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org.biojava.nbio.aaproperties.Constraints Maven / Gradle / Ivy
/*
* 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.PeptideProperties.SingleLetterAACode;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
import java.util.HashMap;
import java.util.Map;
/**
* This class is used to support the implementation of properties stated in IPeptideProperties.
* It initializes several values that would be needed for the computation of properties such as
*
* Molecular weight aa2ExtinctionCoefficient = new HashMap();
public static Map aa2MolecularWeight = new HashMap();
public static Map aa2Hydrophathicity = new HashMap();
public static Map aa2PKa = new HashMap();
public static Map diAA2Instability = new HashMap();
public static Map aa2NTerminalPka = new HashMap();
public static Map aa2CTerminalPka = new HashMap();
static{
initMolecularWeight();
initHydropathicity();
initPKa();
initInstability();
initExtinctionCoefficient();
}
/**
* Does the initialization of molecular weights based on http://au.expasy.org/tools/findmod/findmod_masses.html#AA
*/
public static void initMolecularWeight(){
// Alanine (A) 71.03711 71.0788
aa2MolecularWeight.put(A, 71.0788);
// Arginine (R) 156.10111 156.1875
aa2MolecularWeight.put(R, 156.1875);
// Asparagine (N) 114.04293 114.1038
aa2MolecularWeight.put(N, 114.1038);
// Aspartic acid (D) 115.02694 115.0886
aa2MolecularWeight.put(D, 115.0886);
// Cysteine (C) 103.00919 103.1388
aa2MolecularWeight.put(C, 103.1388);
// Glutamic acid (E) 129.04259 129.1155
aa2MolecularWeight.put(E, 129.1155);
// Glutamine (Q) 128.05858 128.1307
aa2MolecularWeight.put(Q, 128.1307);
// Glycine (G) 57.02146 57.0519
aa2MolecularWeight.put(G, 57.0519);
// Histidine (H) 137.05891 137.1411
aa2MolecularWeight.put(H, 137.1411);
// Isoleucine (I) 113.08406 113.1594
aa2MolecularWeight.put(I, 113.1594);
// Leucine (L) 113.08406 113.1594
aa2MolecularWeight.put(L, 113.1594);
// Lysine (K) 128.09496 128.1741
aa2MolecularWeight.put(K, 128.1741);
// Methionine (M) 131.04049 131.1926
aa2MolecularWeight.put(M, 131.1926);
// Phenylalanine (F) 147.06841 147.1766
aa2MolecularWeight.put(F, 147.1766);
// Proline (P) 97.05276 97.1167
aa2MolecularWeight.put(P, 97.1167);
// Serine (S) 87.03203 87.0782
aa2MolecularWeight.put(S, 87.0782);
// Threonine (T) 101.04768 101.1051
aa2MolecularWeight.put(T, 101.1051);
// Tryptophan (W) 186.07931 186.2132
aa2MolecularWeight.put(W, 186.2132);
// Tyrosine (Y) 163.06333 163.1760
aa2MolecularWeight.put(Y, 163.1760);
// Valine (V) 99.06841 99.1326
aa2MolecularWeight.put(V, 99.1326);
}
/**
* Does the initialization of hydropathicity based on http://web.expasy.org/protscale/pscale/Hphob.Doolittle.html
*/
private static void initHydropathicity(){
// Ala(A): 1.800
aa2Hydrophathicity.put(A, 1.800);
// Arg(R): -4.500
aa2Hydrophathicity.put(R, -4.500);
// Asn(N): -3.500
aa2Hydrophathicity.put(N, -3.500);
// Asp(D): -3.500
aa2Hydrophathicity.put(D, -3.500);
// Cys(C): 2.500
aa2Hydrophathicity.put(C, 2.500);
// Gln(E): -3.500
aa2Hydrophathicity.put(E, -3.500);
// Glu(Q): -3.500
aa2Hydrophathicity.put(Q, -3.500);
// Gly(G): -0.400
aa2Hydrophathicity.put(G, -0.400);
// His(H): -3.200
aa2Hydrophathicity.put(H, -3.200);
// Ile(I): 4.500
aa2Hydrophathicity.put(I, 4.500);
// Leu(L): 3.800
aa2Hydrophathicity.put(L, 3.800);
// Lys(K): -3.900
aa2Hydrophathicity.put(K, -3.900);
// Met(M): 1.900
aa2Hydrophathicity.put(M, 1.900);
// Phe(F): 2.800
aa2Hydrophathicity.put(F, 2.800);
// Pro(P): -1.600
aa2Hydrophathicity.put(P, -1.600);
// Ser(S): -0.800
aa2Hydrophathicity.put(S, -0.800);
// Thr(T): -0.700
aa2Hydrophathicity.put(T, -0.700);
// Trp(W): -0.900
aa2Hydrophathicity.put(W, -0.900);
// Tyr(Y): -1.300
aa2Hydrophathicity.put(Y, -1.300);
// Val(V): 4.200
aa2Hydrophathicity.put(V, 4.200);
}
/**
* Does the initialization of PKa based on
* http://www.innovagen.se/custom-peptide-synthesis/peptide-property-calculator/peptide-property-calculator-notes.asp#NetCharge
*/
private static void initPKaInnovagen(){
/*
* A.Lehninger, Principles of Biochemistry, 4th Edition (2005), Chapter 3, page78, Table 3-1.
*/
//(NH2-) 9.69 (-COOH) 2.34
aa2CTerminalPka.put(G, 2.34);
aa2CTerminalPka.put(A, 2.34);
aa2CTerminalPka.put(P, 1.99);
aa2CTerminalPka.put(V, 2.32);
aa2CTerminalPka.put(L, 2.36);
aa2CTerminalPka.put(I, 2.36);
aa2CTerminalPka.put(M, 2.28);
aa2CTerminalPka.put(F, 1.83);
aa2CTerminalPka.put(Y, 2.20);
aa2CTerminalPka.put(W, 2.38);
aa2CTerminalPka.put(S, 2.21);
aa2CTerminalPka.put(T, 2.11);
aa2CTerminalPka.put(C, 1.96);
aa2CTerminalPka.put(N, 2.02);
aa2CTerminalPka.put(Q, 2.17);
aa2CTerminalPka.put(K, 2.18);
aa2CTerminalPka.put(H, 1.82);
aa2CTerminalPka.put(R, 2.17);
aa2CTerminalPka.put(D, 1.88);
aa2CTerminalPka.put(E, 2.19);
aa2NTerminalPka.put(G, 9.60);
aa2NTerminalPka.put(A, 9.69);
aa2NTerminalPka.put(P, 10.96);
aa2NTerminalPka.put(V, 9.62);
aa2NTerminalPka.put(L, 9.60);
aa2NTerminalPka.put(I, 9.68);
aa2NTerminalPka.put(M, 9.21);
aa2NTerminalPka.put(F, 9.13);
aa2NTerminalPka.put(Y, 9.11);
aa2NTerminalPka.put(W, 9.39);
aa2NTerminalPka.put(S, 9.15);
aa2NTerminalPka.put(T, 9.62);
aa2NTerminalPka.put(C, 10.28);
aa2NTerminalPka.put(N, 8.80);
aa2NTerminalPka.put(Q, 9.13);
aa2NTerminalPka.put(K, 8.95);
aa2NTerminalPka.put(H, 9.17);
aa2NTerminalPka.put(R, 9.04);
aa2NTerminalPka.put(D, 9.60);
aa2NTerminalPka.put(E, 9.67);
// K, Lys 10.53
aa2PKa.put(K, 10.53);
// D, Asp 3.65
aa2PKa.put(D, 3.65);
// R, Arg 12.48
aa2PKa.put(R, 12.48);
// E, Glu 4.25
aa2PKa.put(E, 4.25);
// H, His 6.00
aa2PKa.put(H, 6.00);
// C, Cys 8.18
aa2PKa.put(C, 8.18);
// Y, Tyr 10.07
aa2PKa.put(Y, 10.07);
}
private static void initPKa(){
initPKaInnovagen();
}
/**
* Does the initialization of dipeptide instability index based on the following paper
*
* Guruprasad, K., Reddy, B.V.B. and Pandit, M.W. (1990)
* Correlation between stability of a protein and its dipeptide composition: a novel approach for predicting in vivo stability of a protein from its primary sequence.
* Protein Eng. 4,155-161. Table III.
*/
private static void initInstability(){
double[][] instability = {
//W C M H Y F Q N I R D P T K E V S G A L
{1.0, 1.0, 24.68, 24.68, 1.0, 1.0, 1.0, 13.34, 1.0, 1.0, 1.0, 1.0, -14.03, 1.0, 1.0, -7.49, 1.0, -9.37, -14.03, 13.34},
{24.68, 1.0, 33.6, 33.6, 1.0, 1.0, -6.54, 1.0, 1.0, 1.0, 20.26, 20.26, 33.6, 1.0, 1.0, -6.54, 1.0, 1.0, 1.0, 20.26},
{1.0, 1.0, -1.88, 58.28, 24.68, 1.0, -6.54, 1.0, 1.0, -6.54, 1.0, 44.94, -1.88, 1.0, 1.0, 1.0, 44.94, 1.0, 13.34, 1.0},
{-1.88, 1.0, 1.0, 1.0, 44.94, -9.37, 1.0, 24.68, 44.94, 1.0, 1.0, -1.88, -6.54, 24.68, 1.0, 1.0, 1.0, -9.37, 1.0, 1.0},
{-9.37, 1.0, 44.94, 13.34, 13.34, 1.0, 1.0, 1.0, 1.0, -15.91, 24.68, 13.34, -7.49, 1.0, -6.54, 1.0, 1.0, -7.49, 24.68, 1.0},
{1.0, 1.0, 1.0, 1.0, 33.6, 1.0, 1.0, 1.0, 1.0, 1.0, 13.34, 20.26, 1.0, -14.03, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0},
{1.0, -6.54, 1.0, 1.0, -6.54, -6.54, 20.26, 1.0, 1.0, 1.0, 20.26, 20.26, 1.0, 1.0, 20.26, -6.54, 44.94, 1.0, 1.0, 1.0},
{-9.37, -1.88, 1.0, 1.0, 1.0, -14.03, -6.54, 1.0, 44.94, 1.0, 1.0, -1.88, -7.49, 24.68, 1.0, 1.0, 1.0, -14.03, 1.0, 1.0},
{1.0, 1.0, 1.0, 13.34, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, -1.88, 1.0, -7.49, 44.94, -7.49, 1.0, 1.0, 1.0, 20.26},
{58.28, 1.0, 1.0, 20.26, -6.54, 1.0, 20.26, 13.34, 1.0, 58.28, 1.0, 20.26, 1.0, 1.0, 1.0, 1.0, 44.94, -7.49, 1.0, 1.0},
{1.0, 1.0, 1.0, 1.0, 1.0, -6.54, 1.0, 1.0, 1.0, -6.54, 1.0, 1.0, -14.03, -7.49, 1.0, 1.0, 20.26, 1.0, 1.0, 1.0},
{-1.88, -6.54, -6.54, 1.0, 1.0, 20.26, 20.26, 1.0, 1.0, -6.54, -6.54, 20.26, 1.0, 1.0, 18.38, 20.26, 20.26, 1.0, 20.26, 1.0},
{-14.03,1.0, 1.0, 1.0, 1.0, 13.34, -6.54, -14.03, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 20.26, 1.0, 1.0, -7.49, 1.0, 1.0},
{1.0, 1.0, 33.6, 1.0, 1.0, 1.0, 24.68, 1.0, -7.49, 33.6, 1.0, -6.54, 1.0, 1.0, 1.0, -7.49, 1.0, -7.49, 1.0, -7.49},
{-14.03,44.94, 1.0, -6.54, 1.0, 1.0, 20.26, 1.0, 20.26, 1.0, 20.26, 20.26, 1.0, 1.0, 33.6, 1.0, 20.26, 1.0, 1.0, 1.0},
{1.0, 1.0, 1.0, 1.0, -6.54, 1.0, 1.0, 1.0, 1.0, 1.0, -14.03, 20.26, -7.49, -1.88, 1.0, 1.0, 1.0, -7.49, 1.0, 1.0},
{1.0, 33.6, 1.0, 1.0, 1.0, 1.0, 20.26, 1.0, 1.0, 20.26, 1.0, 44.94, 1.0, 1.0, 20.26, 1.0, 20.26, 1.0, 1.0, 1.0},
{13.34, 1.0, 1.0, 1.0, -7.49, 1.0, 1.0, -7.49, -7.49, 1.0, 1.0, 1.0, -7.49, -7.49, -6.54, 1.0, 1.0, 13.34, -7.49, 1.0},
{1.0, 44.94, 1.0, -7.49, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, -7.49, 20.26, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0},
{24.68, 1.0, 1.0, 1.0, 1.0, 1.0, 33.6, 1.0, 1.0, 20.26, 1.0, 20.26, 1.0, -7.49, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0}
};
SingleLetterAACode[] aa = SingleLetterAACode.values();
for(int i = 0; i < aa.length; i++){
for(int j = 0; j < aa.length; j++){
diAA2Instability.put("" + aa[i] + aa[j], instability[i][j]);
}
}
}
/**
* Does the initialization of extinction coefficient based on
* http://au.expasy.org/tools/protparam-doc.html
*/
public static void initExtinctionCoefficient(){
aa2ExtinctionCoefficient.put(Y, 1490.0);
aa2ExtinctionCoefficient.put(W, 5500.0);
aa2ExtinctionCoefficient.put(C, 125.0);
}
}
