private void addBond(PDBPolymer obp, int bondAtomNo, int bondedAtomNo)
{
IAtom firstAtom = (PDBAtom)atomNumberMap[(System.Int32)bondAtomNo];
IAtom secondAtom = (PDBAtom)atomNumberMap[(System.Int32)bondedAtomNo];
if (firstAtom == null)
{
//logger.error("Could not find bond start atom in map with serial id: ", bondAtomNo);
}
if (secondAtom == null)
{
//logger.error("Could not find bond target atom in map with serial id: ", bondAtomNo);
}
obp.addBond(firstAtom.Builder.newBond(firstAtom, secondAtom, 1));
}
public /*Chem*/ Frame(Org.OpenScience.CDK.Interfaces.IChemFile chemFile, Device graphicsDevice)
{
shapes = new Shape[JmolConstants.SHAPE_MAX];
this.g3d = new NuGraphics3D(graphicsDevice);
this.frameRenderer = new FrameRenderer();
for (int i = MAX_BONDS_LENGTH_TO_CACHE; --i > 0;) // .GT. 0
{
freeBonds[i] = new Bond[MAX_NUM_TO_CACHE][];
}
// convert to jmol native
mmset = new Mmset(this);
// set properties
mmset.ModelSetProperties = new System.Collections.Specialized.NameValueCollection();
// init build
currentModelIndex = -1;
currentModel = null;
currentChainID = '\uFFFF';
currentChain = null;
currentGroupSequenceNumber = -1;
currentGroupInsertionCode = '\uFFFF';
int atomCountEstimate = 0;
for (int seq = 0; seq < chemFile.ChemSequenceCount; seq++)
{
for (int model = 0; model < chemFile.ChemSequences[seq].ChemModelCount; model++)
{
Org.OpenScience.CDK.Interfaces.IChemModel chemModel = chemFile.ChemSequences[seq].ChemModels[model];
for (int atomC = 0; atomC < chemModel.SetOfMolecules.AtomContainerCount; atomC++)
{
atomCountEstimate += chemModel.SetOfMolecules.AtomContainers[atomC].AtomCount;
}
}
}
if (atomCountEstimate <= 0)
{
atomCountEstimate = ATOM_GROWTH_INCREMENT;
}
atoms = new Atom[atomCountEstimate];
bonds = new Bond[2 * atomCountEstimate];
htAtomMap.Clear();
// translate IChemSequence[] into Model[]
mmset.ModelCount = chemFile.ChemSequenceCount;
for (int seq = 0; seq < chemFile.ChemSequenceCount; ++seq)
{
int modelNumber = seq + 1;
string modelName = modelNumber.ToString();
NameValueCollection modelProperties = new NameValueCollection(); // FIXME: Loading property values
mmset.setModelNameNumberProperties(seq, modelName, modelNumber, modelProperties);
}
// translate Atoms
Dictionary <Org.OpenScience.CDK.Interfaces.IAtom, Atom> atomsList = new Dictionary <Org.OpenScience.CDK.Interfaces.IAtom, Atom>();
//try
//{
for (int seq = 0; seq < chemFile.ChemSequenceCount; seq++)
{
for (int model = 0; model < chemFile.ChemSequences[seq].ChemModelCount; model++)
{
Org.OpenScience.CDK.Interfaces.IChemModel chemModel = chemFile.ChemSequences[seq].ChemModels[model];
for (int atomC = 0; atomC < chemModel.SetOfMolecules.AtomContainerCount; atomC++)
{
for (int atomIdx = 0; atomIdx < chemModel.SetOfMolecules.AtomContainers[atomC].AtomCount; atomIdx++)
{
Org.OpenScience.CDK.Interfaces.IAtom atom = chemModel.SetOfMolecules.AtomContainers[atomC].Atoms[atomIdx];
sbyte elementNumber = (sbyte)atom.AtomicNumber;
if (elementNumber <= 0)
{
elementNumber = JmolConstants.elementNumberFromSymbol(atom.Symbol);
}
char alternateLocation = '\0';
int sequenceNumber = int.MinValue;
char groupInsertionCode = '\0';
string atomName = null;
string group3Name = null;
char chainID = '\0';
if (atom is PDBAtom)
{
PDBAtom pdbAtom = (PDBAtom)atom;
if (pdbAtom.ResSeq != null && pdbAtom.ResSeq.Length > 0)
{
sequenceNumber = int.Parse(pdbAtom.ResSeq);
}
if (pdbAtom.ICode != null && pdbAtom.ICode.Length > 0)
{
groupInsertionCode = pdbAtom.ICode[0];
}
atomName = pdbAtom.Name;
group3Name = pdbAtom.ResName;
if (pdbAtom.ChainID != null && pdbAtom.ChainID.Length >= 1)
{
chainID = pdbAtom.ChainID[0];
}
}
else
{
atomName = atom.AtomTypeName;
}
atomsList[atom] = AddAtom(model, atom, elementNumber, atomName, atom.getFormalCharge(),
(float)atom.getCharge(), 100, float.NaN, (float)atom.X3d, (float)atom.Y3d,
(float)atom.Z3d, false, int.MinValue, chainID, group3Name, sequenceNumber,
groupInsertionCode, float.NaN, float.NaN, float.NaN, alternateLocation, null);
}
}
}
}
//}
//catch (Exception e)
//{
// throw new ApplicationException("Problem translating atoms", e);
//}
fileHasHbonds = false;
// translate bonds
try
{
for (int seq = 0; seq < chemFile.ChemSequenceCount; seq++)
{
for (int model = 0; model < chemFile.ChemSequences[seq].ChemModelCount; model++)
{
Org.OpenScience.CDK.Interfaces.IChemModel chemModel = chemFile.ChemSequences[seq].ChemModels[model];
for (int atomC = 0; atomC < chemModel.SetOfMolecules.AtomContainerCount; atomC++)
{
for (int bondIdx = 0; bondIdx < chemModel.SetOfMolecules.AtomContainers[atomC].Bonds.Length; bondIdx++)
{
Org.OpenScience.CDK.Interfaces.IBond bond = chemModel.SetOfMolecules.AtomContainers[atomC].Bonds[bondIdx];
Org.OpenScience.CDK.Interfaces.IAtom[] cdkAtoms = bond.getAtoms();
// locate translated atoms
Atom atom1, atom2;
atomsList.TryGetValue(cdkAtoms[0], out atom1);
atomsList.TryGetValue(cdkAtoms[1], out atom2);
bondAtoms(atom1, atom2, (int)bond.Order);
}
}
}
}
}
catch (Exception e)
{
throw new ApplicationException("Problem translating bonds", e);
}
atomsList.Clear();
// translate structures of PDBPolymer only
for (int seq = 0; seq < chemFile.ChemSequenceCount; seq++)
{
for (int model = 0; model < chemFile.ChemSequences[seq].ChemModelCount; model++)
{
Org.OpenScience.CDK.Interfaces.IChemModel chemModel = chemFile.ChemSequences[seq].ChemModels[model];
foreach (Org.OpenScience.CDK.Interfaces.IMolecule molecule in chemModel.SetOfMolecules.Molecules)
{
if (molecule is PDBPolymer)
{
PDBPolymer pdbPolymer = (PDBPolymer)molecule;
if (pdbPolymer.Structures != null && pdbPolymer.Structures.Count > 0)
{
structuresDefined = true;
foreach (PDBStructure pdbStruct in pdbPolymer.Structures)
{
structuresDefined = true;
mmset.defineStructure(pdbStruct.StructureType, pdbStruct.StartChainID,
pdbStruct.StartSequenceNumber, pdbStruct.StartInsertionCode,
pdbStruct.EndChainID, pdbStruct.EndSequenceNumber, pdbStruct.EndInsertionCode);
}
}
}
}
}
}
autoBond(null, null);
// build groups
FinalizeGroupBuild();
BuildPolymers();
Freeze();
finalizeBuild();
// create ribbon shapes
try
{
setShapeSize(JmolConstants.SHAPE_RIBBONS, -1, new BitArray(0));
setShapeSize(JmolConstants.SHAPE_CARTOON, -1, new BitArray(0));
}
catch (Exception) { }
}
/// <summary>
/// Read a <see cref="IChemFile"/> from a file in PDB format. The molecules
/// in the file are stored as <see cref="IBioPolymer"/>s in the
/// <see cref="IChemFile"/>. The residues are the monomers of the
/// <see cref="IBioPolymer"/>, and their names are the concatenation of the
/// residue, chain id, and the sequence number. Separate chains (denoted by
/// TER records) are stored as separate <see cref="IBioPolymer"/> molecules.
/// </summary>
/// <remarks>
/// Connectivity information is not currently read.
/// </remarks>
/// <returns>The ChemFile that was read from the PDB file.</returns>
private IChemFile ReadChemFile(IChemFile oFile)
{
// initialize all containers
var oSeq = oFile.Builder.NewChemSequence();
var oModel = oFile.Builder.NewChemModel();
var oSet = oFile.Builder.NewAtomContainerSet();
// some variables needed
var oBP = new PDBPolymer();
var molecularStructure = oFile.Builder.NewAtomContainer();
string cRead = "";
char chain = 'A'; // To ensure stringent name giving of monomers
int lineLength = 0;
bool isProteinStructure = false;
atomNumberMap = new Dictionary <int, IAtom>();
if (readConnect.IsSet)
{
bondsFromConnectRecords = new List <IBond>();
}
// do the reading of the Input
try
{
do
{
cRead = oInput.ReadLine();
Debug.WriteLine($"Read line: {cRead}");
if (cRead != null)
{
lineLength = cRead.Length;
// make sure the record name is 6 characters long
if (lineLength < 6)
{
cRead = cRead + " ";
}
// check the first column to decide what to do
var cCol = cRead.Substring(0, 6);
switch (cCol.ToUpperInvariant())
{
case "SEQRES":
{
isProteinStructure = true;
}
break;
case "ATOM ":
{
#region
// read an atom record
var oAtom = ReadAtom(cRead, lineLength);
if (isProteinStructure)
{
// construct a string describing the residue
var cResidue = new StringBuilder(8);
var oObj = oAtom.ResName;
if (oObj != null)
{
cResidue = cResidue.Append(oObj.Trim());
}
oObj = oAtom.ChainID;
if (oObj != null)
{
// cResidue = cResidue.Append(((string)oObj).Trim());
cResidue = cResidue.Append(chain);
}
oObj = oAtom.ResSeq;
if (oObj != null)
{
cResidue = cResidue.Append(oObj.Trim());
}
// search for an existing strand or create a new one.
var strandName = oAtom.ChainID;
if (strandName == null || strandName.Length == 0)
{
strandName = chain.ToString(NumberFormatInfo.InvariantInfo);
}
var oStrand = oBP.GetStrand(strandName);
if (oStrand == null)
{
oStrand = new PDBStrand
{
StrandName = strandName,
Id = chain.ToString(NumberFormatInfo.InvariantInfo)
};
}
// search for an existing monomer or create a new one.
var oMonomer = oBP.GetMonomer(cResidue.ToString(), chain.ToString(NumberFormatInfo.InvariantInfo));
if (oMonomer == null)
{
var monomer = new PDBMonomer
{
MonomerName = cResidue.ToString(),
MonomerType = oAtom.ResName,
ChainID = oAtom.ChainID,
ICode = oAtom.ICode,
ResSeq = oAtom.ResSeq
};
oMonomer = monomer;
}
// add the atom
oBP.AddAtom(oAtom, oMonomer, oStrand);
}
else
{
molecularStructure.Atoms.Add(oAtom);
}
if (readConnect.IsSet)
{
var isDup = atomNumberMap.ContainsKey(oAtom.Serial.Value);
atomNumberMap[oAtom.Serial.Value] = oAtom;
if (isDup)
{
Trace.TraceWarning($"Duplicate serial ID found for atom: {oAtom}");
}
}
Debug.WriteLine($"Added ATOM: {oAtom}");
// As HETATMs cannot be considered to either belong to a certain monomer or strand,
// they are dealt with separately.
#endregion
}
break;
case "HETATM":
{
#region
// read an atom record
var oAtom = ReadAtom(cRead, lineLength);
oAtom.HetAtom = true;
if (isProteinStructure)
{
oBP.Atoms.Add(oAtom);
}
else
{
molecularStructure.Atoms.Add(oAtom);
}
var isDup = atomNumberMap.ContainsKey(oAtom.Serial.Value);
atomNumberMap[oAtom.Serial.Value] = oAtom;
if (isDup)
{
Trace.TraceWarning($"Duplicate serial ID found for atom: {oAtom}");
}
Debug.WriteLine($"Added HETATM: {oAtom}");
#endregion
}
break;
case "TER ":
{
#region
// start new strand
chain++;
var oStrand = new PDBStrand
{
StrandName = chain.ToString(NumberFormatInfo.InvariantInfo)
};
Debug.WriteLine("Added new STRAND");
#endregion
}
break;
case "END ":
{
#region
atomNumberMap.Clear();
if (isProteinStructure)
{
// create bonds and finish the molecule
oSet.Add(oBP);
if (useRebondTool.IsSet)
{
try
{
if (!CreateBondsWithRebondTool(oBP))
{
// Get rid of all potentially created bonds.
Trace.TraceInformation("Bonds could not be created using the RebondTool when PDB file was read.");
oBP.Bonds.Clear();
}
}
catch (Exception exception)
{
Trace.TraceInformation("Bonds could not be created when PDB file was read.");
Debug.WriteLine(exception);
}
}
}
else
{
if (useRebondTool.IsSet)
{
CreateBondsWithRebondTool(molecularStructure);
}
oSet.Add(molecularStructure);
}
#endregion
}
break;
case "MODEL ":
{
#region
// OK, start a new model and save the current one first *if* it contains atoms
if (isProteinStructure)
{
if (oBP.Atoms.Count > 0)
{
// save the model
oSet.Add(oBP);
oModel.MoleculeSet = oSet;
oSeq.Add(oModel);
// setup a new one
oBP = new PDBPolymer();
oModel = oFile.Builder.NewChemModel();
oSet = oFile.Builder.NewAtomContainerSet();
// avoid duplicate atom warnings
atomNumberMap.Clear();
}
}
else
{
if (molecularStructure.Atoms.Count > 0)
{
// save the model
oSet.Add(molecularStructure);
oModel.MoleculeSet = oSet;
oSeq.Add(oModel);
// setup a new one
molecularStructure = oFile.Builder.NewAtomContainer();
oModel = oFile.Builder.NewChemModel();
oSet = oFile.Builder.NewAtomContainerSet();
}
}
#endregion
}
break;
case "REMARK":
{
#region
var comment = oFile.GetProperty <string>(CDKPropertyName.Comment, "");
if (lineLength > 12)
{
comment = comment + cRead.Substring(11).Trim()
+ "\n";
oFile.SetProperty(CDKPropertyName.Comment, comment);
}
else
{
Trace.TraceWarning("REMARK line found without any comment!");
}
#endregion
}
break;
case "COMPND":
{
#region
var title = cRead.Substring(10).Trim();
oFile.SetProperty(CDKPropertyName.Title, title);
#endregion
}
break;
case "CONECT":
{
#region
// Read connectivity information from CONECT records. Only
// covalent bonds are dealt with. Perhaps salt bridges
// should be dealt with in the same way..?
if (!readConnect.IsSet)
{
break;
}
cRead = cRead.Trim();
if (cRead.Length < 16)
{
Debug.WriteLine($"Skipping unexpected empty CONECT line! : {cRead}");
}
else
{
int lineIndex = 6;
int atomFromNumber = -1;
int atomToNumber = -1;
var molecule = (isProteinStructure) ? oBP : molecularStructure;
while (lineIndex + 5 <= cRead.Length)
{
var part = cRead.Substring(lineIndex, 5).Trim();
if (atomFromNumber == -1)
{
try
{
atomFromNumber = int.Parse(part, NumberFormatInfo.InvariantInfo);
}
catch (FormatException)
{
}
}
else
{
try
{
atomToNumber = int.Parse(part, NumberFormatInfo.InvariantInfo);
}
catch (FormatException)
{
atomToNumber = -1;
}
if (atomFromNumber != -1 && atomToNumber != -1)
{
AddBond(molecule, atomFromNumber, atomToNumber);
Debug.WriteLine($"Bonded {atomFromNumber} with {atomToNumber}");
}
}
lineIndex += 5;
}
}
#endregion
}
break;
case "HELIX ":
{
#region
// HELIX 1 H1A CYS A 11 LYS A 18 1 RESIDUE 18 HAS POSITIVE PHI 1D66 72
// 1 2 3 4 5 6 7
// 01234567890123456789012345678901234567890123456789012345678901234567890123456789
var structure = new PDBStructure
{
StructureType = PDBStructure.Helix,
StartChainID = cRead[19],
StartSequenceNumber = int.Parse(cRead.Substring(21, 4).Trim(), NumberFormatInfo.InvariantInfo),
StartInsertionCode = cRead[25],
EndChainID = cRead[31],
EndSequenceNumber = int.Parse(cRead.Substring(33, 4).Trim(), NumberFormatInfo.InvariantInfo),
EndInsertionCode = cRead[37]
};
oBP.Add(structure);
#endregion
}
break;
case "SHEET ":
{
#region
var structure = new PDBStructure
{
StructureType = PDBStructure.Sheet,
StartChainID = cRead[21],
StartSequenceNumber = int.Parse(cRead.Substring(22, 4).Trim(), NumberFormatInfo.InvariantInfo),
StartInsertionCode = cRead[26],
EndChainID = cRead[32],
EndSequenceNumber = int.Parse(cRead.Substring(33, 4).Trim(), NumberFormatInfo.InvariantInfo),
EndInsertionCode = cRead[37]
};
oBP.Add(structure);
#endregion
}
break;
case "TURN ":
{
#region
var structure = new PDBStructure
{
StructureType = PDBStructure.Turn,
StartChainID = cRead[19],
StartSequenceNumber = int.Parse(cRead.Substring(20, 4).Trim(), NumberFormatInfo.InvariantInfo),
StartInsertionCode = cRead[24],
EndChainID = cRead[30],
EndSequenceNumber = int.Parse(cRead.Substring(31, 4).Trim(), NumberFormatInfo.InvariantInfo),
EndInsertionCode = cRead[35]
};
oBP.Add(structure);
#endregion
}
break;
default:
break; // ignore all other commands
}
}
} while (cRead != null);
}
catch (Exception e)
{
if (e is IOException || e is ArgumentException)
{
Trace.TraceError("Found a problem at line:");
Trace.TraceError(cRead);
Trace.TraceError("01234567890123456789012345678901234567890123456789012345678901234567890123456789");
Trace.TraceError(" 1 2 3 4 5 6 7 ");
Trace.TraceError($" error: {e.Message}");
Debug.WriteLine(e);
Console.Error.WriteLine(e.StackTrace);
}
else
{
throw;
}
}
// try to close the Input
try
{
oInput.Close();
}
catch (Exception e)
{
Debug.WriteLine(e);
}
// Set all the dependencies
oModel.MoleculeSet = oSet;
oSeq.Add(oModel);
oFile.Add(oSeq);
return(oFile);
}
/// <summary> Read a <code>ChemFile</code> from a file in PDB format. The molecules
/// in the file are stored as <code>BioPolymer</code>s in the
/// <code>ChemFile</code>. The residues are the monomers of the
/// <code>BioPolymer</code>, and their names are the concatenation of the
/// residue, chain id, and the sequence number. Separate chains (denoted by
/// TER records) are stored as separate <code>BioPolymer</code> molecules.
///
/// <p>Connectivity information is not currently read.
///
/// </summary>
/// <returns> The ChemFile that was read from the PDB file.
/// </returns>
private IChemFile readChemFile(IChemFile oFile)
{
int bonds = 0;
// initialize all containers
IChemSequence oSeq = oFile.Builder.newChemSequence();
IChemModel oModel = oFile.Builder.newChemModel();
ISetOfMolecules oSet = oFile.Builder.newSetOfMolecules();
// some variables needed
string cCol;
PDBAtom oAtom;
PDBPolymer oBP = new PDBPolymer();
System.Text.StringBuilder cResidue;
string oObj;
IMonomer oMonomer;
string cRead = "";
char chain = 'A'; // To ensure stringent name giving of monomers
IStrand oStrand;
int lineLength = 0;
atomNumberMap = System.Collections.Hashtable.Synchronized(new System.Collections.Hashtable());
// do the reading of the Input
try
{
do
{
cRead = _oInput.ReadLine();
//logger.debug("Read line: ", cRead);
if (cRead != null)
{
lineLength = cRead.Length;
if (lineLength < 80)
{
//logger.warn("Line is not of the expected length 80!");
}
// make sure the record name is 6 characters long
if (lineLength < 6)
{
cRead = cRead + " ";
}
// check the first column to decide what to do
cCol = cRead.Substring(0, (6) - (0));
if ("ATOM ".ToUpper().Equals(cCol.ToUpper()))
{
// read an atom record
oAtom = readAtom(cRead, lineLength);
// construct a string describing the residue
cResidue = new System.Text.StringBuilder(8);
oObj = oAtom.ResName;
if (oObj != null)
{
cResidue = cResidue.Append(oObj.Trim());
}
oObj = oAtom.ChainID;
if (oObj != null)
{
// cResidue = cResidue.append(((String)oObj).trim());
cResidue = cResidue.Append(System.Convert.ToString(chain));
}
oObj = oAtom.ResSeq;
if (oObj != null)
{
cResidue = cResidue.Append(oObj.Trim());
}
// search for an existing strand or create a new one.
oStrand = oBP.getStrand(System.Convert.ToString(chain));
if (oStrand == null)
{
oStrand = new PDBStrand();
oStrand.StrandName = System.Convert.ToString(chain);
}
// search for an existing monomer or create a new one.
oMonomer = oBP.getMonomer(cResidue.ToString(), System.Convert.ToString(chain));
if (oMonomer == null)
{
PDBMonomer monomer = new PDBMonomer();
monomer.MonomerName = cResidue.ToString();
monomer.MonomerType = oAtom.ResName;
monomer.ChainID = oAtom.ChainID;
monomer.ICode = oAtom.ICode;
oMonomer = monomer;
}
// add the atom
oBP.addAtom(oAtom, oMonomer, oStrand);
System.Object tempObject;
//UPGRADE_WARNING: At least one expression was used more than once in the target code. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1181'"
tempObject = atomNumberMap[(System.Int32)oAtom.Serial];
atomNumberMap[(System.Int32)oAtom.Serial] = oAtom;
if (readConnect.Set && tempObject != null)
{
//logger.warn("Duplicate serial ID found for atom: ", oAtom);
}
// //logger.debug("Added ATOM: ", oAtom);
/** As HETATMs cannot be considered to either belong to a certain monomer or strand,
* they are dealt with seperately.*/
}
else if ("HETATM".ToUpper().Equals(cCol.ToUpper()))
{
// read an atom record
oAtom = readAtom(cRead, lineLength);
oAtom.HetAtom = true;
oBP.addAtom(oAtom);
System.Object tempObject2;
//UPGRADE_WARNING: At least one expression was used more than once in the target code. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1181'"
tempObject2 = atomNumberMap[(System.Int32)oAtom.Serial];
atomNumberMap[(System.Int32)oAtom.Serial] = oAtom;
if (tempObject2 != null)
{
//logger.warn("Duplicate serial ID found for atom: ", oAtom);
}
//logger.debug("Added HETATM: ", oAtom);
}
else if ("TER ".ToUpper().Equals(cCol.ToUpper()))
{
// start new strand
chain++;
oStrand = new PDBStrand();
oStrand.StrandName = System.Convert.ToString(chain);
//logger.debug("Added new STRAND");
}
else if ("END ".ToUpper().Equals(cCol.ToUpper()))
{
atomNumberMap.Clear();
// create bonds and finish the molecule
if (deduceBonding.Set)
{
// OK, try to deduce the bonding patterns
if (oBP.AtomCount != 0)
{
// Create bonds. If bonds could not be created, all bonds are deleted.
try
{
if (useRebondTool.Set)
{
if (!createBondsWithRebondTool(oBP))
{
// Get rid of all potentially created bonds.
//logger.info("Bonds could not be created using the RebondTool when PDB file was read.");
oBP.removeAllBonds();
}
}
else
{
if (!createBonds(oBP))
{
// Get rid of all potentially created bonds.
//logger.info("Bonds could not be created when PDB file was read.");
oBP.removeAllBonds();
}
}
}
catch (System.Exception exception)
{
//logger.info("Bonds could not be created when PDB file was read.");
//logger.debug(exception);
}
}
}
oSet.addMolecule(oBP);
// oBP = new BioPolymer();
// } else if (cCol.equals("USER ")) {
// System.out.println(cLine);
// System.out.println(cLine);
// } else if (cCol.equals("ENDMDL")) {
// System.out.println(cLine);
}
else if (cCol.Equals("MODEL "))
{
// OK, start a new model and save the current one first *if* it contains atoms
if (oBP.AtomCount > 0)
{
// save the model
oSet.addAtomContainer(oBP);
oModel.SetOfMolecules = oSet;
oSeq.addChemModel(oModel);
// setup a new one
oBP = new PDBPolymer();
oModel = oFile.Builder.newChemModel();
oSet = oFile.Builder.newSetOfMolecules();
}
}
else if ("REMARK".ToUpper().Equals(cCol.ToUpper()))
{
System.Object comment = oFile.getProperty(CDKConstants.COMMENT);
if (comment == null)
{
comment = "";
}
if (lineLength > 12)
{
//UPGRADE_TODO: The equivalent in .NET for method 'java.lang.Object.toString' may return a different value. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1043'"
comment = comment.ToString() + cRead.Substring(11).Trim() + "\n";
oFile.setProperty(CDKConstants.COMMENT, comment);
}
else
{
//logger.warn("REMARK line found without any comment!");
}
}
else if ("COMPND".ToUpper().Equals(cCol.ToUpper()))
{
string title = cRead.Substring(10).Trim();
oFile.setProperty(CDKConstants.TITLE, title);
}
/*************************************************************
* Read connectivity information from CONECT records.
* Only covalent bonds are dealt with. Perhaps salt bridges
* should be dealt with in the same way..?
*/
else if (readConnect.Set && "CONECT".ToUpper().Equals(cCol.ToUpper()))
{
cRead.Trim();
if (cRead.Length < 16)
{
//logger.debug("Skipping unexpected empty CONECT line! : ", cRead);
}
else
{
string bondAtom = cRead.Substring(7, 5).Trim();
int bondAtomNo = System.Int32.Parse(bondAtom);
for (int b = 0; b < 9; b += (b == 5 ? 2 : 1))
{
string bondedAtom = cRead.Substring((b * 5) + 11, 5).Trim();
int bondedAtomNo;
if (int.TryParse(bondedAtom, out bondedAtomNo))
{
bonds++;
addBond(oBP, bondAtomNo, bondedAtomNo);
}
}
//string bondedAtom = cRead.Substring(12, 5).Trim();
//int bondedAtomNo = -1;
//try
//{
// bondedAtomNo = System.Int32.Parse(bondedAtom);
//}
//catch (System.Exception e)
//{
// bondedAtomNo = -1;
//}
//if (bondedAtomNo != -1)
//{
// bonds++;
// addBond(oBP, bondAtomNo, bondedAtomNo);
// //logger.warn("Bonded " + bondAtomNo + " with " + bondedAtomNo);
//}
//else
//{
//}
//if (cRead.Length > 17)
//{
// bondedAtom = cRead.Substring(16, 5);
// bondedAtom = bondedAtom.Trim();
// try
// {
// bondedAtomNo = System.Int32.Parse(bondedAtom);
// }
// catch (System.Exception e)
// {
// bondedAtomNo = -1;
// }
// if (bondedAtomNo != -1)
// {
// bonds++;
// addBond(oBP, bondAtomNo, bondedAtomNo);
// //logger.warn("Bonded " + bondAtomNo + " with " + bondedAtomNo);
// }
//}
//if (cRead.Length > 22)
//{
// bondedAtom = cRead.Substring(22, 5);
// bondedAtom = bondedAtom.Trim();
// try
// {
// bondedAtomNo = System.Int32.Parse(bondedAtom);
// }
// catch (System.Exception e)
// {
// bondedAtomNo = -1;
// }
// if (bondedAtomNo != -1)
// {
// bonds++;
// addBond(oBP, bondAtomNo, bondedAtomNo);
// //logger.warn("Bonded " + bondAtomNo + " with " + bondedAtomNo);
// }
//}
//if (cRead.Length > 27)
//{
// bondedAtom = cRead.Substring(27, 5);
// bondedAtom = bondedAtom.Trim();
// try
// {
// bondedAtomNo = System.Int32.Parse(bondedAtom);
// }
// catch (System.Exception e)
// {
// bondedAtomNo = -1;
// }
// if (bondedAtomNo != -1)
// {
// bonds++;
// addBond(oBP, bondAtomNo, bondedAtomNo);
// //logger.warn("Bonded " + bondAtomNo + " with " + bondedAtomNo);
// }
//}
}
}
/*************************************************************/
else if ("HELIX ".ToUpper().Equals(cCol.ToUpper()))
{
// HELIX 1 H1A CYS A 11 LYS A 18 1 RESIDUE 18 HAS POSITIVE PHI 1D66 72
// 1 2 3 4 5 6 7
// 01234567890123456789012345678901234567890123456789012345678901234567890123456789
PDBStructure structure = new PDBStructure();
structure.StructureType = PDBStructure.HELIX;
structure.StartChainID = cRead[19];
structure.StartSequenceNumber = System.Int32.Parse(cRead.Substring(21, (25) - (21)).Trim());
structure.StartInsertionCode = cRead[25];
structure.EndChainID = cRead[31];
structure.EndSequenceNumber = System.Int32.Parse(cRead.Substring(33, (37) - (33)).Trim());
structure.EndInsertionCode = cRead[37];
oBP.addStructure(structure);
}
else if ("SHEET ".ToUpper().Equals(cCol.ToUpper()))
{
PDBStructure structure = new PDBStructure();
structure.StructureType = PDBStructure.SHEET;
structure.StartChainID = cRead[21];
structure.StartSequenceNumber = System.Int32.Parse(cRead.Substring(22, (26) - (22)).Trim());
structure.StartInsertionCode = cRead[26];
structure.EndChainID = cRead[32];
structure.EndSequenceNumber = System.Int32.Parse(cRead.Substring(33, (37) - (33)).Trim());
structure.EndInsertionCode = cRead[37];
oBP.addStructure(structure);
}
else if ("TURN ".ToUpper().Equals(cCol.ToUpper()))
{
PDBStructure structure = new PDBStructure();
structure.StructureType = PDBStructure.TURN;
structure.StartChainID = cRead[19];
structure.StartSequenceNumber = System.Int32.Parse(cRead.Substring(20, (24) - (20)).Trim());
structure.StartInsertionCode = cRead[24];
structure.EndChainID = cRead[30];
structure.EndSequenceNumber = System.Int32.Parse(cRead.Substring(31, (35) - (31)).Trim());
structure.EndInsertionCode = cRead[35];
oBP.addStructure(structure);
} // ignore all other commands
}
}while (_oInput.Peek() != -1 && (cRead != null));
}
catch (System.Exception e)
{
//logger.error("Found a problem at line:\n");
//logger.error(cRead);
//logger.error("01234567890123456789012345678901234567890123456789012345678901234567890123456789");
//logger.error(" 1 2 3 4 5 6 7 ");
//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(" error: " + e.Message);
//logger.debug(e);
}
// try to close the Input
try
{
_oInput.Close();
}
catch (System.Exception e)
{
//logger.debug(e);
}
// Set all the dependencies
oModel.SetOfMolecules = oSet;
oSeq.addChemModel(oModel);
oFile.addChemSequence(oSeq);
return(oFile);
}