public static Molecule ReadMDLMOL(StreamReader in_Renamed)
{
Molecule mol = new Molecule();
//UPGRADE_NOTE: Final was removed from the declaration of 'GENERIC_ERROR '. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1003'"
System.String GENERIC_ERROR = "Invalid MDL MOL file.";
try
{
System.String line = null;
for (int n = 0; n < 4; n++)
line = in_Renamed.ReadLine();
if (line == null || !line.Substring(34, (39) - (34)).Equals("V2000"))
throw new System.IO.IOException(GENERIC_ERROR);
int numAtoms = System.Int32.Parse(line.Substring(0, (3) - (0)).Trim());
int numBonds = System.Int32.Parse(line.Substring(3, (6) - (3)).Trim());
for (int n = 0; n < numAtoms; n++)
{
line = in_Renamed.ReadLine();
double x = System.Double.Parse(line.Substring(0, (10) - (0)).Trim());
double y = System.Double.Parse(line.Substring(10, (20) - (10)).Trim());
System.String el = line.Substring(31, (33) - (31)).Trim();
int chg = System.Int32.Parse(line.Substring(36, (39) - (36)).Trim()), rad = 0;
if (chg <= 3)
{
}
else if (chg == 4)
{
chg = 0; rad = 2;
}
else
chg = 4 - chg;
mol.AddAtom(el, x, y, chg, rad);
}
for (int n = 0; n < numBonds; n++)
{
line = in_Renamed.ReadLine();
int from = System.Int32.Parse(line.Substring(0, (3) - (0)).Trim()), to = System.Int32.Parse(line.Substring(3, (6) - (3)).Trim());
int type = System.Int32.Parse(line.Substring(6, (9) - (6)).Trim()), stereo = System.Int32.Parse(line.Substring(9, (12) - (9)).Trim());
if (from == to || from < 1 || from > numAtoms || to < 1 || to > numAtoms)
throw new System.IO.IOException(GENERIC_ERROR);
int order = type >= 1 && type <= 3?type:1;
int style = Molecule.BONDTYPE_NORMAL;
if (stereo == 1)
style = Molecule.BONDTYPE_INCLINED;
else if (stereo == 6)
style = Molecule.BONDTYPE_DECLINED;
else if (stereo == 3 || stereo == 4)
style = Molecule.BONDTYPE_UNKNOWN;
mol.AddBond(from, to, order, style);
}
while (true)
{
line = in_Renamed.ReadLine();
if (line.StartsWith("M END"))
break;
int type = 0;
if (line.StartsWith("M CHG"))
type = 1;
else if (line.StartsWith("M RAD"))
type = 2;
if (type > 0)
{
int len = System.Int32.Parse(line.Substring(6, (9) - (6)).Trim());
for (int n = 0; n < len; n++)
{
int apos = System.Int32.Parse(line.Substring(9 + 8 * n, (13 + 8 * n) - (9 + 8 * n)).Trim());
int aval = System.Int32.Parse(line.Substring(13 + 8 * n, (17 + 8 * n) - (13 + 8 * n)).Trim());
if (type == 1)
mol.SetAtomCharge(apos, aval);
else
mol.SetAtomUnpaired(apos, aval);
}
}
}
}
catch (System.Exception)
{
throw new System.IO.IOException(GENERIC_ERROR);
}
return mol;
}