/// <summary>
/// Sets the modification at specific sites on this amino acid polymer
/// </summary>
/// <param name="modification">The modification to set</param>
/// <param name="sites">The sites to set the modification at</param>
/// <returns>The number of modifications added to this amino acid polymer</returns>
public virtual int SetModification(IHasMass modification, ModificationSites sites)
{
int count = 0;
if ((sites & ModificationSites.NPep) == ModificationSites.NPep)
{
NTerminusModification = modification;
count++;
}
for (int i = 0; i < Length; i++)
{
ModificationSites site = residues[i].Site;
if ((sites & site) == site)
{
ReplaceMod(i + 1, modification);
count++;
}
}
if ((sites & ModificationSites.PepC) == ModificationSites.PepC)
{
CTerminusModification = modification;
count++;
}
return(count);
}
/// <summary>
/// Clear the modifications from the specified sites(s)
/// </summary>
/// <param name="sites">The sites to remove modifications from</param>
public void ClearModifications(ModificationSites sites)
{
if ((sites & ModificationSites.NPep) == ModificationSites.NPep || (sites & ModificationSites.NProt) == ModificationSites.NProt)
{
ReplaceMod(0, null);
}
for (int i = 0; i < Length; i++)
{
int modIndex = i + 1;
if (_modifications[modIndex] == null)
{
continue;
}
ModificationSites curSite = residues[i].Site;
if ((curSite & sites) == curSite)
{
ReplaceMod(modIndex, null);
}
}
if ((sites & ModificationSites.PepC) == ModificationSites.PepC || (sites & ModificationSites.ProtC) == ModificationSites.ProtC)
{
ReplaceMod(Length + 1, null);
}
}
public static void LoadOmssaModifications(Stream stream, bool userMod = true)
{
XmlDocument mods_xml = new XmlDocument();
mods_xml.Load(stream);
XmlNamespaceManager mods_xml_ns = new XmlNamespaceManager(mods_xml.NameTable);
mods_xml_ns.AddNamespace("omssa", mods_xml.ChildNodes[1].Attributes["xmlns"].Value);
foreach (XmlNode mod_node in mods_xml.SelectNodes("/omssa:MSModSpecSet/omssa:MSModSpec", mods_xml_ns))
{
string name = mod_node.SelectSingleNode("./omssa:MSModSpec_name", mods_xml_ns).FirstChild.Value;
int id = int.Parse(mod_node.SelectSingleNode("./omssa:MSModSpec_mod/omssa:MSMod", mods_xml_ns).FirstChild.Value);
double mono = double.Parse(mod_node.SelectSingleNode("./omssa:MSModSpec_monomass", mods_xml_ns).FirstChild.Value);
double average = double.Parse(mod_node.SelectSingleNode("./omssa:MSModSpec_averagemass", mods_xml_ns).FirstChild.Value);
ModificationSites sites = ModificationSites.None;
foreach (
XmlNode node in
mod_node.SelectNodes("./omssa:MSModSpec_residues/omssa:MSModSpec_residues_E", mods_xml_ns))
{
string aa = node.FirstChild.Value;
sites = sites.Set(aa[0]);
}
OmssaModification mod = new OmssaModification(name, id, mono, average, userMod, sites);
Modifications.Add(name, mod);
_modificationKeyDicitonary[id] = name;
}
}
public ModificationWithLocation(string id, Tuple <string, string> accession, ModificationMotif motif, ModificationSites terminusLocalization, IDictionary <string, IList <string> > linksToOtherDbs, string modificationType) : base(id, modificationType)
{
this.accession = accession;
this.motif = motif;
this.terminusLocalization = terminusLocalization;
this.linksToOtherDbs = linksToOtherDbs;
}
public Residue(string name, char oneLetterAbbreviation, string threeLetterAbbreviation, ChemicalFormula chemicalFormula, ModificationSites site)
{
Name = name;
Letter = oneLetterAbbreviation;
Symbol = threeLetterAbbreviation;
ThisChemicalFormula = chemicalFormula;
MonoisotopicMass = ThisChemicalFormula.MonoisotopicMass;
Site = site;
}
internal AminoAcid(string name, char oneLetterAbbreviation, string threeLetterAbbreviation, ChemicalFormula chemicalFormula, ModificationSites site)
{
Name = name;
Letter = oneLetterAbbreviation;
Symbol = threeLetterAbbreviation;
ChemicalFormula = chemicalFormula;
MonoisotopicMass = ChemicalFormula.MonoisotopicMass;
Site = site;
}
public IMass AddFixedModification(int modID, ModificationSites sites)
{
OmssaModification modification = null;
if (OmssaModification.TryGetModification(modID, out modification))
{
_fixedMods.Add(modification);
}
return modification;
}
internal AminoAcid(string name, char oneLetterAbbreviation, string threeLetterAbbreviation, ChemicalFormula chemicalFormula, ModificationSites site)
{
Name = name;
Letter = oneLetterAbbreviation;
Symbol = threeLetterAbbreviation;
ChemicalFormula = chemicalFormula;
MonoisotopicMass = ChemicalFormula.MonoisotopicMass;
Site = site;
}
public static ModificationSites Set(this ModificationSites sites, AminoAcid aminoacid)
{
if (aminoacid != null)
{
sites |= aminoacid.Site;
}
return(sites);
}
public static ModificationSites Set(this ModificationSites sites, char aminoacid)
{
AminoAcid aa;
if (AminoAcid.TryGetResidue(aminoacid, out aa))
{
sites |= aa.Site;
}
return(sites);
}
public static bool ContainsSite(this ModificationSites sites, ModificationSites otherSites)
{
// By convention, if the other site is 'Any', they are always equal
if (otherSites == ModificationSites.Any)
return true;
if (otherSites == ModificationSites.None)
return sites == ModificationSites.None;
return sites == otherSites;
}
public static void LoadOmssaModifications(string file, bool userMod = true)
{
XmlDocument mods_xml = new XmlDocument();
mods_xml.Load(file);
XmlNamespaceManager mods_xml_ns = new XmlNamespaceManager(mods_xml.NameTable);
mods_xml_ns.AddNamespace("omssa", mods_xml.ChildNodes[1].Attributes["xmlns"].Value);
foreach (XmlNode mod_node in mods_xml.SelectNodes("/omssa:MSModSpecSet/omssa:MSModSpec", mods_xml_ns))
{
string name = mod_node.SelectSingleNode("./omssa:MSModSpec_name", mods_xml_ns).FirstChild.Value;
int id = int.Parse(mod_node.SelectSingleNode("./omssa:MSModSpec_mod/omssa:MSMod", mods_xml_ns).FirstChild.Value);
double mono = double.Parse(mod_node.SelectSingleNode("./omssa:MSModSpec_monomass", mods_xml_ns).FirstChild.Value);
double average = double.Parse(mod_node.SelectSingleNode("./omssa:MSModSpec_averagemass", mods_xml_ns).FirstChild.Value);
int modType = int.Parse(mod_node.SelectSingleNode("./omssa:MSModSpec_type/omssa:MSModType", mods_xml_ns).FirstChild.Value);
ModificationSites sites = ModificationSites.None;
switch (modType)
{
case 0:
foreach (
XmlNode node in
mod_node.SelectNodes("./omssa:MSModSpec_residues/omssa:MSModSpec_residues_E", mods_xml_ns))
{
string aa = node.FirstChild.Value;
sites = sites.Set(aa[0]);
}
break;
case 1:
sites |= ModificationSites.NProt;
break;
case 3:
sites |= ModificationSites.ProtC;
break;
case 5:
sites |= ModificationSites.NPep;
break;
case 6:
sites |= ModificationSites.PepC;
break;
}
OmssaModification mod = new OmssaModification(name, id, mono, average, userMod, sites);
Modifications[name] = mod;
_modificationKeyDicitonary[id] = name;
}
}
public static IEnumerable <ModificationSites> EnumerateActiveSites(this ModificationSites sites)
{
foreach (ModificationSites site in Enum.GetValues(typeof(ModificationSites)))
{
if (site == ModificationSites.None)
{
continue;
}
if ((sites & site) == site)
{
yield return(site);
}
}
}
/// <summary>
/// Load a modification file
/// </summary>
/// <param name="filePath">The path to the modification file</param>
public static void Load(string filePath)
{
try
{
var modsXml = new XmlDocument();
modsXml.Load(filePath);
foreach (XmlNode modNode in modsXml.SelectNodes("//Modifications/Modification"))
{
string modName = modNode.Attributes["name"].Value;
string chemicalFormula = "";
bool isChemicalFormula = false;
double mass = 0;
var chemModNode = modNode.SelectSingleNode("ChemicalFormula");
if (chemModNode != null)
{
chemicalFormula = modNode.SelectSingleNode("ChemicalFormula").InnerText;
isChemicalFormula = true;
}
else
{
mass = double.Parse(modNode.SelectSingleNode("DeltaMass").InnerText);
}
ModificationSites sites = ModificationSites.None;
foreach (XmlNode siteNode in modNode.SelectNodes("ModificationSite"))
{
string modSite = siteNode.InnerText;
var site = (ModificationSites)Enum.Parse(typeof(ModificationSites), modSite);
sites |= site;
}
var modification = isChemicalFormula ? new ChemicalFormulaModification(chemicalFormula, modName, sites) : new Modification(mass, modName, sites);
Modifications.Add(modName, modification);
foreach (XmlNode modAltNameNode in modNode.SelectNodes("AlternativeName"))
{
string altName = modAltNameNode.InnerText;
Modifications.Add(altName, modification);
}
}
OnModificationsChanged(false);
}
catch (XmlException)
{
//RestoreDefaults();
}
}
public static bool ContainsSites(this ModificationSites sites, ModificationSites otherSites)
{
// By convention, if the other site is 'Any', they are always equal
if (otherSites == ModificationSites.Any)
{
return(true);
}
if (otherSites == ModificationSites.None)
{
return(sites == ModificationSites.None);
}
return((~sites & otherSites) == ModificationSites.None);
}
public void WriteModification(IMass modification, ModificationSites sites, bool fixedModification = true)
{
if (CurrentStage != Stage.SearchSummary)
{
throw new ArgumentException("You must be in the Search Summary stage to write modifications");
}
foreach (ModificationSites singleSite in sites.GetActiveSites())
{
double basemass = 0;
if (singleSite >= ModificationSites.NPep)
{
_writer.WriteStartElement("terminal_modification");
if (singleSite.HasFlag(ModificationSites.NPep) || singleSite.HasFlag(ModificationSites.NProt))
{
_writer.WriteAttributeString("terminus", "N");
basemass += AminoAcidPolymer.DefaultNTerminus.MonoisotopicMass;
}
else
{
_writer.WriteAttributeString("terminus", "C");
basemass += AminoAcidPolymer.DefaultCTerminus.MonoisotopicMass;
}
_writer.WriteAttributeString("protein_terminus", (singleSite.HasFlag(ModificationSites.NProt) || singleSite.HasFlag(ModificationSites.ProtC)) ? "Y" : "N");
}
else
{
string letter = Enum.GetName(typeof(ModificationSites), singleSite);
AminoAcid aa = AminoAcid.GetResidue(letter);
_writer.WriteStartElement("aminoacid_modification");
_writer.WriteAttributeString("aminoacid", letter);
basemass += aa.MonoisotopicMass;
}
double massshift = modification.MonoisotopicMass;
_writer.WriteAttributeString("variable", (fixedModification) ? "N" : "Y");
_writer.WriteAttributeString("mass", (basemass + massshift).ToString());
_writer.WriteAttributeString("massdiff", massshift.ToString());
_writer.WriteAttributeString("description", modification.ToString());
_writer.WriteEndElement();
}
}
public void TestClearModifications()
{
Peptide a = new Peptide("ACDEFGHIKLMNPQRSTVWY");
a.AddModification(new OldSchoolChemicalFormulaModification(ChemicalFormula.ParseFormula("O"), ModificationSites.D));
a.AddModification(new OldSchoolChemicalFormulaModification(ChemicalFormula.ParseFormula("H"), ModificationSites.E));
Assert.AreEqual(2, a.ModificationCount());
a.ClearModifications();
Assert.AreEqual(0, a.ModificationCount());
a.AddModification(new OldSchoolChemicalFormulaModification(ChemicalFormula.ParseFormula("O"), ModificationSites.NTerminus));
a.AddModification(new OldSchoolModification(1), ModificationSites.TerminusC);
Assert.AreEqual(2, a.ModificationCount());
a.Fragment(FragmentTypes.y);
Peptide peptide = new Peptide("[C2H3NO]-LLL-[C2H3NO]");
ModificationSites ff = ModificationSites.NPep | ModificationSites.PepC;
peptide.ClearModifications(ff);
Assert.AreEqual("LLL", peptide.GetSequenceWithModifications());
}
public virtual int AddModification(IHasMass modification, ModificationSites sites)
{
if (_modifications == null)
{
_modifications = new IHasMass[Length + 2];
}
int count = 0;
IHasMass currentMod;
if ((sites & ModificationSites.NPep) == ModificationSites.NPep)
{
currentMod = NTerminusModification;
NTerminusModification = currentMod == null ? modification : new ModificationCollection(currentMod, modification);
count++;
}
for (int i = 0; i < Length; i++)
{
ModificationSites site = residues[i].Site;
if ((sites & site) == site)
{
currentMod = _modifications[i + 1];
ReplaceMod(i + 1, currentMod == null ? modification : new ModificationCollection(currentMod, modification));
count++;
}
}
if ((sites & ModificationSites.PepC) == ModificationSites.PepC)
{
currentMod = CTerminusModification;
CTerminusModification = currentMod == null ? modification : new ModificationCollection(currentMod, modification);
count++;
}
return(count);
}
public ChemicalFormulaModification(string chemicalFormula, ModificationSites sites = ModificationSites.Any)
: this(new ChemicalFormula(chemicalFormula), "", sites)
{
Name = ChemicalFormula.ToString();
}
public ChemicalFormulaModification(string chemicalFormula, string name, ModificationSites sites = ModificationSites.Any)
: this(new ChemicalFormula(chemicalFormula), name, sites)
{
}
internal AminoAcid(string name, char oneLetterAbbreviation, string threeLetterAbbreviation, string chemicalFormula, ModificationSites site)
: this(name, oneLetterAbbreviation, threeLetterAbbreviation, new ChemicalFormula(chemicalFormula), site)
{
}
public OmssaModification(string name, int id, double mono, double average, bool userMod, ModificationSites sites = ModificationSites.None)
: base(mono, name, sites)
{
ID = id;
UserMod = userMod;
}
public ChemicalFormulaModification(ChemicalFormula chemicalFormula, string name, ModificationSites sites = ModificationSites.Any)
: base(chemicalFormula.MonoisotopicMass, name, sites)
{
ChemicalFormula = chemicalFormula;
}
public Modification(double monoMass = 0.0, string name = "", ModificationSites sites = ModificationSites.Any)
{
MonoisotopicMass = monoMass;
Name = name;
Sites = sites;
}
public OldSchoolModification(double monoMass, string name, ModificationSites sites)
{
MonoisotopicMass = monoMass;
Name = name;
Sites = sites;
}
public OldSchoolChemicalFormulaModification(ChemicalFormula chemicalFormula, string name, ModificationSites sites)
: base(chemicalFormula.MonoisotopicMass, name, sites)
{
ThisChemicalFormula = chemicalFormula;
}
public ChemicalFormulaModification(string chemicalFormula, string name, ModificationSites sites = ModificationSites.Any)
: this(new ChemicalFormula(chemicalFormula), name, sites)
{
}
public void AddVariableModification(IMass modificaiton, ModificationSites sites)
{
}
public ModificationWithMassAndCf(string id, Tuple <string, string> accession, ModificationMotif motif, ModificationSites site, ChemicalFormula chemicalFormula, double mm, IDictionary <string, IList <string> > linksToOtherDbs, IEnumerable <double> neutralLosses, IEnumerable <double> diagnosticIons, string modificationType)
: base(id, accession, motif, site, mm, linksToOtherDbs, neutralLosses, diagnosticIons, modificationType)
{
this.chemicalFormula = chemicalFormula;
}
public void WriteModification(IMass modification, ModificationSites sites, bool fixedModification = true)
{
if (CurrentStage != Stage.SearchSummary)
throw new ArgumentException("You must be in the Search Summary stage to write modifications");
foreach (ModificationSites singleSite in sites.GetActiveSites())
{
double basemass = 0;
if (singleSite >= ModificationSites.NPep)
{
_writer.WriteStartElement("terminal_modification");
if (singleSite.HasFlag(ModificationSites.NPep) || singleSite.HasFlag(ModificationSites.NProt))
{
_writer.WriteAttributeString("terminus", "N");
basemass += AminoAcidPolymer.DefaultNTerminus.MonoisotopicMass;
}
else
{
_writer.WriteAttributeString("terminus", "C");
basemass += AminoAcidPolymer.DefaultCTerminus.MonoisotopicMass;
}
_writer.WriteAttributeString("protein_terminus", (singleSite.HasFlag(ModificationSites.NProt) || singleSite.HasFlag(ModificationSites.ProtC)) ? "Y" : "N");
}
else
{
string letter = Enum.GetName(typeof(ModificationSites), singleSite);
AminoAcid aa = AminoAcid.GetResidue(letter);
_writer.WriteStartElement("aminoacid_modification");
_writer.WriteAttributeString("aminoacid", letter);
basemass += aa.MonoisotopicMass;
}
double massshift = modification.MonoisotopicMass;
_writer.WriteAttributeString("variable", (fixedModification) ? "N" : "Y");
_writer.WriteAttributeString("mass", (basemass + massshift).ToString());
_writer.WriteAttributeString("massdiff", massshift.ToString());
_writer.WriteAttributeString("description", modification.ToString());
_writer.WriteEndElement();
}
}
public Isotopologue(string name, ModificationSites sites = ModificationSites.None)
: base(0, name, sites)
{
_modifications = new SortedList <double, Modification>();
}
public ChemicalFormulaModification(ChemicalFormula chemicalFormula, string name, ModificationSites sites = ModificationSites.Any)
: base(chemicalFormula.MonoisotopicMass, name, sites)
{
ChemicalFormula = chemicalFormula;
}
public ModificationWithMultiplePossibilitiesCollection(string name, ModificationSites sites)
: base(0, name, sites)
{
_modifications = new SortedList <double, OldSchoolModification>();
}
public OldSchoolChemicalFormulaModification(ChemicalFormula chemicalFormula, ModificationSites sites)
: this(chemicalFormula, "", sites)
{
Name = ThisChemicalFormula.Formula;
}
public OmssaModification(string name, int id, double mono, double average, bool userMod, ModificationSites sites = ModificationSites.None)
: base(mono, name, sites)
{
ID = id;
UserMod = userMod;
}
public void AddVariableModification(IMass modificaiton, ModificationSites sites)
{
}
public static AminoAcid AddResidue(string name, char oneLetterAbbreviation, string threeLetterAbbreviation, string chemicalFormula, ModificationSites site)
{
var residue = new AminoAcid(name, oneLetterAbbreviation, threeLetterAbbreviation, chemicalFormula, site);
AddResidueToDictionary(residue);
return residue;
}
public ModificationWithMass(string id, Tuple <string, string> accession, ModificationMotif motif, ModificationSites modificationSites, double monoisotopicMass, IDictionary <string, IList <string> > externalDatabaseReferences, IEnumerable <double> neutralLosses, IEnumerable <double> diagnosticIons, string modificationType)
: base(id, accession, motif, modificationSites, externalDatabaseReferences, modificationType)
{
this.monoisotopicMass = monoisotopicMass;
if (neutralLosses == null || neutralLosses.Count() == 0)
{
neutralLosses = new List <double> {
0
}
}
;
this.neutralLosses = neutralLosses;
this.diagnosticIons = diagnosticIons;
}
internal AminoAcid(string name, char oneLetterAbbreviation, string threeLetterAbbreviation, string chemicalFormula, ModificationSites site)
: this(name, oneLetterAbbreviation, threeLetterAbbreviation, new ChemicalFormula(chemicalFormula), site)
{
}
public ChemicalFormulaModification(string chemicalFormula, ModificationSites sites = ModificationSites.Any)
: this(new ChemicalFormula(chemicalFormula), "", sites)
{
Name = ChemicalFormula.ToString();
}
public static AminoAcid AddResidue(string name, char oneLetterAbbreviation, string threeLetterAbbreviation, string chemicalFormula, ModificationSites site)
{
var residue = new AminoAcid(name, oneLetterAbbreviation, threeLetterAbbreviation, chemicalFormula, site);
AddResidueToDictionary(residue);
return(residue);
}
