/// <summary> Adds a product to this reaction.
///
/// </summary>
/// <param name="product"> Molecule added as product to this reaction
/// </param>
/// <param name="coefficient">Stoichiometry coefficient for this molecule
/// </param>
/// <seealso cref="getProducts">
/// </seealso>
public virtual void addProduct(IMolecule product, double coefficient)
{
products.addAtomContainer(product, coefficient);
/* notifyChanged() is called by
* addReactant(Molecule reactant, double coefficient) */
}
public static IChemModel newChemModel(IAtomContainer molecule)
{
IChemModel model = molecule.Builder.newChemModel();
ISetOfMolecules moleculeSet = model.Builder.newSetOfMolecules();
moleculeSet.addAtomContainer(molecule);
model.SetOfMolecules = moleculeSet;
return(model);
}
/// <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);
}
/// <summary> Adds a reactant to this reaction with a stoichiometry coefficient.
///
/// </summary>
/// <param name="reactant"> Molecule added as reactant to this reaction
/// </param>
/// <param name="coefficient">Stoichiometry coefficient for this molecule
/// </param>
/// <seealso cref="getReactants">
/// </seealso>
public virtual void addReactant(IMolecule reactant, double coefficient)
{
reactants.addAtomContainer(reactant, coefficient);
notifyChanged();
}
/// <summary> Adds an agent to this reaction.
///
/// </summary>
/// <param name="agent"> Molecule added as agent to this reaction
/// </param>
/// <seealso cref="getAgents">
/// </seealso>
public virtual void addAgent(IMolecule agent)
{
agents.addAtomContainer(agent);
notifyChanged();
}