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Yana Valasatava
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Serializable Jronn
1 parent ef3b83a commit 4c7dc72

4 files changed

Lines changed: 126 additions & 3 deletions

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‎biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/AminoAcidProperties.java‎

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package org.biojava.nbio.aaproperties;
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import java.util.Set;
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import java.util.stream.Collectors;
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import java.util.stream.Stream;
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/**
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* This class provides the protein properties at the level of individual amino acids.
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*
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* @author Yana Valasatava
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*/
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public class AminoAcidProperties {
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private static final Set<String> negChargedAAs = Stream.of("D", "E", "K", "R", "H").collect(Collectors.toSet());
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private static final Set<String> posChargedAAs = Stream.of("D", "E", "K", "R", "H").collect(Collectors.toSet());
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private static final Set<String> polarAAs = Stream.of("D", "E", "K", "R", "H", "N", "Q", "S", "T", "Y")
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.collect(Collectors.toSet());
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/**
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* At pH=7, two are negative charged: aspartic acid (Asp, D) and glutamic acid (Glu, E) (acidic side chains),
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* and three are positive charged: lysine (Lys, K), arginine (Arg, R) and histidine (His, H) (basic side chains).
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*
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* @param aa The one-letter amino acid code
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*
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* @return true if amino acid is charged
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*/
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public static final boolean isCharged(char aa) {
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if (negChargedAAs.contains(aa)) {
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return true;
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}
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else if (posChargedAAs.contains(aa)) {
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return true;
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}
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return false;
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}
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/**
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* 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),
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* and three are positive charged: lysine (Lys, K), arginine (Arg, R) and histidine (His, H) (basic side chains).
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*
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* @param aa The one-letter amino acid code
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*
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* @return the charge of amino acid (1 if positively charged, -1 if negatively charged, 0 if not charged)
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*/
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public static final int getChargeOfAminoAcid(char aa) {
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if (negChargedAAs.contains(aa)) {
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return -1;
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}
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else if (posChargedAAs.contains(aa)) {
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return 1;
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}
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return 0;
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}
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/**
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* Returns the array of charges of each amino acid in a protein. At pH=7, two are negative charged: aspartic acid (Asp, D) and glutamic acid (Glu, E) (acidic side chains),
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* and three are positive charged: lysine (Lys, K), arginine (Arg, R) and histidine (His, H) (basic side chains).
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*
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* @param aa The one-letter amino acid code
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*
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* @return the array of charges of amino acids in the protein (1 if amino acid is positively charged,
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* -1 if negatively charged, 0 if not charged)
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*/
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public static final int[] getChargesOfAminoAcidsInProtein(String protein) {
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int[] charges = new int[protein.length()];
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for ( int i=0; i < protein.length(); i++ ) {
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char aa = protein.toCharArray()[i];
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charges[i] = getChargeOfAminoAcid(aa);
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}
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return charges;
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}
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/**
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* There are 10 polar amino acids: D, E, H, K, R, N, Q, S, T, Y, that are polar.
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*
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* @param aa The one-letter amino acid code
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*
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* @return true if amino acid is polar
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*/
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public static final boolean isPolar(char aa) {
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if (polarAAs.contains(aa)) {
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return true;
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}
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return false;
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}
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/**
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* There are 10 polar amino acids: D, E, H, K, R, N, Q, S, T, Y, that are polar.
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*
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* @param aa The one-letter amino acid code
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*
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* @return the polarity of amino acid (1 if polar, 0 if not polar)
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*/
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public static final int getPolarityOfAminoAcid(char aa) {
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if (polarAAs.contains(aa)) {
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return 1;
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}
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return 0;
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}
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/**
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* Returns the array of polarity of each amino acid in a protein.
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*
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* @param aa The one-letter amino acid code
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*
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* @return the array of polarity of amino acids in the protein (1 if amino acid is polar, 0 if not)
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*/
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public static final int[] getPolarityOfAminoAcidsInProtein(String protein) {
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int[] polarity = new int[protein.length()];
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for ( int i=0; i < protein.length(); i++ ) {
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char aa = protein.toCharArray()[i];
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polarity[i] = getPolarityOfAminoAcid(aa);
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}
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return polarity;
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}
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}

‎biojava-protein-disorder/pom.xml‎

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<parent>
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<artifactId>biojava</artifactId>
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<groupId>org.biojava</groupId>
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<version>5.0.0-SNAPSHOT</version>
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<version>5.0.0-YV-SNAPSHOT</version>
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</parent>
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<artifactId>biojava-protein-disorder</artifactId>
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<packaging>jar</packaging>

‎biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/Jronn.java‎

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import java.io.FileInputStream;
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import java.io.FileNotFoundException;
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import java.io.IOException;
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import java.io.Serializable;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.Map;
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* @since 3.0.2
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*
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*/
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public class Jronn {
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public class Jronn implements Serializable {
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/**
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*
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*/
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private static final long serialVersionUID = 8104272449130849946L;
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// Load models
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private static final ModelLoader loader = new ModelLoader();
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static {

‎pom.xml‎

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<groupId>org.biojava</groupId>
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<artifactId>biojava</artifactId>
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<packaging>pom</packaging>
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<version>5.0.0-SNAPSHOT</version>
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<version>5.0.0-YV-SNAPSHOT</version>
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<name>biojava</name>
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<description>BioJava is an open-source project dedicated to providing a Java framework for processing biological
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data. It provides analytical and statistical routines, parsers for common file formats and allows the

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