/* * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation, either version 3 * of the License, or (at your option) any later version. * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with Jalview. If not, see . * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.schemes; import java.awt.Color; import java.util.ArrayList; import java.util.Arrays; import java.util.Enumeration; import java.util.HashMap; import java.util.Hashtable; import java.util.List; import java.util.Map; import java.util.Vector; public class ResidueProperties { // Stores residue codes/names and colours and other things public static final int[] aaIndex; // aaHash version 2.1.1 and below public static final int[] nucleotideIndex; public static final int[] purinepyrimidineIndex; public static final Map aa3Hash = new HashMap<>(); public static final Map aa2Triplet = new HashMap<>(); public static final Map nucleotideName = new HashMap<>(); // lookup from modified amino acid (e.g. MSE) to canonical form (e.g. MET) public static final Map modifications = new HashMap<>(); // residue background frequencies across different alphabets public static final Map> backgroundFrequencies = new HashMap<>(); static { aaIndex = new int[255]; for (int i = 0; i < 255; i++) { aaIndex[i] = 23; } aaIndex['A'] = 0; aaIndex['R'] = 1; aaIndex['N'] = 2; aaIndex['D'] = 3; aaIndex['C'] = 4; aaIndex['Q'] = 5; aaIndex['E'] = 6; aaIndex['G'] = 7; aaIndex['H'] = 8; aaIndex['I'] = 9; aaIndex['L'] = 10; aaIndex['K'] = 11; aaIndex['M'] = 12; aaIndex['F'] = 13; aaIndex['P'] = 14; aaIndex['S'] = 15; aaIndex['T'] = 16; aaIndex['W'] = 17; aaIndex['Y'] = 18; aaIndex['V'] = 19; aaIndex['B'] = 20; aaIndex['Z'] = 21; aaIndex['X'] = 22; aaIndex['U'] = 22; aaIndex['a'] = 0; aaIndex['r'] = 1; aaIndex['n'] = 2; aaIndex['d'] = 3; aaIndex['c'] = 4; aaIndex['q'] = 5; aaIndex['e'] = 6; aaIndex['g'] = 7; aaIndex['h'] = 8; aaIndex['i'] = 9; aaIndex['l'] = 10; aaIndex['k'] = 11; aaIndex['m'] = 12; aaIndex['f'] = 13; aaIndex['p'] = 14; aaIndex['s'] = 15; aaIndex['t'] = 16; aaIndex['w'] = 17; aaIndex['y'] = 18; aaIndex['v'] = 19; aaIndex['b'] = 20; aaIndex['z'] = 21; aaIndex['x'] = 22; aaIndex['u'] = 22; // TODO: selenocystine triplet and codons needed. also // extend subt. matrices } /** * maximum (gap) index for matrices involving protein alphabet */ public final static int maxProteinIndex = 23; /** * maximum (gap) index for matrices involving nucleotide alphabet */ public final static int maxNucleotideIndex = 10; static { nucleotideIndex = new int[255]; for (int i = 0; i < 255; i++) { nucleotideIndex[i] = 10; // non-nucleotide symbols are all non-gap gaps. } nucleotideIndex['A'] = 0; nucleotideIndex['a'] = 0; nucleotideIndex['C'] = 1; nucleotideIndex['c'] = 1; nucleotideIndex['G'] = 2; nucleotideIndex['g'] = 2; nucleotideIndex['T'] = 3; nucleotideIndex['t'] = 3; nucleotideIndex['U'] = 4; nucleotideIndex['u'] = 4; nucleotideIndex['I'] = 5; nucleotideIndex['i'] = 5; nucleotideIndex['X'] = 6; nucleotideIndex['x'] = 6; nucleotideIndex['R'] = 7; nucleotideIndex['r'] = 7; nucleotideIndex['Y'] = 8; nucleotideIndex['y'] = 8; nucleotideIndex['N'] = 9; nucleotideIndex['n'] = 9; nucleotideName.put("A", "Adenine"); nucleotideName.put("a", "Adenine"); nucleotideName.put("G", "Guanine"); nucleotideName.put("g", "Guanine"); nucleotideName.put("C", "Cytosine"); nucleotideName.put("c", "Cytosine"); nucleotideName.put("T", "Thymine"); nucleotideName.put("t", "Thymine"); nucleotideName.put("U", "Uracil"); nucleotideName.put("u", "Uracil"); nucleotideName.put("I", "Inosine"); nucleotideName.put("i", "Inosine"); nucleotideName.put("X", "Xanthine"); nucleotideName.put("x", "Xanthine"); nucleotideName.put("R", "Unknown Purine"); nucleotideName.put("r", "Unknown Purine"); nucleotideName.put("Y", "Unknown Pyrimidine"); nucleotideName.put("y", "Unknown Pyrimidine"); nucleotideName.put("N", "Unknown"); nucleotideName.put("n", "Unknown"); nucleotideName.put("W", "Weak nucleotide (A or T)"); nucleotideName.put("w", "Weak nucleotide (A or T)"); nucleotideName.put("S", "Strong nucleotide (G or C)"); nucleotideName.put("s", "Strong nucleotide (G or C)"); nucleotideName.put("M", "Amino (A or C)"); nucleotideName.put("m", "Amino (A or C)"); nucleotideName.put("K", "Keto (G or T)"); nucleotideName.put("k", "Keto (G or T)"); nucleotideName.put("B", "Not A (G or C or T)"); nucleotideName.put("b", "Not A (G or C or T)"); nucleotideName.put("H", "Not G (A or C or T)"); nucleotideName.put("h", "Not G (A or C or T)"); nucleotideName.put("D", "Not C (A or G or T)"); nucleotideName.put("d", "Not C (A or G or T)"); nucleotideName.put("V", "Not T (A or G or C"); nucleotideName.put("v", "Not T (A or G or C"); } static { purinepyrimidineIndex = new int[255]; for (int i = 0; i < 255; i++) { purinepyrimidineIndex[i] = 3; // non-nucleotide symbols are all non-gap // gaps. } purinepyrimidineIndex['A'] = 0; purinepyrimidineIndex['a'] = 0; purinepyrimidineIndex['C'] = 1; purinepyrimidineIndex['c'] = 1; purinepyrimidineIndex['G'] = 0; purinepyrimidineIndex['g'] = 0; purinepyrimidineIndex['T'] = 1; purinepyrimidineIndex['t'] = 1; purinepyrimidineIndex['U'] = 1; purinepyrimidineIndex['u'] = 1; purinepyrimidineIndex['I'] = 2; purinepyrimidineIndex['i'] = 2; purinepyrimidineIndex['X'] = 2; purinepyrimidineIndex['x'] = 2; purinepyrimidineIndex['R'] = 0; purinepyrimidineIndex['r'] = 0; purinepyrimidineIndex['Y'] = 1; purinepyrimidineIndex['y'] = 1; purinepyrimidineIndex['N'] = 2; purinepyrimidineIndex['n'] = 2; } private static final Integer ONE = Integer.valueOf(1); private static final Integer ZERO = Integer.valueOf(0); static { aa3Hash.put("ALA", ZERO); aa3Hash.put("ARG", ONE); aa3Hash.put("ASN", Integer.valueOf(2)); aa3Hash.put("ASP", Integer.valueOf(3)); // D aa3Hash.put("CYS", Integer.valueOf(4)); aa3Hash.put("GLN", Integer.valueOf(5)); // Q aa3Hash.put("GLU", Integer.valueOf(6)); // E aa3Hash.put("GLY", Integer.valueOf(7)); aa3Hash.put("HIS", Integer.valueOf(8)); aa3Hash.put("ILE", Integer.valueOf(9)); aa3Hash.put("LEU", Integer.valueOf(10)); aa3Hash.put("LYS", Integer.valueOf(11)); aa3Hash.put("MET", Integer.valueOf(12)); aa3Hash.put("PHE", Integer.valueOf(13)); aa3Hash.put("PRO", Integer.valueOf(14)); aa3Hash.put("SER", Integer.valueOf(15)); aa3Hash.put("THR", Integer.valueOf(16)); aa3Hash.put("TRP", Integer.valueOf(17)); aa3Hash.put("TYR", Integer.valueOf(18)); aa3Hash.put("VAL", Integer.valueOf(19)); // IUB Nomenclature for ambiguous peptides aa3Hash.put("ASX", Integer.valueOf(20)); // "B"; aa3Hash.put("GLX", Integer.valueOf(21)); // Z aa3Hash.put("XAA", Integer.valueOf(22)); // X unknown aa3Hash.put("-", Integer.valueOf(23)); aa3Hash.put("*", Integer.valueOf(23)); aa3Hash.put(".", Integer.valueOf(23)); aa3Hash.put(" ", Integer.valueOf(23)); aa3Hash.put("Gap", Integer.valueOf(23)); aa3Hash.put("UR3", Integer.valueOf(24)); } static { aa2Triplet.put("A", "ALA"); aa2Triplet.put("a", "ALA"); aa2Triplet.put("R", "ARG"); aa2Triplet.put("r", "ARG"); aa2Triplet.put("N", "ASN"); aa2Triplet.put("n", "ASN"); aa2Triplet.put("D", "ASP"); aa2Triplet.put("d", "ASP"); aa2Triplet.put("C", "CYS"); aa2Triplet.put("c", "CYS"); aa2Triplet.put("Q", "GLN"); aa2Triplet.put("q", "GLN"); aa2Triplet.put("E", "GLU"); aa2Triplet.put("e", "GLU"); aa2Triplet.put("G", "GLY"); aa2Triplet.put("g", "GLY"); aa2Triplet.put("H", "HIS"); aa2Triplet.put("h", "HIS"); aa2Triplet.put("I", "ILE"); aa2Triplet.put("i", "ILE"); aa2Triplet.put("L", "LEU"); aa2Triplet.put("l", "LEU"); aa2Triplet.put("K", "LYS"); aa2Triplet.put("k", "LYS"); aa2Triplet.put("M", "MET"); aa2Triplet.put("m", "MET"); aa2Triplet.put("F", "PHE"); aa2Triplet.put("f", "PHE"); aa2Triplet.put("P", "PRO"); aa2Triplet.put("p", "PRO"); aa2Triplet.put("S", "SER"); aa2Triplet.put("s", "SER"); aa2Triplet.put("T", "THR"); aa2Triplet.put("t", "THR"); aa2Triplet.put("W", "TRP"); aa2Triplet.put("w", "TRP"); aa2Triplet.put("Y", "TYR"); aa2Triplet.put("y", "TYR"); aa2Triplet.put("V", "VAL"); aa2Triplet.put("v", "VAL"); } public static final String[] aa = { "A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V", "B", "Z", "X", "_", "*", ".", " ", "U" }; public static final Color midBlue = new Color(100, 100, 255); // not currently in use // public static final Vector scaleColours = new Vector(); // static // { // scaleColours.addElement(new Color(114, 0, 147)); // scaleColours.addElement(new Color(156, 0, 98)); // scaleColours.addElement(new Color(190, 0, 0)); // scaleColours.addElement(Color.red); // scaleColours.addElement(new Color(255, 125, 0)); // scaleColours.addElement(Color.orange); // scaleColours.addElement(new Color(255, 194, 85)); // scaleColours.addElement(Color.yellow); // scaleColours.addElement(new Color(255, 255, 181)); // scaleColours.addElement(Color.white); // } public static final Color[] taylor = { new Color(204, 255, 0), // A Greenish-yellowy-yellow new Color(0, 0, 255), // R Blueish-bluey-blue new Color(204, 0, 255), // N Blueish-reddy-blue new Color(255, 0, 0), // D Reddish-reddy-red new Color(255, 255, 0), // C Yellowish-yellowy-yellow new Color(255, 0, 204), // Q Reddish-bluey-red new Color(255, 0, 102), // E Blueish-reddy-red new Color(255, 153, 0), // G Yellowy-reddy-yellow new Color(0, 102, 255), // H Greenish-bluey-blue new Color(102, 255, 0), // I Greenish-yellowy-green new Color(51, 255, 0), // L Yellowish-greeny-green new Color(102, 0, 255), // K Reddish-bluey-blue new Color(0, 255, 0), // M Greenish-greeny-green new Color(0, 255, 102), // F Blueish-greeny-green new Color(255, 204, 0), // P Reddish-yellowy-yellow new Color(255, 51, 0), // S Yellowish-reddy-red new Color(255, 102, 0), // T Reddish-yellowy-red new Color(0, 204, 255), // W Blueish-greeny-green new Color(0, 255, 204), // Y Greenish-bluey-green new Color(153, 255, 0), // V Yellowish-greeny-yellow Color.white, // B Color.white, // Z Color.white, // X Color.white, // - Color.white, // * Color.white // . }; public static final Color[] nucleotide = { new Color(100, 247, 63), // A new Color(255, 179, 64), // C new Color(235, 65, 60), // G new Color(60, 136, 238), // T new Color(60, 136, 238), // U Color.white, // I (inosine) Color.white, // X (xanthine) Color.white, // R Color.white, // Y Color.white, // N Color.white, // Gap }; // Added for PurinePyrimidineColourScheme public static final Color[] purinepyrimidine = { new Color(255, 131, 250), // A, // G, // R // purines // purplish/orchid new Color(64, 224, 208), // C,U, T, Y pyrimidines turquoise Color.white, // all other nucleotides Color.white // Gap }; // Zappo public static final Color[] zappo = { Color.pink, // A midBlue, // R Color.green, // N Color.red, // D Color.yellow, // C Color.green, // Q Color.red, // E Color.magenta, // G midBlue, // Color.red, // H Color.pink, // I Color.pink, // L midBlue, // K Color.pink, // M Color.orange, // F Color.magenta, // P Color.green, // S Color.green, // T Color.orange, // W Color.orange, // Y Color.pink, // V Color.white, // B Color.white, // Z Color.white, // X Color.white, // - Color.white, // * Color.white, // . Color.white // ' ' }; // Dunno where I got these numbers from public static final double[] hyd2 = { 0.62, // A 0.29, // R -0.90, // N -0.74, // D 1.19, // C 0.48, // Q -0.40, // E 1.38, // G -1.50, // H 1.06, // I 0.64, // L -0.78, // K 0.12, // M -0.85, // F -2.53, // P -0.18, // S -0.05, // T 1.08, // W 0.81, // Y 0.0, // V 0.26, // B 0.0, // Z 0.0 // X }; public static final double[] helix = { 1.42, 0.98, 0.67, 1.01, 0.70, 1.11, 1.51, 0.57, 1.00, 1.08, 1.21, 1.16, 1.45, 1.13, 0.57, 0.77, 0.83, 1.08, 0.69, 1.06, 0.84, 1.31, 1.00, 0.0 }; public static final double helixmin = 0.57; public static final double helixmax = 1.51; public static final double[] strand = { 0.83, 0.93, 0.89, 0.54, 1.19, 1.10, 0.37, 0.75, 0.87, 1.60, 1.30, 0.74, 1.05, 1.38, 0.55, 0.75, 1.19, 1.37, 1.47, 1.70, 0.72, 0.74, 1.0, 0.0 }; public static final double strandmin = 0.37; public static final double strandmax = 1.7; public static final double[] turn = { 0.66, 0.95, 1.56, 1.46, 1.19, 0.98, 0.74, 1.56, 0.95, 0.47, 0.59, 1.01, 0.60, 0.60, 1.52, 1.43, 0.96, 0.96, 1.14, 0.50, 1.51, 0.86, 1.00, 0, 0 }; public static final double turnmin = 0.47; public static final double turnmax = 1.56; public static final double[] buried = { 1.7, 0.1, 0.4, 0.4, 4.6, 0.3, 0.3, 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, 0.3, 1.358, 0.00 }; public static final double buriedmin = 0.05; public static final double buriedmax = 4.6; // This is hydropathy index // Kyte, J., and Doolittle, R.F., J. Mol. Biol. // 1157, 105-132, 1982 public static final double[] hyd = { 1.8, -4.5, -3.5, -3.5, 2.5, -3.5, -3.5, -0.4, -3.2, 4.5, 3.8, -3.9, 1.9, 2.8, -1.6, -0.8, -0.7, -0.9, -1.3, 4.2, -3.5, -3.5, -0.49, 0.0 }; public static final double hydmax = 4.5; public static final double hydmin = -3.9; // public static final double hydmax = 1.38; // public static final double hydmin = -2.53; // not currently used // public static final Map ssHash = new Hashtable(); // static // { // ssHash.put("H", Color.magenta); // ssHash.put("E", Color.yellow); // ssHash.put("-", Color.white); // ssHash.put(".", Color.white); // ssHash.put("S", Color.cyan); // ssHash.put("T", Color.blue); // ssHash.put("G", Color.pink); // ssHash.put("I", Color.pink); // ssHash.put("B", Color.yellow); // } /* * new Color(60, 136, 238), // U Color.white, // I Color.white, // X * Color.white, // R Color.white, // Y Color.white, // N Color.white, // Gap */ public static String STOP = "STOP"; public static List STOP_CODONS = Arrays.asList("TGA", "TAA", "TAG"); public static String START = "ATG"; /** * Nucleotide Ambiguity Codes */ public static final Map ambiguityCodes = new Hashtable<>(); /** * Codon triplets with additional symbols for unambiguous codons that include * ambiguity codes */ public static final Hashtable codonHash2 = new Hashtable<>(); /** * all ambiguity codes for a given base */ public final static Hashtable> _ambiguityCodes = new Hashtable<>(); static { /* * Ambiguity codes as per http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html */ ambiguityCodes.put("R", new String[] { "A", "G" }); ambiguityCodes.put("Y", new String[] { "T", "C" }); ambiguityCodes.put("W", new String[] { "A", "T" }); ambiguityCodes.put("S", new String[] { "G", "C" }); ambiguityCodes.put("M", new String[] { "A", "C" }); ambiguityCodes.put("K", new String[] { "G", "T" }); ambiguityCodes.put("H", new String[] { "A", "T", "C" }); ambiguityCodes.put("B", new String[] { "G", "T", "C" }); ambiguityCodes.put("V", new String[] { "G", "A", "C" }); ambiguityCodes.put("D", new String[] { "G", "A", "T" }); ambiguityCodes.put("N", new String[] { "G", "A", "T", "C" }); // Now build codon translation table codonHash2.put("AAA", "K"); codonHash2.put("AAG", "K"); codonHash2.put("AAC", "N"); codonHash2.put("AAT", "N"); codonHash2.put("CAA", "Q"); codonHash2.put("CAG", "Q"); codonHash2.put("CAC", "H"); codonHash2.put("CAT", "H"); codonHash2.put("GAA", "E"); codonHash2.put("GAG", "E"); codonHash2.put("GAC", "D"); codonHash2.put("GAT", "D"); codonHash2.put("TAC", "Y"); codonHash2.put("TAT", "Y"); codonHash2.put("ACA", "T"); codonHash2.put("ACC", "T"); codonHash2.put("ACT", "T"); codonHash2.put("ACG", "T"); codonHash2.put("CCA", "P"); codonHash2.put("CCG", "P"); codonHash2.put("CCC", "P"); codonHash2.put("CCT", "P"); codonHash2.put("GCA", "A"); codonHash2.put("GCG", "A"); codonHash2.put("GCC", "A"); codonHash2.put("GCT", "A"); codonHash2.put("TCA", "S"); codonHash2.put("TCG", "S"); codonHash2.put("TCC", "S"); codonHash2.put("TCT", "S"); codonHash2.put("AGC", "S"); codonHash2.put("AGT", "S"); codonHash2.put("AGA", "R"); codonHash2.put("AGG", "R"); codonHash2.put("CGA", "R"); codonHash2.put("CGG", "R"); codonHash2.put("CGC", "R"); codonHash2.put("CGT", "R"); codonHash2.put("GGA", "G"); codonHash2.put("GGG", "G"); codonHash2.put("GGC", "G"); codonHash2.put("GGT", "G"); codonHash2.put("TGA", "*"); codonHash2.put("TAA", "*"); codonHash2.put("TAG", "*"); codonHash2.put("TGG", "W"); codonHash2.put("TGC", "C"); codonHash2.put("TGT", "C"); codonHash2.put("ATA", "I"); codonHash2.put("ATC", "I"); codonHash2.put("ATT", "I"); codonHash2.put("ATG", "M"); codonHash2.put("CTA", "L"); codonHash2.put("CTG", "L"); codonHash2.put("CTC", "L"); codonHash2.put("CTT", "L"); codonHash2.put("TTA", "L"); codonHash2.put("TTG", "L"); codonHash2.put("GTA", "V"); codonHash2.put("GTG", "V"); codonHash2.put("GTC", "V"); codonHash2.put("GTT", "V"); codonHash2.put("TTC", "F"); codonHash2.put("TTT", "F"); buildAmbiguityCodonSet(); } /** * programmatic generation of codons including ambiguity codes */ public static void buildAmbiguityCodonSet() { if (_ambiguityCodes.size() > 0) { System.err .println("Ignoring multiple calls to buildAmbiguityCodonSet"); return; } // Invert the ambiguity code set for (Map.Entry acode : ambiguityCodes.entrySet()) { for (String r : acode.getValue()) { List codesfor = _ambiguityCodes.get(r); if (codesfor == null) { _ambiguityCodes.put(r, codesfor = new ArrayList<>()); } if (!codesfor.contains(acode.getKey())) { codesfor.add(acode.getKey()); } else { System.err.println( "Inconsistency in the IUBMB ambiguity code nomenclature table: collision for " + acode.getKey() + " in residue " + r); } } } // and programmatically add in the ambiguity codes that yield the same amino // acid String[] unambcodons = codonHash2.keySet() .toArray(new String[codonHash2.size()]); for (String codon : unambcodons) { String residue = codonHash2.get(codon); String acodon[][] = new String[codon.length()][]; for (int i = 0, iSize = codon.length(); i < iSize; i++) { String _ac = "" + codon.charAt(i); List acodes = _ambiguityCodes.get(_ac); if (acodes != null) { acodon[i] = acodes.toArray(new String[acodes.size()]); } else { acodon[i] = new String[] {}; } } // enumerate all combinations and test for veracity of translation int tpos[] = new int[codon.length()], cpos[] = new int[codon.length()]; for (int i = 0; i < tpos.length; i++) { tpos[i] = -1; } tpos[acodon.length - 1] = 0; int ipos, j; while (tpos[0] < acodon[0].length) { // make all codons for this combination char allres[][] = new char[tpos.length][]; String _acodon = ""; for (ipos = 0; ipos < tpos.length; ipos++) { if (acodon[ipos].length == 0 || tpos[ipos] < 0) { _acodon += codon.charAt(ipos); allres[ipos] = new char[] { codon.charAt(ipos) }; } else { _acodon += acodon[ipos][tpos[ipos]]; String[] altbase = ambiguityCodes.get(acodon[ipos][tpos[ipos]]); allres[ipos] = new char[altbase.length]; j = 0; for (String ab : altbase) { allres[ipos][j++] = ab.charAt(0); } } } // test all codons for this combination for (ipos = 0; ipos < cpos.length; ipos++) { cpos[ipos] = 0; } boolean valid = true; do { String _codon = ""; for (j = 0; j < cpos.length; j++) { _codon += allres[j][cpos[j]]; } String tr = codonHash2.get(_codon); if (valid = (tr != null && tr.equals(residue))) { // advance to next combination ipos = acodon.length - 1; while (++cpos[ipos] >= allres[ipos].length && ipos > 0) { cpos[ipos] = 0; ipos--; } } } while (valid && cpos[0] < allres[0].length); if (valid) { // Add this to the set of codons we will translate // System.out.println("Adding ambiguity codon: " + _acodon + " for " // + residue); codonHash2.put(_acodon, residue); } else { // System.err.println("Rejecting ambiguity codon: " + _acodon // + " for " + residue); } // next combination ipos = acodon.length - 1; while (++tpos[ipos] >= acodon[ipos].length && ipos > 0) { tpos[ipos] = -1; ipos--; } } } } // Stores residue codes/names and colours and other things public static Map> propHash = new Hashtable<>(); public static Map hydrophobic = new Hashtable<>(); public static Map polar = new Hashtable<>(); public static Map small = new Hashtable<>(); public static Map positive = new Hashtable<>(); public static Map negative = new Hashtable<>(); public static Map charged = new Hashtable<>(); public static Map aromatic = new Hashtable<>(); public static Map aliphatic = new Hashtable<>(); public static Map tiny = new Hashtable<>(); public static Map proline = new Hashtable<>(); static { hydrophobic.put("I", ONE); hydrophobic.put("L", ONE); hydrophobic.put("V", ONE); hydrophobic.put("C", ONE); hydrophobic.put("A", ONE); hydrophobic.put("G", ONE); hydrophobic.put("M", ONE); hydrophobic.put("F", ONE); hydrophobic.put("Y", ONE); hydrophobic.put("W", ONE); hydrophobic.put("H", ONE); hydrophobic.put("K", ONE); hydrophobic.put("X", ONE); hydrophobic.put("-", ONE); hydrophobic.put("*", ONE); hydrophobic.put("R", ZERO); hydrophobic.put("E", ZERO); hydrophobic.put("Q", ZERO); hydrophobic.put("D", ZERO); hydrophobic.put("N", ZERO); hydrophobic.put("S", ZERO); hydrophobic.put("T", ONE); hydrophobic.put("P", ZERO); } static { polar.put("Y", ONE); polar.put("W", ONE); polar.put("H", ONE); polar.put("K", ONE); polar.put("R", ONE); polar.put("E", ONE); polar.put("Q", ONE); polar.put("D", ONE); polar.put("N", ONE); polar.put("S", ONE); polar.put("T", ONE); polar.put("X", ONE); polar.put("-", ONE); polar.put("*", ONE); polar.put("I", ZERO); polar.put("L", ZERO); polar.put("V", ZERO); polar.put("C", ZERO); polar.put("A", ZERO); polar.put("G", ZERO); polar.put("M", ZERO); polar.put("F", ZERO); polar.put("P", ZERO); } static { small.put("I", ZERO); small.put("L", ZERO); small.put("V", ONE); small.put("C", ONE); small.put("A", ONE); small.put("G", ONE); small.put("M", ZERO); small.put("F", ZERO); small.put("Y", ZERO); small.put("W", ZERO); small.put("H", ZERO); small.put("K", ZERO); small.put("R", ZERO); small.put("E", ZERO); small.put("Q", ZERO); small.put("D", ONE); small.put("N", ONE); small.put("S", ONE); small.put("T", ONE); small.put("P", ONE); small.put("-", ONE); small.put("*", ONE); } static { positive.put("I", ZERO); positive.put("L", ZERO); positive.put("V", ZERO); positive.put("C", ZERO); positive.put("A", ZERO); positive.put("G", ZERO); positive.put("M", ZERO); positive.put("F", ZERO); positive.put("Y", ZERO); positive.put("W", ZERO); positive.put("H", ONE); positive.put("K", ONE); positive.put("R", ONE); positive.put("E", ZERO); positive.put("Q", ZERO); positive.put("D", ZERO); positive.put("N", ZERO); positive.put("S", ZERO); positive.put("T", ZERO); positive.put("P", ZERO); positive.put("-", ONE); positive.put("*", ONE); } static { negative.put("I", ZERO); negative.put("L", ZERO); negative.put("V", ZERO); negative.put("C", ZERO); negative.put("A", ZERO); negative.put("G", ZERO); negative.put("M", ZERO); negative.put("F", ZERO); negative.put("Y", ZERO); negative.put("W", ZERO); negative.put("H", ZERO); negative.put("K", ZERO); negative.put("R", ZERO); negative.put("E", ONE); negative.put("Q", ZERO); negative.put("D", ONE); negative.put("N", ZERO); negative.put("S", ZERO); negative.put("T", ZERO); negative.put("P", ZERO); negative.put("-", ONE); negative.put("*", ONE); } static { charged.put("I", ZERO); charged.put("L", ZERO); charged.put("V", ZERO); charged.put("C", ZERO); charged.put("A", ZERO); charged.put("G", ZERO); charged.put("M", ZERO); charged.put("F", ZERO); charged.put("Y", ZERO); charged.put("W", ZERO); charged.put("H", ONE); charged.put("K", ONE); charged.put("R", ONE); charged.put("E", ONE); charged.put("Q", ZERO); charged.put("D", ONE); charged.put("N", ZERO); // Asparagine is polar but not // charged. // Alternative would be charged and // negative (in basic form)? charged.put("S", ZERO); charged.put("T", ZERO); charged.put("P", ZERO); charged.put("-", ONE); charged.put("*", ONE); } static { aromatic.put("I", ZERO); aromatic.put("L", ZERO); aromatic.put("V", ZERO); aromatic.put("C", ZERO); aromatic.put("A", ZERO); aromatic.put("G", ZERO); aromatic.put("M", ZERO); aromatic.put("F", ONE); aromatic.put("Y", ONE); aromatic.put("W", ONE); aromatic.put("H", ONE); aromatic.put("K", ZERO); aromatic.put("R", ZERO); aromatic.put("E", ZERO); aromatic.put("Q", ZERO); aromatic.put("D", ZERO); aromatic.put("N", ZERO); aromatic.put("S", ZERO); aromatic.put("T", ZERO); aromatic.put("P", ZERO); aromatic.put("-", ONE); aromatic.put("*", ONE); } static { aliphatic.put("I", ONE); aliphatic.put("L", ONE); aliphatic.put("V", ONE); aliphatic.put("C", ZERO); aliphatic.put("A", ZERO); aliphatic.put("G", ZERO); aliphatic.put("M", ZERO); aliphatic.put("F", ZERO); aliphatic.put("Y", ZERO); aliphatic.put("W", ZERO); aliphatic.put("H", ZERO); aliphatic.put("K", ZERO); aliphatic.put("R", ZERO); aliphatic.put("E", ZERO); aliphatic.put("Q", ZERO); aliphatic.put("D", ZERO); aliphatic.put("N", ZERO); aliphatic.put("S", ZERO); aliphatic.put("T", ZERO); aliphatic.put("P", ZERO); aliphatic.put("-", ONE); aliphatic.put("*", ONE); } static { tiny.put("I", ZERO); tiny.put("L", ZERO); tiny.put("V", ZERO); tiny.put("C", ZERO); tiny.put("A", ONE); tiny.put("G", ONE); tiny.put("M", ZERO); tiny.put("F", ZERO); tiny.put("Y", ZERO); tiny.put("W", ZERO); tiny.put("H", ZERO); tiny.put("K", ZERO); tiny.put("R", ZERO); tiny.put("E", ZERO); tiny.put("Q", ZERO); tiny.put("D", ZERO); tiny.put("N", ZERO); tiny.put("S", ONE); tiny.put("T", ZERO); tiny.put("P", ZERO); tiny.put("-", ONE); tiny.put("*", ONE); } static { proline.put("I", ZERO); proline.put("L", ZERO); proline.put("V", ZERO); proline.put("C", ZERO); proline.put("A", ZERO); proline.put("G", ZERO); proline.put("M", ZERO); proline.put("F", ZERO); proline.put("Y", ZERO); proline.put("W", ZERO); proline.put("H", ZERO); proline.put("K", ZERO); proline.put("R", ZERO); proline.put("E", ZERO); proline.put("Q", ZERO); proline.put("D", ZERO); proline.put("N", ZERO); proline.put("S", ZERO); proline.put("T", ZERO); proline.put("P", ONE); proline.put("-", ONE); proline.put("*", ONE); } static { propHash.put("hydrophobic", hydrophobic); propHash.put("small", small); propHash.put("positive", positive); propHash.put("negative", negative); propHash.put("charged", charged); propHash.put("aromatic", aromatic); propHash.put("aliphatic", aliphatic); propHash.put("tiny", tiny); propHash.put("proline", proline); propHash.put("polar", polar); } static { int[][] propMatrixF = new int[maxProteinIndex][maxProteinIndex], propMatrixPos = new int[maxProteinIndex][maxProteinIndex], propMatrixEpos = new int[maxProteinIndex][maxProteinIndex]; for (int i = 0; i < maxProteinIndex; i++) { int maxF = 0, maxP = 0, maxEP = 0; String ic = ""; if (aa.length > i) { ic += aa[i]; } else { ic = "-"; } for (int j = i + 1; j < maxProteinIndex; j++) { String jc = ""; if (aa.length > j) { jc += aa[j]; } else { jc = "-"; } propMatrixF[i][j] = 0; propMatrixPos[i][j] = 0; propMatrixEpos[i][j] = 0; for (String ph : propHash.keySet()) { Map pph = propHash.get(ph); if (pph.get(ic) != null && pph.get(jc) != null) { int icp = pph.get(ic).intValue(), jcp = pph.get(jc).intValue(); // Still working on these definitions. propMatrixPos[i][j] += icp == jcp && icp > 0 ? 2 : 0; propMatrixPos[j][i] += icp == jcp && icp > 0 ? 2 : 0; propMatrixF[i][j] += icp == jcp ? 2 : 0; propMatrixF[j][i] += icp == jcp ? 2 : 0; propMatrixEpos[i][j] += icp == jcp ? (1 + icp * 2) : 0; propMatrixEpos[j][i] += icp == jcp ? (1 + icp * 2) : 0; } } if (maxF < propMatrixF[i][j]) { maxF = propMatrixF[i][j]; } if (maxP < propMatrixPos[i][j]) { maxP = propMatrixPos[i][j]; } if (maxEP < propMatrixEpos[i][j]) { maxEP = propMatrixEpos[i][j]; } } propMatrixF[i][i] = maxF; propMatrixPos[i][i] = maxP; propMatrixEpos[i][i] = maxEP; } } private ResidueProperties() { } public static double getHydmax() { return hydmax; } public static double getHydmin() { return hydmin; } public static double[] getHyd() { return hyd; } public static Map getAA3Hash() { return aa3Hash; } public static String codonTranslate(String lccodon) { String cdn = codonHash2.get(lccodon.toUpperCase()); if ("*".equals(cdn)) { return STOP; } return cdn; } public static Hashtable toDssp3State; static { toDssp3State = new Hashtable<>(); toDssp3State.put("H", "H"); toDssp3State.put("E", "E"); toDssp3State.put("C", " "); toDssp3State.put(" ", " "); toDssp3State.put("T", " "); toDssp3State.put("B", "E"); toDssp3State.put("G", "H"); toDssp3State.put("I", "H"); toDssp3State.put("X", " "); } /** * translate from other dssp secondary structure alphabets to 3-state * * @param ssstring * @return ssstring as a three-state secondary structure assignment. */ public static String getDssp3state(String ssstring) { if (ssstring == null) { return null; } StringBuffer ss = new StringBuffer(); for (int i = 0; i < ssstring.length(); i++) { String ssc = ssstring.substring(i, i + 1); if (toDssp3State.containsKey(ssc)) { ss.append(toDssp3State.get(ssc)); } else { ss.append(" "); } } return ss.toString(); } static { modifications.put("MSE", "MET"); // Selenomethionine // the rest tbc; from // http://sourceforge.net/p/jmol/mailman/message/12833570/ // modifications.put("CSE", "CYS"); // Selenocysteine // modifications.put("PTR", "TYR"); // Phosphotyrosine // modifications.put("SEP", "SER"); // Phosphoserine // modifications.put("HYP", "PRO"); // 4-hydroxyproline // modifications.put("5HP", "GLU"); // Pyroglutamic acid; 5-hydroxyproline // modifications.put("PCA", "GLU"); // Pyroglutamic acid // modifications.put("LYZ", "LYS"); // 5-hydroxylysine // Additional protein alphabets used in the SCOP database and PDB files // source: // https://github.com/biopython/biopython/blob/master/Bio/Data/SCOPData.py modifications.put("00C", "CYS"); modifications.put("01W", "XAA"); modifications.put("02K", "ALA"); modifications.put("03Y", "CYS"); modifications.put("07O", "CYS"); modifications.put("08P", "CYS"); modifications.put("0A0", "ASP"); modifications.put("0A1", "TYR"); modifications.put("0A2", "LYS"); modifications.put("0A8", "CYS"); modifications.put("0AA", "VAL"); modifications.put("0AB", "VAL"); modifications.put("0AC", "GLY"); modifications.put("0AD", "GLY"); modifications.put("0AF", "TRP"); modifications.put("0AG", "LEU"); modifications.put("0AH", "SER"); modifications.put("0AK", "ASP"); modifications.put("0AM", "ALA"); modifications.put("0AP", "CYS"); modifications.put("0AU", "UR3"); modifications.put("0AV", "ALA"); modifications.put("0AZ", "PRO"); modifications.put("0BN", "PHE"); modifications.put("0C ", "CYS"); modifications.put("0CS", "ALA"); modifications.put("0DC", "CYS"); modifications.put("0DG", "GLY"); modifications.put("0DT", "THR"); modifications.put("0FL", "ALA"); modifications.put("0G ", "GLY"); modifications.put("0NC", "ALA"); modifications.put("0SP", "ALA"); modifications.put("0U ", "UR3"); modifications.put("0YG", "YG"); modifications.put("10C", "CYS"); modifications.put("125", "UR3"); modifications.put("126", "UR3"); modifications.put("127", "UR3"); modifications.put("128", "ASN"); modifications.put("12A", "ALA"); modifications.put("143", "CYS"); modifications.put("175", "ASG"); modifications.put("193", "XAA"); modifications.put("1AP", "ALA"); modifications.put("1MA", "ALA"); modifications.put("1MG", "GLY"); modifications.put("1PA", "PHE"); modifications.put("1PI", "ALA"); modifications.put("1PR", "ASN"); modifications.put("1SC", "CYS"); modifications.put("1TQ", "TRP"); modifications.put("1TY", "TYR"); modifications.put("1X6", "SER"); modifications.put("200", "PHE"); modifications.put("23F", "PHE"); modifications.put("23S", "XAA"); modifications.put("26B", "THR"); modifications.put("2AD", "XAA"); modifications.put("2AG", "ALA"); modifications.put("2AO", "XAA"); modifications.put("2AR", "ALA"); modifications.put("2AS", "XAA"); modifications.put("2AT", "THR"); modifications.put("2AU", "UR3"); modifications.put("2BD", "ILE"); modifications.put("2BT", "THR"); modifications.put("2BU", "ALA"); modifications.put("2CO", "CYS"); modifications.put("2DA", "ALA"); modifications.put("2DF", "ASN"); modifications.put("2DM", "ASN"); modifications.put("2DO", "XAA"); modifications.put("2DT", "THR"); modifications.put("2EG", "GLY"); modifications.put("2FE", "ASN"); modifications.put("2FI", "ASN"); modifications.put("2FM", "MET"); modifications.put("2GT", "THR"); modifications.put("2HF", "HIS"); modifications.put("2LU", "LEU"); modifications.put("2MA", "ALA"); modifications.put("2MG", "GLY"); modifications.put("2ML", "LEU"); modifications.put("2MR", "ARG"); modifications.put("2MT", "PRO"); modifications.put("2MU", "UR3"); modifications.put("2NT", "THR"); modifications.put("2OM", "UR3"); modifications.put("2OT", "THR"); modifications.put("2PI", "XAA"); modifications.put("2PR", "GLY"); modifications.put("2SA", "ASN"); modifications.put("2SI", "XAA"); modifications.put("2ST", "THR"); modifications.put("2TL", "THR"); modifications.put("2TY", "TYR"); modifications.put("2VA", "VAL"); modifications.put("2XA", "CYS"); modifications.put("32S", "XAA"); modifications.put("32T", "XAA"); modifications.put("3AH", "HIS"); modifications.put("3AR", "XAA"); modifications.put("3CF", "PHE"); modifications.put("3DA", "ALA"); modifications.put("3DR", "ASN"); modifications.put("3GA", "ALA"); modifications.put("3MD", "ASP"); modifications.put("3ME", "UR3"); modifications.put("3NF", "TYR"); modifications.put("3QN", "LYS"); modifications.put("3TY", "XAA"); modifications.put("3XH", "GLY"); modifications.put("4AC", "ASN"); modifications.put("4BF", "TYR"); modifications.put("4CF", "PHE"); modifications.put("4CY", "MET"); modifications.put("4DP", "TRP"); modifications.put("4F3", "GYG"); modifications.put("4FB", "PRO"); modifications.put("4FW", "TRP"); modifications.put("4HT", "TRP"); modifications.put("4IN", "TRP"); modifications.put("4MF", "ASN"); modifications.put("4MM", "XAA"); modifications.put("4OC", "CYS"); modifications.put("4PC", "CYS"); modifications.put("4PD", "CYS"); modifications.put("4PE", "CYS"); modifications.put("4PH", "PHE"); modifications.put("4SC", "CYS"); modifications.put("4SU", "UR3"); modifications.put("4TA", "ASN"); modifications.put("4U7", "ALA"); modifications.put("56A", "HIS"); modifications.put("5AA", "ALA"); modifications.put("5AB", "ALA"); modifications.put("5AT", "THR"); modifications.put("5BU", "UR3"); modifications.put("5CG", "GLY"); modifications.put("5CM", "CYS"); modifications.put("5CS", "CYS"); modifications.put("5FA", "ALA"); modifications.put("5FC", "CYS"); modifications.put("5FU", "UR3"); modifications.put("5HP", "GLU"); modifications.put("5HT", "THR"); modifications.put("5HU", "UR3"); modifications.put("5IC", "CYS"); modifications.put("5IT", "THR"); modifications.put("5IU", "UR3"); modifications.put("5MC", "CYS"); modifications.put("5MD", "ASN"); modifications.put("5MU", "UR3"); modifications.put("5NC", "CYS"); modifications.put("5PC", "CYS"); modifications.put("5PY", "THR"); modifications.put("5SE", "UR3"); modifications.put("5ZA", "TWG"); modifications.put("64T", "THR"); modifications.put("6CL", "LYS"); modifications.put("6CT", "THR"); modifications.put("6CW", "TRP"); modifications.put("6HA", "ALA"); modifications.put("6HC", "CYS"); modifications.put("6HG", "GLY"); modifications.put("6HN", "LYS"); modifications.put("6HT", "THR"); modifications.put("6IA", "ALA"); modifications.put("6MA", "ALA"); modifications.put("6MC", "ALA"); modifications.put("6MI", "ASN"); modifications.put("6MT", "ALA"); modifications.put("6MZ", "ASN"); modifications.put("6OG", "GLY"); modifications.put("70U", "UR3"); modifications.put("7DA", "ALA"); modifications.put("7GU", "GLY"); modifications.put("7JA", "ILE"); modifications.put("7MG", "GLY"); modifications.put("8AN", "ALA"); modifications.put("8FG", "GLY"); modifications.put("8MG", "GLY"); modifications.put("8OG", "GLY"); modifications.put("9NE", "GLU"); modifications.put("9NF", "PHE"); modifications.put("9NR", "ARG"); modifications.put("9NV", "VAL"); modifications.put("A ", "ALA"); modifications.put("A1P", "ASN"); modifications.put("A23", "ALA"); modifications.put("A2L", "ALA"); modifications.put("A2M", "ALA"); modifications.put("A34", "ALA"); modifications.put("A35", "ALA"); modifications.put("A38", "ALA"); modifications.put("A39", "ALA"); modifications.put("A3A", "ALA"); modifications.put("A3P", "ALA"); modifications.put("A40", "ALA"); modifications.put("A43", "ALA"); modifications.put("A44", "ALA"); modifications.put("A47", "ALA"); modifications.put("A5L", "ALA"); modifications.put("A5M", "CYS"); modifications.put("A5N", "ASN"); modifications.put("A5O", "ALA"); modifications.put("A66", "XAA"); modifications.put("AA3", "ALA"); modifications.put("AA4", "ALA"); modifications.put("AAR", "ARG"); modifications.put("AB7", "XAA"); modifications.put("ABA", "ALA"); modifications.put("ABR", "ALA"); modifications.put("ABS", "ALA"); modifications.put("ABT", "ASN"); modifications.put("ACB", "ASP"); modifications.put("ACL", "ARG"); modifications.put("AD2", "ALA"); modifications.put("ADD", "XAA"); modifications.put("ADX", "ASN"); modifications.put("AEA", "XAA"); modifications.put("AEI", "ASP"); modifications.put("AET", "ALA"); modifications.put("AFA", "ASN"); modifications.put("AFF", "ASN"); modifications.put("AFG", "GLY"); modifications.put("AGM", "ARG"); modifications.put("AGT", "CYS"); modifications.put("AHB", "ASN"); modifications.put("AHH", "XAA"); modifications.put("AHO", "ALA"); modifications.put("AHP", "ALA"); modifications.put("AHS", "XAA"); modifications.put("AHT", "XAA"); modifications.put("AIB", "ALA"); modifications.put("AKL", "ASP"); modifications.put("AKZ", "ASP"); modifications.put("ALA", "ALA"); modifications.put("ALC", "ALA"); modifications.put("ALM", "ALA"); modifications.put("ALN", "ALA"); modifications.put("ALO", "THR"); modifications.put("ALQ", "XAA"); modifications.put("ALS", "ALA"); modifications.put("ALT", "ALA"); modifications.put("ALV", "ALA"); modifications.put("ALY", "LYS"); modifications.put("AN8", "ALA"); modifications.put("AP7", "ALA"); modifications.put("APE", "XAA"); modifications.put("APH", "ALA"); modifications.put("API", "LYS"); modifications.put("APK", "LYS"); modifications.put("APM", "XAA"); modifications.put("APP", "XAA"); modifications.put("AR2", "ARG"); modifications.put("AR4", "GLU"); modifications.put("AR7", "ARG"); modifications.put("ARG", "ARG"); modifications.put("ARM", "ARG"); modifications.put("ARO", "ARG"); modifications.put("ARV", "XAA"); modifications.put("AS ", "ALA"); modifications.put("AS2", "ASP"); modifications.put("AS9", "XAA"); modifications.put("ASA", "ASP"); modifications.put("ASB", "ASP"); modifications.put("ASI", "ASP"); modifications.put("ASK", "ASP"); modifications.put("ASL", "ASP"); modifications.put("ASM", "XAA"); modifications.put("ASN", "ASN"); modifications.put("ASP", "ASP"); modifications.put("ASQ", "ASP"); modifications.put("ASU", "ASN"); modifications.put("ASX", "ASX"); modifications.put("ATD", "THR"); modifications.put("ATL", "THR"); modifications.put("ATM", "THR"); modifications.put("AVC", "ALA"); modifications.put("AVN", "XAA"); modifications.put("AYA", "ALA"); modifications.put("AYG", "AYG"); modifications.put("AZK", "LYS"); modifications.put("AZS", "SER"); modifications.put("AZY", "TYR"); modifications.put("B1F", "PHE"); modifications.put("B1P", "ASN"); modifications.put("B2A", "ALA"); modifications.put("B2F", "PHE"); modifications.put("B2I", "ILE"); modifications.put("B2V", "VAL"); modifications.put("B3A", "ALA"); modifications.put("B3D", "ASP"); modifications.put("B3E", "GLU"); modifications.put("B3K", "LYS"); modifications.put("B3L", "XAA"); modifications.put("B3M", "XAA"); modifications.put("B3Q", "XAA"); modifications.put("B3S", "SER"); modifications.put("B3T", "XAA"); modifications.put("B3U", "HIS"); modifications.put("B3X", "ASN"); modifications.put("B3Y", "TYR"); modifications.put("BB6", "CYS"); modifications.put("BB7", "CYS"); modifications.put("BB8", "PHE"); modifications.put("BB9", "CYS"); modifications.put("BBC", "CYS"); modifications.put("BCS", "CYS"); modifications.put("BE2", "XAA"); modifications.put("BFD", "ASP"); modifications.put("BG1", "SER"); modifications.put("BGM", "GLY"); modifications.put("BH2", "ASP"); modifications.put("BHD", "ASP"); modifications.put("BIF", "PHE"); modifications.put("BIL", "XAA"); modifications.put("BIU", "ILE"); modifications.put("BJH", "XAA"); modifications.put("BLE", "LEU"); modifications.put("BLY", "LYS"); modifications.put("BMP", "ASN"); modifications.put("BMT", "THR"); modifications.put("BNN", "PHE"); modifications.put("BNO", "XAA"); modifications.put("BOE", "THR"); modifications.put("BOR", "ARG"); modifications.put("BPE", "CYS"); modifications.put("BRU", "UR3"); modifications.put("BSE", "SER"); modifications.put("BT5", "ASN"); modifications.put("BTA", "LEU"); modifications.put("BTC", "CYS"); modifications.put("BTR", "TRP"); modifications.put("BUC", "CYS"); modifications.put("BUG", "VAL"); modifications.put("BVP", "UR3"); modifications.put("BZG", "ASN"); modifications.put("C ", "CYS"); modifications.put("C12", "TYG"); modifications.put("C1X", "LYS"); modifications.put("C25", "CYS"); modifications.put("C2L", "CYS"); modifications.put("C2S", "CYS"); modifications.put("C31", "CYS"); modifications.put("C32", "CYS"); modifications.put("C34", "CYS"); modifications.put("C36", "CYS"); modifications.put("C37", "CYS"); modifications.put("C38", "CYS"); modifications.put("C3Y", "CYS"); modifications.put("C42", "CYS"); modifications.put("C43", "CYS"); modifications.put("C45", "CYS"); modifications.put("C46", "CYS"); modifications.put("C49", "CYS"); modifications.put("C4R", "CYS"); modifications.put("C4S", "CYS"); modifications.put("C5C", "CYS"); modifications.put("C66", "XAA"); modifications.put("C6C", "CYS"); modifications.put("C99", "TFG"); modifications.put("CAF", "CYS"); modifications.put("CAL", "XAA"); modifications.put("CAR", "CYS"); modifications.put("CAS", "CYS"); modifications.put("CAV", "XAA"); modifications.put("CAY", "CYS"); modifications.put("CB2", "CYS"); modifications.put("CBR", "CYS"); modifications.put("CBV", "CYS"); modifications.put("CCC", "CYS"); modifications.put("CCL", "LYS"); modifications.put("CCS", "CYS"); modifications.put("CCY", "CYG"); modifications.put("CDE", "XAA"); modifications.put("CDV", "XAA"); modifications.put("CDW", "CYS"); modifications.put("CEA", "CYS"); modifications.put("CFL", "CYS"); modifications.put("CFY", "FCYG"); // check modifications.put("CG1", "GLY"); modifications.put("CGA", "GLU"); modifications.put("CGU", "GLU"); modifications.put("CH ", "CYS"); modifications.put("CH6", "MYG"); modifications.put("CH7", "KYG"); modifications.put("CHF", "XAA"); modifications.put("CHG", "XAA"); modifications.put("CHP", "GLY"); modifications.put("CHS", "XAA"); modifications.put("CIR", "ARG"); modifications.put("CJO", "GYG"); modifications.put("CLE", "LEU"); modifications.put("CLG", "LYS"); modifications.put("CLH", "LYS"); modifications.put("CLV", "AFG"); modifications.put("CM0", "ASN"); modifications.put("CME", "CYS"); modifications.put("CMH", "CYS"); modifications.put("CML", "CYS"); modifications.put("CMR", "CYS"); modifications.put("CMT", "CYS"); modifications.put("CNU", "UR3"); modifications.put("CP1", "CYS"); modifications.put("CPC", "XAA"); modifications.put("CPI", "XAA"); modifications.put("CQR", "GYG"); modifications.put("CR0", "TLG"); modifications.put("CR2", "GYG"); modifications.put("CR5", "GLY"); modifications.put("CR7", "KYG"); modifications.put("CR8", "HYG"); modifications.put("CRF", "TWG"); modifications.put("CRG", "THG"); modifications.put("CRK", "MYG"); modifications.put("CRO", "GYG"); modifications.put("CRQ", "QYG"); modifications.put("CRU", "EYG"); modifications.put("CRW", "ASG"); modifications.put("CRX", "ASG"); modifications.put("CS0", "CYS"); modifications.put("CS1", "CYS"); modifications.put("CS3", "CYS"); modifications.put("CS4", "CYS"); modifications.put("CS8", "ASN"); modifications.put("CSA", "CYS"); modifications.put("CSB", "CYS"); modifications.put("CSD", "CYS"); modifications.put("CSE", "CYS"); modifications.put("CSF", "CYS"); modifications.put("CSH", "SHG"); modifications.put("CSI", "GLY"); modifications.put("CSJ", "CYS"); modifications.put("CSL", "CYS"); modifications.put("CSO", "CYS"); modifications.put("CSP", "CYS"); modifications.put("CSR", "CYS"); modifications.put("CSS", "CYS"); modifications.put("CSU", "CYS"); modifications.put("CSW", "CYS"); modifications.put("CSX", "CYS"); modifications.put("CSY", "SYG"); modifications.put("CSZ", "CYS"); modifications.put("CTE", "TRP"); modifications.put("CTG", "THR"); modifications.put("CTH", "THR"); modifications.put("CUC", "XAA"); modifications.put("CWR", "SER"); modifications.put("CXM", "MET"); modifications.put("CY0", "CYS"); modifications.put("CY1", "CYS"); modifications.put("CY3", "CYS"); modifications.put("CY4", "CYS"); modifications.put("CYA", "CYS"); modifications.put("CYD", "CYS"); modifications.put("CYF", "CYS"); modifications.put("CYG", "CYS"); modifications.put("CYJ", "XAA"); modifications.put("CYM", "CYS"); modifications.put("CYQ", "CYS"); modifications.put("CYR", "CYS"); modifications.put("CYS", "CYS"); modifications.put("CZ2", "CYS"); modifications.put("CZO", "GYG"); modifications.put("CZZ", "CYS"); modifications.put("D11", "THR"); modifications.put("D1P", "ASN"); modifications.put("D3 ", "ASN"); modifications.put("D33", "ASN"); modifications.put("D3P", "GLY"); modifications.put("D3T", "THR"); modifications.put("D4M", "THR"); modifications.put("D4P", "XAA"); modifications.put("DA ", "ALA"); modifications.put("DA2", "XAA"); modifications.put("DAB", "ALA"); modifications.put("DAH", "PHE"); modifications.put("DAL", "ALA"); modifications.put("DAR", "ARG"); modifications.put("DAS", "ASP"); modifications.put("DBB", "THR"); modifications.put("DBM", "ASN"); modifications.put("DBS", "SER"); modifications.put("DBU", "THR"); modifications.put("DBY", "TYR"); modifications.put("DBZ", "ALA"); modifications.put("DC ", "CYS"); modifications.put("DC2", "CYS"); modifications.put("DCG", "GLY"); modifications.put("DCI", "XAA"); modifications.put("DCL", "XAA"); modifications.put("DCT", "CYS"); modifications.put("DCY", "CYS"); modifications.put("DDE", "HIS"); modifications.put("DDG", "GLY"); modifications.put("DDN", "UR3"); modifications.put("DDX", "ASN"); modifications.put("DFC", "CYS"); modifications.put("DFG", "GLY"); modifications.put("DFI", "XAA"); modifications.put("DFO", "XAA"); modifications.put("DFT", "ASN"); modifications.put("DG ", "GLY"); modifications.put("DGH", "GLY"); modifications.put("DGI", "GLY"); modifications.put("DGL", "GLU"); modifications.put("DGN", "GLN"); modifications.put("DHA", "SER"); modifications.put("DHI", "HIS"); modifications.put("DHL", "XAA"); modifications.put("DHN", "VAL"); modifications.put("DHP", "XAA"); modifications.put("DHU", "UR3"); modifications.put("DHV", "VAL"); modifications.put("DI ", "ILE"); modifications.put("DIL", "ILE"); modifications.put("DIR", "ARG"); modifications.put("DIV", "VAL"); modifications.put("DLE", "LEU"); modifications.put("DLS", "LYS"); modifications.put("DLY", "LYS"); modifications.put("DM0", "LYS"); modifications.put("DMH", "ASN"); modifications.put("DMK", "ASP"); modifications.put("DMT", "XAA"); modifications.put("DN ", "ASN"); modifications.put("DNE", "LEU"); modifications.put("DNG", "LEU"); modifications.put("DNL", "LYS"); modifications.put("DNM", "LEU"); modifications.put("DNP", "ALA"); modifications.put("DNR", "CYS"); modifications.put("DNS", "LYS"); modifications.put("DOA", "XAA"); modifications.put("DOC", "CYS"); modifications.put("DOH", "ASP"); modifications.put("DON", "LEU"); modifications.put("DPB", "THR"); modifications.put("DPH", "PHE"); modifications.put("DPL", "PRO"); modifications.put("DPP", "ALA"); modifications.put("DPQ", "TYR"); modifications.put("DPR", "PRO"); modifications.put("DPY", "ASN"); modifications.put("DRM", "UR3"); modifications.put("DRP", "ASN"); modifications.put("DRT", "THR"); modifications.put("DRZ", "ASN"); modifications.put("DSE", "SER"); modifications.put("DSG", "ASN"); modifications.put("DSN", "SER"); modifications.put("DSP", "ASP"); modifications.put("DT ", "THR"); modifications.put("DTH", "THR"); modifications.put("DTR", "TRP"); modifications.put("DTY", "TYR"); modifications.put("DU ", "UR3"); modifications.put("DVA", "VAL"); modifications.put("DXD", "ASN"); modifications.put("DXN", "ASN"); modifications.put("DYG", "DYG"); modifications.put("DYS", "CYS"); modifications.put("DZM", "ALA"); modifications.put("E ", "ALA"); modifications.put("E1X", "ALA"); modifications.put("ECC", "GLN"); modifications.put("EDA", "ALA"); modifications.put("EFC", "CYS"); modifications.put("EHP", "PHE"); modifications.put("EIT", "THR"); modifications.put("ENP", "ASN"); modifications.put("ESB", "TYR"); modifications.put("ESC", "MET"); modifications.put("EXB", "XAA"); modifications.put("EXY", "LEU"); modifications.put("EY5", "ASN"); modifications.put("EYS", "XAA"); modifications.put("F2F", "PHE"); modifications.put("FA2", "ALA"); modifications.put("FA5", "ASN"); modifications.put("FAG", "ASN"); modifications.put("FAI", "ASN"); modifications.put("FB5", "ALA"); modifications.put("FB6", "ALA"); modifications.put("FCL", "PHE"); modifications.put("FFD", "ASN"); modifications.put("FGA", "GLU"); modifications.put("FGL", "GLY"); modifications.put("FGP", "SER"); modifications.put("FHL", "XAA"); modifications.put("FHO", "LYS"); modifications.put("FHU", "UR3"); modifications.put("FLA", "ALA"); modifications.put("FLE", "LEU"); modifications.put("FLT", "TYR"); modifications.put("FME", "MET"); modifications.put("FMG", "GLY"); modifications.put("FMU", "ASN"); modifications.put("FOE", "CYS"); modifications.put("FOX", "GLY"); modifications.put("FP9", "PRO"); modifications.put("FPA", "PHE"); modifications.put("FRD", "XAA"); modifications.put("FT6", "TRP"); modifications.put("FTR", "TRP"); modifications.put("FTY", "TYR"); modifications.put("FVA", "VAL"); modifications.put("FZN", "LYS"); modifications.put("G ", "GLY"); modifications.put("G25", "GLY"); modifications.put("G2L", "GLY"); modifications.put("G2S", "GLY"); modifications.put("G31", "GLY"); modifications.put("G32", "GLY"); modifications.put("G33", "GLY"); modifications.put("G36", "GLY"); modifications.put("G38", "GLY"); modifications.put("G42", "GLY"); modifications.put("G46", "GLY"); modifications.put("G47", "GLY"); modifications.put("G48", "GLY"); modifications.put("G49", "GLY"); modifications.put("G4P", "ASN"); modifications.put("G7M", "GLY"); modifications.put("GAO", "GLY"); modifications.put("GAU", "GLU"); modifications.put("GCK", "CYS"); modifications.put("GCM", "XAA"); modifications.put("GDP", "GLY"); modifications.put("GDR", "GLY"); modifications.put("GFL", "GLY"); modifications.put("GGL", "GLU"); modifications.put("GH3", "GLY"); modifications.put("GHG", "GLN"); modifications.put("GHP", "GLY"); modifications.put("GL3", "GLY"); modifications.put("GLH", "GLN"); modifications.put("GLJ", "GLU"); modifications.put("GLK", "GLU"); modifications.put("GLM", "XAA"); modifications.put("GLN", "GLN"); modifications.put("GLQ", "GLU"); modifications.put("GLU", "GLU"); modifications.put("GLX", "GLX"); modifications.put("GLY", "GLY"); modifications.put("GLZ", "GLY"); modifications.put("GMA", "GLU"); modifications.put("GMS", "GLY"); modifications.put("GMU", "UR3"); modifications.put("GN7", "GLY"); modifications.put("GND", "XAA"); modifications.put("GNE", "ASN"); modifications.put("GOM", "GLY"); modifications.put("GPL", "LYS"); modifications.put("GS ", "GLY"); modifications.put("GSC", "GLY"); modifications.put("GSR", "GLY"); modifications.put("GSS", "GLY"); modifications.put("GSU", "GLU"); modifications.put("GT9", "CYS"); modifications.put("GTP", "GLY"); modifications.put("GVL", "XAA"); modifications.put("GYC", "CYG"); modifications.put("GYS", "SYG"); modifications.put("H2U", "UR3"); modifications.put("H5M", "PRO"); modifications.put("HAC", "ALA"); modifications.put("HAR", "ARG"); modifications.put("HBN", "HIS"); modifications.put("HCS", "XAA"); modifications.put("HDP", "UR3"); modifications.put("HEU", "UR3"); modifications.put("HFA", "XAA"); modifications.put("HGL", "XAA"); modifications.put("HHI", "HIS"); modifications.put("HHK", "AK"); // check modifications.put("HIA", "HIS"); modifications.put("HIC", "HIS"); modifications.put("HIP", "HIS"); modifications.put("HIQ", "HIS"); modifications.put("HIS", "HIS"); modifications.put("HL2", "LEU"); modifications.put("HLU", "LEU"); modifications.put("HMR", "ARG"); modifications.put("HOL", "ASN"); modifications.put("HPC", "PHE"); modifications.put("HPE", "PHE"); modifications.put("HPH", "PHE"); modifications.put("HPQ", "PHE"); modifications.put("HQA", "ALA"); modifications.put("HRG", "ARG"); modifications.put("HRP", "TRP"); modifications.put("HS8", "HIS"); modifications.put("HS9", "HIS"); modifications.put("HSE", "SER"); modifications.put("HSL", "SER"); modifications.put("HSO", "HIS"); modifications.put("HTI", "CYS"); modifications.put("HTN", "ASN"); modifications.put("HTR", "TRP"); modifications.put("HV5", "ALA"); modifications.put("HVA", "VAL"); modifications.put("HY3", "PRO"); modifications.put("HYP", "PRO"); modifications.put("HZP", "PRO"); modifications.put("I ", "ILE"); modifications.put("I2M", "ILE"); modifications.put("I58", "LYS"); modifications.put("I5C", "CYS"); modifications.put("IAM", "ALA"); modifications.put("IAR", "ARG"); modifications.put("IAS", "ASP"); modifications.put("IC ", "CYS"); modifications.put("IEL", "LYS"); modifications.put("IEY", "HYG"); modifications.put("IG ", "GLY"); modifications.put("IGL", "GLY"); modifications.put("IGU", "GLY"); modifications.put("IIC", "SHG"); modifications.put("IIL", "ILE"); modifications.put("ILE", "ILE"); modifications.put("ILG", "GLU"); modifications.put("ILX", "ILE"); modifications.put("IMC", "CYS"); modifications.put("IML", "ILE"); modifications.put("IOY", "PHE"); modifications.put("IPG", "GLY"); modifications.put("IPN", "ASN"); modifications.put("IRN", "ASN"); modifications.put("IT1", "LYS"); modifications.put("IU ", "UR3"); modifications.put("IYR", "TYR"); modifications.put("IYT", "THR"); modifications.put("IZO", "MET"); modifications.put("JJJ", "CYS"); modifications.put("JJK", "CYS"); modifications.put("JJL", "CYS"); modifications.put("JW5", "ASN"); modifications.put("K1R", "CYS"); modifications.put("KAG", "GLY"); modifications.put("KCX", "LYS"); modifications.put("KGC", "LYS"); modifications.put("KNB", "ALA"); modifications.put("KOR", "MET"); modifications.put("KPI", "LYS"); modifications.put("KST", "LYS"); modifications.put("KYQ", "LYS"); modifications.put("L2A", "XAA"); modifications.put("LA2", "LYS"); modifications.put("LAA", "ASP"); modifications.put("LAL", "ALA"); modifications.put("LBY", "LYS"); modifications.put("LC ", "CYS"); modifications.put("LCA", "ALA"); modifications.put("LCC", "ASN"); modifications.put("LCG", "GLY"); modifications.put("LCH", "ASN"); modifications.put("LCK", "LYS"); modifications.put("LCX", "LYS"); modifications.put("LDH", "LYS"); modifications.put("LED", "LEU"); modifications.put("LEF", "LEU"); modifications.put("LEH", "LEU"); modifications.put("LEI", "VAL"); modifications.put("LEM", "LEU"); modifications.put("LEN", "LEU"); modifications.put("LET", "XAA"); modifications.put("LEU", "LEU"); modifications.put("LEX", "LEU"); modifications.put("LG ", "GLY"); modifications.put("LGP", "GLY"); modifications.put("LHC", "XAA"); modifications.put("LHU", "UR3"); modifications.put("LKC", "ASN"); modifications.put("LLP", "LYS"); modifications.put("LLY", "LYS"); modifications.put("LME", "GLU"); modifications.put("LMF", "LYS"); modifications.put("LMQ", "GLN"); modifications.put("LMS", "ASN"); modifications.put("LP6", "LYS"); modifications.put("LPD", "PRO"); modifications.put("LPG", "GLY"); modifications.put("LPL", "XAA"); modifications.put("LPS", "SER"); modifications.put("LSO", "XAA"); modifications.put("LTA", "XAA"); modifications.put("LTR", "TRP"); modifications.put("LVG", "GLY"); modifications.put("LVN", "VAL"); modifications.put("LYF", "LYS"); modifications.put("LYK", "LYS"); modifications.put("LYM", "LYS"); modifications.put("LYN", "LYS"); modifications.put("LYR", "LYS"); modifications.put("LYS", "LYS"); modifications.put("LYX", "LYS"); modifications.put("LYZ", "LYS"); modifications.put("M0H", "CYS"); modifications.put("M1G", "GLY"); modifications.put("M2G", "GLY"); modifications.put("M2L", "LYS"); modifications.put("M2S", "MET"); modifications.put("M30", "GLY"); modifications.put("M3L", "LYS"); modifications.put("M5M", "CYS"); modifications.put("MA ", "ALA"); modifications.put("MA6", "ALA"); modifications.put("MA7", "ALA"); modifications.put("MAA", "ALA"); modifications.put("MAD", "ALA"); modifications.put("MAI", "ARG"); modifications.put("MBQ", "TYR"); modifications.put("MBZ", "ASN"); modifications.put("MC1", "SER"); modifications.put("MCG", "XAA"); modifications.put("MCL", "LYS"); modifications.put("MCS", "CYS"); modifications.put("MCY", "CYS"); modifications.put("MD3", "CYS"); modifications.put("MD6", "GLY"); modifications.put("MDH", "XAA"); modifications.put("MDO", "ASG"); modifications.put("MDR", "ASN"); modifications.put("MEA", "PHE"); modifications.put("MED", "MET"); modifications.put("MEG", "GLU"); modifications.put("MEN", "ASN"); modifications.put("MEP", "UR3"); modifications.put("MEQ", "GLN"); modifications.put("MET", "MET"); modifications.put("MEU", "GLY"); modifications.put("MF3", "XAA"); modifications.put("MFC", "GYG"); modifications.put("MG1", "GLY"); modifications.put("MGG", "ARG"); modifications.put("MGN", "GLN"); modifications.put("MGQ", "ALA"); modifications.put("MGV", "GLY"); modifications.put("MGY", "GLY"); modifications.put("MHL", "LEU"); modifications.put("MHO", "MET"); modifications.put("MHS", "HIS"); modifications.put("MIA", "ALA"); modifications.put("MIS", "SER"); modifications.put("MK8", "LEU"); modifications.put("ML3", "LYS"); modifications.put("MLE", "LEU"); modifications.put("MLL", "LEU"); modifications.put("MLY", "LYS"); modifications.put("MLZ", "LYS"); modifications.put("MME", "MET"); modifications.put("MMO", "ARG"); modifications.put("MMT", "THR"); modifications.put("MND", "ASN"); modifications.put("MNL", "LEU"); modifications.put("MNU", "UR3"); modifications.put("MNV", "VAL"); modifications.put("MOD", "XAA"); modifications.put("MP8", "PRO"); modifications.put("MPH", "XAA"); modifications.put("MPJ", "XAA"); modifications.put("MPQ", "GLY"); modifications.put("MRG", "GLY"); modifications.put("MSA", "GLY"); modifications.put("MSE", "MET"); modifications.put("MSL", "MET"); modifications.put("MSO", "MET"); modifications.put("MSP", "XAA"); modifications.put("MT2", "MET"); modifications.put("MTR", "THR"); modifications.put("MTU", "ALA"); modifications.put("MTY", "TYR"); modifications.put("MVA", "VAL"); modifications.put("N ", "ASN"); modifications.put("N10", "SER"); modifications.put("N2C", "XAA"); modifications.put("N5I", "ASN"); modifications.put("N5M", "CYS"); modifications.put("N6G", "GLY"); modifications.put("N7P", "PRO"); modifications.put("NA8", "ALA"); modifications.put("NAL", "ALA"); modifications.put("NAM", "ALA"); modifications.put("NB8", "ASN"); modifications.put("NBQ", "TYR"); modifications.put("NC1", "SER"); modifications.put("NCB", "ALA"); modifications.put("NCX", "ASN"); modifications.put("NCY", "XAA"); modifications.put("NDF", "PHE"); modifications.put("NDN", "UR3"); modifications.put("NEM", "HIS"); modifications.put("NEP", "HIS"); modifications.put("NF2", "ASN"); modifications.put("NFA", "PHE"); modifications.put("NHL", "GLU"); modifications.put("NIT", "XAA"); modifications.put("NIY", "TYR"); modifications.put("NLE", "LEU"); modifications.put("NLN", "LEU"); modifications.put("NLO", "LEU"); modifications.put("NLP", "LEU"); modifications.put("NLQ", "GLN"); modifications.put("NMC", "GLY"); modifications.put("NMM", "ARG"); modifications.put("NMS", "THR"); modifications.put("NMT", "THR"); modifications.put("NNH", "ARG"); modifications.put("NP3", "ASN"); modifications.put("NPH", "CYS"); modifications.put("NPI", "ALA"); modifications.put("NRP", "LYG"); modifications.put("NRQ", "MYG"); modifications.put("NSK", "XAA"); modifications.put("NTY", "TYR"); modifications.put("NVA", "VAL"); modifications.put("NYC", "TWG"); modifications.put("NYG", "NYG"); modifications.put("NYM", "ASN"); modifications.put("NYS", "CYS"); modifications.put("NZH", "HIS"); modifications.put("O12", "XAA"); modifications.put("O2C", "ASN"); modifications.put("O2G", "GLY"); modifications.put("OAD", "ASN"); modifications.put("OAS", "SER"); modifications.put("OBF", "XAA"); modifications.put("OBS", "XAA"); modifications.put("OCS", "CYS"); modifications.put("OCY", "CYS"); modifications.put("ODP", "ASN"); modifications.put("OHI", "HIS"); modifications.put("OHS", "ASP"); modifications.put("OIC", "XAA"); modifications.put("OIP", "ILE"); modifications.put("OLE", "XAA"); modifications.put("OLT", "THR"); modifications.put("OLZ", "SER"); modifications.put("OMC", "CYS"); modifications.put("OMG", "GLY"); modifications.put("OMT", "MET"); modifications.put("OMU", "UR3"); modifications.put("ONE", "UR3"); modifications.put("ONH", "ALA"); modifications.put("ONL", "XAA"); modifications.put("OPR", "ARG"); modifications.put("ORN", "ALA"); modifications.put("ORQ", "ARG"); modifications.put("OSE", "SER"); modifications.put("OTB", "XAA"); modifications.put("OTH", "THR"); modifications.put("OTY", "TYR"); modifications.put("OXX", "ASP"); modifications.put("P ", "GLY"); modifications.put("P1L", "CYS"); modifications.put("P1P", "ASN"); modifications.put("P2T", "THR"); modifications.put("P2U", "UR3"); modifications.put("P2Y", "PRO"); modifications.put("P5P", "ALA"); modifications.put("PAQ", "TYR"); modifications.put("PAS", "ASP"); modifications.put("PAT", "TRP"); modifications.put("PAU", "ALA"); modifications.put("PBB", "CYS"); modifications.put("PBF", "PHE"); modifications.put("PBT", "ASN"); modifications.put("PCA", "GLU"); modifications.put("PCC", "PRO"); modifications.put("PCE", "XAA"); modifications.put("PCS", "PHE"); modifications.put("PDL", "XAA"); modifications.put("PDU", "UR3"); modifications.put("PEC", "CYS"); modifications.put("PF5", "PHE"); modifications.put("PFF", "PHE"); modifications.put("PFX", "XAA"); modifications.put("PG1", "SER"); modifications.put("PG7", "GLY"); modifications.put("PG9", "GLY"); modifications.put("PGL", "XAA"); modifications.put("PGN", "GLY"); modifications.put("PGP", "GLY"); modifications.put("PGY", "GLY"); modifications.put("PHA", "PHE"); modifications.put("PHD", "ASP"); modifications.put("PHE", "PHE"); modifications.put("PHI", "PHE"); modifications.put("PHL", "PHE"); modifications.put("PHM", "PHE"); modifications.put("PIA", "AYG"); modifications.put("PIV", "XAA"); modifications.put("PLE", "LEU"); modifications.put("PM3", "PHE"); modifications.put("PMT", "CYS"); modifications.put("POM", "PRO"); modifications.put("PPN", "PHE"); modifications.put("PPU", "ALA"); modifications.put("PPW", "GLY"); modifications.put("PQ1", "ASN"); modifications.put("PR3", "CYS"); modifications.put("PR5", "ALA"); modifications.put("PR9", "PRO"); modifications.put("PRN", "ALA"); modifications.put("PRO", "PRO"); modifications.put("PRS", "PRO"); modifications.put("PSA", "PHE"); modifications.put("PSH", "HIS"); modifications.put("PST", "THR"); modifications.put("PSU", "UR3"); modifications.put("PSW", "CYS"); modifications.put("PTA", "XAA"); modifications.put("PTH", "TYR"); modifications.put("PTM", "TYR"); modifications.put("PTR", "TYR"); modifications.put("PU ", "ALA"); modifications.put("PUY", "ASN"); modifications.put("PVH", "HIS"); modifications.put("PVL", "XAA"); modifications.put("PYA", "ALA"); modifications.put("PYO", "UR3"); modifications.put("PYX", "CYS"); modifications.put("PYY", "ASN"); modifications.put("QLG", "QLG"); modifications.put("QMM", "GLN"); modifications.put("QPA", "CYS"); modifications.put("QPH", "PHE"); modifications.put("QUO", "GLY"); modifications.put("R ", "ALA"); modifications.put("R1A", "CYS"); modifications.put("R4K", "TRP"); modifications.put("RC7", "HYG"); modifications.put("RE0", "TRP"); modifications.put("RE3", "TRP"); modifications.put("RIA", "ALA"); modifications.put("RMP", "ALA"); modifications.put("RON", "XAA"); modifications.put("RT ", "THR"); modifications.put("RTP", "ASN"); modifications.put("S1H", "SER"); modifications.put("S2C", "CYS"); modifications.put("S2D", "ALA"); modifications.put("S2M", "THR"); modifications.put("S2P", "ALA"); modifications.put("S4A", "ALA"); modifications.put("S4C", "CYS"); modifications.put("S4G", "GLY"); modifications.put("S4U", "UR3"); modifications.put("S6G", "GLY"); modifications.put("SAC", "SER"); modifications.put("SAH", "CYS"); modifications.put("SAR", "GLY"); modifications.put("SBL", "SER"); modifications.put("SC ", "CYS"); modifications.put("SCH", "CYS"); modifications.put("SCS", "CYS"); modifications.put("SCY", "CYS"); modifications.put("SD2", "XAA"); modifications.put("SDG", "GLY"); modifications.put("SDP", "SER"); modifications.put("SEB", "SER"); modifications.put("SEC", "ALA"); modifications.put("SEG", "ALA"); modifications.put("SEL", "SER"); modifications.put("SEM", "SER"); modifications.put("SEN", "SER"); modifications.put("SEP", "SER"); modifications.put("SER", "SER"); modifications.put("SET", "SER"); modifications.put("SGB", "SER"); modifications.put("SHC", "CYS"); modifications.put("SHP", "GLY"); modifications.put("SHR", "LYS"); modifications.put("SIB", "CYS"); modifications.put("SIC", "DC"); // check modifications.put("SLA", "PRO"); modifications.put("SLR", "PRO"); modifications.put("SLZ", "LYS"); modifications.put("SMC", "CYS"); modifications.put("SME", "MET"); modifications.put("SMF", "PHE"); modifications.put("SMP", "ALA"); modifications.put("SMT", "THR"); modifications.put("SNC", "CYS"); modifications.put("SNN", "ASN"); modifications.put("SOC", "CYS"); modifications.put("SOS", "ASN"); modifications.put("SOY", "SER"); modifications.put("SPT", "THR"); modifications.put("SRA", "ALA"); modifications.put("SSU", "UR3"); modifications.put("STY", "TYR"); modifications.put("SUB", "XAA"); modifications.put("SUI", "DG"); modifications.put("SUN", "SER"); modifications.put("SUR", "UR3"); modifications.put("SVA", "SER"); modifications.put("SVV", "SER"); modifications.put("SVW", "SER"); modifications.put("SVX", "SER"); modifications.put("SVY", "SER"); modifications.put("SVZ", "XAA"); modifications.put("SWG", "SWG"); modifications.put("SYS", "CYS"); modifications.put("T ", "THR"); modifications.put("T11", "PHE"); modifications.put("T23", "THR"); modifications.put("T2S", "THR"); modifications.put("T2T", "ASN"); modifications.put("T31", "UR3"); modifications.put("T32", "THR"); modifications.put("T36", "THR"); modifications.put("T37", "THR"); modifications.put("T38", "THR"); modifications.put("T39", "THR"); modifications.put("T3P", "THR"); modifications.put("T41", "THR"); modifications.put("T48", "THR"); modifications.put("T49", "THR"); modifications.put("T4S", "THR"); modifications.put("T5O", "UR3"); modifications.put("T5S", "THR"); modifications.put("T66", "XAA"); modifications.put("T6A", "ALA"); modifications.put("TA3", "THR"); modifications.put("TA4", "XAA"); modifications.put("TAF", "THR"); modifications.put("TAL", "ASN"); modifications.put("TAV", "ASP"); modifications.put("TBG", "VAL"); modifications.put("TBM", "THR"); modifications.put("TC1", "CYS"); modifications.put("TCP", "THR"); modifications.put("TCQ", "TYR"); modifications.put("TCR", "TRP"); modifications.put("TCY", "ALA"); modifications.put("TDD", "LEU"); modifications.put("TDY", "THR"); modifications.put("TFE", "THR"); modifications.put("TFO", "ALA"); modifications.put("TFQ", "PHE"); modifications.put("TFT", "THR"); modifications.put("TGP", "GLY"); modifications.put("TH6", "THR"); modifications.put("THC", "THR"); modifications.put("THO", "XAA"); modifications.put("THR", "THR"); modifications.put("THX", "ASN"); modifications.put("THZ", "ARG"); modifications.put("TIH", "ALA"); modifications.put("TLB", "ASN"); modifications.put("TLC", "THR"); modifications.put("TLN", "UR3"); modifications.put("TMB", "THR"); modifications.put("TMD", "THR"); modifications.put("TNB", "CYS"); modifications.put("TNR", "SER"); modifications.put("TOX", "TRP"); modifications.put("TP1", "THR"); modifications.put("TPC", "CYS"); modifications.put("TPG", "GLY"); modifications.put("TPH", "XAA"); modifications.put("TPL", "TRP"); modifications.put("TPO", "THR"); modifications.put("TPQ", "TYR"); modifications.put("TQI", "TRP"); modifications.put("TQQ", "TRP"); modifications.put("TRF", "TRP"); modifications.put("TRG", "LYS"); modifications.put("TRN", "TRP"); modifications.put("TRO", "TRP"); modifications.put("TRP", "TRP"); modifications.put("TRQ", "TRP"); modifications.put("TRW", "TRP"); modifications.put("TRX", "TRP"); modifications.put("TS ", "ASN"); modifications.put("TST", "XAA"); modifications.put("TT ", "ASN"); modifications.put("TTD", "THR"); modifications.put("TTI", "UR3"); modifications.put("TTM", "THR"); modifications.put("TTQ", "TRP"); modifications.put("TTS", "TYR"); modifications.put("TY1", "TYR"); modifications.put("TY2", "TYR"); modifications.put("TY3", "TYR"); modifications.put("TY5", "TYR"); modifications.put("TYB", "TYR"); modifications.put("TYI", "TYR"); modifications.put("TYJ", "TYR"); modifications.put("TYN", "TYR"); modifications.put("TYO", "TYR"); modifications.put("TYQ", "TYR"); modifications.put("TYR", "TYR"); modifications.put("TYS", "TYR"); modifications.put("TYT", "TYR"); modifications.put("TYU", "ASN"); modifications.put("TYW", "TYR"); modifications.put("TYX", "XAA"); modifications.put("TYY", "TYR"); modifications.put("TZB", "XAA"); modifications.put("TZO", "XAA"); modifications.put("U ", "UR3"); modifications.put("U25", "UR3"); modifications.put("U2L", "UR3"); modifications.put("U2N", "UR3"); modifications.put("U2P", "UR3"); modifications.put("U31", "UR3"); modifications.put("U33", "UR3"); modifications.put("U34", "UR3"); modifications.put("U36", "UR3"); modifications.put("U37", "UR3"); modifications.put("U8U", "UR3"); modifications.put("UAR", "UR3"); modifications.put("UCL", "UR3"); modifications.put("UD5", "UR3"); modifications.put("UDP", "ASN"); modifications.put("UFP", "ASN"); modifications.put("UFR", "UR3"); modifications.put("UFT", "UR3"); modifications.put("UMA", "ALA"); modifications.put("UMP", "UR3"); modifications.put("UMS", "UR3"); modifications.put("UN1", "XAA"); modifications.put("UN2", "XAA"); modifications.put("UNK", "XAA"); modifications.put("UR3", "UR3"); modifications.put("URD", "UR3"); modifications.put("US1", "UR3"); modifications.put("US2", "UR3"); modifications.put("US3", "THR"); modifications.put("US5", "UR3"); modifications.put("USM", "UR3"); modifications.put("VAD", "VAL"); modifications.put("VAF", "VAL"); modifications.put("VAL", "VAL"); modifications.put("VB1", "LYS"); modifications.put("VDL", "XAA"); modifications.put("VLL", "XAA"); modifications.put("VLM", "XAA"); modifications.put("VMS", "XAA"); modifications.put("VOL", "XAA"); modifications.put("WCR", "GYG"); modifications.put("X ", "GLY"); modifications.put("X2W", "GLU"); modifications.put("X4A", "ASN"); modifications.put("X9Q", "AFG"); modifications.put("XAD", "ALA"); modifications.put("XAE", "ASN"); modifications.put("XAL", "ALA"); modifications.put("XAR", "ASN"); modifications.put("XCL", "CYS"); modifications.put("XCN", "CYS"); modifications.put("XCP", "XAA"); modifications.put("XCR", "CYS"); modifications.put("XCS", "ASN"); modifications.put("XCT", "CYS"); modifications.put("XCY", "CYS"); modifications.put("XGA", "ASN"); modifications.put("XGL", "GLY"); modifications.put("XGR", "GLY"); modifications.put("XGU", "GLY"); modifications.put("XPR", "PRO"); modifications.put("XSN", "ASN"); modifications.put("XTH", "THR"); modifications.put("XTL", "THR"); modifications.put("XTR", "THR"); modifications.put("XTS", "GLY"); modifications.put("XTY", "ASN"); modifications.put("XUA", "ALA"); modifications.put("XUG", "GLY"); modifications.put("XX1", "LYS"); modifications.put("XXY", "THG"); modifications.put("XYG", "DYG"); modifications.put("Y ", "ALA"); modifications.put("YCM", "CYS"); modifications.put("YG ", "GLY"); modifications.put("YOF", "TYR"); modifications.put("YRR", "ASN"); modifications.put("YYG", "GLY"); modifications.put("Z ", "CYS"); modifications.put("Z01", "ALA"); modifications.put("ZAD", "ALA"); modifications.put("ZAL", "ALA"); modifications.put("ZBC", "CYS"); modifications.put("ZBU", "UR3"); modifications.put("ZCL", "PHE"); modifications.put("ZCY", "CYS"); modifications.put("ZDU", "UR3"); modifications.put("ZFB", "XAA"); modifications.put("ZGU", "GLY"); modifications.put("ZHP", "ASN"); modifications.put("ZTH", "THR"); modifications.put("ZU0", "THR"); modifications.put("ZZJ", "ALA"); } static { Map amino = new HashMap<>(); amino.put('A', 0.0826f); amino.put('Q', 0.0393f); amino.put('L', 0.0965f); amino.put('S', 0.0661f); amino.put('R', 0.0553f); amino.put('E', 0.0674f); amino.put('K', 0.0582f); amino.put('T', 0.0535f); amino.put('N', 0.0406f); amino.put('G', 0.0708f); amino.put('M', 0.0241f); amino.put('W', 0.0109f); amino.put('D', 0.0546f); amino.put('H', 0.0227f); amino.put('F', 0.0386f); amino.put('Y', 0.0292f); amino.put('C', 0.0137f); amino.put('I', 0.0593f); amino.put('P', 0.0472f); amino.put('V', 0.0686f); backgroundFrequencies.put("amino", amino); } // TODO get correct frequencies static { Map dna = new HashMap<>(); dna.put('A', 0.25f); dna.put('C', 0.25f); dna.put('T', 0.25f); dna.put('G', 0.25f); backgroundFrequencies.put("DNA", dna); } static { Map rna = new HashMap<>(); rna.put('A', 0.25f); rna.put('C', 0.25f); rna.put('T', 0.25f); rna.put('G', 0.25f); backgroundFrequencies.put("RNA", rna); } public static String getCanonicalAminoAcid(String aA) { String canonical = modifications.get(aA); return canonical == null ? aA : canonical; } // main method generates perl representation of residue property hash // / cut here public static void main(String[] args) { Hashtable> aaProps = new Hashtable<>(); System.out.println("my %aa = {"); // invert property hashes for (String pname : propHash.keySet()) { Map phash = propHash.get(pname); for (String rname : phash.keySet()) { Vector aprops = aaProps.get(rname); if (aprops == null) { aprops = new Vector<>(); aaProps.put(rname, aprops); } Integer hasprop = phash.get(rname); if (hasprop.intValue() == 1) { aprops.addElement(pname); } } } Enumeration res = aaProps.keys(); while (res.hasMoreElements()) { String rname = res.nextElement(); System.out.print("'" + rname + "' => ["); Enumeration props = aaProps.get(rname).elements(); while (props.hasMoreElements()) { System.out.print("'" + props.nextElement() + "'"); if (props.hasMoreElements()) { System.out.println(", "); } } System.out.println("]" + (res.hasMoreElements() ? "," : "")); } System.out.println("};"); } // to here /** * Returns a list of residue characters for the specified inputs * * @param forNucleotide * @param includeAmbiguous * @return */ public static List getResidues(boolean forNucleotide, boolean includeAmbiguous) { List result = new ArrayList<>(); if (forNucleotide) { for (String nuc : nucleotideName.keySet()) { int val = nucleotideIndex[nuc.charAt(0)]; if ((!includeAmbiguous && val > 4) || (val >= maxNucleotideIndex)) { continue; } nuc = nuc.toUpperCase(); if (!result.contains(nuc)) { result.add(nuc); } } } else { /* * Peptide */ for (String res : aa3Hash.keySet()) { int index = aa3Hash.get(res).intValue(); if ((!includeAmbiguous && index >= 20) || index >= maxProteinIndex) { continue; } res = res.toUpperCase(); if (!result.contains(res)) { result.add(res); } } } return result; } /** * Returns the single letter code for a three letter code, or '0' if not known * * @param threeLetterCode * not case sensitive * @return */ public static char getSingleCharacterCode(String threeLetterCode) { if (threeLetterCode == null) { return '0'; } Integer index = ResidueProperties.aa3Hash .get(threeLetterCode.toUpperCase()); return index == null ? '0' : aa[index].charAt(0); } }