Hi everyone
TPSA values of imidazole from different SMILES strings gave different
values.
c1nccn1 24.72A
C1=NC=CN1 25.78A
in this case one hydrogen is not added correctly as a known bug
C1=NC=CN1 28.68A
After temporary addition of hydrogen addition subroutine as followed
int numatoms = mol.getAtomCount();
Atom atomH = new Atom("H");
for (int i=0; i<mol.getAtomCount(); i++) {
Atom atom = (Atom)mol.getAtomAt(i);
if(mol.getBondOrderSum(atom)-atom.getFormalCharge() ==2.&&
atom.getSymbol().equals("N")) {
mol.addAtom(atomH);
mol.addBond(i, numatoms, 1);
numatoms++;
}
http://www.daylight.com/meetings/emug00/Ertl/tpsa.html gave 28.68A
Thanks in advance.
Takayuki KOTANI
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