/// <summary> Read a Reaction from a file in MDL RXN format
///
/// </summary>
/// <returns> The Reaction that was read from the MDL file.
/// </returns>
private IMolecule readMolecule(IMolecule molecule)
{
AtomTypeFactory atFactory = null;
try
{
atFactory = AtomTypeFactory.getInstance("mol2_atomtypes.xml", molecule.Builder);
}
catch (System.Exception exception)
{
System.String error = "Could not instantiate an AtomTypeFactory";
//logger.error(error);
//logger.debug(exception);
throw new CDKException(error, exception);
}
try
{
System.String line = input.ReadLine();
int atomCount = 0;
int bondCount = 0;
while (line != null)
{
if (line.StartsWith("@<TRIPOS>MOLECULE"))
{
//logger.info("Reading molecule block");
// second line has atom/bond counts?
input.ReadLine(); // disregard the name line
System.String counts = input.ReadLine();
SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(counts);
try
{
atomCount = System.Int32.Parse(tokenizer.NextToken());
}
catch (System.FormatException nfExc)
{
System.String error = "Error while reading atom count from MOLECULE block";
//logger.error(error);
//logger.debug(nfExc);
throw new CDKException(error, nfExc);
}
if (tokenizer.HasMoreTokens())
{
try
{
bondCount = System.Int32.Parse(tokenizer.NextToken());
}
catch (System.FormatException nfExc)
{
System.String error = "Error while reading atom and bond counts";
//logger.error(error);
//logger.debug(nfExc);
throw new CDKException(error, nfExc);
}
}
else
{
bondCount = 0;
}
//logger.info("Reading #atoms: ", atomCount);
//logger.info("Reading #bonds: ", bondCount);
//logger.warn("Not reading molecule qualifiers");
}
else if (line.StartsWith("@<TRIPOS>ATOM"))
{
//logger.info("Reading atom block");
for (int i = 0; i < atomCount; i++)
{
line = input.ReadLine().Trim();
SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(line);
tokenizer.NextToken(); // disregard the id token
System.String nameStr = tokenizer.NextToken();
System.String xStr = tokenizer.NextToken();
System.String yStr = tokenizer.NextToken();
System.String zStr = tokenizer.NextToken();
System.String atomTypeStr = tokenizer.NextToken();
IAtomType atomType = atFactory.getAtomType(atomTypeStr);
if (atomType == null)
{
atomType = atFactory.getAtomType("X");
//logger.error("Could not find specified atom type: ", atomTypeStr);
}
IAtom atom = molecule.Builder.newAtom("X");
atom.ID = nameStr;
atom.AtomTypeName = atomTypeStr;
atFactory.configure(atom);
try
{
double x = System.Double.Parse(xStr);
double y = System.Double.Parse(yStr);
double z = System.Double.Parse(zStr);
atom.setPoint3d(new Point3d(x, y, z));
}
catch (System.FormatException nfExc)
{
System.String error = "Error while reading atom coordinates";
//logger.error(error);
//logger.debug(nfExc);
throw new CDKException(error, nfExc);
}
molecule.addAtom(atom);
}
}
else if (line.StartsWith("@<TRIPOS>BOND"))
{
//logger.info("Reading bond block");
for (int i = 0; i < bondCount; i++)
{
line = input.ReadLine();
SupportClass.Tokenizer tokenizer = new SupportClass.Tokenizer(line);
tokenizer.NextToken(); // disregard the id token
System.String atom1Str = tokenizer.NextToken();
System.String atom2Str = tokenizer.NextToken();
System.String orderStr = tokenizer.NextToken();
try
{
int atom1 = System.Int32.Parse(atom1Str);
int atom2 = System.Int32.Parse(atom2Str);
double order = 0;
if ("1".Equals(orderStr))
{
order = CDKConstants.BONDORDER_AROMATIC;
}
else if ("2".Equals(orderStr))
{
order = CDKConstants.BONDORDER_DOUBLE;
}
else if ("3".Equals(orderStr))
{
order = CDKConstants.BONDORDER_TRIPLE;
}
else if ("am".Equals(orderStr))
{
order = CDKConstants.BONDORDER_SINGLE;
}
else if ("ar".Equals(orderStr))
{
order = CDKConstants.BONDORDER_AROMATIC;
}
else if ("du".Equals(orderStr))
{
order = CDKConstants.BONDORDER_SINGLE;
}
else if ("un".Equals(orderStr))
{
order = CDKConstants.BONDORDER_SINGLE;
}
else if ("nc".Equals(orderStr))
{
// not connected
order = 0;
}
if (order != 0)
{
molecule.addBond(atom1 - 1, atom2 - 1, order);
}
}
catch (System.FormatException nfExc)
{
System.String error = "Error while reading bond information";
//logger.error(error);
//logger.debug(nfExc);
throw new CDKException(error, nfExc);
}
}
}
line = input.ReadLine();
}
}
catch (System.IO.IOException exception)
{
System.String error = "Error while reading general structure";
//logger.error(error);
//logger.debug(exception);
throw new CDKException(error, exception);
}
return(molecule);
}
/// <summary> Creates an <code>Atom</code> and sets properties to their values from
/// the ATOM record. If the line is shorter than 80 characters, the information
/// past 59 characters is treated as optional. If the line is shorter than 59
/// characters, a <code>RuntimeException</code> is thrown.
///
/// </summary>
/// <param name="cLine"> the PDB ATOM record.
/// </param>
/// <returns> the <code>Atom</code> created from the record.
/// </returns>
/// <throws> RuntimeException if the line is too short (less than 59 characters). </throws>
private PDBAtom readAtom(string cLine, int lineLength)
{
// a line looks like:
// 0 1 2 3 4
// 01234567890123456789012345678901234567890123456789012345678901234567890123456789
// ATOM 1 O5* C A 1 20.662 36.632 23.475 1.00 10.00 114D 45
// ATOM 1186 1H ALA 1 10.105 5.945 -6.630 1.00 0.00 1ALE1288
if (lineLength < 59)
{
throw new System.SystemException("PDBReader error during readAtom(): line too short");
}
string elementSymbol = cLine.Substring(12, 4).Trim();
if (elementSymbol.Length == 2)
{
// ensure that the second char is lower case
elementSymbol = elementSymbol[0] + elementSymbol.Substring(1).ToLower();
}
string rawAtomName = cLine.Substring(12, 4).Trim();
string resName = cLine.Substring(17, 3).Trim();
try
{
IAtomType type = pdbFactory.getAtomType(resName + "." + rawAtomName);
elementSymbol = type.Symbol;
}
catch (NoSuchAtomTypeException e)
{
// try 1 char
try
{
elementSymbol = rawAtomName.Substring(0, 1);//pdbFactory.getAtomType(rawAtomName.Substring(0, 1)).Symbol;
}
catch
{
elementSymbol = "Xx";
}
//System.Console.Out.WriteLine("Did not recognize PDB atom type: " + resName + "." + rawAtomName);
}
PDBAtom oAtom = new PDBAtom(elementSymbol, new Point3d(System.Double.Parse(cLine.Substring(30, (38) - (30))), System.Double.Parse(cLine.Substring(38, (46) - (38))), System.Double.Parse(cLine.Substring(46, (54) - (46)))));
oAtom.Record = cLine;
oAtom.Serial = System.Int32.Parse(cLine.Substring(6, 5).Trim());
oAtom.Name = rawAtomName.Trim();
oAtom.AltLoc = cLine.Substring(16, 1).Trim();
oAtom.ResName = resName;
oAtom.ChainID = cLine.Substring(21, (22) - (21)).Trim();
oAtom.ResSeq = cLine.Substring(22, (26) - (22)).Trim();
oAtom.ICode = cLine.Substring(26, (27) - (26)).Trim();
oAtom.AtomTypeName = oAtom.ResName + "." + rawAtomName;
if (lineLength >= 59)
{
string frag = cLine.Substring(54, (60) - (54)).Trim();
if (frag.Length > 0)
{
oAtom.Occupancy = System.Double.Parse(frag);
}
}
if (lineLength >= 65)
{
string frag = cLine.Substring(60, (66) - (60)).Trim();
if (frag.Length > 0)
{
oAtom.TempFactor = System.Double.Parse(frag);
}
}
if (lineLength >= 75)
{
oAtom.SegID = cLine.Substring(72, (76) - (72)).Trim();
}
// if (lineLength >= 78) {
// oAtom.setSymbol((new String(cLine.substring(76, 78))).trim());
// }
if (lineLength >= 79)
{
string frag = cLine.Substring(78, (80) - (78)).Trim();
if (frag.Length > 0)
{
oAtom.setCharge(System.Double.Parse(frag));
}
}
/*************************************************************************************
* It sets a flag in the property content of an atom,
* which is used when bonds are created to check if the atom is an OXT-record => needs
* special treatment.
*/
string oxt = cLine.Substring(13, (16) - (13)).Trim();
if (oxt.Equals("OXT"))
{
oAtom.Oxt = true;
}
else
{
oAtom.Oxt = false;
}
/*************************************************************************************/
return(oAtom);
}