public static Crosslinker ParseCrosslinkerFromString(string line)
{
var split = line.Split('\t');
bool cleavable = true;
if (split[3] == "F")
{
cleavable = false;
}
Crosslinker crosslinker = new Crosslinker(
crosslinkerName: split[0],
crosslinkerModSites: split[1],
crosslinkerModSites2: split[2],
cleavable: cleavable,
dissociationTypes: split[4],
totalMass: double.Parse(split[5]),
cleaveMassShort: double.Parse(split[6]),
cleaveMassLong: double.Parse(split[7]),
loopMass: double.Parse(split[5]),
deadendMassH2O: double.Parse(split[8]),
deadendMassNH2: double.Parse(split[9]),
deadendMassTris: double.Parse(split[10]));
return(crosslinker);
}
/// <summary>
/// Deadend and loop crosslink are changed to a type of modification and searched as a modified peptide.
/// </summary>
/// <param name="crosslinker"></param>
public static void GenerateCrosslinkModifications(Crosslinker crosslinker, out Modification TrisDeadEnd, out Modification H2ODeadEnd, out Modification NH2DeadEnd, out Modification Loop)
{
ModificationMotif.TryGetMotif("X", out var motif);
TrisDeadEnd = new Modification(_originalId: "Tris Dead End", _modificationType: "Crosslink", _locationRestriction: "Anywhere.", _target: motif, _monoisotopicMass: crosslinker.DeadendMassTris);
H2ODeadEnd = new Modification(_originalId: "H2O Dead End", _modificationType: "Crosslink", _locationRestriction: "Anywhere.", _target: motif, _monoisotopicMass: crosslinker.DeadendMassH2O);
NH2DeadEnd = new Modification(_originalId: "NH2 Dead End", _modificationType: "Crosslink", _locationRestriction: "Anywhere.", _target: motif, _monoisotopicMass: crosslinker.DeadendMassNH2);
Loop = new Modification(_originalId: "Loop", _modificationType: "Crosslink", _locationRestriction: "Anywhere.", _target: motif, _monoisotopicMass: crosslinker.LoopMass);
}
private static void LoadCrosslinkers()
{
_KnownCrosslinkers = new List <Crosslinker>();
// load default crosslinkers
string crosslinkerLocation = Path.Combine(DataDir, @"Data", @"Crosslinkers.tsv");
AddCrosslinkers(Crosslinker.LoadCrosslinkers(crosslinkerLocation));
// load custom crosslinkers
string customCrosslinkerLocation = Path.Combine(DataDir, @"Data", @"CustomCrosslinkers.tsv");
if (File.Exists(customCrosslinkerLocation))
{
AddCrosslinkers(Crosslinker.LoadCrosslinkers(customCrosslinkerLocation));
}
}
static GlobalVariables()
{
MetaMorpheusVersion = typeof(GlobalVariables).Assembly.GetName().Version.ToString();
if (MetaMorpheusVersion.Equals("1.0.0.0"))
{
#if DEBUG
MetaMorpheusVersion = "Not a release version. DEBUG.";
#else
MetaMorpheusVersion = "Not a release version.";
#endif
}
else
{
// as of 0.0.277, AppVeyor appends the build number
// this is intentional; it's to avoid conflicting AppVeyor build numbers
// trim the build number off the version number for displaying/checking versions, etc
var foundIndexes = new List <int>();
for (int i = 0; i < MetaMorpheusVersion.Length; i++)
{
if (MetaMorpheusVersion[i] == '.')
{
foundIndexes.Add(i);
}
}
MetaMorpheusVersion = MetaMorpheusVersion.Substring(0, foundIndexes.Last());
}
{
var pathToProgramFiles = Environment.GetFolderPath(Environment.SpecialFolder.ProgramFiles);
if (!String.IsNullOrWhiteSpace(pathToProgramFiles) && AppDomain.CurrentDomain.BaseDirectory.Contains(pathToProgramFiles) && !AppDomain.CurrentDomain.BaseDirectory.Contains("Jenkins"))
{
DataDir = Path.Combine(Environment.GetFolderPath(Environment.SpecialFolder.LocalApplicationData), "MetaMorpheus");
}
else
{
DataDir = AppDomain.CurrentDomain.BaseDirectory;
}
}
ElementsLocation = Path.Combine(DataDir, @"Data", @"elements.dat");
UsefulProteomicsDatabases.Loaders.LoadElements();
AddSeparationTypes(new List <string> {
{ "HPLC" }, { "CZE" }
});
// load default crosslinkers
string crosslinkerLocation = Path.Combine(DataDir, @"Data", @"Crosslinkers.tsv");
AddCrosslinkers(Crosslinker.LoadCrosslinkers(crosslinkerLocation));
// load custom crosslinkers
string customCrosslinkerLocation = Path.Combine(DataDir, @"Data", @"CustomCrosslinkers.tsv");
if (File.Exists(customCrosslinkerLocation))
{
AddCrosslinkers(Crosslinker.LoadCrosslinkers(customCrosslinkerLocation));
}
OGlycanLocations = new List <string>();
foreach (var glycanFile in Directory.GetFiles(Path.Combine(DataDir, @"Glycan_Mods", @"OGlycan")))
{
OGlycanLocations.Add(glycanFile);
}
NGlycanLocations = new List <string>();
foreach (var glycanFile in Directory.GetFiles(Path.Combine(DataDir, @"Glycan_Mods", @"NGlycan")))
{
NGlycanLocations.Add(glycanFile);
}
ExperimentalDesignFileName = "ExperimentalDesign.tsv";
UnimodDeserialized = UsefulProteomicsDatabases.Loaders.LoadUnimod(Path.Combine(DataDir, @"Data", @"unimod.xml")).ToList();
PsiModDeserialized = UsefulProteomicsDatabases.Loaders.LoadPsiMod(Path.Combine(DataDir, @"Data", @"PSI-MOD.obo.xml"));
var formalChargesDictionary = UsefulProteomicsDatabases.Loaders.GetFormalChargesDictionary(PsiModDeserialized);
UniprotDeseralized = UsefulProteomicsDatabases.Loaders.LoadUniprot(Path.Combine(DataDir, @"Data", @"ptmlist.txt"), formalChargesDictionary).ToList();
foreach (var modFile in Directory.GetFiles(Path.Combine(DataDir, @"Mods")))
{
AddMods(UsefulProteomicsDatabases.PtmListLoader.ReadModsFromFile(modFile, out var errorMods), false);
}
AddMods(UniprotDeseralized.OfType <Modification>(), false);
AddMods(UnimodDeserialized.OfType <Modification>(), false);
// populate dictionaries of known mods/proteins for deserialization
AllModsKnownDictionary = new Dictionary <string, Modification>();
foreach (Modification mod in AllModsKnown)
{
if (!AllModsKnownDictionary.ContainsKey(mod.IdWithMotif))
{
AllModsKnownDictionary.Add(mod.IdWithMotif, mod);
}
// no error thrown if multiple mods with this ID are present - just pick one
}
//Add Glycan mod into AllModsKnownDictionary, currently this is for MetaDraw.
//The reason why not include Glycan into modification database is for users to apply their own database.
foreach (var path in OGlycanLocations)
{
var og = GlycanDatabase.LoadGlycan(path, false, false);
foreach (var g in og)
{
var ogmod = Glycan.OGlycanToModification(g);
if (!AllModsKnownDictionary.ContainsKey(ogmod.IdWithMotif))
{
AllModsKnownDictionary.Add(ogmod.IdWithMotif, ogmod);
}
}
}
foreach (var path in NGlycanLocations)
{
var og = GlycanDatabase.LoadGlycan(path, false, false);
foreach (var g in og)
{
var ogmod = Glycan.OGlycanToModification(g);
if (!AllModsKnownDictionary.ContainsKey(ogmod.IdWithMotif))
{
AllModsKnownDictionary.Add(ogmod.IdWithMotif, ogmod);
}
}
}
RefreshAminoAcidDictionary();
string settingsPath = Path.Combine(DataDir, @"settings.toml");
if (!File.Exists(settingsPath))
{
Toml.WriteFile <GlobalSettings>(new GlobalSettings(), settingsPath);
}
GlobalSettings = Toml.ReadFile <GlobalSettings>(settingsPath);
AllSupportedDissociationTypes = new Dictionary <string, DissociationType> {
{ DissociationType.CID.ToString(), DissociationType.CID },
{ DissociationType.ECD.ToString(), DissociationType.ECD },
{ DissociationType.ETD.ToString(), DissociationType.ETD },
{ DissociationType.HCD.ToString(), DissociationType.HCD },
{ DissociationType.EThcD.ToString(), DissociationType.EThcD },
{ DissociationType.Custom.ToString(), DissociationType.Custom },
{ DissociationType.LowCID.ToString(), DissociationType.LowCID }
// TODO: allow reading from scan header (autodetect dissociation type)
};
}
