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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 org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable;
import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
import org.biojava.nbio.core.sequence.ProteinSequence;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import javax.xml.bind.JAXBException;
import java.io.File;
import java.io.FileNotFoundException;
import java.util.Arrays;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
import java.util.Set;
import java.util.stream.Collectors;
import java.util.stream.Stream;
/**
* This is an adaptor class which enable the ease of generating protein properties.
* At least one adaptor method is written for each available properties provided in IPeptideProperties.
*
* @author kohchuanhock
* @version 2011.08.22
* @since 3.0.2
* @see IPeptideProperties
* @see PeptidePropertiesImpl
*/
public class PeptideProperties {
private final static Logger logger = LoggerFactory.getLogger(PeptideProperties.class);
/**
* Enumeration of 20 standard amino acid code
*/
public enum SingleLetterAACode { W, C, M, H, Y, F, Q, N, I, R, D, P, T, K, E, V, S, G, A, L}
/**
* Contains the 20 standard AA code in a set
*/
public static Set standardAASet;
/**
* To initialize the standardAASet
*/
static{
standardAASet = Arrays.stream(SingleLetterAACode.values())
.map(singleLetterAACode -> singleLetterAACode.toString().charAt(0))
.collect(Collectors.toCollection(HashSet::new));
}
/**
* An adaptor method to return the molecular weight of sequence.
* The sequence argument must be a protein sequence consisting of only non-ambiguous characters.
* This method will sum the molecular weight of each amino acid in the
* sequence. Molecular weights are based on here.
*
* @param sequence
* a protein sequence consisting of non-ambiguous characters only
* @return the total molecular weight of sequence + weight of water molecule
*/
public static final double getMolecularWeight(String sequence){
sequence = Utils.checkSequence(sequence);
ProteinSequence pSequence = null;
try {
pSequence = new ProteinSequence(sequence);
} catch (CompoundNotFoundException e) {
// the sequence was checked with Utils.checkSequence, this shouldn't happen
logger.error("The protein sequence contains invalid characters ({}), this should not happen. This is most likely a bug in Utils.checkSequence()", e.getMessage());
}
IPeptideProperties pp = new PeptidePropertiesImpl();
return pp.getMolecularWeight(pSequence);
}
/**
* An adaptor method to return the molecular weight of sequence.
* The sequence argument must be a protein sequence consisting of only non-ambiguous characters.
* This method will sum the molecular weight of each amino acid in the
* sequence. Molecular weights are based on the input xml file.
*
* @param sequence
* a protein sequence consisting of non-ambiguous characters only
* @param elementMassFile
* xml file that details the mass of each elements and isotopes
* @param aminoAcidCompositionFile
* xml file that details the composition of amino acids
* @return the total molecular weight of sequence + weight of water molecule
* @throws FileNotFoundException
* thrown if either elementMassFile or aminoAcidCompositionFile are not found
* @throws JAXBException
* thrown if unable to properly parse either elementMassFile or aminoAcidCompositionFile
*/
public static final double getMolecularWeight(String sequence, File elementMassFile, File aminoAcidCompositionFile)
throws FileNotFoundException, JAXBException{
sequence = Utils.checkSequence(sequence);
ProteinSequence pSequence = null;
try {
pSequence = new ProteinSequence(sequence);
} catch (CompoundNotFoundException e) {
// the sequence was checked with Utils.checkSequence, this shouldn't happen
logger.error("The protein sequence contains invalid characters ({}), this should not happen. This is most likely a bug in Utils.checkSequence()", e.getMessage());
}
IPeptideProperties pp = new PeptidePropertiesImpl();
return pp.getMolecularWeight(pSequence, elementMassFile, aminoAcidCompositionFile);
}
/**
* An adaptor method to return the molecular weight of sequence. The sequence argument must be a protein sequence consisting of only non-ambiguous characters.
* This method will sum the molecular weight of each amino acid in the
* sequence. Molecular weights are based on the input files. These input files must be XML using the defined schema.
* Note that it assumes that ElementMass.xml file can be found in default location.
*
* @param sequence
* a protein sequence consisting of non-ambiguous characters only
* xml file that details the mass of each elements and isotopes
* @param aminoAcidCompositionFile
* xml file that details the composition of amino acids
* @return the total molecular weight of sequence + weight of water molecule
* @throws JAXBException
* thrown if unable to properly parse either elementMassFile or aminoAcidCompositionFile
* @throws FileNotFoundException
* thrown if either elementMassFile or aminoAcidCompositionFile are not found
*/
public static final double getMolecularWeight(String sequence, File aminoAcidCompositionFile) throws FileNotFoundException, JAXBException{
sequence = Utils.checkSequence(sequence);
ProteinSequence pSequence = null;
try {
pSequence = new ProteinSequence(sequence);
} catch (CompoundNotFoundException e) {
// the sequence was checked with Utils.checkSequence, this shouldn't happen
logger.error("The protein sequence contains invalid characters ({}), this should not happen. This is most likely a bug in Utils.checkSequence()", e.getMessage());
}
IPeptideProperties pp = new PeptidePropertiesImpl();
return pp.getMolecularWeight(pSequence, aminoAcidCompositionFile);
}
/**
* An adaptor method would initialize amino acid composition table based on the input xml files and stores the table for usage in future calls to
* IPeptideProperties.getMolecularWeightBasedOnXML(ProteinSequence, AminoAcidCompositionTable).
* Note that ElementMass.xml is assumed to be able to be seen in default location.
*
* @param aminoAcidCompositionFile
* xml file that details the composition of amino acids
* @return the initialized amino acid composition table
* @throws JAXBException
* thrown if unable to properly parse either elementMassFile or aminoAcidCompositionFile
* @throws FileNotFoundException
* thrown if either elementMassFile or aminoAcidCompositionFile are not found
*/
public static final AminoAcidCompositionTable obtainAminoAcidCompositionTable(File aminoAcidCompositionFile)
throws JAXBException, FileNotFoundException{
IPeptideProperties pp = new PeptidePropertiesImpl();
return pp.obtainAminoAcidCompositionTable(aminoAcidCompositionFile);
}
/**
* An adaptor method would initialize amino acid composition table based on the input xml files and stores the table for usage in future calls to
* IPeptideProperties.getMolecularWeightBasedOnXML(ProteinSequence, AminoAcidCompositionTable).
*
* @param elementMassFile
* xml file that details the mass of each elements and isotopes
* @param aminoAcidCompositionFile
* xml file that details the composition of amino acids
* @return the initialized amino acid composition table
* @throws JAXBException
* thrown if unable to properly parse either elementMassFile or aminoAcidCompositionFile
* @throws FileNotFoundException
* thrown if either elementMassFile or aminoAcidCompositionFile are not found
*/
public static final AminoAcidCompositionTable obtainAminoAcidCompositionTable(File elementMassFile, File aminoAcidCompositionFile)
throws JAXBException, FileNotFoundException{
IPeptideProperties pp = new PeptidePropertiesImpl();
return pp.obtainAminoAcidCompositionTable(elementMassFile, aminoAcidCompositionFile);
}
/**
* An adaptor method that returns the molecular weight of sequence. The sequence argument must be a protein sequence consisting of only non-ambiguous characters.
* This method will sum the molecular weight of each amino acid in the
* sequence. Molecular weights are based on the AminoAcidCompositionTable.
* Those input files must be XML using the defined schema.
*
* @param sequence
* a protein sequence consisting of non-ambiguous characters only
* @param aminoAcidCompositionTable
* a amino acid composition table obtained by calling IPeptideProperties.obtainAminoAcidCompositionTable
* @return the total molecular weight of sequence + weight of water molecule
* thrown if the method IPeptideProperties.setMolecularWeightXML(File, File) is not successfully called before calling this method.
*/
public static double getMolecularWeightBasedOnXML(String sequence, AminoAcidCompositionTable aminoAcidCompositionTable){
sequence = Utils.checkSequence(sequence, aminoAcidCompositionTable.getSymbolSet());
ProteinSequence pSequence = null;
try {
pSequence = new ProteinSequence(sequence, aminoAcidCompositionTable.getAminoAcidCompoundSet());
} catch (CompoundNotFoundException e) {
// the sequence was checked with Utils.checkSequence, this shouldn't happen
logger.error("The protein sequence contains invalid characters ({}), this should not happen. This is most likely a bug in Utils.checkSequence()", e.getMessage());
}
IPeptideProperties pp = new PeptidePropertiesImpl();
return pp.getMolecularWeightBasedOnXML(pSequence, aminoAcidCompositionTable);
}
/**
* An adaptor method to returns the absorbance (optical density) of sequence. The sequence argument
* must be a protein sequence consisting of only non-ambiguous characters.
* The computation of absorbance (optical density) follows the
* documentation in here.
*
* @param sequence
* a protein sequence consisting of non-ambiguous characters only
* @param assumeCysReduced
* true if Cys are assumed to be reduced and false if Cys are assumed to form cystines
* @return the absorbance (optical density) of sequence
*/
public static final double getAbsorbance(String sequence, boolean assumeCysReduced){
sequence = Utils.checkSequence(sequence);
ProteinSequence pSequence = null;
try {
pSequence = new ProteinSequence(sequence);
} catch (CompoundNotFoundException e) {
// the sequence was checked with Utils.checkSequence, this shouldn't happen
logger.error("The protein sequence contains invalid characters ({}), this should not happen. This is most likely a bug in Utils.checkSequence()", e.getMessage());
}
IPeptideProperties pp = new PeptidePropertiesImpl();
return pp.getAbsorbance(pSequence, assumeCysReduced);
}
/**
* An adaptor method to return the extinction coefficient of sequence. The sequence argument
* must be a protein sequence consisting of only non-ambiguous characters.
* The extinction coefficient indicates how much light a protein absorbs at
* a certain wavelength. It is useful to have an estimation of this
* coefficient for following a protein which a spectrophotometer when
* purifying it. The computation of extinction coefficient follows the
* documentation in here.
*
* @param sequence
* a protein sequence consisting of non-ambiguous characters only
* @param assumeCysReduced
* true if Cys are assumed to be reduced and false if Cys are
* assumed to form cystines
* @return the extinction coefficient of sequence
*/
public static final double getExtinctionCoefficient(String sequence, boolean assumeCysReduced) {
sequence = Utils.checkSequence(sequence);
ProteinSequence pSequence = null;
try {
pSequence = new ProteinSequence(sequence);
} catch (CompoundNotFoundException e) {
// the sequence was checked with Utils.checkSequence, this shouldn't happen
logger.error("The protein sequence contains invalid characters ({}), this should not happen. This is most likely a bug in Utils.checkSequence()", e.getMessage());
}
IPeptideProperties pp = new PeptidePropertiesImpl();
return pp.getExtinctionCoefficient(pSequence, assumeCysReduced);
}
/**
* An adaptor method to return the instability index of sequence. The sequence argument must be
* a protein sequence consisting of only non-ambiguous characters.
* The instability index provides an estimate of the stability of your
* protein in a test tube. The computation of instability index follows the
* documentation in here.
*
* @param sequence
* a protein sequence consisting of non-ambiguous characters only
* @return the instability index of sequence
*/
public static final double getInstabilityIndex(String sequence) {
sequence = Utils.checkSequence(sequence);
ProteinSequence pSequence = null;
try {
pSequence = new ProteinSequence(sequence);
} catch (CompoundNotFoundException e) {
// the sequence was checked with Utils.checkSequence, this shouldn't happen
logger.error("The protein sequence contains invalid characters ({}), this should not happen. This is most likely a bug in Utils.checkSequence()", e.getMessage());
}
IPeptideProperties pp = new PeptidePropertiesImpl();
return pp.getInstabilityIndex(pSequence);
}
/**
* An adaptor method to return the apliphatic index of sequence. The sequence argument must be a
* protein sequence consisting of only non-ambiguous characters.
* The aliphatic index of a protein is defined as the relative volume
* occupied by aliphatic side chains (alanine, valine, isoleucine, and
* leucine). It may be regarded as a positive factor for the increase of
* thermostability of globular proteins. The computation of aliphatic index
* follows the documentation in here.
* A protein whose instability index is smaller than 40 is predicted as stable, a value above 40 predicts that the protein may be unstable.
*
* @param sequence
* a protein sequence consisting of non-ambiguous characters only
* @return the aliphatic index of sequence
*/
public static final double getApliphaticIndex(String sequence) {
sequence = Utils.checkSequence(sequence);
ProteinSequence pSequence = null;
try {
pSequence = new ProteinSequence(sequence);
} catch (CompoundNotFoundException e) {
// the sequence was checked with Utils.checkSequence, this shouldn't happen
logger.error("The protein sequence contains invalid characters ({}), this should not happen. This is most likely a bug in Utils.checkSequence()", e.getMessage());
}
IPeptideProperties pp = new PeptidePropertiesImpl();
return pp.getApliphaticIndex(pSequence);
}
/**
* An adaptor method to return the average hydropathy value of sequence. The sequence argument
* must be a protein sequence consisting of only non-ambiguous characters.
* The average value for a sequence is calculated as the sum of hydropathy
* values of all the amino acids, divided by the number of residues in the
* sequence. Hydropathy values are based on (Kyte, J. and Doolittle, R.F.
* (1982) A simple method for displaying the hydropathic character of a
* protein. J. Mol. Biol. 157, 105-132).
*
* @param sequence
* a protein sequence consisting of non-ambiguous characters only
* @return the average hydropathy value of sequence
*/
public static final double getAvgHydropathy(String sequence) {
sequence = Utils.checkSequence(sequence);
ProteinSequence pSequence = null;
try {
pSequence = new ProteinSequence(sequence);
} catch (CompoundNotFoundException e) {
// the sequence was checked with Utils.checkSequence, this shouldn't happen
logger.error("The protein sequence contains invalid characters ({}), this should not happen. This is most likely a bug in Utils.checkSequence()", e.getMessage());
}
IPeptideProperties pp = new PeptidePropertiesImpl();
return pp.getAvgHydropathy(pSequence);
}
/**
* An adaptor method to return the isoelectric point of sequence. The sequence argument must be
* a protein sequence consisting of only non-ambiguous characters.
* The isoelectric point is the pH at which the protein carries no net
* electrical charge. The isoelectric point will be computed based on
* approach stated in
* here
*
* pKa values used will be either
* those used by Expasy which referenced "Electrophoresis 1994, 15, 529-539"
* OR
* A.Lehninger, Principles of Biochemistry, 4th Edition (2005), Chapter 3, page78, Table 3-1.
*
* @param sequence
* a protein sequence consisting of non-ambiguous characters only
* @param useExpasyValues
* whether to use Expasy values (Default) or Innovagen values
* @return the isoelectric point of sequence
*/
public static final double getIsoelectricPoint(String sequence, boolean useExpasyValues) {
sequence = Utils.checkSequence(sequence);
ProteinSequence pSequence = null;
try {
pSequence = new ProteinSequence(sequence);
} catch (CompoundNotFoundException e) {
// the sequence was checked with Utils.checkSequence, this shouldn't happen
logger.error("The protein sequence contains invalid characters ({}), this should not happen. This is most likely a bug in Utils.checkSequence()", e.getMessage());
}
IPeptideProperties pp = new PeptidePropertiesImpl();
return pp.getIsoelectricPoint(pSequence, useExpasyValues);
}
public static final double getIsoelectricPoint(String sequence){
return getIsoelectricPoint(sequence, true);
}
/**
* An adaptor method to return the net charge of sequence at pH 7. The sequence argument must be
* a protein sequence consisting of only non-ambiguous characters.
* The net charge will be computed using the approach stated in
* here
*
* pKa values used will be either
* those used by Expasy which referenced "Electrophoresis 1994, 15, 529-539"
* OR
* A.Lehninger, Principles of Biochemistry, 4th Edition (2005), Chapter 3, page78, Table 3-1.
*
* @param sequence
* a protein sequence consisting of non-ambiguous characters only
* @param useExpasyValues
* whether to use Expasy values (Default) or Innovagen values
* @param pHPoint
* the pH value to use for computation of the net charge. Default at 7.
* @return the net charge of sequence at given pHPoint
*/
public static final double getNetCharge(String sequence, boolean useExpasyValues, double pHPoint){
sequence = Utils.checkSequence(sequence);
ProteinSequence pSequence = null;
try {
pSequence = new ProteinSequence(sequence);
} catch (CompoundNotFoundException e) {
// the sequence was checked with Utils.checkSequence, this shouldn't happen
logger.error("The protein sequence contains invalid characters ({}), this should not happen. This is most likely a bug in Utils.checkSequence()", e.getMessage());
}
IPeptideProperties pp = new PeptidePropertiesImpl();
return pp.getNetCharge(pSequence, useExpasyValues, pHPoint);
}
public static final double getNetCharge(String sequence, boolean useExpasyValues) {
return getNetCharge(sequence, useExpasyValues, 7.0);
}
public static final double getNetCharge(String sequence){
return getNetCharge(sequence, true);
}
/**
* An adaptor method to return the composition of specified amino acid in the sequence. The
* sequence argument must be a protein sequence consisting of only
* non-ambiguous characters. The aminoAcidCode must be a non-ambiguous
* character.
* The composition of an amino acid is the total number of its occurrence,
* divided by the total length of the sequence.
*
* @param sequence
* a protein sequence consisting of non-ambiguous characters only
* @param aminoAcidCode
* the code of the amino acid to compute
* @return the composition of specified amino acid in the sequence
* @see SingleLetterAACode
*/
public static final double getEnrichment(String sequence, SingleLetterAACode aminoAcidCode) {
return getEnrichment(sequence, aminoAcidCode.toString());
}
/**
* An adaptor method to return the composition of specified amino acid in the sequence. The
* sequence argument must be a protein sequence consisting of only
* non-ambiguous characters. The aminoAcidCode must be a non-ambiguous
* character.
* The composition of an amino acid is the total number of its occurrence,
* divided by the total length of the sequence.
*
* @param sequence
* a protein sequence consisting of non-ambiguous characters only
* @param aminoAcidCode
* the code of the amino acid to compute
* @return the composition of specified amino acid in the sequence
*/
public static final double getEnrichment(String sequence, char aminoAcidCode){
return getEnrichment(sequence, aminoAcidCode);
}
/**
* An adaptor method to return the composition of specified amino acid in the sequence. The
* sequence argument must be a protein sequence consisting of only
* non-ambiguous characters. The aminoAcidCode must be a non-ambiguous
* character.
* The composition of an amino acid is the total number of its occurrence,
* divided by the total length of the sequence.
*
* @param sequence
* a protein sequence consisting of non-ambiguous characters only
* @param aminoAcidCode
* the code of the amino acid to compute
* @return the composition of specified amino acid in the sequence
*/
public static final double getEnrichment(String sequence, String aminoAcidCode){
sequence = Utils.checkSequence(sequence);
ProteinSequence pSequence = null;
try {
pSequence = new ProteinSequence(sequence);
} catch (CompoundNotFoundException e) {
// the sequence was checked with Utils.checkSequence, this shouldn't happen
logger.error("The protein sequence contains invalid characters ({}), this should not happen. This is most likely a bug in Utils.checkSequence()", e.getMessage());
}
IPeptideProperties pp = new PeptidePropertiesImpl();
AminoAcidCompoundSet aaSet = new AminoAcidCompoundSet();
return pp.getEnrichment(pSequence, aaSet.getCompoundForString(aminoAcidCode));
}
/**
* An adaptor method to return the composition of the 20 standard amino acid in the sequence.
* The sequence argument must be a protein sequence consisting of only
* non-ambiguous characters.
* The composition of an amino acid is the total number of its occurrence,
* divided by the total length of the sequence.
*
* @param sequence
* a protein sequence consisting of non-ambiguous characters only
* @return the composition of the 20 standard amino acid in the sequence
* @see AminoAcidCompound
*/
public static final Map getAAComposition(String sequence) {
sequence = Utils.checkSequence(sequence);
ProteinSequence pSequence = null;
try {
pSequence = new ProteinSequence(sequence);
} catch (CompoundNotFoundException e) {
// the sequence was checked with Utils.checkSequence, this shouldn't happen
logger.error("The protein sequence contains invalid characters ({}), this should not happen. This is most likely a bug in Utils.checkSequence()", e.getMessage());
}
IPeptideProperties pp = new PeptidePropertiesImpl();
return pp.getAAComposition(pSequence);
}
/**
* An adaptor method to return the composition of the 20 standard amino acid in the sequence.
* The sequence argument must be a protein sequence consisting of only
* non-ambiguous characters.
* The composition of an amino acid is the total number of its occurrence,
* divided by the total length of the sequence.
*
* @param sequence
* a protein sequence consisting of non-ambiguous characters only
* @return the composition of the 20 standard amino acid in the sequence
*/
public static final Map getAACompositionString(String sequence){
Map aa2Composition = getAAComposition(sequence);
Map aaString2Composition = new HashMap();
aaString2Composition = aa2Composition.keySet().stream() .collect(Collectors.toMap(aaCompound -> aaCompound.getShortName(),aaCompound ->aa2Composition.get(aaCompound)));
return aaString2Composition;
}
/**
* An adaptor method to return the composition of the 20 standard amino acid in the sequence.
* The sequence argument must be a protein sequence consisting of only
* non-ambiguous characters.
* The composition of an amino acid is the total number of its occurrence,
* divided by the total length of the sequence.
*
* @param sequence
* a protein sequence consisting of non-ambiguous characters only
* @return the composition of the 20 standard amino acid in the sequence
*/
public static final Map getAACompositionChar(String sequence){
Map aa2Composition = getAAComposition(sequence);
Map aaChar2Composition = new HashMap();
for(AminoAcidCompound aaCompound:aa2Composition.keySet()){
aaChar2Composition.put(aaCompound.getShortName().charAt(0), aa2Composition.get(aaCompound));
}
return aaChar2Composition;
}
/**
* 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),
* and three are positive charged: lysine (Lys, K), arginine (Arg, R) and histidine (His, H) (basic side chains).
*
* @param sequence
* a protein sequence consisting of non-ambiguous characters only
* @return the array of charges of amino acids in the protein (1 if amino acid is positively charged, -1 if negatively charged, 0 if not charged)
*/
public static final int[] getChargesOfAminoAcids(String sequence) {
int[] charges = new int[sequence.length()];
for ( int i=0; i < sequence.length(); i++ ) {
char aa = sequence.toCharArray()[i];
charges[i] = AminoAcidProperties.getChargeOfAminoAcid(aa);
}
return charges;
}
/**
* Returns the array of polarity values of each amino acid in a protein sequence.
*
* @param sequence
* a protein sequence consisting of non-ambiguous characters only
* @return the array of polarity of amino acids in the protein (1 if amino acid is polar, 0 if not)
*/
public static final int[] getPolarityOfAminoAcids(String sequence) {
int[] polarity = new int[sequence.length()];
for ( int i=0; i < sequence.length(); i++ ) {
char aa = sequence.toCharArray()[i];
polarity[i] = AminoAcidProperties.getPolarityOfAminoAcid(aa);
}
return polarity;
}
}
