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/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package org.biojava.nbio.aaproperties;
import java.util.Set;
import java.util.stream.Collectors;
import java.util.stream.Stream;
/**
* This class provides the protein properties at the level of individual amino acids.
*
* @author Yana Valasatava
*/
public class AminoAcidProperties {
private static final Set negChargedAAs = Stream.of("D", "E").collect(Collectors.toSet());
private static final Set posChargedAAs = Stream.of("K", "R", "H").collect(Collectors.toSet());
private static final Set polarAAs = Stream.of("D", "E", "K", "R", "H", "N", "Q", "S", "T", "Y")
.collect(Collectors.toSet());
/**
* At pH=7, two are negative charged: aspartic acid (Asp, D) and glutamic acid (Glu, E) (acidic side chains),
* and three are positive charged: lysine (Lys, K), arginine (Arg, R) and histidine (His, H) (basic side chains).
*
* @param aa The one-letter amino acid code
* @return true if amino acid is charged
*/
public static final boolean isCharged(char aa) {
if (negChargedAAs.contains(String.valueOf(aa))) {
return true;
}
else if (posChargedAAs.contains(String.valueOf(aa))) {
return true;
}
return false;
}
/**
* 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),
* and three are positive charged: lysine (Lys, K), arginine (Arg, R) and histidine (His, H) (basic side chains).
*
* @param aa The one-letter amino acid code
* @return the charge of amino acid (1 if positively charged, -1 if negatively charged, 0 if not charged)
*/
public static final int getChargeOfAminoAcid(char aa) {
if (negChargedAAs.contains(String.valueOf(aa))) {
return -1;
}
else if (posChargedAAs.contains(String.valueOf(aa))) {
return 1;
}
return 0;
}
/**
* There are 10 amino acids: D, E, H, K, R, N, Q, S, T, Y, that are polar.
*
* @param aa The one-letter amino acid code
* @return true if amino acid is polar
*/
public static final boolean isPolar(char aa) {
if (polarAAs.contains(String.valueOf(aa))) {
return true;
}
return false;
}
/**
* There are 10 amino acids: D, E, H, K, R, N, Q, S, T, Y, that are polar.
*
* @param aa The one-letter amino acid code
* @return the polarity of amino acid (1 if polar, 0 if not polar)
*/
public static final int getPolarityOfAminoAcid(char aa) {
if (polarAAs.contains(String.valueOf(aa))) {
return 1;
}
return 0;
}
}
