/*
* 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/
*
* Created on 2011.05.09 by kohchuanhock
*
*/
package org.biojava.nbio.aaproperties;
import org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable;
import org.biojava.nbio.core.sequence.ProteinSequence;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
import javax.xml.bind.JAXBException;
import java.io.File;
import java.io.FileNotFoundException;
import java.util.Map;
/**
* An interface to generate some basic physico-chemical properties of protein sequences.<br/>
* The following properties could be generated:
* <p/>
* Molecular weight<br/>
* Absorbance<br/>
* Extinction coefficient<br/>
* Instability index<br/>
* Apliphatic index<br/>
* Average hydropathy value<br/>
* Isoelectric point<br/>
* Net charge at pH 7<br/>
* Composition of specified amino acid<br/>
* Composition of the 20 standard amino acid<br/>
* @author kohchuanhock
* @version 2011.05.09
* @see PeptideProperties
*/
public interface IPeptideProperties{
/**
* 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 <a href="http://web.expasy.org/findmod/findmod_masses.html">here</a>.
*
* @param sequence
* a protein sequence consisting of non-ambiguous characters only
* @return the total molecular weight of sequence + weight of water molecule
* @see ProteinSequence
*/
public double getMolecularWeight(ProteinSequence sequence);
/**
* 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 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 double getMolecularWeight(ProteinSequence sequence, File aminoAcidCompositionFile) throws JAXBException, FileNotFoundException;
/**
* 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 input files. These input files must be XML using the defined schema.
*
* @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 JAXBException
* thrown if unable to properly parse either elementMassFile or aminoAcidCompositionFile
* @throws FileNotFoundException
* thrown if either elementMassFile or aminoAcidCompositionFile are not found
*/
public double getMolecularWeight(ProteinSequence sequence, File elementMassFile, File aminoAcidCompositionFile)
throws JAXBException, FileNotFoundException;
/**
* 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
*/
public double getMolecularWeightBasedOnXML(ProteinSequence sequence, AminoAcidCompositionTable aminoAcidCompositionTable);
/**
* This 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 AminoAcidCompositionTable obtainAminoAcidCompositionTable(File aminoAcidCompositionFile)
throws JAXBException, FileNotFoundException;
/**
* This 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 AminoAcidCompositionTable obtainAminoAcidCompositionTable(File elementMassFile, File aminoAcidCompositionFile)
throws JAXBException, FileNotFoundException;
/**
* Returns 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 <a href="http://web.expasy.org/protparam/protparam-doc.html">here</a>.
*
* @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
* @see ProteinSequence
*/
public double getExtinctionCoefficient(ProteinSequence sequence, boolean assumeCysReduced);
/**
* 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 <a href="http://web.expasy.org/protparam/protparam-doc.html">here</a>.
*
* @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
* @see ProteinSequence
*/
public double getAbsorbance(ProteinSequence sequence, boolean assumeCysReduced);
/**
* Returns 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 <a href="http://web.expasy.org/protparam/protparam-doc.html">here</a>.
*
* @param sequence
* a protein sequence consisting of non-ambiguous characters only
* @return the instability index of sequence
* @see ProteinSequence
*/
public double getInstabilityIndex(ProteinSequence sequence);
/**
* Returns 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 <a href="http://web.expasy.org/protparam/protparam-doc.html">here</a>.
* 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
* @see ProteinSequence
*/
public double getApliphaticIndex(ProteinSequence sequence);
/**
* Returns 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
* @see ProteinSequence
*/
public double getAvgHydropathy(ProteinSequence sequence);
/**
* Returns 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
* <a href="http://www.innovagen.se/custom-peptide-synthesis/peptide-property-calculator/peptide-property-calculator-notes.asp#PI">here</a>
*
* 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
* @see ProteinSequence
*/
public double getIsoelectricPoint(ProteinSequence sequence, boolean useExpasyValues);
public double getIsoelectricPoint(ProteinSequence seuqence);
/**
* Returns 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
* <a href="http://www.innovagen.se/custom-peptide-synthesis/peptide-property-calculator/peptide-property-calculator-notes.asp#NetCharge>here</a>
*
* 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
* @see ProteinSequence
*/
public double getNetCharge(ProteinSequence sequence, boolean useExpasyValues, double pHPoint);
public double getNetCharge(ProteinSequence sequence, boolean useExpasyValues);
public double getNetCharge(ProteinSequence sequence);
/**
* Returns 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 ProteinSequence
* @see AminoAcidCompound
*/
public double getEnrichment(ProteinSequence sequence, AminoAcidCompound aminoAcidCode);
/**
* Returns 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 ProteinSequence
* @see AminoAcidCompound
*/
public Map<AminoAcidCompound, Double> getAAComposition(ProteinSequence sequence);
}