public IChemFile GetChemFile(string filename, bool useRebond)
{
using (var reader = new PDBReader(ResourceLoader.GetAsStream(filename)))
{
return(GetChemFile(reader, useRebond));
}
}
public void ReadFinalPump()
{
using (var reader = new PDBReader(ResourceLoader.GetAsStream(GetType(), "finalPump96.09.06.pdb")))
{
var chemFile = reader.Read(builder.NewChemFile());
}
}
public IChemFile GetChemFileFromString(string data)
{
var stringReader = new StringReader(data);
var reader = new PDBReader(stringReader);
Assert.IsNotNull(reader);
return(GetChemFile(reader));
}
public void TestProtein()
{
var filename = "NCDK.Data.PDB.Test-1crn.pdb";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new PDBReader(ins);
Assert.IsNotNull(reader);
var chemFile = (IChemFile)reader.Read(builder.NewChemFile());
Assert.IsNotNull(chemFile);
Assert.AreEqual(1, chemFile.Count);
var seq = chemFile[0];
Assert.IsNotNull(seq);
Assert.AreEqual(1, seq.Count);
var model = seq[0];
Assert.IsNotNull(model);
Assert.AreEqual(1, model.MoleculeSet.Count());
var container = model.MoleculeSet[0];
Assert.IsTrue(container is IBioPolymer);
var mol = (IBioPolymer)container;
Assert.IsNotNull(mol);
Assert.AreEqual(327, mol.Atoms.Count);
Assert.AreEqual(46, mol.GetMonomerMap().Count());
Assert.IsNotNull(mol.GetMonomer("THRA1", "A"));
Assert.AreEqual(7, mol.GetMonomer("THRA1", "A").Atoms.Count);
Assert.IsNotNull(mol.GetMonomer("ILEA7", "A"));
Assert.AreEqual(8, mol.GetMonomer("ILEA7", "A").Atoms.Count);
var nAtom = mol.Atoms[94];
Assert.IsNotNull(nAtom);
Assert.IsTrue(nAtom is IPDBAtom);
var atom = (IPDBAtom)nAtom;
Assert.AreEqual("C", atom.Symbol);
Assert.AreEqual(95, atom.Serial.Value);
Assert.AreEqual("CZ", atom.Name);
Assert.AreEqual("PHE", atom.ResName);
Assert.AreEqual("13", atom.ResSeq);
Assert.AreEqual(1.0, atom.Occupancy.Value, 0.001);
Assert.AreEqual(6.84, atom.TempFactor.Value, 0.001);
}
public void MolfactoryRoundtripTest()
{
IAtomContainer original = TestMoleculeFactory.MakePyrrole();
SetCoordinatesToZero(original);
StringWriter stringWriter = new StringWriter();
PDBWriter writer = new PDBWriter(stringWriter);
writer.WriteMolecule(original);
writer.Close();
string output = stringWriter.ToString();
PDBReader reader = new PDBReader(new StringReader(output));
var chemFile = reader.Read(builder.NewChemFile());
reader.Close();
IAtomContainer reconstructed = chemFile[0][0].MoleculeSet[0];
Assert.AreEqual(original.Atoms.Count, reconstructed.Atoms.Count);
Assert.AreEqual(original.Bonds.Count, reconstructed.Bonds.Count);
}
public void TestRoundTrip_fractionalCoordinates()
{
StringWriter sWriter = new StringWriter();
PDBWriter writer = new PDBWriter(sWriter);
Crystal crystal = new Crystal();
crystal.A = new Vector3(0, 1, 0);
crystal.B = new Vector3(1, 0, 0);
crystal.C = new Vector3(0, 0, 2);
IAtom atom = new Atom("C");
atom.FractionalPoint3D = new Vector3(0.1, 0.1, 0.3);
crystal.Atoms.Add(atom);
writer.Write(crystal);
writer.Close();
string output = sWriter.ToString();
Assert.IsNotNull(output);
Assert.IsTrue(output.Length > 0);
PDBReader reader = new PDBReader(new StringReader(""));
var chemFile = reader.Read(builder.NewChemFile());
reader.Close();
Assert.IsNotNull(chemFile);
Assert.AreEqual(1, chemFile.Count);
IChemSequence sequence = chemFile[0];
Assert.AreEqual(1, sequence.Count);
IChemModel chemModel = sequence[0];
Assert.IsNotNull(chemModel);
// can't do further testing as the PDBReader does not read
// Crystal structures :(
}
public void TestConnectRecords()
{
string data = "SEQRES 111111111111111111111111111111111111111111111111111111111111111 \n"
+ "ATOM 1 N SER A 326 103.777 74.304 20.170 1.00 21.58 N\n"
+ "ATOM 2 CA SER A 326 102.613 74.991 20.586 1.00 18.59 C\n"
+ "ATOM 3 C SER A 326 101.631 74.211 21.431 1.00 17.75 C\n"
+ "ATOM 4 O SER A 326 101.653 74.549 22.634 1.00 18.51 O\n"
+ "CONECT 1 4\n" + "CONECT 4 1\n" + "END \n";
IChemFile obj;
using (var reader = new PDBReader(new StringReader(data)))
{
reader.IOSettings["UseRebondTool"].Setting = "false"; // UseRebondTool
reader.IOSettings["ReadConnectSection"].Setting = "true"; // ReadConnectSection
obj = builder.NewChemFile();
reader.Read(obj);
}
Assert.IsNotNull(obj);
var bondCount = obj[0][0].MoleculeSet[0].Bonds.Count;
Assert.AreEqual(1, bondCount);
}
public void Test1D66()
{
var filename = "NCDK.Data.PDB.1D66.pdb";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new PDBReader(ins);
Assert.IsNotNull(reader);
var chemFile = (IChemFile)reader.Read(builder.NewChemFile());
Assert.IsNotNull(chemFile);
Assert.AreEqual(1, chemFile.Count);
var seq = chemFile[0];
Assert.IsNotNull(seq);
Assert.AreEqual(1, seq.Count);
var model = seq[0];
Assert.IsNotNull(model);
Assert.AreEqual(1, model.MoleculeSet.Count());
var container = model.MoleculeSet[0];
Assert.IsTrue(container is IBioPolymer);
var polymer = (IBioPolymer)container;
Assert.IsTrue(polymer is IPDBPolymer);
var pdb = (IPDBPolymer)polymer;
Assert.AreEqual(4, pdb.GetStrandMap().Count);
Assert.IsTrue(polymer.GetStrandNames().Contains("D"));
Assert.IsTrue(polymer.GetStrand("D") is IPDBStrand, "Strand D is not a PDBStrand");
Assert.IsTrue(polymer.GetStrandNames().Contains("E"));
Assert.IsTrue(polymer.GetStrand("E") is IPDBStrand, "Strand E is not a PDBStrand");
Assert.IsTrue(polymer.GetStrandNames().Contains("A"));
Assert.IsTrue(polymer.GetStrand("A") is IPDBStrand, "Strand A is not a PDBStrand");
Assert.IsTrue(polymer.GetStrandNames().Contains("B"));
Assert.IsTrue(polymer.GetStrand("B") is IPDBStrand, "Strand B is not a PDBStrand");
//Check to pick up all 4 strands
Assert.AreEqual(polymer.GetStrandMap().Count, 4);
//The following check is to see that the first monomers in a strand
//can be accessed consecutively
//i.e. their resSeq numbering follows that in the File
//Strand A
var strandA = (IPDBStrand)polymer.GetStrand("A");
var lst = strandA.GetMonomerNamesInSequentialOrder();
//Should be 57 monomers in strand A
Assert.AreEqual(57, lst.Count);
var lstIter = lst.GetEnumerator();
lstIter.MoveNext();
var monomer1 = lstIter.Current;
var mono1 = strandA.GetMonomer(monomer1);
Assert.IsNotNull(mono1);
Assert.IsNotNull(mono1.MonomerName);
Assert.IsTrue(mono1 is IPDBMonomer, "Monomer is not a PDBMonomer");
var pdbMonomer = (IPDBMonomer)mono1;
Assert.AreEqual("A", pdbMonomer.ChainID);
Assert.AreEqual("8", pdbMonomer.ResSeq);
lstIter.MoveNext();
monomer1 = lstIter.Current;
mono1 = strandA.GetMonomer(monomer1);
pdbMonomer = (IPDBMonomer)mono1;
Assert.AreEqual("A", pdbMonomer.ChainID);
Assert.AreEqual("9", pdbMonomer.ResSeq);
lstIter.MoveNext();
monomer1 = lstIter.Current;
mono1 = strandA.GetMonomer(monomer1);
pdbMonomer = (IPDBMonomer)mono1;
Assert.AreEqual("A", pdbMonomer.ChainID);
Assert.AreEqual("10", pdbMonomer.ResSeq);
//Strand B
var strandB = (IPDBStrand)polymer.GetStrand("B");
lst = strandB.GetMonomerNamesInSequentialOrder();
//Should be 57 monomers in strand B
Assert.AreEqual(57, lst.Count);
lstIter = lst.GetEnumerator();
lstIter.MoveNext();
monomer1 = lstIter.Current;
mono1 = strandB.GetMonomer(monomer1);
Assert.IsNotNull(mono1);
Assert.IsNotNull(mono1.MonomerName);
Assert.IsTrue(mono1 is IPDBMonomer, "Monomer is not a PDBMonomer");
pdbMonomer = (IPDBMonomer)mono1;
Assert.AreEqual("B", pdbMonomer.ChainID);
Assert.AreEqual("8", pdbMonomer.ResSeq);
lstIter.MoveNext();
monomer1 = lstIter.Current;
mono1 = strandB.GetMonomer(monomer1);
pdbMonomer = (IPDBMonomer)mono1;
Assert.AreEqual("B", pdbMonomer.ChainID);
Assert.AreEqual("9", pdbMonomer.ResSeq);
lstIter.MoveNext();
monomer1 = lstIter.Current;
mono1 = strandB.GetMonomer(monomer1);
pdbMonomer = (IPDBMonomer)mono1;
Assert.AreEqual("B", pdbMonomer.ChainID);
Assert.AreEqual("10", pdbMonomer.ResSeq);
//Strand E
var strandE = (IPDBStrand)polymer.GetStrand("E");
lst = strandE.GetMonomerNamesInSequentialOrder();
//Should be 19 monomers in strand E
Assert.AreEqual(19, lst.Count);
lstIter = lst.GetEnumerator();
lstIter.MoveNext();
monomer1 = lstIter.Current;
mono1 = strandE.GetMonomer(monomer1);
Assert.IsNotNull(mono1);
Assert.IsNotNull(mono1.MonomerName);
Assert.IsTrue(mono1 is IPDBMonomer, "Monomer is not a PDBMonomer");
pdbMonomer = (IPDBMonomer)mono1;
Assert.AreEqual("E", pdbMonomer.ChainID);
Assert.AreEqual("20", pdbMonomer.ResSeq);
lstIter.MoveNext();
monomer1 = lstIter.Current;
mono1 = strandE.GetMonomer(monomer1);
pdbMonomer = (IPDBMonomer)mono1;
Assert.AreEqual("E", pdbMonomer.ChainID);
Assert.AreEqual("21", pdbMonomer.ResSeq);
lstIter.MoveNext();
monomer1 = lstIter.Current;
mono1 = strandE.GetMonomer(monomer1);
pdbMonomer = (IPDBMonomer)mono1;
Assert.AreEqual("E", pdbMonomer.ChainID);
Assert.AreEqual("22", pdbMonomer.ResSeq);
//Chain D should be 1,2,3...19
var strandD = (IPDBStrand)polymer.GetStrand("D");
lst = strandD.GetMonomerNamesInSequentialOrder();
//Should be 19 monomers in strand D
Assert.AreEqual(19, lst.Count);
lstIter = lst.GetEnumerator();
lstIter.MoveNext();
monomer1 = lstIter.Current;
mono1 = strandD.GetMonomer(monomer1);
Assert.IsNotNull(mono1);
Assert.IsNotNull(mono1.MonomerName);
Assert.IsTrue(mono1 is IPDBMonomer, "Monomer is not a PDBMonomer");
pdbMonomer = (IPDBMonomer)mono1;
Assert.AreEqual("D", pdbMonomer.ChainID);
Assert.AreEqual("1", pdbMonomer.ResSeq);
lstIter.MoveNext();
monomer1 = lstIter.Current;
mono1 = strandD.GetMonomer(monomer1);
pdbMonomer = (IPDBMonomer)mono1;
Assert.AreEqual("D", pdbMonomer.ChainID);
Assert.AreEqual("2", pdbMonomer.ResSeq);
lstIter.MoveNext();
monomer1 = lstIter.Current;
mono1 = strandD.GetMonomer(monomer1);
pdbMonomer = (IPDBMonomer)mono1;
Assert.AreEqual("D", pdbMonomer.ChainID);
Assert.AreEqual("3", pdbMonomer.ResSeq);
// PDB Structures validation
//Should have 6 helices
Assert.AreEqual(6, pdb.GetStructures().Count());
}
public void Test114D()
{
var filename = "NCDK.Data.PDB.114D.pdb";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new PDBReader(ins);
Assert.IsNotNull(reader);
var chemFile = (IChemFile)reader.Read(builder.NewChemFile());
Assert.IsNotNull(chemFile);
Assert.AreEqual(1, chemFile.Count);
var seq = chemFile[0];
Assert.IsNotNull(seq);
Assert.AreEqual(1, seq.Count);
var model = seq[0];
Assert.IsNotNull(model);
Assert.AreEqual(1, model.MoleculeSet.Count());
var container = model.MoleculeSet[0];
Assert.IsTrue(container is IBioPolymer);
var polymer = (IBioPolymer)container;
Assert.IsTrue(polymer.GetStrand("A") is IPDBStrand, "Strand A is not a PDBStrand");
var strandA = (IPDBStrand)polymer.GetStrand("A");
var lst = strandA.GetMonomerNamesInSequentialOrder().GetEnumerator();
lst.MoveNext();
var monomer1 = lst.Current;
var mono1 = strandA.GetMonomer(monomer1);
Assert.IsNotNull(mono1);
Assert.IsNotNull(mono1.MonomerName);
Assert.IsTrue(mono1 is IPDBMonomer, "Monomer is not a PDBMonomer");
var pdbMonomer = (IPDBMonomer)mono1;
Assert.AreEqual(pdbMonomer.ResSeq, "1");
lst.MoveNext();
var monomer2 = lst.Current;
var mono2 = strandA.GetMonomer(monomer2);
Assert.IsTrue(mono2 is IPDBMonomer, "Monomer is not a PDBMonomer");
var pdbMonomer2 = (IPDBMonomer)mono2;
Assert.AreEqual(pdbMonomer2.ResSeq, "2");
// chemical validation
Assert.AreEqual(552, ChemFileManipulator.GetAtomCount(chemFile));
Assert.AreEqual(2, polymer.GetStrandMap().Count());
Assert.AreEqual(24, polymer.GetMonomerMap().Count());
Assert.IsTrue(polymer.GetStrandNames().Contains("A"));
Assert.IsTrue(polymer.GetStrandNames().Contains("B"));
Assert.IsFalse(polymer.GetStrandNames().Contains("C"));
Assert.AreEqual(24, polymer.GetMonomerMap().Count());
Assert.IsTrue(polymer is IPDBPolymer);
var pdb = (IPDBPolymer)polymer;
// PDB validation
Assert.AreEqual(0, pdb.GetStructures().Count());
}
public void TestPDBFileCoffein()
{
var filename = "NCDK.Data.PDB.coffeine.pdb";
var ins = ResourceLoader.GetAsStream(filename);
var oReader = new PDBReader(ins);
Assert.IsNotNull(oReader);
var oChemFile = (IChemFile)oReader.Read(builder.NewChemFile());
Assert.IsNotNull(oChemFile);
Assert.AreEqual(oChemFile.Count, 1);
var oSeq = oChemFile[0];
Assert.IsNotNull(oSeq);
Assert.AreEqual(oSeq.Count, 1);
var oModel = oSeq[0];
Assert.IsNotNull(oModel);
Assert.AreEqual(1, oModel.MoleculeSet.Count);
var container = oModel.MoleculeSet[0];
Assert.IsFalse(container is IBioPolymer);
Assert.IsTrue(container is IAtomContainer);
var oMol = (IAtomContainer)container;
Assert.IsNotNull(oMol);
Assert.AreEqual(oMol.Atoms.Count, 14);
var nAtom = oMol.Atoms[0];
Assert.IsNotNull(nAtom);
Assert.IsTrue(nAtom is IPDBAtom);
var oAtom = (IPDBAtom)nAtom;
Assert.AreEqual("C", oAtom.Symbol);
Assert.AreEqual(1, oAtom.Serial.Value);
Assert.AreEqual("C1", oAtom.Name);
Assert.AreEqual("MOL", oAtom.ResName);
Assert.AreEqual("1", oAtom.ResSeq);
Assert.AreEqual(1.0, oAtom.Occupancy.Value, 0);
Assert.AreEqual(0.0, oAtom.TempFactor.Value, 0);
nAtom = oMol.Atoms[3];
Assert.IsNotNull(nAtom);
Assert.IsTrue(nAtom is IPDBAtom);
oAtom = (IPDBAtom)nAtom;
Assert.AreEqual("O", oAtom.Symbol);
Assert.AreEqual(4, oAtom.Serial.Value);
Assert.AreEqual("O4", oAtom.Name);
Assert.AreEqual("MOL", oAtom.ResName);
Assert.AreEqual("1", oAtom.ResSeq);
Assert.AreEqual(1.0, oAtom.Occupancy.Value, 0);
Assert.AreEqual(0.0, oAtom.TempFactor.Value, 0);
nAtom = oMol.Atoms[oMol.Atoms.Count - 1];
Assert.IsNotNull(nAtom);
Assert.IsTrue(nAtom is IPDBAtom);
oAtom = (IPDBAtom)nAtom;
Assert.AreEqual("N", oAtom.Symbol);
Assert.AreEqual(14, oAtom.Serial.Value);
Assert.AreEqual("N14", oAtom.Name);
Assert.AreEqual("MOL", oAtom.ResName);
Assert.AreEqual("1", oAtom.ResSeq);
Assert.AreEqual(1.0, oAtom.Occupancy.Value, 0);
Assert.AreEqual(0.0, oAtom.TempFactor.Value, 0);
}
public void TestAccepts()
{
var reader = new PDBReader(new StringReader(""));
Assert.IsTrue(reader.Accepts(typeof(IChemFile)));
}
