Hi there,
It would be nice if I had the ability to write (canonical) SMILES strings
without any bond order information, as a "round trip" to another format
(say, .xyz with gen3D) may cause this information to be lost and I end up
with different strings for the same molecule. For example,
[NH3]
Hello,
Your first SMILES string contains a pentavalent carbon, so I would argue that
that one isn’t correct in any file format…
Kind regards,
Fredrik
31 mar 2014 kl. 13:59 skrev Lee-Ping Wang :
> Hi there,
>
> It would be nice if I had the ability to write (canonical) SMILES strings
> witho
> It would be nice if I had the ability to write (canonical) SMILES strings
> without any bond order information, as a "round trip" to another format
> (say, .xyz with gen3D) may cause this information to be lost and I end up
> with different strings for the same molecule. For example,
> [NH3][CH2
Hi,
FYI, Helium support this by default. For example, the following python
script illustrates this:
from helium import *
SMILES = Smiles()
mol1 = Molecule()
if not SMILES.read('[NH3][CH2][C](=O)=O', mol1):
print SMILES.error()
exit()
mol2 = Molecule()
if not SMILES.read('[NH3][CH2]C(=O
