void AddMonosaccharide(Monosaccharide sugar)
{
if (composite.ContainsKey(sugar))
{
composite[sugar] += 1;
}
else
{
composite[sugar] = 1;
}
}
public override List <IGlycan> Grow(Monosaccharide monosaccharide)
{
List <IGlycan> glycans = new List <IGlycan>();
switch (monosaccharide)
{
case Monosaccharide.GlcNAc:
if (ValidAddGlcNAc())
{
NHighMannose ptr = CreateByAddGlcNAc();
glycans.Add(ptr);
}
break;
case Monosaccharide.Man:
if (ValidAddManCore())
{
NHighMannose ptr = CreateByAddManCore();
glycans.Add(ptr);
}
else if (ValidAddManBranch())
{
List <NHighMannose> gs = CreateByAddManBranch();
glycans.AddRange(gs);
}
break;
case Monosaccharide.Fuc:
if (ValidAddFucCore())
{
NHighMannose ptr = CreateByAddFucCore();
glycans.Add(ptr);
}
break;
default:
break;
}
return(glycans);
}
public Dictionary <Element, int> Compositions(Monosaccharide sugar)
{
// GlcNAc C8H15NO6, Man/Gal C6H12O6, Fuc C6H12O5, NeuAc C11H19NO9, NeuGc C11H19NO10
switch (sugar)
{
case Monosaccharide.HexNAc:
return(new Dictionary <Element, int>()
{
{ new C(), 8 }, { new H(), 15 }, { new N(), 1 }, { new O(), 6 }
});
case Monosaccharide.Hex:
return(new Dictionary <Element, int>()
{
{ new C(), 6 }, { new H(), 12 }, { new O(), 6 }
});
case Monosaccharide.Fuc:
return(new Dictionary <Element, int>()
{
{ new C(), 6 }, { new H(), 12 }, { new O(), 5 }
});
case Monosaccharide.NeuAc:
return(new Dictionary <Element, int>()
{
{ new C(), 11 }, { new H(), 19 }, { new N(), 1 }, { new O(), 9 }
});
case Monosaccharide.NeuGc:
return(new Dictionary <Element, int>()
{
{ new C(), 11 }, { new H(), 19 }, { new N(), 1 }, { new O(), 10 }
});
}
return(new Dictionary <Element, int>());
}
public abstract List <IGlycan> Grow(Monosaccharide monosaccharide);
// composition in a glycan
public Dictionary <Element, int> SubCompositions(Monosaccharide sugar, bool permethylated)
{
// GlcNAc C8H15NO6, Man/Gal C6H12O6, Fuc C6H12O5, NeuAc C11H19NO9, NeuGc C11H19NO10
if (permethylated)
{
switch (sugar)
{
case Monosaccharide.HexNAc:
return(new Dictionary <Element, int>()
{
{ new C(), 11 }, { new H(), 19 }, { new N(), 1 }, { new O(), 5 }
});
case Monosaccharide.Hex:
return(new Dictionary <Element, int>()
{
{ new C(), 9 }, { new H(), 16 }, { new O(), 5 }
});
case Monosaccharide.Fuc:
return(new Dictionary <Element, int>()
{
{ new C(), 8 }, { new H(), 14 }, { new O(), 4 }
});
case Monosaccharide.NeuAc:
return(new Dictionary <Element, int>()
{
{ new C(), 16 }, { new H(), 27 }, { new N(), 1 }, { new O(), 8 }
});
case Monosaccharide.NeuGc:
return(new Dictionary <Element, int>()
{
{ new C(), 17 }, { new H(), 29 }, { new N(), 1 }, { new O(), 9 }
});
}
}
else
{
switch (sugar)
{
case Monosaccharide.HexNAc:
return(new Dictionary <Element, int>()
{
{ new C(), 8 }, { new H(), 13 }, { new N(), 1 }, { new O(), 5 }
});
case Monosaccharide.Hex:
return(new Dictionary <Element, int>()
{
{ new C(), 6 }, { new H(), 10 }, { new O(), 5 }
});
case Monosaccharide.Fuc:
return(new Dictionary <Element, int>()
{
{ new C(), 6 }, { new H(), 10 }, { new O(), 4 }
});
case Monosaccharide.NeuAc:
return(new Dictionary <Element, int>()
{
{ new C(), 11 }, { new H(), 17 }, { new N(), 1 }, { new O(), 8 }
});
case Monosaccharide.NeuGc:
return(new Dictionary <Element, int>()
{
{ new C(), 11 }, { new H(), 17 }, { new N(), 1 }, { new O(), 9 }
});
}
}
return(new Dictionary <Element, int>());
}
public Compound Compounds(Monosaccharide sugar)
{
Dictionary <Element, int> composition = Compositions(sugar);
return(new Compound(composition));
}
public override List <IGlycan> Grow(Monosaccharide monosaccharide)
{
List <IGlycan> glycans = new List <IGlycan>();
switch (monosaccharide)
{
case Monosaccharide.GlcNAc:
if (ValidAddGlcNAcCore())
{
NGlycanComplex ptr = CreateByAddGlcNAcCore();
glycans.Add(ptr);
}
else if (ValidAddGlcNAc())
{
if (ValidAddGlcNAcBisect())
{
NGlycanComplex ptr = CreateByAddGlcNAcBisect();
glycans.Add(ptr);
}
if (ValidAddGlcNAcBranch())
{
List <NGlycanComplex> gs = CreateByAddGlcNAcBranch();
glycans.AddRange(gs);
}
}
break;
case Monosaccharide.Man:
if (ValidAddMan())
{
NGlycanComplex ptr = CreateByAddMan();
glycans.Add(ptr);
}
break;
case Monosaccharide.Gal:
if (ValidAddGal())
{
List <NGlycanComplex> gs = CreateByAddGal();
glycans.AddRange(gs);
}
break;
case Monosaccharide.Fuc:
if (ValidAddFucCore())
{
NGlycanComplex ptr = CreateByAddFucCore();
glycans.Add(ptr);
}
if (ValidAddFucTerminal())
{
List <NGlycanComplex> gs = CreateByAddFucTerminal();
glycans.AddRange(gs);
}
break;
case Monosaccharide.NeuAc:
if (ValidAddNeuAc())
{
List <NGlycanComplex> gs = CreateByAddNeuAc();
glycans.AddRange(gs);
}
break;
case Monosaccharide.NeuGc:
if (ValidAddNeuGc())
{
List <NGlycanComplex> gs = CreateByAddNeuGc();
glycans.AddRange(gs);
}
break;
default:
break;
}
return(glycans);
}
