I think the underlying problem is that the current aromaticity code is
optimized for the situation where the location of hydrogens is
unknown. This is useful for PDB files, but in the general case, it is
solving a more difficult problem than we need to.
I'm not 100% sure of the interaction
Hello.
Yes, an input flag (at least for some input formats like cif or smiles)
meaning please keep hydrogens as they are in the input and do not add
or remove hydrogens even if you think that they may be missing or wrong
will surely help.
Best wishes,
Miguel Quirós
El mié, 05-12-2012 a las
Hi Chris,
Thanks for your reply and apologies for the delayed response. Converting
the cif to xyz and viewing the molecule shows the correct structure but
converting the xyz file to smi and then generating coordinates and viewing
shows the addition of a H atom.
The correct smiles is:
Scott
Your correct smiles is not right. The sum of the bond orders to the
charged nitrogen should be 4, and is only 3 (it has no H attached). The
correct SMILES is in my post below. Even with it, the round trip via xyz:
obabel -:C(=O)(O)C[C@@H](C(=O)[O-])n1c[nH+]cc1 -oxyz --gen3D
| obabel
Your problem is the incorrect conversion of a cif file, but you haven't
shown one yet. (Not that I know much about cif files, but others may.)
Conversions in OB go through an internal data structure, OBMol. It sound
like the problem is in the cif to OBMol part, not in the OBMol to SMILES.
Chris
Apologies, it was attached in the e-mail before last but had an identifier
name (SOXGES.search2.cif) and so may have caused confusion. I've attached
it again in this e-mail.
As a general question, is it possible to convert coordinates to smiles that
will always preserve the elements present (but
Dear all,
The conversion of (S)-3-carboxy-2-(imidazol-3-ium-1-yl)propanoate from a
.cif file to .smi and subsequent generation of coordinates from the .smi
file results in the addition of an extra H to one of the ring C atoms. The
original cif formula is C7H8N2O4 but this changes to C7H9N2O4,
On 30/11/2012 12:03, scott_m wrote:
Dear all,
The conversion of (S)-3-carboxy-2-(imidazol-3-ium-1-yl)propanoate from a
.cif file to .smi and subsequent generation of coordinates from the .smi
file results in the addition of an extra H to one of the ring C atoms. The
original cif formula is
