The Alias feature is for display. That is if you draw the structure from the
information in the SDF file (or any of the MDL formats)
you are supposed to use the alias name instead of the atomic symbol in the
drawing only. However for all other purposes you should use the real atomic
number/symbol
For example this feature allows you to annotate the structure drawing with
labelled atoms "C1", "C2", "C3" etc
Open Babel would do better to ignore the A records and just keep mum! unless
the intent is to convert to a graphical format (PNG etc), then the default
should be to use the Alias symbol unless explicity told not to
This is all old hat standard stuff with MDL molecule/reaction formats. Sounds
like from the comments that this knowledge has been lost/confused in the mists
of time!
Tony
> Date: Tue, 13 Mar 2012 12:08:55 +0000
> From: c.mor...@gaseq.co.uk
> To: openbabel-discuss@lists.sourceforge.net
> Subject: Re: [Open Babel] Trouble converting .sdf files downloaded from PDB
> website
>
> On 12/03/2012 23:18, baratron wrote:
> > Hi all,
> >
> > I'm trying to find the quickest way to get ligands from the PDB website into
> > .mol2 format for use in another program.
> >
> If I run the OpenBabel program from command line, I get lots of
> > warning messages:
> > ==============================
> > *** Open Babel Warning in Expand
> > Alias CL1 was not chemically interpreted
> >
>
> > And then the output .mol2 file is missing all of the information about
> > chemical elements. They are all replaced with dummy atoms:
> > 1 XX 6.3250 11.0900 22.6650 Du 1 LIG1 0.0000
> > 2 XX 4.6490 11.0350 23.3060 Du 1 LIG1 0.0000
> > 3 XX 4.0200 9.8040 23.4780 Du 1 LIG1 0.0000
> > etc.
> >
> > I searched on Google and the Nabble site& couldn't find anyone else having
> > problems converting from .sdf to .mol2. I'm assuming there's something
> > "special" or "different" about the ligand .sdf files from the PDB website,
> > but I don't know what that is.
>
> The entries in the SDF file like
>
> A 14
> C5'
>
> are being interpreted as an alternative representation (alias) rather
> than additional information (atom types?), which OpenBabel does not
> understand. It sets the original atom to 0 atomic number, which is
> perhaps unnecessary. The is now altered in the development code, so that
> the basic structure is converted properly, although the warnings are
> still there. Is there a need for an option to capture the additional
> information?
>
> Chris
>
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