public void GeneratePdbForPeptide()
{
var peptide = PeptideBuilder.PeptideFromString(
"MQRSPLEKASVVSKLFFSWTRPILRKGYRQRLELSDIYQIPSVDSADNLSEKLEREWDRE"
+ "LASKKNPKLINALRRCFFWRFMFYGIFLYLGEVTKAVQPLLLGRIIASYDPDNKEERSIA"
+ "IYLGIGLCLLFIVRTLLLHPAIFGLHHIGMQMRIAMFSLIYKKTLKLSSRVLDKISIGQL"
+ "VSLLSNNLNKFDEGLALAHFVWIAPLQVALLMGLIWELLQASAFCGLGFLIVLALFQAGL"
+ "GRMMMKYRDQRAGKISERLVITSEMIENIQSVKAYCWEEAMEKMIENLRQTELKLTRKAA"
+ "YVRYFNSSAFFFSGFFVVFLSVLPYALIKGIILRKIFTTISFCIVLRMAVTRQFPWAVQT"
+ "WYDSLGAINKIQDFLQKQEYKTLEYNLTTTEVVMENVTAFWEEGFGELFEKAKQNNNNRK"
+ "TSNGDDSLFFSNFSLLGTPVLKDINFKIERGQLLAVAGSTGAGKTSLLMVIMGELEPSEG"
+ "KIKHSGRISFCSQFSWIMPGTIKENIIFGVSYDEYRYRSVIKACQLEEDISKFAEKDNIV"
+ "LGEGGITLSGGQRARISLARAVYKDADLYLLDSPFGYLDVLTEKEIFESCVCKLMANKTR"
+ "ILVTSKMEHLKKADKILILHEGSSYFYGTFSELQNLQPDFSSKLMGCDSFDQFSAERRNS"
+ "ILTETLHRFSLEGDAPVSWTETKKQSFKQTGEFGEKRKNSILNPINSIRKFSIVQKTPLQ"
+ "MNGIEEDSDEPLERRLSLVPDSEQGEAILPRISVISTGPTLQARRRQSVLNLMTHSVNQG"
+ "QNIHRKTTASTRKVSLAPQANLTELDIYSRRLSQETGLEISEEINEEDLKECFFDDMESI"
+ "PAVTTWNTYLRYITVHKSLIFVLIWCLVIFLAEVAASLVVLWLLGNTPLQDKGNSTHSRN"
+ "NSYAVIITSTSSYYVFYIYVGVADTLLAMGFFRGLPLVHTLITVSKILHHKMLHSVLQAP"
+ "MSTLNTLKAGGILNRFSKDIAILDDLLPLTIFDFIQLLLIVIGAIAVVAVLQPYIFVATV"
+ "PVIVAFIMLRAYFLQTSQQLKQLESEGRSPIFTHLVTSLKGLWTLRAFGRQPYFETLFHK"
+ "ALNLHTANWFLYLSTLRWFQMRIEMIFVIFFIAVTFISILTTGEGEGRVGIILTLAMNIM"
+ "STLQWAVNSSIDVDSLMRSVSRVFKFIDMPTEGKPTKSTKPYKNGQLSKVMIIENSHVKK"
+ "DDIWPSGGQMTVKDLTAKYTEGGNAILENISFSISPGQRVGLLGRTGSGKSTLLSAFLRL"
+ "LNTEGEIQIDGVSWDSITLQQWRKAFGVIPQKVFIFSGTFRKNLDPYEQWSDQEIWKVAD"
+ "EVGLRSVIEQFPGKLDFVLVDGGCVLSHGHKQLMCLARSVLSKAKILLLDEPSAHLDPVT"
+ "YQIIRRTLKQAFADCTVILCEHRIEAMLECQQFLVIEENKVRQYDSIQKLLNERSLFRQA"
+ "ISPSDRVKLFPHRNSSKCKSKPQIAALKEETEEEVQDTRL");
peptide.Molecule.PositionAtoms(peptide.MoleculeReference.FirstAtomId, peptide.MoleculeReference.LastAtomId);
File.WriteAllText(@"G:\Projects\HumanGenome\cftr.pdb", PdbSerializer.Serialize("cftr", peptide));
}
public void AlignPdbSubsequences()
{
var pdbCode1 = "1xmj";
var startIndex1 = 48;
var pdbCode2 = "2bbo";
var startIndex2 = 60;
var length = 40;
var outputDirectory = @"C:\Temp";
var pdbFile1 = $@"G:\Projects\HumanGenome\Protein-PDBs\HumanProteins\SingleChain\FullyPositioned\pdb{pdbCode1}.ent";
var pdbFile2 = $@"G:\Projects\HumanGenome\Protein-PDBs\HumanProteins\SingleChain\FullyPositioned\pdb{pdbCode2}.ent";
var peptide1 = PdbReader.ReadFile(pdbFile1).Models.First().Chains.First();
var peptide2 = PdbReader.ReadFile(pdbFile2).Models.First().Chains.First();
var proteinAligner = new ProteinAligner();
var proteinAlignerResult = proteinAligner.AlignSubsequence(peptide1, startIndex1, peptide2, startIndex2, length);
var alignmentTransform = proteinAlignerResult.Transformation;
peptide2.Molecule.Atoms
.Where(atom => atom.IsPositioned)
.ForEach(atom =>
{
atom.IsPositionFixed = false;
atom.Position = alignmentTransform.Apply(atom.Position.In(SIPrefix.Pico, Unit.Meter)).To(SIPrefix.Pico, Unit.Meter);
});
var repositionedPdb = PdbSerializer.Serialize(pdbCode2, peptide2);
File.Copy(pdbFile1, Path.Combine(outputDirectory, $@"pdb{pdbCode1}.ent"), true);
File.WriteAllText(
Path.Combine(outputDirectory, $@"pdb{pdbCode2}_repositioned_{pdbCode1}_sub{startIndex1}-{startIndex2}-{length}.ent"),
repositionedPdb);
}
public void RunSimulationForSequence(string pdbCode, string sequenceString, string outputFilePath)
{
var distributionDirectory = @"G:\Projects\HumanGenome\ramachadranDistributions";
var sut = new MultiLevelGrowingFoldingSimulator(distributionDirectory);
var settings = new MultiLevelGrowingFoldingSimulatorSettings
{
};
var aminoAcidSequence = sequenceString
.Select(c => c.ToAminoAcidName())
.ToList();
var peptide = sut.Simulate(aminoAcidSequence, settings);
var approximatePeptideCompleter = new ApproximatePeptideCompleter(peptide);
var completedPeptide = approximatePeptideCompleter.GetBackbone();
File.WriteAllText(outputFilePath, PdbSerializer.Serialize(pdbCode, completedPeptide));
}
public void AlignAllModelsOfProtein(string proteinName, bool storeIndividualAlignedPdb)
{
var outputDirectory = Path.Combine(@"G:\Projects\HumanGenome\Protein-PDBs\HumanProteins\SingleChain\FullyPositioned\AlignedProteins", proteinName);
if (!Directory.Exists(outputDirectory))
{
Directory.CreateDirectory(outputDirectory);
}
var proteinListDirectory = @"G:\Projects\HumanGenome\Protein-PDBs\HumanProteins\SingleChain\FullyPositioned\ByProtein";
var pdbListFile = Path.Combine(proteinListDirectory, proteinName + ".csv");
var pdbFiles = File.ReadLines(pdbListFile).ToList();
var firstPeptide = PdbReader.ReadFile(pdbFiles.First()).Models.First().Chains.First();
File.Copy(pdbFiles.First(), Path.Combine(outputDirectory, Path.GetFileName(pdbFiles.First())), true);
var proteinAligner = new ProteinAligner();
var combinedModels = new List <Peptide> {
firstPeptide
};
var modelErrors = new Dictionary <string, UnitValue> {
{ pdbFiles.First(), 0.To(Unit.Meter) }
};
foreach (var pdbFile in pdbFiles.Skip(1))
{
var peptide = PdbReader.ReadFile(pdbFile).Models.First().Chains.First();
var proteinAlignerResult = proteinAligner.Align(firstPeptide, peptide);
var alignmentTransform = proteinAlignerResult.Transformation;
peptide.Molecule.Atoms
.Where(atom => atom.IsPositioned)
.ForEach(atom =>
{
atom.IsPositionFixed = false;
atom.Position = alignmentTransform.Apply(atom.Position.In(SIPrefix.Pico, Unit.Meter)).To(SIPrefix.Pico, Unit.Meter);
});
var modelError = proteinAlignerResult.IsTransformationValid
? proteinAlignerResult.AveragePositionError
: double.PositiveInfinity.To(Unit.Meter);
modelErrors.Add(pdbFile, modelError);
combinedModels.Add(peptide);
if (storeIndividualAlignedPdb)
{
var pdbId = Path.GetFileNameWithoutExtension(pdbFile).Replace("pdb", "");
var repositionedPdb = PdbSerializer.Serialize(pdbId, peptide);
File.WriteAllText(
Path.Combine(outputDirectory, $"pdb{pdbId}.ent"),
repositionedPdb);
}
}
var medianError = modelErrors.Values.Select(x => x.In(SIPrefix.Pico, Unit.Meter)).Median();
var stdError = modelErrors.Values
.Select(x => x.In(SIPrefix.Pico, Unit.Meter))
.Average(x => x.Square()).Sqrt();
var validModels = pdbFiles
.Select((pdbFile, idx) => new
{
PdbFile = pdbFile,
Model = combinedModels[idx],
Error = modelErrors[pdbFile].In(SIPrefix.Pico, Unit.Meter)
})
.Where(x => x.Error < Math.Min(medianError + 2 * stdError, 1000))
.Select(x => x.Model)
.ToArray();
var combinedPdb = PdbSerializer.Serialize("1234", validModels);
File.WriteAllText(
Path.Combine(outputDirectory, "pdb_combined.ent"),
combinedPdb);
File.WriteAllLines(
Path.Combine(outputDirectory, "averageError.csv"),
modelErrors.Select(kvp => $"{kvp.Key};{kvp.Value.In(SIPrefix.Pico, Unit.Meter)}"));
}