private static void ParseMMFFPPROP(Stream ins, MmffProp[] props)
{
using (var br = new StreamReader(ins, Encoding.UTF8))
{
string line;
while ((line = br.ReadLine()) != null)
{
if (line.Length == 0 || line[0] == '*')
{
continue;
}
var cols = Strings.Tokenize(line);
if (cols.Count != 9)
{
throw new IOException("Malformed MMFFPROP.PAR file.");
}
int type = int.Parse(cols[0], NumberFormatInfo.InvariantInfo);
props[type] = new MmffProp(int.Parse(cols[1], NumberFormatInfo.InvariantInfo),
int.Parse(cols[2], NumberFormatInfo.InvariantInfo),
int.Parse(cols[3], NumberFormatInfo.InvariantInfo),
int.Parse(cols[4], NumberFormatInfo.InvariantInfo),
int.Parse(cols[5], NumberFormatInfo.InvariantInfo),
int.Parse(cols[6], NumberFormatInfo.InvariantInfo),
int.Parse(cols[7], NumberFormatInfo.InvariantInfo),
int.Parse(cols[8], NumberFormatInfo.InvariantInfo));
}
}
}
/// <summary>
/// see. MMFF Part V - p 620, a nonstandard bond-type index of “1” is
/// assigned whenever a single bond (formal bond order 1) is found: (a)
/// between atoms i and j of types that are not both aromatic and for which
/// ”sbmb” entries of ”1” appear in Table I; or (b) between pairs of atoms
/// belonging to different aromatic rings (as in the case of the connecting
/// C-C bond in biphenyl).
/// </summary>
public int GetBondCls(int type1, int type2, int bord, bool barom)
{
MmffProp prop1 = properties[CheckType(type1)];
MmffProp prop2 = properties[CheckType(type2)];
// non-arom atoms with sbmb (single-bond-multi-bond)
if (bord == 1 && !prop1.arom && prop1.sbmb && !prop2.arom && prop2.sbmb)
{
return(1);
}
// non-arom bond between arom atoms
if (bord == 1 && !barom && prop1.arom && prop2.arom)
{
return(1);
}
return(0);
}
