public override bool Equals(object obj)
{
if (this == obj)
{
return(true);
}
if (obj is AminoAcid)
{
AminoAcid other = (AminoAcid)obj;
return(other.letter == letter);
}
return(false);
}
private static AminoAcid[] InitAminoAcids()
{
AminoAcid alanine = new AminoAcid("C3H5NO", "Alanine", "Ala", 'A', 7.4, new[] { "GCT", "GCC", "GCA", "GCG" },
"hydrophobic aliphatic", true, 1.8);
AminoAcid arginine = new AminoAcid("C6H12N4O", "Arginine", "Arg", 'R', 4.2,
new[] { "CGT", "CGC", "CGA", "CGG", "AGA", "AGG" }, "charged basic", true, -4.5);
AminoAcid asparagine = new AminoAcid("C4H6N2O2", "Asparagine", "Asn", 'N', 4.4, new[] { "AAT", "AAC" }, "polar neutral",
true, -3.5);
AminoAcid asparticAcid = new AminoAcid("C4H5NO3", "Aspartic acid", "Asp", 'D', 5.9, new[] { "GAT", "GAC" },
"charged acidic", true, -3.5);
AminoAcid cysteine = new AminoAcid("C3H5NOS", "Cysteine", "Cys", 'C', 3.3, new[] { "TGT", "TGC" }, "polar neutral", true,
2.5);
AminoAcid glutamicAcid = new AminoAcid("C5H7NO3", "Glutamic acid", "Glu", 'E', 5.8, new[] { "GAA", "GAG" },
"charged acidic", true, -3.5);
AminoAcid glutamine = new AminoAcid("C5H8N2O2", "Glutamine", "Gln", 'Q', 3.7, new[] { "CAA", "CAG" }, "polar neutral",
true, -3.5);
AminoAcid glycine = new AminoAcid("C2H3NO", "Glycine", "Gly", 'G', 7.4, new[] { "GGT", "GGC", "GGA", "GGG" }, "", true,
-0.4);
AminoAcid histidine = new AminoAcid("C6H7N3O", "Histidine", "His", 'H', 2.9, new[] { "CAT", "CAC" }, "charged basic",
true, -3.2);
AminoAcid isoleucine = new AminoAcid("C6H11NO", "Isoleucine", "Ile", 'I', 3.8, new[] { "ATT", "ATC", "ATA" },
"hydrophobic aliphatic", true, 4.5);
AminoAcid leucine = new AminoAcid("C6H11NO", "Leucine", "Leu", 'L', 7.6,
new[] { "TTA", "TTG", "CTT", "CTC", "CTA", "CTG" }, "hydrophobic aliphatic", true, 3.8);
AminoAcid lysine = new AminoAcid("C6H12N2O", "Lysine", "Lys", 'K', 7.2, new[] { "AAA", "AAG" }, "charged basic", true,
-3.9);
AminoAcid methionine = new AminoAcid("C5H9NOS", "Methionine", "Met", 'M', 1.8, new[] { "ATG" }, "polar neutral", true,
1.9);
AminoAcid phenylalanine = new AminoAcid("C9H9NO", "Phenylalanine", "Phe", 'F', 4, new[] { "TTT", "TTC" },
"hydrophobic aromatic", true, 2.8);
AminoAcid proline = new AminoAcid("C5H7NO", "Proline", "Pro", 'P', 5, new[] { "CCT", "CCC", "CCA", "CCG" }, "", true,
-1.6);
AminoAcid serine = new AminoAcid("C3H5NO2", "Serine", "Ser", 'S', 8.1,
new[] { "TCT", "TCC", "TCA", "TCG", "AGT", "AGC" }, "polar neutral", true, -0.8);
AminoAcid threonine = new AminoAcid("C4H7NO2", "Threonine", "Thr", 'T', 6.2, new[] { "ACT", "ACC", "ACA", "ACG" },
"polar neutral", true, -0.7);
AminoAcid tryptophan = new AminoAcid("C11H10N2O", "Tryptophan", "Trp", 'W', 1.3, new[] { "TGG" }, "hydrophobic aromatic",
true, -0.9);
AminoAcid tyrosine = new AminoAcid("C9H9NO2", "Tyrosine", "Tyr", 'Y', 3.3, new[] { "TAT", "TAC" },
"hydrophobic aromatic", true, -1.3);
AminoAcid valine = new AminoAcid("C5H9NO", "Valine", "Val", 'V', 6.8, new[] { "GTT", "GTC", "GTA", "GTG" },
"hydrophobic aliphatic", true, 4.2);
AminoAcid selenocysteine = new AminoAcid("C3H7NO2Se", "Selenocysteine", "Sec", 'U', 0.0, new[] { "TGA" }, "", false, 0.0);
AminoAcid[] aas = new[] {
alanine, arginine, asparagine, asparticAcid, cysteine, glutamine, glutamicAcid, glycine, histidine, isoleucine,
leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine, valine, selenocysteine
};
return(aas);
}
public static Image GetImage(AminoAcid aa)
{
object resource = Resources.ResourceManager.GetObject(aa.Letter.ToString(CultureInfo.InvariantCulture));
return(resource is Image ? (Image)resource : null);
}
private static AminoAcid[] InitAminoAcids()
{
AminoAcid alanine = new AminoAcid("C3H5NO", "Alanine", "Ala", 'A', 7.4, new[]{"GCT", "GCC", "GCA", "GCG"},
"hydrophobic aliphatic", true, 1.8);
AminoAcid arginine = new AminoAcid("C6H12N4O", "Arginine", "Arg", 'R', 4.2,
new[]{"CGT", "CGC", "CGA", "CGG", "AGA", "AGG"}, "charged basic", true, -4.5);
AminoAcid asparagine = new AminoAcid("C4H6N2O2", "Asparagine", "Asn", 'N', 4.4, new[]{"AAT", "AAC"}, "polar neutral",
true, -3.5);
AminoAcid asparticAcid = new AminoAcid("C4H5NO3", "Aspartic acid", "Asp", 'D', 5.9, new[]{"GAT", "GAC"},
"charged acidic", true, -3.5);
AminoAcid cysteine = new AminoAcid("C3H5NOS", "Cysteine", "Cys", 'C', 3.3, new[]{"TGT", "TGC"}, "polar neutral", true,
2.5);
AminoAcid glutamicAcid = new AminoAcid("C5H7NO3", "Glutamic acid", "Glu", 'E', 5.8, new[]{"GAA", "GAG"},
"charged acidic", true, -3.5);
AminoAcid glutamine = new AminoAcid("C5H8N2O2", "Glutamine", "Gln", 'Q', 3.7, new[]{"CAA", "CAG"}, "polar neutral",
true, -3.5);
AminoAcid glycine = new AminoAcid("C2H3NO", "Glycine", "Gly", 'G', 7.4, new[]{"GGT", "GGC", "GGA", "GGG"}, "", true,
-0.4);
AminoAcid histidine = new AminoAcid("C6H7N3O", "Histidine", "His", 'H', 2.9, new[]{"CAT", "CAC"}, "charged basic",
true, -3.2);
AminoAcid isoleucine = new AminoAcid("C6H11NO", "Isoleucine", "Ile", 'I', 3.8, new[]{"ATT", "ATC", "ATA"},
"hydrophobic aliphatic", true, 4.5);
AminoAcid leucine = new AminoAcid("C6H11NO", "Leucine", "Leu", 'L', 7.6,
new[]{"TTA", "TTG", "CTT", "CTC", "CTA", "CTG"}, "hydrophobic aliphatic", true, 3.8);
AminoAcid lysine = new AminoAcid("C6H12N2O", "Lysine", "Lys", 'K', 7.2, new[]{"AAA", "AAG"}, "charged basic", true,
-3.9);
AminoAcid methionine = new AminoAcid("C5H9NOS", "Methionine", "Met", 'M', 1.8, new[]{"ATG"}, "polar neutral", true,
1.9);
AminoAcid phenylalanine = new AminoAcid("C9H9NO", "Phenylalanine", "Phe", 'F', 4, new[]{"TTT", "TTC"},
"hydrophobic aromatic", true, 2.8);
AminoAcid proline = new AminoAcid("C5H7NO", "Proline", "Pro", 'P', 5, new[]{"CCT", "CCC", "CCA", "CCG"}, "", true,
-1.6);
AminoAcid serine = new AminoAcid("C3H5NO2", "Serine", "Ser", 'S', 8.1,
new[]{"TCT", "TCC", "TCA", "TCG", "AGT", "AGC"}, "polar neutral", true, -0.8);
AminoAcid threonine = new AminoAcid("C4H7NO2", "Threonine", "Thr", 'T', 6.2, new[]{"ACT", "ACC", "ACA", "ACG"},
"polar neutral", true, -0.7);
AminoAcid tryptophan = new AminoAcid("C11H10N2O", "Tryptophan", "Trp", 'W', 1.3, new[]{"TGG"}, "hydrophobic aromatic",
true, -0.9);
AminoAcid tyrosine = new AminoAcid("C9H9NO2", "Tyrosine", "Tyr", 'Y', 3.3, new[]{"TAT", "TAC"},
"hydrophobic aromatic", true, -1.3);
AminoAcid valine = new AminoAcid("C5H9NO", "Valine", "Val", 'V', 6.8, new[]{"GTT", "GTC", "GTA", "GTG"},
"hydrophobic aliphatic", true, 4.2);
AminoAcid selenocysteine = new AminoAcid("C3H7NO2Se", "Selenocysteine", "Sec", 'U', 0.0, new[]{"TGA"}, "", false, 0.0);
AminoAcid[] aas = new[]{
alanine, arginine, asparagine, asparticAcid, cysteine, glutamine, glutamicAcid, glycine, histidine, isoleucine,
leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine, valine, selenocysteine
};
return aas;
}
public static char[] GetSingleLetters(AminoAcid[] aas)
{
char[] result = new char[aas.Length];
for (int i = 0; i < aas.Length; i++){
result[i] = aas[i].letter;
}
return result;
}
public static Image GetImage(AminoAcid aa)
{
object resource = Resources.ResourceManager.GetObject(aa.Letter.ToString(CultureInfo.InvariantCulture));
return resource is Image ? (Image) resource : null;
}
public static AminoAcid[] FromLetters(char[] c)
{
AminoAcid[] result = new AminoAcid[c.Length];
for (int i = 0; i < c.Length; i++){
result[i] = FromLetter(c[i]);
}
return result;
}
