public static string FindProteinInterfaceAminoAcidCommonPropertiesMotif(List <string> proteinInterfaceSequenceList, AminoAcidPropertyMatchType aminoAcidPropertyMatchType, double matchValue = 0)
{
if (proteinInterfaceSequenceList == null)
{
throw new ArgumentNullException(nameof(proteinInterfaceSequenceList));
}
var totalProteinInterfaces = proteinInterfaceSequenceList.Count;
var proteinInterfaceLength = proteinInterfaceSequenceList.Select(a => a.Length).Max();
var aminoAcidObjects = new AminoAcidProperties <bool> [TotalAminoAcids];
for (var aaIndex = 0; aaIndex < aminoAcidObjects.Length; aaIndex++)
{
aminoAcidObjects[aaIndex] = AminoAcidConversions.AminoAcidNumberToAminoAcidObject(aaIndex + 1);
}
var aminoAcidPositionCount = new AminoAcidProperties <int> [proteinInterfaceLength];
for (var position = 0; position < aminoAcidPositionCount.Length; position++)
{
aminoAcidPositionCount[position] = new AminoAcidProperties <int>();
}
var motifs = new List <string>();
for (int positionIndex = 0; positionIndex < proteinInterfaceLength; positionIndex++)
{
string positionMotif = "";
foreach (var aaCode in proteinInterfaceSequenceList.Where(a => a.Length > positionIndex).Select(a => a[positionIndex]).Distinct().ToArray())
{
if (!char.IsLetterOrDigit(aaCode) || NonStandardAminoAcids.Contains(aaCode))
{
continue;
}
var aminoAcid = aminoAcidObjects[AminoAcidConversions.AminoAcidNameToNumber(aaCode) - 1];
var matches = AminoAcidConversions.ListAminoAcidsByProperty(aminoAcid, aminoAcidPropertyMatchType, matchValue);
positionMotif += string.Join("", matches.Where(a => !positionMotif.Contains(a) && !NonStandardAminoAcids.Contains(a)).ToArray());
}
motifs.Add(positionMotif);
}
return(MotifFormatter(motifs));
}
public void TestAminoAcids()
{
//int intAcidic = 0;
int intAliphatic = 0;
int intAromatic = 0;
int intCharged = 0;
int intHydrophobic = 0;
int intHydroxylic = 0;
int intNegative = 0;
int intPolar = 0;
int intPositive = 0;
int intSmall = 0;
int intSulphur = 0;
int intTiny = 0;
//string strAcidic = "";
string strAliphatic = "";
string strAromatic = "";
string strCharged = "";
string strHydrophobic = "";
string strHydroxylic = "";
string strNegative = "";
string strPolar = "";
string strPositive = "";
string strSmall = "";
string strSulphur = "";
string strTiny = "";
for (var i = 1; i <= 26; i++)
{
var x = AminoAcidConversions.AminoAcidNumberToAminoAcidObject(i);
//if (x.Acidic)
//{
//intAcidic++;
//strAcidic += x.Code1L;
//}
if (x.Aliphatic)
{
intAliphatic++;
strAliphatic += x.Code1L;
}
if (x.Aromatic)
{
intAromatic++;
strAromatic += x.Code1L;
}
if (x.Charged)
{
intCharged++;
strCharged += x.Code1L;
}
if (x.Hydrophobic)
{
intHydrophobic++;
strHydrophobic += x.Code1L;
}
if (x.Hydroxylic)
{
intHydroxylic++;
strHydroxylic += x.Code1L;
}
if (x.Negative)
{
intNegative++;
strNegative += x.Code1L;
}
if (x.Polar)
{
intPolar++;
strPolar += x.Code1L;
}
if (x.Positive)
{
intPositive++;
strPositive += x.Code1L;
}
if (x.Small)
{
intSmall++;
strSmall += x.Code1L;
}
if (x.Sulphur)
{
intSulphur++;
strSulphur += x.Code1L;
}
if (x.Tiny)
{
intTiny++;
strTiny += x.Code1L;
}
}
//Console.WriteLine("Acidic: " + intAcidic + " " + strAcidic);
Console.WriteLine("Aliphatic: " + intAliphatic + " " + strAliphatic);
Console.WriteLine("Aromatic: " + intAromatic + " " + strAromatic);
Console.WriteLine("Charged: " + intCharged + " " + strCharged);
Console.WriteLine("Hydrophobic: " + intHydrophobic + " " + strHydrophobic);
Console.WriteLine("Hydroxylic: " + intHydroxylic + " " + strHydroxylic);
Console.WriteLine("Negative: " + intNegative + " " + strNegative);
Console.WriteLine("Polar: " + intPolar + " " + strPolar);
Console.WriteLine("Positive: " + intPositive + " " + strPositive);
Console.WriteLine("Small: " + intSmall + " " + strSmall);
Console.WriteLine("Sulphur: " + intSulphur + " " + strSulphur);
Console.WriteLine("Tiny: " + intTiny + " " + strTiny);
}
public void TestListAminoAcidsByProperty()
{
var x = new AminoAcidProperties<string>()
{
//Acidic = AminoAcidConversions.ListAminoAcidsByProperty(new AminoAcidProperties<bool>() {Acidic = true}),
Aliphatic = AminoAcidConversions.ListAminoAcidsByProperty(new AminoAcidProperties<bool>() {Aliphatic = true}),
Aromatic = AminoAcidConversions.ListAminoAcidsByProperty(new AminoAcidProperties<bool>() {Aromatic = true}),
Charged = AminoAcidConversions.ListAminoAcidsByProperty(new AminoAcidProperties<bool>() {Charged = true}),
Hydrophobic = AminoAcidConversions.ListAminoAcidsByProperty(new AminoAcidProperties<bool>() {Hydrophobic = true}),
Hydroxylic = AminoAcidConversions.ListAminoAcidsByProperty(new AminoAcidProperties<bool>() {Hydroxylic = true}),
Negative = AminoAcidConversions.ListAminoAcidsByProperty(new AminoAcidProperties<bool>() {Negative = true}),
Polar = AminoAcidConversions.ListAminoAcidsByProperty(new AminoAcidProperties<bool>() {Polar = true}),
Positive = AminoAcidConversions.ListAminoAcidsByProperty(new AminoAcidProperties<bool>() {Positive = true}),
Small = AminoAcidConversions.ListAminoAcidsByProperty(new AminoAcidProperties<bool>() {Small = true}),
Sulphur = AminoAcidConversions.ListAminoAcidsByProperty(new AminoAcidProperties<bool>() {Sulphur = true}),
Tiny = AminoAcidConversions.ListAminoAcidsByProperty(new AminoAcidProperties<bool>() { Tiny = true }),
};
var uncommon = AminoAcidConversions.ListAminoAcidsByProperty(new AminoAcidProperties<bool>() {}, AminoAcidPropertyMatchType.AllMatch);
var y = new AminoAcidProperties<string>()
{
};
for (var i = 0; i < AminoAcidTotals.TotalAminoAcids(); i++)
{
var aa = AminoAcidConversions.AminoAcidNumberToAminoAcidObject(i + 1);
//if (aa.Acidic) y.Acidic += aa.Code1L;
if (aa.Aliphatic) y.Aliphatic += aa.Code1L;
if (aa.Aromatic) y.Aromatic += aa.Code1L;
if (aa.Charged) y.Charged += aa.Code1L;
if (aa.Hydrophobic) y.Hydrophobic += aa.Code1L;
if (aa.Hydroxylic) y.Hydroxylic += aa.Code1L;
if (aa.Negative) y.Negative += aa.Code1L;
if (aa.Polar) y.Polar += aa.Code1L;
if (aa.Positive) y.Positive += aa.Code1L;
if (aa.Small) y.Small += aa.Code1L;
if (aa.Sulphur) y.Sulphur += aa.Code1L;
if (aa.Tiny) y.Tiny += aa.Code1L;
}
//Console.WriteLine("Acidic: " + x.Acidic);
Console.WriteLine("Aliphatic: " + x.Aliphatic);
Console.WriteLine("Aromatic: " + x.Aromatic);
Console.WriteLine("Charged: " + x.Charged);
Console.WriteLine("Hydrophobic: " + x.Hydrophobic);
Console.WriteLine("Hydroxylic: " + x.Hydroxylic);
Console.WriteLine("Negative: " + x.Negative);
Console.WriteLine("Polar: " + x.Polar);
Console.WriteLine("Positive: " + x.Positive);
Console.WriteLine("Small: " + x.Small);
Console.WriteLine("Sulphur: " + x.Sulphur);
Console.WriteLine("Tiny: " + x.Tiny);
Console.WriteLine("Others: " + uncommon);
//Assert.AreEqual(string.Join(" ", y.Acidic.OrderBy(a=>a).ToArray()), string.Join(" ", x.Acidic.OrderBy(a=>a).ToArray()));
Assert.AreEqual(string.Join(" ", y.Aliphatic.OrderBy(a=>a).ToArray()), string.Join(" ", x.Aliphatic.OrderBy(a=>a).ToArray()));
Assert.AreEqual(string.Join(" ", y.Aromatic.OrderBy(a=>a).ToArray()), string.Join(" ", x.Aromatic.OrderBy(a=>a).ToArray()));
Assert.AreEqual(string.Join(" ", y.Charged.OrderBy(a=>a).ToArray()), string.Join(" ", x.Charged.OrderBy(a=>a).ToArray()));
Assert.AreEqual(string.Join(" ", y.Hydrophobic.OrderBy(a=>a).ToArray()), string.Join(" ", x.Hydrophobic.OrderBy(a=>a).ToArray()));
Assert.AreEqual(string.Join(" ", y.Hydroxylic.OrderBy(a=>a).ToArray()), string.Join(" ", x.Hydroxylic.OrderBy(a=>a).ToArray()));
Assert.AreEqual(string.Join(" ", y.Negative.OrderBy(a=>a).ToArray()), string.Join(" ", x.Negative.OrderBy(a=>a).ToArray()));
Assert.AreEqual(string.Join(" ", y.Polar.OrderBy(a=>a).ToArray()), string.Join(" ", x.Polar.OrderBy(a=>a).ToArray()));
Assert.AreEqual(string.Join(" ", y.Positive.OrderBy(a=>a).ToArray()), string.Join(" ", x.Positive.OrderBy(a=>a).ToArray()));
Assert.AreEqual(string.Join(" ", y.Small.OrderBy(a=>a).ToArray()), string.Join(" ", x.Small.OrderBy(a=>a).ToArray()));
Assert.AreEqual(string.Join(" ", y.Sulphur.OrderBy(a=>a).ToArray()), string.Join(" ", x.Sulphur.OrderBy(a=>a).ToArray()));
Assert.AreEqual(string.Join(" ", y.Tiny.OrderBy(a=>a).ToArray()), string.Join(" ", x.Tiny.OrderBy(a=>a).ToArray()));
}