/// <summary> Returns a new Reaction object which is the reverse of the given
/// Reaction.
/// </summary>
public static IReaction reverse(IReaction reaction)
{
IReaction reversedReaction = reaction.Builder.newReaction();
if (reaction.Direction == IReaction_Fields.BIDIRECTIONAL)
{
reversedReaction.Direction = IReaction_Fields.BIDIRECTIONAL;
}
else if (reaction.Direction == IReaction_Fields.FORWARD)
{
reversedReaction.Direction = IReaction_Fields.BACKWARD;
}
else if (reaction.Direction == IReaction_Fields.BACKWARD)
{
reversedReaction.Direction = IReaction_Fields.FORWARD;
}
IMolecule[] reactants = reaction.Reactants.Molecules;
for (int i = 0; i < reactants.Length; i++)
{
double coefficient = reaction.getReactantCoefficient(reactants[i]);
reversedReaction.addProduct(reactants[i], coefficient);
}
IMolecule[] products = reaction.Products.Molecules;
for (int i = 0; i < products.Length; i++)
{
double coefficient = reaction.getProductCoefficient(products[i]);
reversedReaction.addReactant(products[i], coefficient);
}
return(reversedReaction);
}
/// <summary> Procedure required by the CDOInterface. This function is only
/// supposed to be called by the JCFL library
/// </summary>
public virtual void endObject(System.String objectType)
{
//logger.debug("END: " + objectType);
if (objectType.Equals("Molecule"))
{
if (currentMolecule is IMolecule)
{
//logger.debug("Adding molecule to set");
currentSetOfMolecules.addMolecule((IMolecule)currentMolecule);
//logger.debug("#mols in set: " + currentSetOfMolecules.MoleculeCount);
}
else if (currentMolecule is ICrystal)
{
//logger.debug("Adding crystal to chemModel");
currentChemModel.Crystal = (ICrystal)currentMolecule;
currentChemSequence.addChemModel(currentChemModel);
}
}
else if (objectType.Equals("SetOfMolecules"))
{
currentChemModel.SetOfMolecules = currentSetOfMolecules;
currentChemSequence.addChemModel(currentChemModel);
}
else if (objectType.Equals("Frame"))
{
// endObject("Molecule");
}
else if (objectType.Equals("Animation"))
{
addChemSequence(currentChemSequence);
//logger.info("This file has " + ChemSequenceCount + " sequence(s).");
}
else if (objectType.Equals("Atom"))
{
currentMolecule.addAtom(currentAtom);
}
else if (objectType.Equals("Bond"))
{
//logger.debug("Bond(" + bond_id + "): " + bond_a1 + ", " + bond_a2 + ", " + bond_order);
if (bond_a1 > currentMolecule.AtomCount || bond_a2 > currentMolecule.AtomCount)
{
//logger.error("Cannot add bond between at least one non-existant atom: " + bond_a1 + " and " + bond_a2);
}
else
{
IAtom a1 = currentMolecule.getAtomAt(bond_a1);
IAtom a2 = currentMolecule.getAtomAt(bond_a2);
IBond b = currentChemFile.Builder.newBond(a1, a2, bond_order);
if (bond_id != null)
{
b.ID = bond_id;
}
if (bond_stereo != -99)
{
b.Stereo = bond_stereo;
}
if (bond_order == CDKConstants.BONDORDER_AROMATIC)
{
b.setFlag(CDKConstants.ISAROMATIC, true);
}
currentMolecule.addBond(b);
}
}
else if (objectType.Equals("a-axis"))
{
// set these variables
if (currentMolecule is ICrystal)
{
ICrystal current = (ICrystal)currentMolecule;
current.A = new Vector3d(crystal_axis_x, crystal_axis_y, crystal_axis_z);
}
else
{
//logger.warn("Current object is not a crystal");
}
}
else if (objectType.Equals("b-axis"))
{
if (currentMolecule is ICrystal)
{
ICrystal current = (ICrystal)currentMolecule;
current.B = new Vector3d(crystal_axis_x, crystal_axis_y, crystal_axis_z);
}
else
{
//logger.warn("Current object is not a crystal");
}
}
else if (objectType.Equals("c-axis"))
{
if (currentMolecule is ICrystal)
{
ICrystal current = (ICrystal)currentMolecule;
current.C = new Vector3d(crystal_axis_x, crystal_axis_y, crystal_axis_z);
}
else
{
//logger.warn("Current object is not a crystal");
}
}
else if (objectType.Equals("SetOfReactions"))
{
currentChemModel.SetOfReactions = currentSetOfReactions;
currentChemSequence.addChemModel(currentChemModel);
/* FIXME: this should be when document is closed! */
}
else if (objectType.Equals("Reaction"))
{
//logger.debug("Adding reaction to SOR");
currentSetOfReactions.addReaction(currentReaction);
}
else if (objectType.Equals("Reactant"))
{
currentReaction.addReactant((IMolecule)currentMolecule);
}
else if (objectType.Equals("Product"))
{
currentReaction.addProduct((IMolecule)currentMolecule);
}
else if (objectType.Equals("Crystal"))
{
//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'"
//logger.debug("Crystal: " + currentMolecule);
}
}
private IReaction readReaction(IChemObjectBuilder builder)
{
IReaction reaction = builder.newReaction();
readLine(); // first line should be $RXN
readLine(); // second line
readLine(); // third line
readLine(); // fourth line
int reactantCount = 0;
int productCount = 0;
bool foundCOUNTS = false;
while (Ready && !foundCOUNTS)
{
System.String command = readCommand();
if (command.StartsWith("COUNTS"))
{
SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(command);
try
{
tokenizer.NextToken();
reactantCount = System.Int32.Parse(tokenizer.NextToken());
//logger.info("Expecting " + reactantCount + " reactants in file");
productCount = System.Int32.Parse(tokenizer.NextToken());
//logger.info("Expecting " + productCount + " products in file");
}
catch (System.Exception exception)
{
//logger.debug(exception);
throw new CDKException("Error while counts line of RXN file", exception);
}
foundCOUNTS = true;
}
else
{
//logger.warn("Waiting for COUNTS line, but found: " + command);
}
}
// now read the reactants
for (int i = 1; i <= reactantCount; i++)
{
System.Text.StringBuilder molFile = new System.Text.StringBuilder();
System.String announceMDLFileLine = readCommand();
if (!announceMDLFileLine.Equals("BEGIN REACTANT"))
{
System.String error = "Excepted start of reactant, but found: " + announceMDLFileLine;
//logger.error(error);
throw new CDKException(error);
}
System.String molFileLine = "";
while (!molFileLine.EndsWith("END REACTANT"))
{
molFileLine = readLine();
molFile.Append(molFileLine);
molFile.Append("\n");
}
;
try
{
// read MDL molfile content
MDLV3000Reader reader = new MDLV3000Reader(new StreamReader(molFile.ToString()));
IMolecule reactant = (IMolecule)reader.read(builder.newMolecule());
// add reactant
reaction.addReactant(reactant);
}
catch (System.Exception exception)
{
//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.String error = "Error while reading reactant: " + exception.Message;
//logger.error(error);
//logger.debug(exception);
throw new CDKException(error, exception);
}
}
// now read the products
for (int i = 1; i <= productCount; i++)
{
System.Text.StringBuilder molFile = new System.Text.StringBuilder();
System.String announceMDLFileLine = readCommand();
if (!announceMDLFileLine.Equals("BEGIN PRODUCT"))
{
System.String error = "Excepted start of product, but found: " + announceMDLFileLine;
//logger.error(error);
throw new CDKException(error);
}
System.String molFileLine = "";
while (!molFileLine.EndsWith("END PRODUCT"))
{
molFileLine = readLine();
molFile.Append(molFileLine);
molFile.Append("\n");
}
;
try
{
// read MDL molfile content
MDLV3000Reader reader = new MDLV3000Reader(new StreamReader(molFile.ToString()));
IMolecule product = (IMolecule)reader.read(builder.newMolecule());
// add product
reaction.addProduct(product);
}
catch (System.Exception exception)
{
//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.String error = "Error while reading product: " + exception.Message;
//logger.error(error);
//logger.debug(exception);
throw new CDKException(error, exception);
}
}
return(reaction);
}
/// <summary> Read a Reaction from a file in MDL RXN format
///
/// </summary>
/// <returns> The Reaction that was read from the MDL file.
/// </returns>
private IReaction readReaction(IChemObjectBuilder builder)
{
IReaction reaction = builder.newReaction();
try
{
input.ReadLine(); // first line should be $RXN
input.ReadLine(); // second line
input.ReadLine(); // third line
input.ReadLine(); // fourth line
}
catch (System.IO.IOException exception)
{
//logger.debug(exception);
throw new CDKException("Error while reading header of RXN file", exception);
}
int reactantCount = 0;
int productCount = 0;
try
{
System.String countsLine = input.ReadLine();
/* this line contains the number of reactants
* and products */
SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(countsLine);
reactantCount = System.Int32.Parse(tokenizer.NextToken());
//logger.info("Expecting " + reactantCount + " reactants in file");
productCount = System.Int32.Parse(tokenizer.NextToken());
//logger.info("Expecting " + productCount + " products in file");
}
catch (System.Exception exception)
{
//logger.debug(exception);
throw new CDKException("Error while counts line of RXN file", exception);
}
// now read the reactants
try
{
for (int i = 1; i <= reactantCount; i++)
{
System.Text.StringBuilder molFile = new System.Text.StringBuilder();
input.ReadLine(); // announceMDLFileLine
System.String molFileLine = "";
do
{
molFileLine = input.ReadLine();
molFile.Append(molFileLine);
molFile.Append("\n");
}while (!molFileLine.Equals("M END"));
// read MDL molfile content
MDLReader reader = new MDLReader(new StreamReader(molFile.ToString()));
IMolecule reactant = (IMolecule)reader.read(builder.newMolecule());
// add reactant
reaction.addReactant(reactant);
}
}
catch (CDKException exception)
{
// rethrow exception from MDLReader
throw exception;
}
catch (System.Exception exception)
{
//logger.debug(exception);
throw new CDKException("Error while reading reactant", exception);
}
// now read the products
try
{
for (int i = 1; i <= productCount; i++)
{
System.Text.StringBuilder molFile = new System.Text.StringBuilder();
input.ReadLine(); // String announceMDLFileLine =
System.String molFileLine = "";
do
{
molFileLine = input.ReadLine();
molFile.Append(molFileLine);
molFile.Append("\n");
}while (!molFileLine.Equals("M END"));
// read MDL molfile content
MDLReader reader = new MDLReader(new StreamReader(molFile.ToString()));
IMolecule product = (IMolecule)reader.read(builder.newMolecule());
// add reactant
reaction.addProduct(product);
}
}
catch (CDKException exception)
{
// rethrow exception from MDLReader
throw exception;
}
catch (System.Exception exception)
{
//logger.debug(exception);
throw new CDKException("Error while reading products", exception);
}
// now try to map things, if wanted
//logger.info("Reading atom-atom mapping from file");
// distribute all atoms over two AtomContainer's
IAtomContainer reactingSide = builder.newAtomContainer();
IMolecule[] molecules = reaction.Reactants.Molecules;
for (int i = 0; i < molecules.Length; i++)
{
reactingSide.add(molecules[i]);
}
IAtomContainer producedSide = builder.newAtomContainer();
molecules = reaction.Products.Molecules;
for (int i = 0; i < molecules.Length; i++)
{
producedSide.add(molecules[i]);
}
// map the atoms
int mappingCount = 0;
IAtom[] reactantAtoms = reactingSide.Atoms;
IAtom[] producedAtoms = producedSide.Atoms;
for (int i = 0; i < reactantAtoms.Length; i++)
{
for (int j = 0; j < producedAtoms.Length; j++)
{
if (reactantAtoms[i].ID != null && reactantAtoms[i].ID.Equals(producedAtoms[j].ID))
{
reaction.addMapping(builder.newMapping(reactantAtoms[i], producedAtoms[j]));
mappingCount++;
break;
}
}
}
//logger.info("Mapped atom pairs: " + mappingCount);
return(reaction);
}