("OXX", "ASP");
1928  18 modifications.put("P ", "GLY");
1929  18 modifications.put("P1L", "CYS");
1930  18 modifications.put("P1P", "ASN");
1931  18 modifications.put("P2T", "THR");
1932  18 modifications.put("P2U", "UR3");
1933  18 modifications.put("P2Y", "PRO");
1934  18 modifications.put("P5P", "ALA");
1935  18 modifications.put("PAQ", "TYR");
1936  18 modifications.put("PAS", "ASP");
1937  18 modifications.put("PAT", "TRP");
1938  18 modifications.put("PAU", "ALA");
1939  18 modifications.put("PBB", "CYS");
1940  18 modifications.put("PBF", "PHE");
1941  18 modifications.put("PBT", "ASN");
1942  18 modifications.put("PCA", "GLU");
1943  18 modifications.put("PCC", "PRO");
1944  18 modifications.put("PCE", "XAA");
1945  18 modifications.put("PCS", "PHE");
1946  18 modifications.put("PDL", "XAA");
1947  18 modifications.put("PDU", "UR3");
1948  18 modifications.put("PEC", "CYS");
1949  18 modifications.put("PF5", "PHE");
1950  18 modifications.put("PFF", "PHE");
1951  18 modifications.put("PFX", "XAA");
1952  18 modifications.put("PG1", "SER");
1953  18 modifications.put("PG7", "GLY");
1954  18 modifications.put("PG9", "GLY");
1955  18 modifications.put("PGL", "XAA");
1956  18 modifications.put("PGN", "GLY");
1957  18 modifications.put("PGP", "GLY");
1958  18 modifications.put("PGY", "GLY");
1959  18 modifications.put("PHA", "PHE");
1960  18 modifications.put("PHD", "ASP");
1961  18 modifications.put("PHE", "PHE");
1962  18 modifications.put("PHI", "PHE");
1963  18 modifications.put("PHL", "PHE");
1964  18 modifications.put("PHM", "PHE");
1965  18 modifications.put("PIA", "AYG");
1966  18 modifications.put("PIV", "XAA");
1967  18 modifications.put("PLE", "LEU");
1968  18 modifications.put("PM3", "PHE");
1969  18 modifications.put("PMT", "CYS");
1970  18 modifications.put("POM", "PRO");
1971  18 modifications.put("PPN", "PHE");
1972  18 modifications.put("PPU", "ALA");
1973  18 modifications.put("PPW", "GLY");
1974  18 modifications.put("PQ1", "ASN");
1975  18 modifications.put("PR3", "CYS");
1976  18 modifications.put("PR5", "ALA");
1977  18 modifications.put("PR9", "PRO");
1978  18 modifications.put("PRN", "ALA");
1979  18 modifications.put("PRO", "PRO");
1980  18 modifications.put("PRS", "PRO");
1981  18 modifications.put("PSA", "PHE");
1982  18 modifications.put("PSH", "HIS");
1983  18 modifications.put("PST", "THR");
1984  18 modifications.put("PSU", "UR3");
1985  18 modifications.put("PSW", "CYS");
1986  18 modifications.put("PTA", "XAA");
1987  18 modifications.put("PTH", "TYR");
1988  18 modifications.put("PTM", "TYR");
1989  18 modifications.put("PTR", "TYR");
1990  18 modifications.put("PU ", "ALA");
1991  18 modifications.put("PUY", "ASN");
1992  18 modifications.put("PVH", "HIS");
1993  18 modifications.put("PVL", "XAA");
1994  18 modifications.put("PYA", "ALA");
1995  18 modifications.put("PYO", "UR3");
1996  18 modifications.put("PYX", "CYS");
1997  18 modifications.put("PYY", "ASN");
1998  18 modifications.put("QLG", "QLG");
1999  18 modifications.put("QMM", "GLN");
2000  18 modifications.put("QPA", "CYS");
2001  18 modifications.put("QPH", "PHE");
2002  18 modifications.put("QUO", "GLY");
2003  18 modifications.put("R ", "ALA");
2004  18 modifications.put("R1A", "CYS");
2005  18 modifications.put("R4K", "TRP");
2006  18 modifications.put("RC7", "HYG");
2007  18 modifications.put("RE0", "TRP");
2008  18 modifications.put("RE3", "TRP");
2009  18 modifications.put("RIA", "ALA");
2010  18 modifications.put("RMP", "ALA");
2011  18 modifications.put("RON", "XAA");
2012  18 modifications.put("RT ", "THR");
2013  18 modifications.put("RTP", "ASN");
2014  18 modifications.put("S1H", "SER");
2015  18 modifications.put("S2C", "CYS");
2016  18 modifications.put("S2D", "ALA");
2017  18 modifications.put("S2M", "THR");
2018  18 modifications.put("S2P", "ALA");
2019  18 modifications.put("S4A", "ALA");
2020  18 modifications.put("S4C", "CYS");
2021  18 modifications.put("S4G", "GLY");
2022  18 modifications.put("S4U", "UR3");
2023  18 modifications.put("S6G", "GLY");
2024  18 modifications.put("SAC", "SER");
2025  18 modifications.put("SAH", "CYS");
2026  18 modifications.put("SAR", "GLY");
2027  18 modifications.put("SBL", "SER");
2028  18 modifications.put("SC ", "CYS");
2029  18 modifications.put("SCH", "CYS");
2030  18 modifications.put("SCS", "CYS");
2031  18 modifications.put("SCY", "CYS");
2032  18 modifications.put("SD2", "XAA");
2033  18 modifications.put("SDG", "GLY");
2034  18 modifications.put("SDP", "SER");
2035  18 modifications.put("SEB", "SER");
2036  18 modifications.put("SEC", "ALA");
2037  18 modifications.put("SEG", "ALA");
2038  18 modifications.put("SEL", "SER");
2039  18 modifications.put("SEM", "SER");
2040  18 modifications.put("SEN", "SER");
2041  18 modifications.put("SEP", "SER");
2042  18 modifications.put("SER", "SER");
2043  18 modifications.put("SET", "SER");
2044  18 modifications.put("SGB", "SER");
2045  18 modifications.put("SHC", "CYS");
2046  18 modifications.put("SHP", "GLY");
2047  18 modifications.put("SHR", "LYS");
2048  18 modifications.put("SIB", "CYS");
2049  18 modifications.put("SIC", "DC"); // check
2050  18 modifications.put("SLA", "PRO");
2051  18 modifications.put("SLR", "PRO");
2052  18 modifications.put("SLZ", "LYS");
2053  18 modifications.put("SMC", "CYS");
2054  18 modifications.put("SME", "MET");
2055  18 modifications.put("SMF", "PHE");
2056  18 modifications.put("SMP", "ALA");
2057  18 modifications.put("SMT", "THR");
2058  18 modifications.put("SNC", "CYS");
2059  18 modifications.put("SNN", "ASN");
2060  18 modifications.put("SOC", "CYS");
2061  18 modifications.put("SOS", "ASN");
2062  18 modifications.put("SOY", "SER");
2063  18 modifications.put("SPT", "THR");
2064  18 modifications.put("SRA", "ALA");
2065  18 modifications.put("SSU", "UR3");
2066  18 modifications.put("STY", "TYR");
2067  18 modifications.put("SUB", "XAA");
2068  18 modifications.put("SUI", "DG");
2069  18 modifications.put("SUN", "SER");
2070  18 modifications.put("SUR", "UR3");
2071  18 modifications.put("SVA", "SER");
2072  18 modifications.put("SVV", "SER");
2073  18 modifications.put("SVW", "SER");
2074  18 modifications.put("SVX", "SER");
2075  18 modifications.put("SVY", "SER");
2076  18 modifications.put("SVZ", "XAA");
2077  18 modifications.put("SWG", "SWG");
2078  18 modifications.put("SYS", "CYS");
2079  18 modifications.put("T ", "THR");
2080  18 modifications.put("T11", "PHE");
2081  18 modifications.put("T23", "THR");
2082  18 modifications.put("T2S", "THR");
2083  18 modifications.put("T2T", "ASN");
2084  18 modifications.put("T31", "UR3");
2085  18 modifications.put("T32", "THR");
2086  18 modifications.put("T36", "THR");
2087  18 modifications.put("T37", "THR");
2088  18 modifications.put("T38", "THR");
2089  18 modifications.put("T39", "THR");
2090  18 modifications.put("T3P", "THR");
2091  18 modifications.put("T41", "THR");
2092  18 modifications.put("T48", "THR");
2093  18 modifications.put("T49", "THR");
2094  18 modifications.put("T4S", "THR");
2095  18 modifications.put("T5O", "UR3");
2096  18 modifications.put("T5S", "THR");
2097  18 modifications.put("T66", "XAA");
2098  18 modifications.put("T6A", "ALA");
2099  18 modifications.put("TA3", "THR");
2100  18 modifications.put("TA4", "XAA");
2101  18 modifications.put("TAF", "THR");
2102  18 modifications.put("TAL", "ASN");
2103  18 modifications.put("TAV", "ASP");
2104  18 modifications.put("TBG", "VAL");
2105  18 modifications.put("TBM", "THR");
2106  18 modifications.put("TC1", "CYS");
2107  18 modifications.put("TCP", "THR");
2108  18 modifications.put("TCQ", "TYR");
2109  18 modifications.put("TCR", "TRP");
2110  18 modifications.put("TCY", "ALA");
2111  18 modifications.put("TDD", "LEU");
2112  18 modifications.put("TDY", "THR");
2113  18 modifications.put("TFE", "THR");
2114  18 modifications.put("TFO", "ALA");
2115  18 modifications.put("TFQ", "PHE");
2116  18 modifications.put("TFT", "THR");
2117  18 modifications.put("TGP", "GLY");
2118  18 modifications.put("TH6", "THR");
2119  18 modifications.put("THC", "THR");
2120  18 modifications.put("THO", "XAA");
2121  18 modifications.put("THR", "THR");
2122  18 modifications.put("THX", "ASN");
2123  18 modifications.put("THZ", "ARG");
2124  18 modifications.put("TIH", "ALA");
2125  18 modifications.put("TLB", "ASN");
2126  18 modifications.put("TLC", "THR");
2127  18 modifications.put("TLN", "UR3");
2128  18 modifications.put("TMB", "THR");
2129  18 modifications.put("TMD", "THR");
2130  18 modifications.put("TNB", "CYS");
2131  18 modifications.put("TNR", "SER");
2132  18 modifications.put("TOX", "TRP");
2133  18 modifications.put("TP1", "THR");
2134  18 modifications.put("TPC", "CYS");
2135  18 modifications.put("TPG", "GLY");
2136  18 modifications.put("TPH", "XAA");
2137  18 modifications.put("TPL", "TRP");
2138  18 modifications.put("TPO", "THR");
2139  18 modifications.put("TPQ", "TYR");
2140  18 modifications.put("TQI", "TRP");
2141  18 modifications.put("TQQ", "TRP");
2142  18 modifications.put("TRF", "TRP");
2143  18 modifications.put("TRG", "LYS");
2144  18 modifications.put("TRN", "TRP");
2145  18 modifications.put("TRO", "TRP");
2146  18 modifications.put("TRP", "TRP");
2147  18 modifications.put("TRQ", "TRP");
2148  18 modifications.put("TRW", "TRP");
2149  18 modifications.put("TRX", "TRP");
2150  18 modifications.put("TS ", "ASN");
2151  18 modifications.put("TST", "XAA");
2152  18 modifications.put("TT ", "ASN");
2153  18 modifications.put("TTD", "THR");
2154  18 modifications.put("TTI", "UR3");
2155  18 modifications.put("TTM", "THR");
2156  18 modifications.put("TTQ", "TRP");
2157  18 modifications.put("TTS", "TYR");
2158  18 modifications.put("TY1", "TYR");
2159  18 modifications.put("TY2", "TYR");
2160  18 modifications.put("TY3", "TYR");
2161  18 modifications.put("TY5", "TYR");
2162  18 modifications.put("TYB", "TYR");
2163  18 modifications.put("TYI", "TYR");
2164  18 modifications.put("TYJ", "TYR");
2165  18 modifications.put("TYN", "TYR");
2166  18 modifications.put("TYO", "TYR");
2167  18 modifications.put("TYQ", "TYR");
2168  18 modifications.put("TYR", "TYR");
2169  18 modifications.put("TYS", "TYR");
2170  18 modifications.put("TYT", "TYR");
2171  18 modifications.put("TYU", "ASN");
2172  18 modifications.put("TYW", "TYR");
2173  18 modifications.put("TYX", "XAA");
2174  18 modifications.put("TYY", "TYR");
2175  18 modifications.put("TZB", "XAA");
2176  18 modifications.put("TZO", "XAA");
2177  18 modifications.put("U ", "UR3");
2178  18 modifications.put("U25", "UR3");
2179  18 modifications.put("U2L", "UR3");
2180  18 modifications.put("U2N", "UR3");
2181  18 modifications.put("U2P", "UR3");
2182  18 modifications.put("U31", "UR3");
2183  18 modifications.put("U33", "UR3");
2184  18 modifications.put("U34", "UR3");
2185  18 modifications.put("U36", "UR3");
2186  18 modifications.put("U37", "UR3");
2187  18 modifications.put("U8U", "UR3");
2188  18 modifications.put("UAR", "UR3");
2189  18 modifications.put("UCL", "UR3");
2190  18 modifications.put("UD5", "UR3");
2191  18 modifications.put("UDP", "ASN");
2192  18 modifications.put("UFP", "ASN");
2193  18 modifications.put("UFR", "UR3");
2194  18 modifications.put("UFT", "UR3");
2195  18 modifications.put("UMA", "ALA");
2196  18 modifications.put("UMP", "UR3");
2197  18 modifications.put("UMS", "UR3");
2198  18 modifications.put("UN1", "XAA");
2199  18 modifications.put("UN2", "XAA");
2200  18 modifications.put("UNK", "XAA");
2201  18 modifications.put("UR3", "UR3");
2202  18 modifications.put("URD", "UR3");
2203  18 modifications.put("US1", "UR3");
2204  18 modifications.put("US2", "UR3");
2205  18 modifications.put("US3", "THR");
2206  18 modifications.put("US5", "UR3");
2207  18 modifications.put("USM", "UR3");
2208  18 modifications.put("VAD", "VAL");
2209  18 modifications.put("VAF", "VAL");
2210  18 modifications.put("VAL", "VAL");
2211  18 modifications.put("VB1", "LYS");
2212  18 modifications.put("VDL", "XAA");
2213  18 modifications.put("VLL", "XAA");
2214  18 modifications.put("VLM", "XAA");
2215  18 modifications.put("VMS", "XAA");
2216  18 modifications.put("VOL", "XAA");
2217  18 modifications.put("WCR", "GYG");
2218  18 modifications.put("X ", "GLY");
2219  18 modifications.put("X2W", "GLU");
2220  18 modifications.put("X4A", "ASN");
2221  18 modifications.put("X9Q", "AFG");
2222  18 modifications.put("XAD", "ALA");
2223  18 modifications.put("XAE", "ASN");
2224  18 modifications.put("XAL", "ALA");
2225  18 modifications.put("XAR", "ASN");
2226  18 modifications.put("XCL", "CYS");
2227  18 modifications.put("XCN", "CYS");
2228  18 modifications.put("XCP", "XAA");
2229  18 modifications.put("XCR", "CYS");
2230  18 modifications.put("XCS", "ASN");
2231  18 modifications.put("XCT", "CYS");
2232  18 modifications.put("XCY", "CYS");
2233  18 modifications.put("XGA", "ASN");
2234  18 modifications.put("XGL", "GLY");
2235  18 modifications.put("XGR", "GLY");
2236  18 modifications.put("XGU", "GLY");
2237  18 modifications.put("XPR", "PRO");
2238  18 modifications.put("XSN", "ASN");
2239  18 modifications.put("XTH", "THR");
2240  18 modifications.put("XTL", "THR");
2241  18 modifications.put("XTR", "THR");
2242  18 modifications.put("XTS", "GLY");
2243  18 modifications.put("XTY", "ASN");
2244  18 modifications.put("XUA", "ALA");
2245  18 modifications.put("XUG", "GLY");
2246  18 modifications.put("XX1", "LYS");
2247  18 modifications.put("XXY", "THG");
2248  18 modifications.put("XYG", "DYG");
2249  18 modifications.put("Y ", "ALA");
2250  18 modifications.put("YCM", "CYS");
2251  18 modifications.put("YG ", "GLY");
2252  18 modifications.put("YOF", "TYR");
2253  18 modifications.put("YRR", "ASN");
2254  18 modifications.put("YYG", "GLY");
2255  18 modifications.put("Z ", "CYS");
2256  18 modifications.put("Z01", "ALA");
2257  18 modifications.put("ZAD", "ALA");
2258  18 modifications.put("ZAL", "ALA");
2259  18 modifications.put("ZBC", "CYS");
2260  18 modifications.put("ZBU", "UR3");
2261  18 modifications.put("ZCL", "PHE");
2262  18 modifications.put("ZCY", "CYS");
2263  18 modifications.put("ZDU", "UR3");
2264  18 modifications.put("ZFB", "XAA");
2265  18 modifications.put("ZGU", "GLY");
2266  18 modifications.put("ZHP", "ASN");
2267  18 modifications.put("ZTH", "THR");
2268  18 modifications.put("ZU0", "THR");
2269  18 modifications.put("ZZJ", "ALA");
2270   
2271    }
2272   
 
2273  8121 toggle public static String getCanonicalAminoAcid(String aA)
2274    {
2275  8121 String canonical = modifications.get(aA);
2276  8121 return canonical == null ? aA : canonical;
2277    }
2278   
2279    // main method generates perl representation of residue property hash
2280    // / cut here
2281    /**
2282    * @j2sIgnore
2283    * @param args
2284    */
 
2285  0 toggle public static void main(String[] args)
2286    {
2287  0 Hashtable<String, Vector<String>> aaProps = new Hashtable<>();
2288  0 System.out.println("my %aa = {");
2289    // invert property hashes
2290  0 for (String pname : propHash.keySet())
2291    {
2292  0 Map<String, Integer> phash = propHash.get(pname);
2293  0 for (String rname : phash.keySet())
2294    {
2295  0 Vector<String> aprops = aaProps.get(rname);
2296  0 if (aprops == null)
2297    {
2298  0 aprops = new Vector<>();
2299  0 aaProps.put(rname, aprops);
2300    }
2301  0 Integer hasprop = phash.get(rname);
2302  0 if (hasprop.intValue() == 1)
2303    {
2304  0 aprops.addElement(pname);
2305    }
2306    }
2307    }
2308  0 Enumeration<String> res = aaProps.keys();
2309  0 while (res.hasMoreElements())
2310    {
2311  0 String rname = res.nextElement();
2312   
2313  0 System.out.print("'" + rname + "' => [");
2314  0 Enumeration<String> props = aaProps.get(rname).elements();
2315  0 while (props.hasMoreElements())
2316    {
2317  0 System.out.print("'" + props.nextElement() + "'");
2318  0 if (props.hasMoreElements())
2319    {
2320  0 System.out.println(", ");
2321    }
2322    }
2323  0 System.out.println("]" + (res.hasMoreElements() ? "," : ""));
2324    }
2325  0 System.out.println("};");
2326    }
2327   
2328    // to here
2329   
2330    /**
2331    * Returns a list of residue characters for the specified inputs
2332    *
2333    * @param forNucleotide
2334    * @param includeAmbiguous
2335    * @return
2336    */
 
2337  4 toggle public static List<String> getResidues(boolean forNucleotide,
2338    boolean includeAmbiguous)
2339    {
2340  4 List<String> result = new ArrayList<>();
2341  4 if (forNucleotide)
2342    {
2343  2 for (String nuc : nucleotideName.keySet())
2344    {
2345  72 int val = nucleotideIndex[nuc.charAt(0)];
2346  72 if ((!includeAmbiguous && val > 4) || (val >= maxNucleotideIndex))
2347    {
2348  42 continue;
2349    }
2350  30 nuc = nuc.toUpperCase();
2351  30 if (!result.contains(nuc))
2352    {
2353  15 result.add(nuc);
2354    }
2355    }
2356    }
2357    else
2358    {
2359    /*
2360    * Peptide
2361    */
2362  2 for (String res : aa3Hash.keySet())
2363    {
2364  58 int index = aa3Hash.get(res).intValue();
2365  58 if ((!includeAmbiguous && index >= 20) || index >= maxProteinIndex)
2366    {
2367  15 continue;
2368    }
2369  43 res = res.toUpperCase();
2370  43 if (!result.contains(res))
2371    {
2372  43 result.add(res);
2373    }
2374    }
2375    }
2376   
2377  4 return result;
2378    }
2379   
2380    /**
2381    * Returns the single letter code for a three letter code, or '0' if not known
2382    *
2383    * @param threeLetterCode
2384    * not case sensitive
2385    * @return
2386    */
 
2387  10 toggle public static char getSingleCharacterCode(String threeLetterCode)
2388    {
2389  10 if (threeLetterCode == null)
2390    {
2391  2 return '0';
2392    }
2393  8 Integer index = ResidueProperties.aa3Hash
2394    .get(threeLetterCode.toUpperCase());
2395  8 return index == null ? '0' : aa[index].charAt(0);
2396    }
2397    }
  • Report generated by OpenClover v 4.4.1 on Thu Aug 13 2020 12:06:48 BST using coverage data from Thu Aug 13 2020 12:06:40 BST.
  • OpenClover is free and open-source software.