001/*
002 *                    BioJava development code
003 *
004 * This code may be freely distributed and modified under the
005 * terms of the GNU Lesser General Public Licence.  This should
006 * be distributed with the code.  If you do not have a copy,
007 * see:
008 *
009 *      http://www.gnu.org/copyleft/lesser.html
010 *
011 * Copyright for this code is held jointly by the individual
012 * authors.  These should be listed in @author doc comments.
013 *
014 * For more information on the BioJava project and its aims,
015 * or to join the biojava-l mailing list, visit the home page
016 * at:
017 *
018 *      http://www.biojava.org/
019 *
020 */
021package org.biojava.nbio.aaproperties;
022
023import java.util.Set;
024import java.util.stream.Collectors;
025import java.util.stream.Stream;
026
027/**
028 * This class provides the protein properties at the level of individual amino acids.
029 *
030 * @author Yana Valasatava
031 */
032public class AminoAcidProperties {
033
034        private static final Set<String> negChargedAAs = Stream.of("D", "E").collect(Collectors.toSet());
035        private static final Set<String> posChargedAAs = Stream.of("K", "R", "H").collect(Collectors.toSet());
036        private static final Set<String> polarAAs = Stream.of("D", "E", "K", "R", "H", "N", "Q", "S", "T", "Y")
037                        .collect(Collectors.toSet());
038
039        /**
040         * At pH=7, two are negative charged: aspartic acid (Asp, D) and glutamic acid (Glu, E) (acidic side chains),
041         * and three are positive charged: lysine (Lys, K), arginine (Arg, R) and histidine (His, H) (basic side chains).
042         *
043         * @param aa The one-letter amino acid code
044         * @return true if amino acid is charged
045         */
046        public static final boolean isCharged(char aa) {
047                if (negChargedAAs.contains(String.valueOf(aa))) {
048                        return true;
049                }
050                else if (posChargedAAs.contains(String.valueOf(aa))) {
051                        return true;
052                }
053                return false;
054        }
055
056        /**
057         * Returns the charge of amino acid. At pH=7, two are negative charged: aspartic acid (Asp, D) and glutamic acid (Glu, E) (acidic side chains),
058         * and three are positive charged: lysine (Lys, K), arginine (Arg, R) and histidine (His, H) (basic side chains).
059         *
060         * @param aa The one-letter amino acid code
061         * @return the charge of amino acid (1 if positively charged, -1 if negatively charged, 0 if not charged)
062         */
063        public static final int getChargeOfAminoAcid(char aa) {
064                if (negChargedAAs.contains(String.valueOf(aa))) {
065                        return -1;
066                }
067                else if (posChargedAAs.contains(String.valueOf(aa))) {
068                        return 1;
069                }
070                return 0;
071        }
072
073        /**
074         * There are 10 amino acids: D, E, H, K, R, N, Q, S, T, Y, that are polar.
075         *
076         * @param aa The one-letter amino acid code
077         * @return true if amino acid is polar
078         */
079        public static final boolean isPolar(char aa) {
080                if (polarAAs.contains(String.valueOf(aa))) {
081                        return true;
082                }
083                return false;
084        }
085
086        /**
087         * There are 10 amino acids: D, E, H, K, R, N, Q, S, T, Y, that are polar.
088         *
089         * @param aa The one-letter amino acid code
090         * @return the polarity of amino acid (1 if polar, 0 if not polar)
091         */
092        public static final int getPolarityOfAminoAcid(char aa) {
093                if (polarAAs.contains(String.valueOf(aa))) {
094                        return 1;
095                }
096                return 0;
097        }
098}