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);
}
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;
}
