public static IEnumerable <Peptide> GenerateIsoforms(Peptide peptide, Modification modification, long ptms)
{
// Get all the possible modified-residues' indices (zero-based)
List <int> sites = modification.GetModifiableSites(peptide).ToList();
// Total number of PTM sites
int ptmsites = sites.Count;
// Exact number of possible isoforms
long isoforms = Combinatorics.BinomCoefficient(ptmsites, ptms);
// For each possible isoform
for (long isoform = 0; isoform < isoforms; isoform++)
{
// Create a new peptide based on the one passed in
Peptide pep = new Peptide(peptide);
long x = isoforms - isoform - 1;
long a = ptmsites;
long b = ptms;
// For each ptm
for (int i = 0; i < ptms; i++)
{
long ans = Combinatorics.LargestV(a, b, x);
int index = sites[(int)(ptmsites - ans - 1)];
if (index == 0)
{
pep.AddModification(modification, Terminus.N);
}
else if (index > pep.Length)
{
pep.AddModification(modification, Terminus.C);
}
else
{
pep.AddModification(modification, index);
}
x -= Combinatorics.BinomCoefficient(ans, b);
a = ans;
b--;
}
yield return(pep);
}
}
public IEnumerable <Peptide> GenerateIsotopologues()
{
// Get all the modifications that are isotopologues
var isotopologues = GetUniqueModifications <IIsotopologue>().ToArray();
// Base condition, no more isotopologues to make, so just return
if (isotopologues.Length < 1)
{
yield break;
}
// Grab the the first isotopologue
IIsotopologue isotopologue = isotopologues[0];
// Loop over each modification in the isotopologue
foreach (Modification mod in isotopologue)
{
// Create a clone of the peptide, cloning modifications as well.
Peptide peptide = new Peptide(this);
// Replace the base isotopologue mod with the specific version
peptide.ReplaceModification(isotopologue, mod);
// There were more than one isotopologue, so we must go deeper
if (isotopologues.Length > 1)
{
// Call the same rotuine on the newly generate peptide that has one less isotopologue
foreach (var subpeptide in peptide.GenerateIsotopologues())
{
yield return(subpeptide);
}
}
else
{
// Return this peptide
yield return(peptide);
}
}
}
public void SetSequenceAndMods(string sequence, IList <Modification> fixedMods, string variableMods)
{
Peptide = new CSMSL.Proteomics.Peptide(sequence);
Peptide.SetModifications(fixedMods);
Modificationstring = variableMods;
foreach (Tuple <Modification, int> modTuple in OmssaModification.ParseModificationLine(variableMods))
{
Modification mod = modTuple.Item1;
int site = modTuple.Item2;
if (site == 1 && mod.Sites.HasFlag(ModificationSites.NPep))
{
Peptide.AddModification(mod, Terminus.N);
}
else if (site == Peptide.Length && mod.Sites.HasFlag(ModificationSites.PepC))
{
Peptide.AddModification(mod, Terminus.C);
}
else
{
Peptide.AddModification(mod, site);
}
}
}
public static IEnumerable <Peptide> GenerateIsoforms(Peptide peptide, bool keepBaseModifications, params Modification[] modifications)
{
// Get the number of modifications to this peptide
int numberOfModifications = modifications.Length;
if (numberOfModifications < 1)
{
// No modifications, return the base peptide
yield return(peptide);
}
else if (numberOfModifications == 1)
{
// Only one modification, use the faster algorithm
foreach (Peptide pep in GenerateIsoforms(peptide, modifications[0], 1))
{
yield return(pep);
}
}
else
{
// More than one ptm case
// Get all the unique modified sites for all the mods
Dictionary <Modification, List <int> > allowedSites = new Dictionary <Modification, List <int> >();
foreach (Modification mod in modifications)
{
List <int> sites;
if (!allowedSites.TryGetValue(mod, out sites))
{
allowedSites.Add(mod, mod.GetModifiableSites(peptide).ToList());
}
}
// Only one type of mod, use the faster algorithm
if (allowedSites.Count == 1)
{
foreach (Peptide pep in GenerateIsoforms(peptide, modifications[0], numberOfModifications))
{
yield return(pep);
}
yield break;
}
HashSet <Modification[]> results = new HashSet <Modification[]>(new ModificationArrayComparer());
// Call out to the recursive helper method, starting with mod 0 and site 0
GenIsoHelper(results, new Modification[peptide.Length + 2], modifications, allowedSites, 0, 0);
// Create correct peptide mappings
foreach (Modification[] modArray in results)
{
Peptide pep = new Peptide(peptide, keepBaseModifications);
for (int i = 0; i < modArray.Length; i++)
{
var mod = modArray[i];
if (mod == null)
{
continue;
}
if (i == 0)
{
pep.AddModification(mod, Terminus.N);
}
else if (i > peptide.Length)
{
pep.AddModification(mod, Terminus.C);
}
else
{
pep.AddModification(mod, i);
}
}
yield return(pep);
}
}
}
