public DonatedSubstitutionInfo(string description, string folder, string @interface, string interfacePadded, InterfaceInterfaceData interfaceInterfaceSequenceIdentityClusteringItem)
{
Description = description;
Folder = folder;
Interface = @interface;
InterfacePadded = interfacePadded;
InterfaceInterfaceSequenceIdentityClusteringItem = interfaceInterfaceSequenceIdentityClusteringItem;
}
public static void Main(string[] args)
{
var resultsFolder = @"C:\r\";
Directory.CreateDirectory(resultsFolder);
var atomsFullFolder = @"C:\dbmk\atoms_all\";
const int atom_chain = 21;
const int atom_chain_len = 1;
const int atom_icode = 26;
const int atom_icode_len = 1;
const int atom_type = 14;
const int atom_type_len = 3;
const int atom_resseq = 22;
const int atom_resseq_len = 4;
var dbmkList = File.ReadAllLines(@"c:\dbmk\dbmk-1to1-list.txt").ToList();
dbmkList = dbmkList.Where(a => !string.IsNullOrWhiteSpace(a)).ToList();
var structureOutputTypes = new List <string>()
{
"all"
};
var sequenceOutputTypes = new List <string> {
"pir"
};
var list = new List <string>();
foreach (var dbmkProtein in dbmkList)
{
var pdbId = dbmkProtein.Substring(0, 4);
var pdbChains = dbmkProtein.Substring(4);
var pdbInterfaceInterfaceData = InterfaceInterfaceData.Load(@"c:\dbmk\interfaces\interface-interface_" + pdbId + ".pdb.csv");
pdbInterfaceInterfaceData = pdbInterfaceInterfaceData.Where(a => !string.IsNullOrWhiteSpace(a.ReceptorPdbId) && !string.IsNullOrWhiteSpace(a.LigandPdbId)).ToList();
pdbInterfaceInterfaceData = pdbInterfaceInterfaceData.Where(a => pdbChains.Contains(a.ReceptorChainId) && pdbChains.Contains(a.LigandChainId)).ToList();
pdbInterfaceInterfaceData = pdbInterfaceInterfaceData.Where(a => ((double)a.LigandInterfaceAllAminoAcidsSuper.Length / (double)a.LigandSequenceSuper.Length) < 0.5).ToList();
for (int index = 0; index < pdbInterfaceInterfaceData.Count; index++)
{
var receptorLigandDimerA = pdbInterfaceInterfaceData[index];
var outputFolder = @"c:\r\" + receptorLigandDimerA.LigandPdbId + "_" + receptorLigandDimerA.LigandChainId + "_" + (index + 1) + "_" + receptorLigandDimerA.LigandInterfaceAllAminoAcidsSuper.Length + "_" + receptorLigandDimerA.LigandSequenceSuper.Length + "_" + receptorLigandDimerA.LigandInterfaceSuperStart + "_" + receptorLigandDimerA.LigandInterfaceSuperEnd + @"\";
var substitutionList = new List <DonatedSubstitutionInfo>();
var receptorLigandDimerChainOrderA = new List <char> {
receptorLigandDimerA.ReceptorChainId, receptorLigandDimerA.LigandChainId
};
for (var interfacePositionIndex = 0; interfacePositionIndex <= receptorLigandDimerA.LigandSequenceSuper.Length - receptorLigandDimerA.LigandInterfaceAllAminoAcidsSuper.Length; interfacePositionIndex++)
{
var subInterface = receptorLigandDimerA.LigandSequenceSuper.Substring(interfacePositionIndex, receptorLigandDimerA.LigandInterfaceAllAminoAcidsSuper.Length);
var description = "Interface Sliding Window " + interfacePositionIndex + " " + (interfacePositionIndex + subInterface.Length);
substitutionList.Add(new DonatedSubstitutionInfo(description, description.Replace(" ", "_"), subInterface, subInterface, receptorLigandDimerA));
}
var receptorLigandFilename = @"" + receptorLigandDimerA.LigandPdbId + ".pdb";
var acceptorTemplateAllAtomPdbFileData = !structureOutputTypes.Contains("all") ? null : File.ReadAllLines(atomsFullFolder + receptorLigandFilename).Where(a => a[atom_icode] == ' ' && ((a[atom_chain] == receptorLigandDimerA.ReceptorChainId) || (a[atom_chain] == receptorLigandDimerA.LigandChainId))).OrderBy(a => receptorLigandDimerChainOrderA.IndexOf(a[atom_chain])).ThenBy(a => int.Parse(a.Substring(atom_resseq, atom_resseq_len))).ToArray();
var monomerAcceptorTemplateLigandAllAtomPdbFile = !structureOutputTypes.Contains("all") ? null : acceptorTemplateAllAtomPdbFileData.Where(a => a[atom_icode] == ' ' && a[atom_chain] == receptorLigandDimerA.LigandChainId).OrderBy(a => receptorLigandDimerChainOrderA.IndexOf(a[atom_chain])).ThenBy(a => int.Parse(a.Substring(atom_resseq, atom_resseq_len))).ToList();
var receptorHeader = ">" + receptorLigandDimerA.ReceptorPdbId + ":" + receptorLigandDimerA.ReceptorChainId;
var ligandHeader = ">" + receptorLigandDimerA.LigandPdbId + ":" + receptorLigandDimerA.LigandChainId;
var dimerAcceptorTemplateDimerSequenceSuper = new List <Sequence> {
new Sequence(receptorHeader, receptorLigandDimerA.ReceptorSequenceSuper), new Sequence(ligandHeader, receptorLigandDimerA.LigandSequenceSuper)
};
foreach (var sub in substitutionList)
{
// align ligand interface sequence and substitution sequence
var offset = AlignInside(receptorLigandDimerA.LigandInterfaceAllAminoAcidsSuper, sub.InterfacePadded);
if (receptorLigandDimerA.LigandInterfaceAllAminoAcidsSuper.Length < sub.InterfacePadded.Length)
{
offset = -offset;
}
var acceptorTemplateSubstitutionStart = receptorLigandDimerA.LigandInterfaceSuperStart + offset;
//var info = string.Join(Environment.NewLine, new string[] { "" + receptorLigandDimerA.ReceptorSequenceClusterIndex, "" + receptorLigandDimerA.ReceptorInterfaceSequenceClusterIndex, "" + receptorLigandDimerA.LigandSequenceClusterIndex, "" + receptorLigandDimerA.LigandInterfaceSequenceClusterIndex, "" + sub.InterfaceInterfaceSequenceIdentityClusteringItem.ReceptorSequenceClusterIndex, "" + sub.InterfaceInterfaceSequenceIdentityClusteringItem.ReceptorInterfaceSequenceClusterIndex, "" + sub.InterfaceInterfaceSequenceIdentityClusteringItem.LigandSequenceClusterIndex, "" + sub.InterfaceInterfaceSequenceIdentityClusteringItem.LigandInterfaceSequenceClusterIndex, receptorLigandDimerA.ReceptorPdbId, "" + receptorLigandDimerA.ReceptorChainId, receptorLigandDimerA.LigandPdbId, "" + receptorLigandDimerA.LigandChainId, sub.InterfaceInterfaceSequenceIdentityClusteringItem.ReceptorPdbId, "" + sub.InterfaceInterfaceSequenceIdentityClusteringItem.ReceptorChainId, sub.InterfaceInterfaceSequenceIdentityClusteringItem.LigandPdbId, "" + sub.InterfaceInterfaceSequenceIdentityClusteringItem.LigandChainId, sub.Description, receptorLigandDimerA.LigandInterfaceAllAminoAcidsSuper, sub.Interface, sub.InterfacePadded });
var modelOutputFolder = outputFolder + sub.Folder + @"\";
Directory.CreateDirectory(modelOutputFolder);
//File.WriteAllText(modelOutputFolder + "substitution.log", info);
if (structureOutputTypes.Contains("all"))
{
File.WriteAllLines(modelOutputFolder + "template_ligand_all.pdb", monomerAcceptorTemplateLigandAllAtomPdbFile);
}
var mutatedLigandSequenceSubLigand = new Sequence(ligandHeader, receptorLigandDimerA.LigandSequenceSuper.Remove(acceptorTemplateSubstitutionStart, sub.InterfacePadded.Length).Insert(acceptorTemplateSubstitutionStart, sub.InterfacePadded));
var dimerSequenceAfterSubstitution = dimerAcceptorTemplateDimerSequenceSuper.Select(a => a.Id == ligandHeader ? mutatedLigandSequenceSubLigand : a).ToList();
if (sequenceOutputTypes.Contains("pir"))
{
File.WriteAllText(modelOutputFolder + "template_ligand_after_substitution.ali", Sequence.GetFormattedSequence(mutatedLigandSequenceSubLigand, Sequence.SequenceFormat.Pir));
}
}
}
}
}
public static void Main(string[] args)
{
var resultsFolder = @"C:\r\";
Directory.CreateDirectory(resultsFolder);
//var clustersCsvFile = @"C:\CategoryM\catm_combined_data.csv";
//var atomsCaTraceFolder = @"C:\dbmk\atoms_ca\";
//var atomsBackBoneFolder = @"C:\dbmk\atoms_mc\";
//var atomsSideChainFolder = @"C:\dbmk\atoms_sc\";
var atomsFullFolder = @"C:\dbmk\atoms_all\";
const int atom_chain = 21;
const int atom_chain_len = 1;
const int atom_icode = 26;
const int atom_icode_len = 1;
const int atom_type = 14;
const int atom_type_len = 3;
const int atom_resseq = 22;
const int atom_resseq_len = 4;
/*
* var data = InterfaceInterfaceData.Load(clustersCsvFile);
*
* // interfaces with length at least five
* data = data.Where(a => a.ReceptorInterfaceResSeqLength >= 5 && a.LigandInterfaceResSeqLength >= 5).ToList();
*
* data = data.Where(a => char.IsLetterOrDigit(a.ReceptorChainId) && char.IsLetterOrDigit(a.LigandChainId)).ToList();
*
* // ensure pdbids are uppercase
* foreach (var d in data)
* {
* d.ReceptorPdbId = d.ReceptorPdbId.ToUpperInvariant();
* d.LigandPdbId = d.LigandPdbId.ToUpperInvariant();
* }
*/
var scripts = new List <string>();
//scripts.AddRange(Directory.GetFiles(@"c:\modeller_scripts\", "*.py*", SearchOption.AllDirectories));
//scripts.AddRange(Directory.GetFiles(@"c:\modeller_scripts\", "*.bat", SearchOption.AllDirectories));
//scripts.AddRange(Directory.GetFiles(@"c:\modeller_scripts\", "*.html*", SearchOption.AllDirectories));
var dbmkList = File.ReadAllLines(@"c:\dbmk\dbmk-1to1-list.txt").ToList();
dbmkList = dbmkList.Where(a => !string.IsNullOrWhiteSpace(a)).ToList();
var scriptsText = scripts.Select(a => new Tuple <string, string>(a, File.ReadAllText(a))).ToList();
/*
* var dataGroupedByReceptorClusterIndex = data.GroupBy(a => a.ReceptorConsensusClusterIndex).Select(a => a.ToList()).ToList();
* var dataGroupedByReceptorClusterIndexAndInterfaceOverlap = new List<List<InterfaceInterfaceData>>();
*
* foreach (var l in dataGroupedByReceptorClusterIndex)
* {
* var overlapClusters = l.Select(a => new List<InterfaceInterfaceData> { a }).ToList();
*
* foreach (var a in l)
* {
* foreach (var b in l)
* {
* if (a == b) continue;
*
* var seqLenDiff = Math.Abs(Sequence.TrimSequence(a.ReceptorSequenceFromSequenceFile).Length - Sequence.TrimSequence(b.ReceptorSequenceFromSequenceFile).Length);
*
*
* var maxMultiBindDist = -seqLenDiff;
* maxMultiBindDist--;
*
* var o = ProteinBioClass.InterfaceOverlap(a.ReceptorInterfaceResSeqStart, a.ReceptorInterfaceResSeqEnd, b.ReceptorInterfaceResSeqStart, b.ReceptorInterfaceResSeqEnd);
*
* if (o >= maxMultiBindDist || a.ReceptorInterfaceSequenceClusterIndex == b.ReceptorInterfaceSequenceClusterIndex)
* {
* var aCluster = overlapClusters.First(c => c.Contains(a));
* var bCluster = overlapClusters.First(c => c.Contains(b));
* if (aCluster == bCluster) continue;
* aCluster.AddRange(bCluster);
* overlapClusters.Remove(bCluster);
* }
* }
* }
*
* dataGroupedByReceptorClusterIndexAndInterfaceOverlap.AddRange(overlapClusters);
* }
*
* // make sure cluster has more than 1 pdb id
* dataGroupedByReceptorClusterIndexAndInterfaceOverlap = dataGroupedByReceptorClusterIndexAndInterfaceOverlap.Where(a => a.Select(b => b.ReceptorPdbId).Distinct().Count() > 1).ToList();
*/
var structureOutputTypes = new List <string>()
{
"all"
};
var sequenceOutputTypes = new List <string> {
"pir"
};
//var calculateReversed = true;
var list = new List <string>();
foreach (var dbmkProtein in dbmkList)
{
var pdbId = dbmkProtein.Substring(0, 4);
var pdbChains = dbmkProtein.Substring(4);
var pdbInterfaceInterfaceData = InterfaceInterfaceData.Load(@"c:\dbmk\interfaces\interface-interface_" + pdbId + ".pdb.csv");
pdbInterfaceInterfaceData = pdbInterfaceInterfaceData.Where(a => !string.IsNullOrWhiteSpace(a.ReceptorPdbId) && !string.IsNullOrWhiteSpace(a.LigandPdbId)).ToList();
pdbInterfaceInterfaceData = pdbInterfaceInterfaceData.Where(a => pdbChains.Contains(a.ReceptorChainId) && pdbChains.Contains(a.LigandChainId)).ToList();
pdbInterfaceInterfaceData = pdbInterfaceInterfaceData.Where(a => ((double)a.LigandInterfaceAllAminoAcidsSuper.Length / (double)a.LigandSequenceSuper.Length) < 0.5).ToList();
for (int index = 0; index < pdbInterfaceInterfaceData.Count; index++)
{
var receptorLigandDimerA = pdbInterfaceInterfaceData[index];
var outputFolder = @"c:\r\" + receptorLigandDimerA.LigandPdbId + "_" + receptorLigandDimerA.LigandChainId + "_" + (index + 1) + "_" + receptorLigandDimerA.LigandInterfaceAllAminoAcidsSuper.Length + "_" + receptorLigandDimerA.LigandSequenceSuper.Length + "_" + receptorLigandDimerA.LigandInterfaceSuperStart + "_" + receptorLigandDimerA.LigandInterfaceSuperEnd + @"\";
//list.Add(outputFolder);
//continue;
var substitutionList = new List <DonatedSubstitutionInfo>();
var receptorLigandDimerChainOrderA = new List <char> {
receptorLigandDimerA.ReceptorChainId, receptorLigandDimerA.LigandChainId
};
for (var interfacePositionIndex = 0; interfacePositionIndex <= receptorLigandDimerA.LigandSequenceSuper.Length - receptorLigandDimerA.LigandInterfaceAllAminoAcidsSuper.Length; interfacePositionIndex++)
{
var subInterface = receptorLigandDimerA.LigandSequenceSuper.Substring(interfacePositionIndex, receptorLigandDimerA.LigandInterfaceAllAminoAcidsSuper.Length);
var description = "Interface Sliding Window " + interfacePositionIndex + " " + (interfacePositionIndex + subInterface.Length);
substitutionList.Add(new DonatedSubstitutionInfo(description, description.Replace(" ", "_"), subInterface, subInterface, receptorLigandDimerA));
}
var receptorLigandFilename = @"" + receptorLigandDimerA.LigandPdbId + ".pdb";
var acceptorTemplateAllAtomPdbFileData = !structureOutputTypes.Contains("all") ? null : File.ReadAllLines(atomsFullFolder + receptorLigandFilename).Where(a => a[atom_icode] == ' ' && ((a[atom_chain] == receptorLigandDimerA.ReceptorChainId) || (a[atom_chain] == receptorLigandDimerA.LigandChainId))).OrderBy(a => receptorLigandDimerChainOrderA.IndexOf(a[atom_chain])).ThenBy(a => int.Parse(a.Substring(atom_resseq, atom_resseq_len))).ToArray();
// monomer
//var monomerAcceptorTemplateReceptorAllAtomPdbFile = !structureOutputTypes.Contains("all") ? null : acceptorTemplateAllAtomPdbFileData.Where(a => a[atom_icode] == ' ' && a[atom_chain] == receptorLigandDimerA.ReceptorChainId).OrderBy(a => receptorLigandDimerChainOrderA.IndexOf(a[atom_chain])).ThenBy(a => int.Parse(a.Substring(atom_resseq, atom_resseq_len))).ToList();
var monomerAcceptorTemplateLigandAllAtomPdbFile = !structureOutputTypes.Contains("all") ? null : acceptorTemplateAllAtomPdbFileData.Where(a => a[atom_icode] == ' ' && a[atom_chain] == receptorLigandDimerA.LigandChainId).OrderBy(a => receptorLigandDimerChainOrderA.IndexOf(a[atom_chain])).ThenBy(a => int.Parse(a.Substring(atom_resseq, atom_resseq_len))).ToList();
// dimer
//var dimerAcceptorTemplateDimerAllAtomPdbFile = !structureOutputTypes.Contains("all") ? null : acceptorTemplateAllAtomPdbFileData.Where(a => a[atom_icode] == ' ' && (a[atom_chain] == receptorLigandDimerA.ReceptorChainId || a[atom_chain] == receptorLigandDimerA.LigandChainId)).OrderBy(a => receptorLigandDimerChainOrderA.IndexOf(a[atom_chain])).ThenBy(a => int.Parse(a.Substring(atom_resseq, atom_resseq_len))).ToList();
var receptorHeader = ">" + receptorLigandDimerA.ReceptorPdbId + ":" + receptorLigandDimerA.ReceptorChainId;
var ligandHeader = ">" + receptorLigandDimerA.LigandPdbId + ":" + receptorLigandDimerA.LigandChainId;
//var monomerAcceptorTemplateLigandSequenceSuper = new Sequence(ligandHeader, receptorLigandDimerA.LigandSequenceSuper);
var dimerAcceptorTemplateDimerSequenceSuper = new List <Sequence> {
new Sequence(receptorHeader, receptorLigandDimerA.ReceptorSequenceSuper), new Sequence(ligandHeader, receptorLigandDimerA.LigandSequenceSuper)
};
/*
* var dimerAcceptorTemplateDimerSequenceSuperLocked = new List<Sequence>
* {
* new Sequence(receptorHeader, new string('-',receptorLigandDimerA.ReceptorSequenceSuper.Length)),
* new Sequence(ligandHeader, new string('-',receptorLigandDimerA.LigandSequenceSuper.Length))
* };
*/
foreach (var sub in substitutionList)
{
// align ligand interface sequence and substitution sequence
var offset = AlignInside(receptorLigandDimerA.LigandInterfaceAllAminoAcidsSuper, sub.InterfacePadded);
if (receptorLigandDimerA.LigandInterfaceAllAminoAcidsSuper.Length < sub.InterfacePadded.Length)
{
offset = -offset;
}
var acceptorTemplateSubstitutionStart = receptorLigandDimerA.LigandInterfaceSuperStart + offset;
//var acceptorTemplateSubstitutionEnd = (acceptorTemplateSubstitutionStart + sub.InterfacePadded.Length) - 1;
var info = string.Join(Environment.NewLine, new string[] { "" + receptorLigandDimerA.ReceptorSequenceClusterIndex, "" + receptorLigandDimerA.ReceptorInterfaceSequenceClusterIndex, "" + receptorLigandDimerA.LigandSequenceClusterIndex, "" + receptorLigandDimerA.LigandInterfaceSequenceClusterIndex, "" + sub.InterfaceInterfaceSequenceIdentityClusteringItem.ReceptorSequenceClusterIndex, "" + sub.InterfaceInterfaceSequenceIdentityClusteringItem.ReceptorInterfaceSequenceClusterIndex, "" + sub.InterfaceInterfaceSequenceIdentityClusteringItem.LigandSequenceClusterIndex, "" + sub.InterfaceInterfaceSequenceIdentityClusteringItem.LigandInterfaceSequenceClusterIndex, receptorLigandDimerA.ReceptorPdbId, "" + receptorLigandDimerA.ReceptorChainId, receptorLigandDimerA.LigandPdbId, "" + receptorLigandDimerA.LigandChainId, sub.InterfaceInterfaceSequenceIdentityClusteringItem.ReceptorPdbId, "" + sub.InterfaceInterfaceSequenceIdentityClusteringItem.ReceptorChainId, sub.InterfaceInterfaceSequenceIdentityClusteringItem.LigandPdbId, "" + sub.InterfaceInterfaceSequenceIdentityClusteringItem.LigandChainId, sub.Description, receptorLigandDimerA.LigandInterfaceAllAminoAcidsSuper, sub.Interface, sub.InterfacePadded });
//var monomerAcceptorTemplateFragmentLigandCaTracePdbFile = !structureOutputTypes.Contains("ca") ? null : monomerAcceptorTemplateLigandCaTracePdbFile.Where(a => int.Parse(a.Substring(atom_resseq, atom_resseq_len)) >= acceptorTemplateSubstitutionStart && int.Parse(a.Substring(atom_resseq, atom_resseq_len)) <= acceptorTemplateSubstitutionEnd).ToList();
//var monomerAcceptorTemplateFragmentLigandBackBonePdbFile = !structureOutputTypes.Contains("mc") ? null : monomerAcceptorTemplateLigandBackBonePdbFile.Where(a => int.Parse(a.Substring(atom_resseq, atom_resseq_len)) >= acceptorTemplateSubstitutionStart && int.Parse(a.Substring(atom_resseq, atom_resseq_len)) <= acceptorTemplateSubstitutionEnd).ToList();
//var monomerAcceptorTemplateFragmentLigandSideChainPdbFile = !structureOutputTypes.Contains("sc") ? null : monomerAcceptorTemplateLigandSideChainPdbFile.Where(a => int.Parse(a.Substring(atom_resseq, atom_resseq_len)) >= acceptorTemplateSubstitutionStart && int.Parse(a.Substring(atom_resseq, atom_resseq_len)) <= acceptorTemplateSubstitutionEnd).ToList();
//var monomerAcceptorTemplateFragmentLigandAllAtomPdbFile = !structureOutputTypes.Contains("all") ? null : monomerAcceptorTemplateLigandAllAtomPdbFile.Where(a => int.Parse(a.Substring(atom_resseq, atom_resseq_len)) >= acceptorTemplateSubstitutionStart && int.Parse(a.Substring(atom_resseq, atom_resseq_len)) <= acceptorTemplateSubstitutionEnd).ToList();
//var dimerAcceptorTemplateFragmentDimerCaTracePdbFile = !structureOutputTypes.Contains("ca") ? null : dimerAcceptorTemplateDimerCaTracePdbFile.Where(a => (a[atom_chain] == receptorLigandDimerA.ReceptorChainId && int.Parse(a.Substring(atom_resseq, atom_resseq_len)) >= receptorLigandDimerA.ReceptorInterfaceResSeqStart && int.Parse(a.Substring(atom_resseq, atom_resseq_len)) <= receptorLigandDimerA.ReceptorInterfaceResSeqEnd) || (a[atom_chain] == receptorLigandDimerA.LigandChainId && int.Parse(a.Substring(atom_resseq, atom_resseq_len)) >= acceptorTemplateSubstitutionStart && int.Parse(a.Substring(atom_resseq, atom_resseq_len)) <= acceptorTemplateSubstitutionEnd)).ToList();
//var dimerAcceptorTemplateFragmentDimerBackBonePdbFile = !structureOutputTypes.Contains("mc") ? null : dimerAcceptorTemplateDimerBackBonePdbFile.Where(a => (a[atom_chain] == receptorLigandDimerA.ReceptorChainId && int.Parse(a.Substring(atom_resseq, atom_resseq_len)) >= receptorLigandDimerA.ReceptorInterfaceResSeqStart && int.Parse(a.Substring(atom_resseq, atom_resseq_len)) <= receptorLigandDimerA.ReceptorInterfaceResSeqEnd) || (a[atom_chain] == receptorLigandDimerA.LigandChainId && int.Parse(a.Substring(atom_resseq, atom_resseq_len)) >= acceptorTemplateSubstitutionStart && int.Parse(a.Substring(atom_resseq, atom_resseq_len)) <= acceptorTemplateSubstitutionEnd)).ToList();
//var dimerAcceptorTemplateFragmentDimerSideChainPdbFile = !structureOutputTypes.Contains("sc") ? null : dimerAcceptorTemplateDimerSideChainPdbFile.Where(a => (a[atom_chain] == receptorLigandDimerA.ReceptorChainId && int.Parse(a.Substring(atom_resseq, atom_resseq_len)) >= receptorLigandDimerA.ReceptorInterfaceResSeqStart && int.Parse(a.Substring(atom_resseq, atom_resseq_len)) <= receptorLigandDimerA.ReceptorInterfaceResSeqEnd) || (a[atom_chain] == receptorLigandDimerA.LigandChainId && int.Parse(a.Substring(atom_resseq, atom_resseq_len)) >= acceptorTemplateSubstitutionStart && int.Parse(a.Substring(atom_resseq, atom_resseq_len)) <= acceptorTemplateSubstitutionEnd)).ToList();
//var dimerAcceptorTemplateFragmentDimerAllAtomPdbFile = !structureOutputTypes.Contains("all") ? null : dimerAcceptorTemplateDimerAllAtomPdbFile.Where(a => (a[atom_chain] == receptorLigandDimerA.ReceptorChainId && int.Parse(a.Substring(atom_resseq, atom_resseq_len)) >= receptorLigandDimerA.ReceptorInterfaceResSeqStart && int.Parse(a.Substring(atom_resseq, atom_resseq_len)) <= receptorLigandDimerA.ReceptorInterfaceResSeqEnd) || (a[atom_chain] == receptorLigandDimerA.LigandChainId && int.Parse(a.Substring(atom_resseq, atom_resseq_len)) >= acceptorTemplateSubstitutionStart && int.Parse(a.Substring(atom_resseq, atom_resseq_len)) <= acceptorTemplateSubstitutionEnd)).ToList();
var modelOutputFolder = outputFolder + sub.Folder + @"\";
Directory.CreateDirectory(modelOutputFolder);
//scriptsText.ForEach(a => File.WriteAllText(modelOutputFolder + Path.GetFileName(a.Item1), a.Item2.Replace("%%chain%%", "" + receptorLigandDimerA.LigandChainId)));
File.WriteAllText(modelOutputFolder + "substitution.log", info);
if (structureOutputTypes.Contains("all"))
{
File.WriteAllLines(modelOutputFolder + "template_ligand_all.pdb", monomerAcceptorTemplateLigandAllAtomPdbFile);
}
//if (structureOutputTypes.Contains("all")) File.WriteAllLines(modelOutputFolder + "template_dimer_all.pdb", dimerAcceptorTemplateDimerAllAtomPdbFile);
//if (structureOutputTypes.Contains("all")) File.WriteAllLines(modelOutputFolder + "template_locked_ligand_all.pdb", monomerAcceptorTemplateLigandAllAtomPdbFile);
//if (structureOutputTypes.Contains("all")) File.WriteAllLines(modelOutputFolder + "template_locked_dimer_all.pdb", dimerAcceptorTemplateDimerAllAtomPdbFile);
//if (structureOutputTypes.Contains("all")) File.WriteAllLines(modelOutputFolder + "template_fragment_ligand_all.pdb", monomerAcceptorTemplateFragmentLigandAllAtomPdbFile);
//if (structureOutputTypes.Contains("all")) File.WriteAllLines(modelOutputFolder + "template_fragment_dimer_all.pdb", dimerAcceptorTemplateFragmentDimerAllAtomPdbFile);
/*
* var mutatedLigandSequenceLocked =
* new Sequence(ligandHeader,
*
* new string('-', receptorLigandDimerA.LigandSequenceSuper.Length)
* .Remove(acceptorTemplateSubstitutionStart, sub.InterfacePadded.Length)
* .Insert(acceptorTemplateSubstitutionStart, sub.InterfacePadded));
*/
var mutatedLigandSequenceSubLigand = new Sequence(ligandHeader, receptorLigandDimerA.LigandSequenceSuper.Remove(acceptorTemplateSubstitutionStart, sub.InterfacePadded.Length).Insert(acceptorTemplateSubstitutionStart, sub.InterfacePadded));
var dimerSequenceAfterSubstitution = dimerAcceptorTemplateDimerSequenceSuper.Select(a => a.Id == ligandHeader ? mutatedLigandSequenceSubLigand : a).ToList();
//var dimerSequenceAfterSubstitutionLocked = dimerAcceptorTemplateDimerSequenceSuperLocked.Select(a => a.Id == ligandHeader ? mutatedLigandSequenceLocked : a).ToList();
/*
* var mutatedMonomerAcceptorTemplateFragmentLigandSequenceSuper = new List<Sequence>
* {
* new Sequence(ligandHeader, sub.InterfacePadded)
* };
*/
/*
* var mutatedDimerAcceptorTemplateFragmentDimerSequenceSuper = new List<Sequence>
* {
* new Sequence(receptorHeader, receptorLigandDimerA.ReceptorInterfaceAllAminoAcidsSuper),
* new Sequence(ligandHeader, sub.InterfacePadded)
* };
*/
// save before
//if (sequenceOutputTypes.Contains("pir")) File.WriteAllText(modelOutputFolder + "template_ligand_before_substitution.ali", Sequence.GetFormattedSequence(monomerAcceptorTemplateLigandSequenceSuper, Sequence.SequenceFormat.Pir));
//if (sequenceOutputTypes.Contains("fasta")) File.WriteAllText(modelOutputFolder + "template_ligand_before_substitution.fasta", Sequence.GetFormattedSequence(monomerAcceptorTemplateLigandSequenceSuper, Sequence.SequenceFormat.Fasta));
if (sequenceOutputTypes.Contains("pir"))
{
File.WriteAllText(modelOutputFolder + "template_ligand_after_substitution.ali", Sequence.GetFormattedSequence(mutatedLigandSequenceSubLigand, Sequence.SequenceFormat.Pir));
}
//if (sequenceOutputTypes.Contains("fasta")) File.WriteAllText(modelOutputFolder + "template_ligand_after_substitution.fasta", Sequence.GetFormattedSequence(mutatedLigandSequenceSubLigand, Sequence.SequenceFormat.Fasta));
//if (sequenceOutputTypes.Contains("pir")) File.WriteAllText(modelOutputFolder + "template_dimer_before_substitution.ali", Sequence.GetFormattedSequence(dimerAcceptorTemplateDimerSequenceSuper, Sequence.SequenceFormat.Pir, ligandHeader));
//if (sequenceOutputTypes.Contains("fasta")) File.WriteAllText(modelOutputFolder + "template_dimer_before_substitution.fasta", Sequence.GetFormattedSequence(dimerAcceptorTemplateDimerSequenceSuper, Sequence.SequenceFormat.Fasta, ligandHeader));
//if (sequenceOutputTypes.Contains("pir")) File.WriteAllText(modelOutputFolder + "template_dimer_after_substitution.ali", Sequence.GetFormattedSequence(dimerSequenceAfterSubstitution, Sequence.SequenceFormat.Pir, ligandHeader));
//if (sequenceOutputTypes.Contains("fasta")) File.WriteAllText(modelOutputFolder + "template_dimer_after_substitution.fasta", Sequence.GetFormattedSequence(dimerSequenceAfterSubstitution, Sequence.SequenceFormat.Fasta));
//if (sequenceOutputTypes.Contains("pir")) File.WriteAllText(modelOutputFolder + "template_fragment_ligand_after_substitution.ali", Sequence.GetFormattedSequence(mutatedMonomerAcceptorTemplateFragmentLigandSequenceSuper, Sequence.SequenceFormat.Pir, ligandHeader));
//if (sequenceOutputTypes.Contains("fasta")) File.WriteAllText(modelOutputFolder + "template_fragment_ligand_after_substitution.fasta", Sequence.GetFormattedSequence(mutatedMonomerAcceptorTemplateFragmentLigandSequenceSuper, Sequence.SequenceFormat.Fasta));
//if (sequenceOutputTypes.Contains("pir")) File.WriteAllText(modelOutputFolder + "template_fragment_dimer_after_substitution.ali", Sequence.GetFormattedSequence(mutatedDimerAcceptorTemplateFragmentDimerSequenceSuper, Sequence.SequenceFormat.Pir, ligandHeader));
//if (sequenceOutputTypes.Contains("fasta")) File.WriteAllText(modelOutputFolder + "template_fragment_dimer_after_substitution.fasta", Sequence.GetFormattedSequence(mutatedDimerAcceptorTemplateFragmentDimerSequenceSuper, Sequence.SequenceFormat.Fasta));
//if (sequenceOutputTypes.Contains("pir")) File.WriteAllText(modelOutputFolder + "template_locked_ligand_after_substitution.ali", Sequence.GetFormattedSequence(mutatedLigandSequenceLocked, Sequence.SequenceFormat.Pir));
//if (sequenceOutputTypes.Contains("fasta")) File.WriteAllText(modelOutputFolder + "template_locked_ligand_after_substitution.fasta", Sequence.GetFormattedSequence(mutatedLigandSequenceLocked, Sequence.SequenceFormat.Fasta));
//if (sequenceOutputTypes.Contains("pir")) File.WriteAllText(modelOutputFolder + "template_locked_dimer_after_substitution.ali", Sequence.GetFormattedSequence(dimerSequenceAfterSubstitutionLocked, Sequence.SequenceFormat.Pir, ligandHeader));
//if (sequenceOutputTypes.Contains("fasta")) File.WriteAllText(modelOutputFolder + "template_locked_dimer_after_substitution.fasta", Sequence.GetFormattedSequence(dimerSequenceAfterSubstitutionLocked, Sequence.SequenceFormat.Fasta));
}
}
}
//File.WriteAllLines(@"c:\r\list.csv", list);
/*
* var batches = new Dictionary<string, string[]>
* {
* //{ resultsFolder + @"call_fs_modeller_monomer_full.bat", Directory.GetFiles(resultsFolder, @"modeller_monomer_full.bat", SearchOption.AllDirectories).Where(a => Path.GetDirectoryName(a).Contains("Full Structure")).ToArray()},
* //{ resultsFolder + @"call_fs_modeller_dimer_full.bat", Directory.GetFiles(resultsFolder, @"modeller_dimer_full.bat", SearchOption.AllDirectories).Where(a => Path.GetDirectoryName(a).Contains("Full Structure")).ToArray()},
* { resultsFolder + @"call_fs_modeller_monomer_and_dimer_full.bat", Directory.GetFiles(resultsFolder, @"modeller_monomer_and_dimer_full.bat", SearchOption.AllDirectories).Where(a => Path.GetDirectoryName(a).Contains("Full Structure")).ToArray()},
* { resultsFolder + @"call_fs_pymol_images.bat", Directory.GetFiles(resultsFolder, @"pymol_images.bat", SearchOption.AllDirectories).Where(a => Path.GetDirectoryName(a).Contains("Full Structure")).ToArray()}
* };
*
* foreach (var batch in batches)
* {
* var outputCmds = new List<string>();
*
* outputCmds.Add(@"echo Running """ + Path.GetFileName(batch.Key) + @"""");
*
* for (var index = 0; index < batch.Value.Length; index++)
* {
* var file = batch.Value[index];
* var pct = (index + 1) / (decimal)batch.Value.Length;
*
* outputCmds.Add(@"echo Processing """ + Path.GetDirectoryName(file) + @""" " + (index + 1) + "/" + batch.Value.Length + " (" + Math.Round(pct * 100, 2) + "%)");
* outputCmds.Add(@"cd """ + Path.GetDirectoryName(file) + @"""");
* outputCmds.Add(@"echo Calling """ + Path.GetFileName(file) + @"""");
* outputCmds.Add(@"call """ + file + @"""");
* outputCmds.Add(@"");
* }
* outputCmds.Add(@"pause");
* outputCmds.Add(@"");
*
* File.WriteAllLines(batch.Key, outputCmds);
* }
*/
}
