static void Main(string[] args)
{
var parameters = new string[, ]
{
{ "[pdb_or_atoms_file]", "input structure for sequence" },
{ "[fasta_file]", "input sequence for structure" },
{ "[[output_file]]", "optional output file" },
};
var maxParamLength = parameters.Cast <string>().Where((a, i) => i % 2 == 0).Max(a => a.Length);
var exeFilename = Path.GetFileName(Process.GetCurrentProcess().MainModule.FileName);
if (args.Length < 1)
{
Console.WriteLine(exeFilename + @" is a program to calculate offset between the sequence and structure.");
Console.WriteLine();
Console.WriteLine(@"Usage:");
Console.WriteLine(ProteinBioClass.WrapConsoleText(exeFilename + @" " + String.Join(" ", parameters.Cast <string>().Where((a, i) => i % 2 == 0)), maxParamLength + 2, 1));
Console.WriteLine();
Console.WriteLine(@"Example:");
Console.WriteLine(ProteinBioClass.WrapConsoleText(exeFilename + @" ""c:\pdb_db\atoms\atoms1a12.pdb"" ""c:\pdb_db\fasta\atoms1a12.fasta""", maxParamLength + 2, 1));
Console.WriteLine();
Console.WriteLine(@"Arguments:");
for (var i = 0; i < parameters.GetLength(0); i++)
{
Console.WriteLine(@" " + parameters[i, 0].PadLeft(maxParamLength, ' ') + " " + ProteinBioClass.WrapConsoleText(parameters[i, 1], maxParamLength + 2, 1, false));
}
Console.WriteLine();
return;
}
// load arguments
var p = 0;
var atomsFilename = args.Length > p && args[p].Length > 0 ? args[p] : "";
atomsFilename = atomsFilename.Replace("\"", "");
Console.WriteLine("; " + parameters[p, 0].PadLeft(maxParamLength, ' ') + " = " + atomsFilename);
p++;
var inputFastaFilename = args.Length > p && args[p].Length > 0 ? args[p] : "";
inputFastaFilename = inputFastaFilename.Replace("\"", "");
Console.WriteLine("; " + parameters[p, 0].PadLeft(maxParamLength, ' ') + " = " + inputFastaFilename);
p++;
var outputDataFilename = args.Length > p && args[p].Length > 0 ? args[p] : "";
outputDataFilename = outputDataFilename.Replace("\"", "");
Console.WriteLine("; " + parameters[p, 0].PadLeft(maxParamLength, ' ') + " = " + outputDataFilename);
Console.WriteLine();
var struct_seq = ProteinBioinformaticsSharedLibrary.ProteinBioClass.StructureFileToAaSequence(atomsFilename, null,
false);
//foreach (var s in struct_seq)
//Console.WriteLine(s);
//var fasta = File.ReadAllLines(inputFastaFilename);
//foreach (var line in fasta)
//{
// if (string.IsNullOrWhiteSpace(line))continue;
// if (line[0] == '>')
// {
// if (line.Contains())
// }
//}
/// not finished!
}
static void Main(string[] args)
{
var parameters = new string[, ]
{
{ "[pdb_file]", "PDB ~v3.3 Protein Data Bank format file [*.pdb, *.ent]" },
{ "[interface-interface_file]", "interface-interface file" },
{ "[[chain_ids]]", "molecule chains to output [* for all]" },
{ "[[output_file]]", "optional output file. use ? for chain id. when ommitted, output to console" },
};
var maxParamLength = parameters.Cast <string>().Where((a, i) => i % 2 == 0).Max(a => a.Length);
var exeFilename = Path.GetFileName(System.Diagnostics.Process.GetCurrentProcess().MainModule.FileName);
if (args.Length == 0)
{
Console.WriteLine(exeFilename + @" is a program to extract ATOM records from a PDB file.");
Console.WriteLine();
Console.WriteLine(@"Usage:");
Console.WriteLine(ProteinBioClass.WrapConsoleText(exeFilename + @" " + String.Join(" ", parameters.Cast <string>().Where((a, i) => i % 2 == 0)), maxParamLength + 2, 1));
Console.WriteLine();
Console.WriteLine(@"Example:");
Console.WriteLine(ProteinBioClass.WrapConsoleText(exeFilename + @" ""c:\pdb_db\pdb1a12.pdb"" 8.0 ""c:\pdb_atoms\atoms1a12.pdb""", maxParamLength + 2, 1));
Console.WriteLine();
Console.WriteLine(@"Arguments:");
for (var i = 0; i < parameters.GetLength(0); i++)
{
Console.WriteLine(@" " + parameters[i, 0].PadLeft(maxParamLength, ' ') + " " + ProteinBioClass.WrapConsoleText(parameters[i, 1], maxParamLength + 2, 1, false));
}
Console.WriteLine();
return;
}
// load and echo arguments
var p = 0;
var pdbFilename = args.Length > p && args[p].Length > 0 ? args[p] : "";
pdbFilename = pdbFilename.Replace("\"", "");
Console.WriteLine("; " + parameters[p, 0].PadLeft(maxParamLength, ' ') + " = " + pdbFilename);
p++;
var interfaceInterfaceFile = args.Length > p && args[p].Length > 0 ? args[p].ToUpperInvariant() : "";
interfaceInterfaceFile = interfaceInterfaceFile.Replace("\"", "");
Console.WriteLine("; " + parameters[p, 0].PadLeft(maxParamLength, ' ') + " = " + interfaceInterfaceFile);
p++;
var chainIds = args.Length > p && args[p].Length > 0 ? args[p] : "";
Console.WriteLine("; " + parameters[p, 0].PadLeft(maxParamLength, ' ') + " = " + chainIds);
p++;
var outputFilename = args.Length > p && args[p].Length > 0 ? args[p] : "";
outputFilename = outputFilename.Replace("\"", "");
Console.WriteLine("; " + parameters[p, 0].PadLeft(maxParamLength, ' ') + " = " + outputFilename);
Console.WriteLine();
if (!File.Exists(pdbFilename))
{
Console.WriteLine("; File not found: " + pdbFilename);
return;
}
if (!File.Exists(interfaceInterfaceFile))
{
Console.WriteLine("; File not found: " + interfaceInterfaceFile);
return;
}
if (string.IsNullOrWhiteSpace(pdbFilename))
{
return;
}
if (chainIds.Contains('*'))
{
chainIds = null;
}
var chainIdWhiteList = !string.IsNullOrEmpty(chainIds) ? chainIds.ToUpperInvariant().Split(new char[] { ' ', ',' }, StringSplitOptions.RemoveEmptyEntries) : null;
var interfaceData = ComplexInterfaces.ComplexInterfaces.InterfaceInterfaceData.Load(interfaceInterfaceFile);
var terminatedChains = new List <string>();
var pdbfilenameShort = Path.GetFileNameWithoutExtension(pdbFilename);
var pdbId = pdbfilenameShort.Substring(pdbfilenameShort.Length - 4).ToUpperInvariant();
var lines = File.ReadAllLines(pdbFilename);
var result = new List <Tuple <string, string> >();
var interfaceDataChains = interfaceData.Select(a => a.ReceptorChainId).Distinct().ToList();
var interfaceDataStart = interfaceDataChains.Select(a => interfaceData.Where(b => b.ReceptorChainId == a).Min(b => b.ReceptorInterfaceResSeqStart)).ToList();
var interfaceDataEnd = interfaceDataChains.Select(a => interfaceData.Where(b => b.ReceptorChainId == a).Max(b => b.ReceptorInterfaceResSeqEnd)).ToList();
foreach (var line in lines)
{
if (line.Length < 22)
{
continue;
}
if (line.Substring(0, 4).ToUpperInvariant() == "TER ")
{
var chainId = ("" + line[21]).ToUpperInvariant();
terminatedChains.Add(chainId);
}
if (line.Substring(0, 5).ToUpperInvariant() == "ATOM ")
{
var chainId = ("" + line[21]).ToUpperInvariant();
if (terminatedChains.Contains(chainId))
{
continue;
}
if (chainIdWhiteList != null && chainIdWhiteList.Length > 0 && !chainIdWhiteList.Contains(chainId))
{
continue;
}
if (!interfaceDataChains.Contains(chainId[0]))
{
continue;
}
//if (caTraceOnlyBool && (line[13] != 'C' || line[14] != 'A')) continue;
var interfaceDataChainIndex = interfaceDataChains.IndexOf(chainId[0]);
var resSeq = int.Parse(line.Substring(22, 4).Trim());
if (resSeq >= interfaceDataStart[interfaceDataChainIndex] && resSeq <= interfaceDataEnd[interfaceDataChainIndex])
{
result.Add(new Tuple <string, string>(chainId, line));
}
}
}
if (!string.IsNullOrWhiteSpace(outputFilename))
{
Directory.CreateDirectory(Path.GetDirectoryName(outputFilename.Replace("?", "")));
if (!outputFilename.Contains("?"))
{
File.WriteAllLines(outputFilename, result.Select(a => a.Item2).ToList());
}
else
{
var chains = result.Select(a => a.Item1).Distinct().ToList();
foreach (var chain in chains)
{
var outputFilename2 = outputFilename.Replace("?", "");
outputFilename2 = Path.GetDirectoryName(outputFilename2) + @"\" + Path.GetFileNameWithoutExtension(outputFilename2) + chain + Path.GetExtension(outputFilename2);
File.WriteAllLines(outputFilename2, result.Where(a => a.Item1 == chain).Select(a => a.Item2).ToList());
}
}
}
else
{
foreach (var line in result)
{
Console.WriteLine(line);
}
Console.WriteLine();
}
}
public static void Main(string[] args)
{
var parameters = new string[, ]
{
{ "[pdb_or_atoms_file]", "standard crystal pdb file or output from the ComplexAtoms program" },
{ "[[pad_missing]]", "Y or N (default: Y)" },
{ "[[output_fasta_file]]", "optional output fasta file. when ommitted, output to console" },
{ "[[append_or_overwrite]]", "optional (A) append or (O) overwrite (default: overwrite)" },
};
var maxParamLength = parameters.Cast <string>().Where((a, i) => i % 2 == 0).Max(a => a.Length);
var exeFilename = Path.GetFileName(System.Diagnostics.Process.GetCurrentProcess().MainModule.FileName);
if (args.Length < 1)
{
Console.WriteLine(exeFilename + @" is a program to extract the protein amino acid fasta sequence from protein structure pdb file.");
Console.WriteLine();
Console.WriteLine(@"Usage:");
Console.WriteLine(ProteinBioClass.WrapConsoleText(exeFilename + @" " + String.Join(" ", parameters.Cast <string>().Where((a, i) => i % 2 == 0)), maxParamLength + 2, 1));
Console.WriteLine();
Console.WriteLine(@"Example:");
Console.WriteLine(ProteinBioClass.WrapConsoleText(exeFilename + @" ""c:\pdb_db\atoms\atoms1a12.pdb"" ""c:\pdb_db\fasta_from_pdb\atoms1a12.pdb.fasta""", maxParamLength + 2, 1));
Console.WriteLine();
Console.WriteLine(@"Arguments:");
for (var i = 0; i < parameters.GetLength(0); i++)
{
Console.WriteLine(@" " + parameters[i, 0].PadLeft(maxParamLength, ' ') + " " + ProteinBioClass.WrapConsoleText(parameters[i, 1], maxParamLength + 2, 1, false));
}
Console.WriteLine();
return;
}
// load arguments
var p = 0;
var atomsFilename = args.Length > p && args[p].Length > 0 ? args[p] : "";
atomsFilename = atomsFilename.Replace("\"", "");
Console.WriteLine("; " + parameters[p, 0].PadLeft(maxParamLength, ' ') + " = " + atomsFilename);
p++;
var padMissing = args.Length > p && args[p].Length > 0 ? args[p] : "Y";
padMissing = padMissing.Replace("\"", "");
Console.WriteLine("; " + parameters[p, 0].PadLeft(maxParamLength, ' ') + " = " + padMissing);
if (padMissing != "Y" && padMissing != "N")
{
padMissing = "Y";
}
var padMissingBool = padMissing == "Y";
p++;
var outputFastaFilename = args.Length > p && args[p].Length > 0 ? args[p] : "";
outputFastaFilename = outputFastaFilename.Replace("\"", "");
Console.WriteLine("; " + parameters[p, 0].PadLeft(maxParamLength, ' ') + " = " + outputFastaFilename);
p++;
var appendOrOverwrite = args.Length > p && args[p].Length > 0 ? args[p] : "";
appendOrOverwrite = appendOrOverwrite.Replace("\"", "");
Console.WriteLine("; " + parameters[p, 0].PadLeft(maxParamLength, ' ') + " = " + appendOrOverwrite);
if (!(string.IsNullOrWhiteSpace(appendOrOverwrite) || appendOrOverwrite == "O" || appendOrOverwrite == "A"))
{
return;
}
Console.WriteLine();
var sequenceList = Sequence.LoadStructureFile(atomsFilename, null, padMissingBool);// ProteinBioClass.StructureFileToAaFastaSequence(atomsFilename, null, padMissingBool);
var output = Sequence.GetAsFasta(sequenceList);
if (string.IsNullOrWhiteSpace(outputFastaFilename))
{
Console.WriteLine();
Console.WriteLine(output);
Console.WriteLine();
}
else
{
Directory.CreateDirectory(Path.GetDirectoryName(outputFastaFilename));
if (appendOrOverwrite == "A" && File.Exists(outputFastaFilename))
{
var data = File.ReadAllText(outputFastaFilename);
if (!data.EndsWith(Environment.NewLine))
{
data = data + Environment.NewLine;
}
output = data + output;
}
File.WriteAllText(outputFastaFilename, output);
}
}
static void Main(string[] args)
{
//var s1 =
// @"XXXXXXXXXXXXXXXXXXXXKKVKVSHRSHSTEPGLVLTLGQGDVGQLGLGENVMERKKPALVSIPEDVVQAEAGGMHTVCLSKSGQVYSFGCNDEGALGRDTSVEGSEMVPGKVELQEKVVQVSAGDSHTAALTDDGRVFLWGSFRDNNGVIGLLEPMKKSMVPVQVQLDVPVVKVASGNDHLVMLTADGDLYTLGCGEQGQLGRVPELFANRGGRQGLERLLVPKCVMLKSRGSRGHVRFQDAFCGAYFTFAISHEGHVYGFGLSNYHQLGTPGTESCFIPQNLTSFKNSTKSWVGFSGGQHHTVCMDSEGKAYSLGRAEYGRLGLGEGAEEKSIPTLISRLPAVSSVACGASVGYAVTKDGRVFAWGMGTNYQLGTGQDEDAWSPVEMMGKQLENRVVLSVSSGGQHTVLLVKDKEQS";
//var s2 = @"RRSPPADAIPKSKKVKVSHRSHSTEPGLVLTLGQGDVGQLGLGENVMERKKPALVSIPEDVVQAEAGGMHTVCLSKSGQVYSFGCNDEGALGRDTSVEGSEMVPGKVELQEKVVQVSAGDSHTAALTDDGRVFLWGSFRDNNGVIGLLEPMKKSMVPVQVQLDVPVVKVASGNDHLVMLTADGDLYTLGCGEQGQLGRVPELFANRGGRQGLERLLVPKCVMLKSRGSRGHVRFQDAFCGAYFTFAISHEGHVYGFGLSNYHQLGTPGTESCFIPQNLTSFKNSTKSWVGFSGGQHHTVCMDSEGKAYSLGRAEYGRLGLGEGAEEKSIPTLISRLPAVSSVACGASVGYAVTKDGRVFAWGMGTNYQLGTGQDEDAWSPVEMMGKQLENRVVLSVSSGGQHTVLLVKDKEQS";
//var x = SimpleAlignmentOffset(s1,s2);
//Console.WriteLine();
//Console.WriteLine(x.Item1);
//Console.WriteLine(x.Item2);
//Console.WriteLine();
//Console.ReadLine();
//return;
// MutateSequence example.fasta start end mutation original (will find closest to start/end in case of sequence/structure index misalignment)
var parameters = new string[, ]
{
{ "[input_fasta_file]", "fasta file with sequence to mutate" },
{ "[chain_ids]", "chain ids to mutate" },
{ "[start_positions]", "mutation start position (one based)" },
{ "[end_positions]", "mutation end position (one based)" },
{ "[offsets]", "offsets (for where pdb index doesn't match fasta sequence index) (one based)" },
{ "[mutation_sequence]", "new amino acids to overwrite with" },
{ "[[output_fasta_file]]", "optional output fasta file. when ommitted, output to console" },
};
var maxParamLength = parameters.Cast <string>().Where((a, i) => i % 2 == 0).Max(a => a.Length);
var exeFilename = Path.GetFileName(System.Diagnostics.Process.GetCurrentProcess().MainModule.FileName);
if (args.Length < 5)
{
Console.WriteLine(exeFilename +
@" is a program to mutate (substitute) a subsequence of a protein amino acid sequence within a fasta file.");
Console.WriteLine();
Console.WriteLine(@"Usage:");
Console.WriteLine(
ProteinBioClass.WrapConsoleText(
exeFilename + @" " + String.Join(" ", parameters.Cast <string>().Where((a, i) => i % 2 == 0)),
maxParamLength + 2, 1));
Console.WriteLine();
Console.WriteLine(@"Example:");
Console.WriteLine(
ProteinBioClass.WrapConsoleText(
exeFilename +
@" ""c:\pdb_db\fasta\fasta_pdb1a12.pdb.fasta"" A,B,C 10,76,100 15,77,102 GBVBGA,AA,GHG ""c:\pdb_db\fasta_mutated\mutated_pdb1a12.pdb.fasta""",
maxParamLength + 2, 1));
Console.WriteLine();
Console.WriteLine(@"Arguments:");
for (var i = 0; i < parameters.GetLength(0); i++)
{
Console.WriteLine(@" " + parameters[i, 0].PadLeft(maxParamLength, ' ') + " " +
ProteinBioClass.WrapConsoleText(parameters[i, 1], maxParamLength + 2, 1, false));
}
Console.WriteLine();
return;
}
var p = 0;
var input_fasta_file = args.Length > p && args[p].Length > 0 ? args[p] : "";
input_fasta_file = input_fasta_file.Replace("\"", "");
Console.WriteLine("; " + parameters[p, 0].PadLeft(maxParamLength, ' ') + " = " + input_fasta_file);
p++;
var chain_ids = args.Length > p && args[p].Length > 0 ? args[p] : "";
chain_ids = chain_ids.Replace("\"", "");
Console.WriteLine("; " + parameters[p, 0].PadLeft(maxParamLength, ' ') + " = " + chain_ids);
var chain_ids_split = chain_ids.ToUpperInvariant().Split(',');
p++;
var start_position = args.Length > p && args[p].Length > 0 ? args[p] : "";
start_position = start_position.Replace("\"", "");
Console.WriteLine("; " + parameters[p, 0].PadLeft(maxParamLength, ' ') + " = " + start_position);
var start_position_split = start_position.Split(',').Select(int.Parse).ToArray();
p++;
var end_position = args.Length > p && args[p].Length > 0 ? args[p] : "";
end_position = end_position.Replace("\"", "");
Console.WriteLine("; " + parameters[p, 0].PadLeft(maxParamLength, ' ') + " = " + end_position);
var end_position_split = end_position.Split(',').Select(int.Parse).ToArray();
p++;
var offset_position = args.Length > p && args[p].Length > 0 ? args[p] : "";
offset_position = offset_position.Replace("\"", "");
Console.WriteLine("; " + parameters[p, 0].PadLeft(maxParamLength, ' ') + " = " + offset_position);
var offset_position_split = offset_position.Split(',').Select(int.Parse).ToArray();
p++;
var mutation_sequence = args.Length > p && args[p].Length > 0 ? args[p] : "";
mutation_sequence = mutation_sequence.Replace("\"", "");
Console.WriteLine("; " + parameters[p, 0].PadLeft(maxParamLength, ' ') + " = " + mutation_sequence);
var mutation_sequence_split = mutation_sequence.Split(',');
p++;
var output_fasta_file = args.Length > p && args[p].Length > 0 ? args[p] : "";
output_fasta_file = output_fasta_file.Replace("\"", "");
Console.WriteLine("; " + parameters[p, 0].PadLeft(maxParamLength, ' ') + " = " + output_fasta_file);
Console.WriteLine();
MutateFastaSequenceSave(input_fasta_file, chain_ids_split, start_position_split, end_position_split,
offset_position_split, mutation_sequence_split, output_fasta_file);
}
static void Main(string[] args)
{
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 parameters = new string[, ]
{
{ "[pdb_file]", "PDB ~v3.3 Protein Data Bank format file [*.pdb, *.ent]" },
{ "[[subset]]", "-, mc, sc, ca" },
{ "[[chain_ids]]", "molecule chains to output [2 formats: - for all, ABC, or A,1,50,B,2,40,C,5,200]" },
{ "[[output_file]]", "optional output file. use ? for chain id. when ommitted, output to console" },
};
var maxParamLength = parameters.Cast <string>().Where((a, i) => i % 2 == 0).Max(a => a.Length);
var exeFilename = Path.GetFileName(System.Diagnostics.Process.GetCurrentProcess().MainModule.FileName);
if (args.Length == 0)
{
Console.WriteLine(exeFilename + @" is a program to extract ATOM records from a PDB file.");
Console.WriteLine();
Console.WriteLine(@"Usage:");
Console.WriteLine(ProteinBioClass.WrapConsoleText(exeFilename + @" " + String.Join(" ", parameters.Cast <string>().Where((a, i) => i % 2 == 0)), maxParamLength + 2, 1));
Console.WriteLine();
Console.WriteLine(@"Example:");
Console.WriteLine(ProteinBioClass.WrapConsoleText(exeFilename + @" ""c:\pdb_db\pdb1a12.pdb"" 8.0 ""c:\pdb_atoms\atoms1a12.pdb""", maxParamLength + 2, 1));
Console.WriteLine();
Console.WriteLine(@"Arguments:");
for (var i = 0; i < parameters.GetLength(0); i++)
{
Console.WriteLine(@" " + parameters[i, 0].PadLeft(maxParamLength, ' ') + " " + ProteinBioClass.WrapConsoleText(parameters[i, 1], maxParamLength + 2, 1, false));
}
Console.WriteLine();
return;
}
// load and echo arguments
var p = 0;
var pdbFilename = args.Length > p && args[p].Length > 0 ? args[p] : "";
pdbFilename = pdbFilename.Replace("\"", "");
Console.WriteLine("; " + parameters[p, 0].PadLeft(maxParamLength, ' ') + " = " + pdbFilename);
p++;
var subset = args.Length > p && args[p].Length > 0 ? args[p].ToUpperInvariant() : "";
Console.WriteLine("; " + parameters[p, 0].PadLeft(maxParamLength, ' ') + " = " + subset);
p++;
var chainIds = args.Length > p && args[p].Length > 0 ? args[p] : "";
Console.WriteLine("; " + parameters[p, 0].PadLeft(maxParamLength, ' ') + " = " + chainIds);
p++;
var outputFilename = args.Length > p && args[p].Length > 0 ? args[p] : "";
outputFilename = outputFilename.Replace("\"", "");
Console.WriteLine("; " + parameters[p, 0].PadLeft(maxParamLength, ' ') + " = " + outputFilename);
Console.WriteLine();
if (string.IsNullOrWhiteSpace(pdbFilename))
{
return;
}
if (!File.Exists(pdbFilename))
{
return;
}
if (chainIds.Contains('-'))
{
chainIds = null;
}
var chainStartEnd = new List <Tuple <char, int, int> >();
var chainIdsSplit = chainIds?.Split(',').ToList();
char[] chainIdWhiteList;
if (chainIdsSplit?.Count > 1)
{
if (chainIdsSplit.Count % 3 != 0)
{
return;
}
for (var i = 0; i < chainIdsSplit.Count; i += 3)
{
var id = chainIdsSplit[i + 0][0];
var start = chainIdsSplit[i + 1];
if (string.IsNullOrWhiteSpace(start))
{
start = "-1";
}
var end = chainIdsSplit[i + 2];
if (string.IsNullOrWhiteSpace(end))
{
end = "-1";
}
chainStartEnd.Add(new Tuple <char, int, int>(id, int.Parse(start), int.Parse(end)));
}
chainIdWhiteList = chainStartEnd.Select(a => a.Item1).Distinct().ToArray();
}
else
{
chainIdWhiteList = chainIds?.Where(char.IsLetter).Distinct().ToArray();//!string.IsNullOrEmpty(chainIds) ? chainIds.ToUpperInvariant().Split(new char[] { ' ', ',' },StringSplitOptions.RemoveEmptyEntries) : null;
}
var terminatedChains = new List <char>();
var pdbfilenameShort = Path.GetFileNameWithoutExtension(pdbFilename);
var pdbId = pdbfilenameShort.Substring(pdbfilenameShort.Length - 4).ToUpperInvariant();
var lines = File.ReadAllLines(pdbFilename);
var result = new List <Tuple <char, string> >();
string[] ca = new string[] { "CA" };
string[] bb = new[] { "N", "CA", "C", "O" };
foreach (var line in lines)
{
if (line.Length < 22)
{
continue;
}
if (line.Substring(0, 4).ToUpperInvariant() == "TER ")
{
var chainId = line[21];//).ToUpperInvariant();
terminatedChains.Add(chainId);
}
if (line.Substring(0, 5).ToUpperInvariant() == "ATOM ")
{
var chainId = line[21];//).ToUpperInvariant();
if (terminatedChains.Contains(chainId))
{
continue;
}
if (chainIdWhiteList != null && chainIdWhiteList.Length > 0 && !chainIdWhiteList.Contains(chainId))
{
continue;
}
//if (subset == "ca" || subset == "sc") && (line[13] != 'C' || line[14] != 'A')) continue;
var add = false;
var atom_type_s = line.Substring(13, 3).Trim();
if (atom_type_s[0] != 'C' && atom_type_s[0] != 'N' && atom_type_s[0] != 'O')
{
continue;
}
// check chainIdsSplit
var resId = int.Parse(line.Substring(atom_resseq, atom_resseq_len));
var chainStartEndItem = chainStartEnd.FirstOrDefault(a => a.Item1 == chainId);
if (chainStartEndItem != null)
{
if (!((chainStartEndItem.Item2 == -1 || resId >= chainStartEndItem.Item2) && (chainStartEndItem.Item3 == -1 || resId <= chainStartEndItem.Item3)))
{
continue;
}
}
if (subset == "-")
{
add = true;
}
else if (subset == "CA" && ca.Contains(atom_type_s))
{
add = true;
}
else if (subset == "MC" && bb.Contains(atom_type_s))
{
add = true;
}
else if (subset == "SC" && !bb.Contains(atom_type_s))
{
add = true;
}
if (add)
{
result.Add(new Tuple <char, string>(chainId, line));
}
}
}
if (!string.IsNullOrWhiteSpace(outputFilename))
{
var outputFilename2 = outputFilename.Replace("?", "");
Directory.CreateDirectory(Path.GetDirectoryName(outputFilename2));
if (!outputFilename.Contains("?"))
{
File.WriteAllLines(outputFilename, result.Select(a => a.Item2).ToList());
}
else if (outputFilename.Contains("??"))
{
var chains = new string(result.Select(a => a.Item1).Where(char.IsLetter).Distinct().OrderBy(a => a).ToArray());
outputFilename2 = Path.GetDirectoryName(outputFilename2) + @"\" + Path.GetFileNameWithoutExtension(outputFilename2) + chains + Path.GetExtension(outputFilename2);
File.WriteAllLines(outputFilename2, result.Select(a => a.Item2).ToList());
}
else if (outputFilename.Contains("?"))
{
var chains = result.Select(a => a.Item1).Distinct().ToList();
foreach (var chain in chains)
{
outputFilename2 = outputFilename.Replace("?", "");
outputFilename2 = Path.GetDirectoryName(outputFilename2) + @"\" + Path.GetFileNameWithoutExtension(outputFilename2) + chain + Path.GetExtension(outputFilename2);
File.WriteAllLines(outputFilename2, result.Where(a => a.Item1 == chain).Select(a => a.Item2).ToList());
}
}
}
else
{
foreach (var line in result)
{
Console.WriteLine(line);
}
Console.WriteLine();
}
}
static void Main(string[] args)
{
var parameters = new string[, ]
{
{ "[pdb_or_atoms_file]", "output from the ComplexAtoms program" },
{ "[max_distance]", "maximum allowed contact distance in angstroms [i.e. 5.0 or 8.0]" },
{ "[[output_file]]", "optional output file. when ommitted, output to console" },
{ "[[overwrite]]", "overwrite if output file exists" }
};
var maxParamLength = parameters.Cast <string>().Where((a, i) => i % 2 == 0).Max(a => a.Length);
var exeFilename = Path.GetFileName(System.Diagnostics.Process.GetCurrentProcess().MainModule.FileName);
if (args.Length == 0)
{
Console.WriteLine(exeFilename + @" is a program to list atomic contacts for a PDB file ATOM records.");
Console.WriteLine();
Console.WriteLine(@"Usage:");
Console.WriteLine(ProteinBioClass.WrapConsoleText(exeFilename + @" " + String.Join(" ", parameters.Cast <string>().Where((a, i) => i % 2 == 0)), maxParamLength + 2, 1));
Console.WriteLine();
Console.WriteLine(@"Example:");
Console.WriteLine(ProteinBioClass.WrapConsoleText(exeFilename + @" ""c:\pdb_db\pdb1a12.pdb"" 8.0 ""c:\pdb_atoms\atoms1a12.pdb""", maxParamLength + 2, 1));
Console.WriteLine();
Console.WriteLine(@"Arguments:");
for (var i = 0; i < parameters.GetLength(0); i++)
{
Console.WriteLine(@" " + parameters[i, 0].PadLeft(maxParamLength, ' ') + " " + ProteinBioClass.WrapConsoleText(parameters[i, 1], maxParamLength + 2, 1, false));
}
Console.WriteLine();
//return;
}
// load arguments
var p = 0;
var atomsFilename = args.Length > p && args[p].Length > 0 ? args[p] : "";
atomsFilename = atomsFilename.Replace("\"", "");
Console.WriteLine("; " + parameters[p, 0].PadLeft(maxParamLength, ' ') + " = " + atomsFilename);
p++;
var maxDistance = args.Length > p && args[p].Length > 0 ? Decimal.Parse(args[p]) : 0.0m;
Console.WriteLine("; " + parameters[p, 0].PadLeft(maxParamLength, ' ') + " = " + maxDistance);
p++;
var outputFilename = args.Length > p && args[p].Length > 0 ? args[p] : "";
outputFilename = outputFilename.Replace("\"", "");
Console.WriteLine("; " + parameters[p, 0].PadLeft(maxParamLength, ' ') + " = " + outputFilename);
p++;
var overwrite = args.Length > p && args[p].Length > 0 ? args[p] : "";
overwrite = overwrite.Replace("\"", "");
Console.WriteLine("; " + parameters[p, 0].PadLeft(maxParamLength, ' ') + " = " + overwrite);
if (!string.IsNullOrWhiteSpace(overwrite) && overwrite.ToUpperInvariant() != "Y" && File.Exists(outputFilename))
{
Console.Write("; File exists, skipping.");
return;
}
Console.WriteLine();
if (!File.Exists(atomsFilename))
{
return;
}
var interactions = ProteinBioClass.FindInteractions(CancellationToken.None, maxDistance, atomsFilename, new Dictionary <string, List <char> >());
if (!string.IsNullOrWhiteSpace(outputFilename))
{
ProteinBioClass.AtomPair.SaveAtomPairList(outputFilename, interactions);
}
else
{
//Console.WriteLine("; Atom pairs with contacts: " + interactions.Count);
foreach (var a in interactions.Select(a => a.ToString()).ToList())
{
Console.WriteLine(a);
}
}
}
