public override void TestClone()
{
IBioPolymer polymer = (IBioPolymer)NewChemObject();
object clone = polymer.Clone();
Assert.IsTrue(clone is IBioPolymer);
}
public override void TestGetMonomerCount()
{
IBioPolymer oBioPolymer = (IBioPolymer)NewChemObject();
Assert.AreEqual(0, oBioPolymer.GetMonomerMap().Count());
IStrand oStrand1 = oBioPolymer.Builder.NewStrand();
oStrand1.StrandName = "A";
IStrand oStrand2 = oBioPolymer.Builder.NewStrand();
oStrand2.StrandName = "B";
IMonomer oMono1 = oBioPolymer.Builder.NewMonomer();
oMono1.MonomerName = "TRP279";
IMonomer oMono2 = oBioPolymer.Builder.NewMonomer();
oMono2.MonomerName = "HOH";
IAtom oAtom1 = oBioPolymer.Builder.NewAtom("C");
IAtom oAtom2 = oBioPolymer.Builder.NewAtom("C");
IAtom oAtom3 = oBioPolymer.Builder.NewAtom("C");
oBioPolymer.Atoms.Add(oAtom1);
oBioPolymer.AddAtom(oAtom2, oMono1, oStrand1);
oBioPolymer.AddAtom(oAtom3, oMono2, oStrand2);
Assert.IsNotNull(oBioPolymer.Atoms[0]);
Assert.IsNotNull(oBioPolymer.Atoms[1]);
Assert.IsNotNull(oBioPolymer.Atoms[2]);
Assert.AreEqual(oAtom1, oBioPolymer.Atoms[0]);
Assert.AreEqual(oAtom2, oBioPolymer.Atoms[1]);
Assert.AreEqual(oAtom3, oBioPolymer.Atoms[2]);
Assert.AreEqual(2, oBioPolymer.GetMonomerMap().Count());
}
public virtual void TestGetStrands()
{
IBioPolymer oBioPolymer = (IBioPolymer)NewChemObject();
IStrand oStrand1 = oBioPolymer.Builder.NewStrand();
IStrand oStrand2 = oBioPolymer.Builder.NewStrand();
oStrand1.StrandName = "A";
oStrand2.StrandName = "B";
IMonomer oMono1 = oBioPolymer.Builder.NewMonomer();
oMono1.MonomerName = "TRP279";
IMonomer oMono2 = oBioPolymer.Builder.NewMonomer();
oMono2.MonomerName = "GLY123";
IAtom oAtom1 = oBioPolymer.Builder.NewAtom("C");
IAtom oAtom2 = oBioPolymer.Builder.NewAtom("C");
oBioPolymer.AddAtom(oAtom1, oMono1, oStrand1);
oBioPolymer.AddAtom(oAtom2, oMono2, oStrand2);
IDictionary <string, IStrand> strands = new Dictionary <string, IStrand>
{
{ "A", oStrand1 },
{ "B", oStrand2 }
};
Assert.IsTrue(Compares.AreDeepEqual(strands, oBioPolymer.GetStrandMap()));
}
public void TestNewBioPolymer()
{
IChemObjectBuilder builder = RootObject.Builder;
IBioPolymer polymer = builder.NewBioPolymer();
Assert.IsNotNull(polymer);
}
public virtual void TestGetMonomer_String_String()
{
IBioPolymer oBioPolymer = (IBioPolymer)NewChemObject();
IStrand oStrand1 = oBioPolymer.Builder.NewStrand();
oStrand1.StrandName = "A";
IStrand oStrand2 = oBioPolymer.Builder.NewStrand();
oStrand2.StrandName = "B";
IMonomer oMono1 = oBioPolymer.Builder.NewMonomer();
oMono1.MonomerName = "TRP279";
IMonomer oMono2 = oBioPolymer.Builder.NewMonomer();
oMono2.MonomerName = "HOH";
IAtom oAtom1 = oBioPolymer.Builder.NewAtom("C");
IAtom oAtom2 = oBioPolymer.Builder.NewAtom("C");
IAtom oAtom3 = oBioPolymer.Builder.NewAtom("C");
oBioPolymer.AddAtom(oAtom1, oMono1, oStrand1);
oBioPolymer.AddAtom(oAtom2, oMono1, oStrand1);
oBioPolymer.AddAtom(oAtom3, oMono2, oStrand2);
Assert.AreEqual(oMono1, oBioPolymer.GetMonomer("TRP279", "A"));
Assert.AreEqual(oMono2, oBioPolymer.GetMonomer("HOH", "B"));
}
public override void TestToString()
{
IBioPolymer bp = (IBioPolymer)NewChemObject();
string description = bp.ToString();
for (int i = 0; i < description.Length; i++)
{
Assert.IsTrue('\n' != description[i]);
Assert.IsTrue('\r' != description[i]);
}
}
public void TestCreateProtein()
{
IBioPolymer protein = ProteinBuilderTool.CreateProtein("GAGA", CDK.Builder);
Assert.IsNotNull(protein);
Assert.AreEqual(4, protein.GetMonomerMap().Count());
Assert.AreEqual(1, protein.GetStrandMap().Count());
Assert.AreEqual(18 + 1, protein.Atoms.Count);
// 1=terminal oxygen
Assert.AreEqual(14 + 3 + 1, protein.Bonds.Count);
// 3 = extra back bone bonds, 1=bond to terminal oxygen
}
public void TestSFBug1085912_1()
{
string filename_pdb = "NCDK.Data.PDB.1CKV.pdb";
var ins1 = ResourceLoader.GetAsStream(this.GetType(), filename_pdb);
ISimpleChemObjectReader reader = new PDBReader(ins1);
IChemFile chemFile1 = (IChemFile)reader.Read(builder.NewChemFile());
reader.Close();
IChemSequence seq1 = chemFile1[0];
IChemModel model1 = seq1[0];
IAtomContainer container = model1.MoleculeSet[0];
IBioPolymer polymer1 = (IBioPolymer)container;
int countchemFile1 = chemFile1.Count;
int countmodel1 = model1.MoleculeSet.Count;
int countpolymer1 = polymer1.Atoms.Count;
StringWriter writer = new StringWriter();
CMLWriter cmlWriter = new CMLWriter(writer);
cmlWriter.RegisterCustomizer(new PDBAtomCustomizer());
cmlWriter.Write(polymer1);
cmlWriter.Close();
string cmlContent1 = writer.ToString();
CMLReader reader2 = new CMLReader(new MemoryStream(Encoding.UTF8.GetBytes(cmlContent1)));
var chemFil2 = reader2.Read(builder.NewChemFile());
reader2.Close();
IChemSequence seq2 = chemFil2[0];
IChemModel model2 = seq2[0];
var polymer2 = (IPDBPolymer)model2.MoleculeSet[0];
int countchemFile2 = chemFil2.Count;
int countmodel2 = model2.MoleculeSet.Count;
int countpolymer2 = polymer2.Atoms.Count;
Assert.AreEqual(countchemFile1, countchemFile2);
Assert.AreEqual(countmodel1, countmodel2);
Assert.AreEqual(countpolymer1, countpolymer2);
writer = new StringWriter();
cmlWriter = new CMLWriter(writer);
cmlWriter.RegisterCustomizer(new PDBAtomCustomizer());
cmlWriter.Write(polymer2);
cmlWriter.Close();
string cmlContent2 = writer.ToString();
string conte1 = cmlContent1.Substring(0, 1000);
string conte2 = cmlContent2.Substring(0, 1000);
Assert.AreEqual(conte1, conte2);
}
private static IBioPolymer AddAminoAcid(IBioPolymer protein, IAminoAcid aaToAdd, IStrand strand)
{
foreach (var atom in aaToAdd.Atoms)
{
protein.AddAtom(atom, aaToAdd, strand);
}
foreach (var bond in aaToAdd.Bonds)
{
protein.Bonds.Add(bond);
}
return(protein);
}
public override void TestAddAtom_IAtom()
{
IBioPolymer oBioPolymer = (IBioPolymer)NewChemObject();
IAtom oAtom1 = oBioPolymer.Builder.NewAtom("C");
IAtom oAtom2 = oBioPolymer.Builder.NewAtom("C");
oBioPolymer.Atoms.Add(oAtom1);
oBioPolymer.Atoms.Add(oAtom2);
Assert.AreEqual(2, oBioPolymer.Atoms.Count);
}
/// <summary>
/// Builds a protein by connecting a new amino acid at the C-terminus of the
/// given strand. The acidic oxygen of the added amino acid is removed so that
/// additional amino acids can be added savely. But this also means that you
/// might want to add an oxygen at the end of the protein building!
/// </summary>
/// <param name="protein">protein to which the strand belongs</param>
/// <param name="aaToAdd">amino acid to add to the strand of the protein</param>
/// <param name="strand">strand to which the protein is added</param>
/// <param name="aaToAddTo"></param>
public static IBioPolymer AddAminoAcidAtCTerminus(IBioPolymer protein, IAminoAcid aaToAdd, IStrand strand, IAminoAcid aaToAddTo)
{
// then add the amino acid
AddAminoAcid(protein, aaToAdd, strand);
// Now think about the protein back bone connection
if (protein.GetMonomerMap().Any() && (aaToAddTo != null))
{
// make the connection between that aminoAcid's N-terminus and the
// protein's C-terminus
protein.Bonds.Add(aaToAdd.Builder.NewBond(aaToAddTo.CTerminus,
aaToAdd.NTerminus, BondOrder.Single));
} // else : no current C-terminus, so nothing special to do
return(protein);
}
public virtual void TestGetStrand_String()
{
IBioPolymer oBioPolymer = (IBioPolymer)NewChemObject();
IStrand oStrand1 = oBioPolymer.Builder.NewStrand();
oStrand1.StrandName = "A";
IMonomer oMono1 = oBioPolymer.Builder.NewMonomer();
oMono1.MonomerName = "TRP279";
IAtom oAtom1 = oBioPolymer.Builder.NewAtom("C");
oBioPolymer.AddAtom(oAtom1, oMono1, oStrand1);
Assert.AreEqual(oStrand1, oBioPolymer.GetStrand("A"));
}
public virtual void TestAddAtom_IAtom_IMonomer_IStrand()
{
IBioPolymer oBioPolymer = (IBioPolymer)NewChemObject();
IStrand oStrand1 = oBioPolymer.Builder.NewStrand();
oStrand1.StrandName = "A";
IMonomer oMono1 = oBioPolymer.Builder.NewMonomer();
oMono1.MonomerName = "TRP279";
IAtom oAtom1 = oBioPolymer.Builder.NewAtom("C");
IAtom oAtom2 = oBioPolymer.Builder.NewAtom("C");
oBioPolymer.AddAtom(oAtom1, oMono1, oStrand1);
oBioPolymer.AddAtom(oAtom2, oMono1, oStrand1);
oBioPolymer.AddAtom(oAtom1, null, oStrand1);
Assert.AreEqual(2, oBioPolymer.GetMonomer("TRP279", "A").Atoms.Count);
Assert.AreEqual(0, oBioPolymer.GetMonomer("", "A").Atoms.Count);
}
public virtual void TestRemoveStrand_String()
{
IBioPolymer oBioPolymer = (IBioPolymer)NewChemObject();
IStrand oStrand1 = oBioPolymer.Builder.NewStrand();
oStrand1.StrandName = "A";
IMonomer oMono1 = oBioPolymer.Builder.NewMonomer();
oMono1.MonomerName = "TRP279";
IAtom oAtom1 = oBioPolymer.Builder.NewAtom("C");
oBioPolymer.AddAtom(oAtom1, oMono1, oStrand1);
Assert.IsTrue(oBioPolymer.GetStrandNames().Contains(oStrand1.StrandName));
Assert.AreEqual(1, oBioPolymer.Atoms.Count);
oBioPolymer.RemoveStrand("A");
Assert.IsFalse(oBioPolymer.GetStrandNames().Contains(oStrand1.StrandName));
Assert.AreEqual(0, oBioPolymer.Atoms.Count);
}
private static List <IMonomer> GetMonomers(IBioPolymer iBioPolymer)
{
var monomList = new List <IMonomer>();
var strands = iBioPolymer.GetStrandMap();
var strandKeys = strands.Keys;
foreach (var key in strandKeys)
{
var aStrand = strands[key];
var tmp = aStrand.GetMonomerMap();
var keys = tmp.Keys;
foreach (var o1 in keys)
{
monomList.Add(tmp[o1]);
}
}
return(monomList);
}
/// <summary>
/// Calculates the 147 TAE descriptors for amino acids.
/// </summary>
/// <returns>The 147 TAE descriptors</returns>
public Result Calculate(IBioPolymer container)
{
container = (IBioPolymer)container.Clone(); // don't mod original
var peptide = container;
// I assume that we get single letter names
var desc = new double[ndesc];
for (int i = 0; i < ndesc; i++)
{
desc[i] = 0.0;
}
var monomers = GetMonomers(peptide);
foreach (var monomer in monomers)
{
string o = monomer.MonomerName;
if (o.Length == 0)
{
continue;
}
var olc = o.Substring(0, 1).ToUpperInvariant();
var tlc = AminoAcids.ConvertOneLetterCodeToThreeLetterCode(olc).ToLowerInvariant();
Debug.WriteLine($"Converted {olc} to {tlc}");
// get the params for this AA
var parameters = taeParams[tlc];
for (int i = 0; i < ndesc; i++)
{
desc[i] += parameters[i];
}
}
return(new Result(desc));
}
private bool createBondsWithRebondTool(IBioPolymer pol)
{
RebondTool tool = new RebondTool(2.0, 0.5, 0.5);
try
{
// configure atoms
AtomTypeFactory factory = AtomTypeFactory.getInstance("jmol_atomtypes.txt", pol.Builder);
IAtom[] atoms = pol.Atoms;
for (int i = 0; i < atoms.Length; i++)
{
try
{
IAtomType[] types = factory.getAtomTypes(atoms[i].Symbol);
if (types.Length > 0)
{
// just pick the first one
AtomTypeManipulator.configure(atoms[i], types[0]);
}
else
{
System.Console.Out.WriteLine("Could not configure atom with symbol: " + atoms[i].Symbol);
}
}
catch (System.Exception e)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.getMessage' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
System.Console.Out.WriteLine("Could not configure atom (but don't care): " + e.Message);
//logger.debug(e);
}
}
tool.rebond(pol);
}
catch (System.Exception e)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.getMessage' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
//logger.error("Could not rebond the polymer: " + e.Message);
//logger.debug(e);
}
return(true);
}
/// <summary> Create bonds when reading a protein PDB file. NB ONLY works for protein
/// PDB files! If you want to read small molecules I recommend using molecule
/// file format where the connectivity is explicitly stated. [This method can
/// however reasonably easily be extended to cover e.g. nucleic acids or your
/// favourite small molecule]. Returns 'false' if bonds could not be created
/// due to incomplete pdb-records or other reasons.
///
/// </summary>
/// <param name="pol">The Biopolymer to work on
/// </param>
public virtual bool createBonds(IBioPolymer pol)
{
//UPGRADE_TODO: Class 'java.util.HashMap' was converted to 'System.Collections.Hashtable' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilHashMap'"
System.Collections.Hashtable AAs = AminoAcids.HashMapByThreeLetterCode;
int[][] AABondInfo = AminoAcids.aaBondInfo();
System.Collections.Hashtable strands = pol.Strands;
System.Collections.IEnumerator strandKeys = strands.Keys.GetEnumerator();
//UPGRADE_TODO: Method 'java.util.Enumeration.hasMoreElements' was converted to 'System.Collections.IEnumerator.MoveNext' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilEnumerationhasMoreElements'"
while (strandKeys.MoveNext())
{
//UPGRADE_TODO: Method 'java.util.Enumeration.nextElement' was converted to 'System.Collections.IEnumerator.Current' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilEnumerationnextElement'"
IStrand strand = (IStrand)strands[strandKeys.Current];
int atoms = 0;
int atomsInLastResidue = 0;
int atomsInPresentResidue = 0;
while (atoms < strand.AtomCount - 1)
{
PDBAtom anAtom = (PDBAtom)strand.getAtomAt(atoms);
// Check that we have bond info about residue/ligand, if not - exit.
if (!AAs.ContainsKey(anAtom.ResName))
{
return(false);
}
//UPGRADE_TODO: Method 'java.util.HashMap.get' was converted to 'System.Collections.Hashtable.Item' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilHashMapget_javalangObject'"
IMonomer monomer = (IMonomer)AAs[anAtom.ResName];
atomsInPresentResidue = System.Int32.Parse((string)monomer.getProperty(AminoAcids.NO_ATOMS));
/* Check if there's something wrong with the residue record (e.g. it doesn't contain the
* correct number of atom records). */
int counter = 1;
while (atoms + counter < strand.AtomCount && anAtom.ResName.Equals(strand.getAtomAt(atoms + counter).getProperty(AminoAcids.RESIDUE_NAME)))
{
counter++;
}
// Check if something is wrong. Remember to deal with possible OXT atom...
if (counter % atomsInPresentResidue != 0 && (atoms + counter == strand.AtomCount && counter % atomsInPresentResidue != 1))
{
return(false);
}
// If nothing's wrong, add bonds
int bondID = System.Int32.Parse((string)monomer.getProperty(AminoAcids.ID));
for (int l = 0; l < System.Int32.Parse((string)monomer.getProperty(AminoAcids.NO_BONDS)); l++)
{
IBond bond = pol.Builder.newBond(strand.getAtomAt(AABondInfo[bondID + l][1] + atoms), strand.getAtomAt(AABondInfo[bondID + l][2] + atoms), (double)(AABondInfo[bondID + l][3]));
pol.addBond(bond);
}
// If not first residue, connect residues
if (atomsInLastResidue != 0)
{
IBond bond = pol.Builder.newBond(strand.getAtomAt(atoms - atomsInLastResidue + 2), strand.getAtomAt(atoms), 1);
pol.addBond(bond);
}
atoms = atoms + atomsInPresentResidue;
atomsInLastResidue = atomsInPresentResidue;
// Check if next atom is an OXT. The reason to why this is seemingly overly complex is because
// not all PDB-files have ending OXT. If that were the case you could just check if
// atoms == mol.getAtomCount()...
if (strand.AtomCount < atoms && ((PDBAtom)strand.getAtomAt(atoms)).Oxt)
{
// if(strand.getAtomCount() < atoms && ((String)strand.getAtomAt(atoms).getProperty("oxt")).equals("1")) {
IBond bond = pol.Builder.newBond(strand.getAtomAt(atoms - atomsInLastResidue + 2), strand.getAtomAt(atoms), 1);
pol.addBond(bond);
}
}
}
return(true);
}
private bool createBondsWithRebondTool(IBioPolymer pol)
{
RebondTool tool = new RebondTool(2.0, 0.5, 0.5);
try
{
// configure atoms
AtomTypeFactory factory = AtomTypeFactory.getInstance("jmol_atomtypes.txt", pol.Builder);
IAtom[] atoms = pol.Atoms;
for (int i = 0; i < atoms.Length; i++)
{
try
{
IAtomType[] types = factory.getAtomTypes(atoms[i].Symbol);
if (types.Length > 0)
{
// just pick the first one
AtomTypeManipulator.configure(atoms[i], types[0]);
}
else
{
System.Console.Out.WriteLine("Could not configure atom with symbol: " + atoms[i].Symbol);
}
}
catch (System.Exception e)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.getMessage' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
System.Console.Out.WriteLine("Could not configure atom (but don't care): " + e.Message);
//logger.debug(e);
}
}
tool.rebond(pol);
}
catch (System.Exception e)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Throwable.getMessage' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
//logger.error("Could not rebond the polymer: " + e.Message);
//logger.debug(e);
}
return true;
}
/// <summary> Create bonds when reading a protein PDB file. NB ONLY works for protein
/// PDB files! If you want to read small molecules I recommend using molecule
/// file format where the connectivity is explicitly stated. [This method can
/// however reasonably easily be extended to cover e.g. nucleic acids or your
/// favourite small molecule]. Returns 'false' if bonds could not be created
/// due to incomplete pdb-records or other reasons.
///
/// </summary>
/// <param name="pol">The Biopolymer to work on
/// </param>
public virtual bool createBonds(IBioPolymer pol)
{
//UPGRADE_TODO: Class 'java.util.HashMap' was converted to 'System.Collections.Hashtable' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilHashMap'"
System.Collections.Hashtable AAs = AminoAcids.HashMapByThreeLetterCode;
int[][] AABondInfo = AminoAcids.aaBondInfo();
System.Collections.Hashtable strands = pol.Strands;
System.Collections.IEnumerator strandKeys = strands.Keys.GetEnumerator();
//UPGRADE_TODO: Method 'java.util.Enumeration.hasMoreElements' was converted to 'System.Collections.IEnumerator.MoveNext' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilEnumerationhasMoreElements'"
while (strandKeys.MoveNext())
{
//UPGRADE_TODO: Method 'java.util.Enumeration.nextElement' was converted to 'System.Collections.IEnumerator.Current' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilEnumerationnextElement'"
IStrand strand = (IStrand)strands[strandKeys.Current];
int atoms = 0;
int atomsInLastResidue = 0;
int atomsInPresentResidue = 0;
while (atoms < strand.AtomCount - 1)
{
PDBAtom anAtom = (PDBAtom)strand.getAtomAt(atoms);
// Check that we have bond info about residue/ligand, if not - exit.
if (!AAs.ContainsKey(anAtom.ResName))
{
return false;
}
//UPGRADE_TODO: Method 'java.util.HashMap.get' was converted to 'System.Collections.Hashtable.Item' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilHashMapget_javalangObject'"
IMonomer monomer = (IMonomer)AAs[anAtom.ResName];
atomsInPresentResidue = System.Int32.Parse((string)monomer.getProperty(AminoAcids.NO_ATOMS));
/* Check if there's something wrong with the residue record (e.g. it doesn't contain the
* correct number of atom records). */
int counter = 1;
while (atoms + counter < strand.AtomCount && anAtom.ResName.Equals(strand.getAtomAt(atoms + counter).getProperty(AminoAcids.RESIDUE_NAME)))
{
counter++;
}
// Check if something is wrong. Remember to deal with possible OXT atom...
if (counter % atomsInPresentResidue != 0 && (atoms + counter == strand.AtomCount && counter % atomsInPresentResidue != 1))
{
return false;
}
// If nothing's wrong, add bonds
int bondID = System.Int32.Parse((string)monomer.getProperty(AminoAcids.ID));
for (int l = 0; l < System.Int32.Parse((string)monomer.getProperty(AminoAcids.NO_BONDS)); l++)
{
IBond bond = pol.Builder.newBond(strand.getAtomAt(AABondInfo[bondID + l][1] + atoms), strand.getAtomAt(AABondInfo[bondID + l][2] + atoms), (double)(AABondInfo[bondID + l][3]));
pol.addBond(bond);
}
// If not first residue, connect residues
if (atomsInLastResidue != 0)
{
IBond bond = pol.Builder.newBond(strand.getAtomAt(atoms - atomsInLastResidue + 2), strand.getAtomAt(atoms), 1);
pol.addBond(bond);
}
atoms = atoms + atomsInPresentResidue;
atomsInLastResidue = atomsInPresentResidue;
// Check if next atom is an OXT. The reason to why this is seemingly overly complex is because
// not all PDB-files have ending OXT. If that were the case you could just check if
// atoms == mol.getAtomCount()...
if (strand.AtomCount < atoms && ((PDBAtom)strand.getAtomAt(atoms)).Oxt)
{
// if(strand.getAtomCount() < atoms && ((String)strand.getAtomAt(atoms).getProperty("oxt")).equals("1")) {
IBond bond = pol.Builder.newBond(strand.getAtomAt(atoms - atomsInLastResidue + 2), strand.getAtomAt(atoms), 1);
pol.addBond(bond);
}
}
}
return true;
}
IDescriptorResult IBioPolymerDescriptor.Calculate(IBioPolymer mol) => Calculate(mol);
public ProteinPocketFinder(IBioPolymer protein, double[][][] grid)
{
this.Protein = protein;
this.Grid = grid;
gridGenerator.Grid = grid;
}