Hello Riccardo,
That sounds very reasonable solution to the issue.
[I replied to rdkit-discuss to bring this thread on the list back again]
Best regards,
Tuomo
From: riccardo.viane...@gmail.com
Date: Wed, 29 Apr 2015 12:08:48 +0200
Subject: Re: [Rdkit-discuss] SDF tags and "->"
To: tkall...@live.com
Hi Tuomo,
yes, I agree the behavior seems a bit inconsistent. I suppose that if the
correctness of the parser is confirmed, then a change could be suggested for
the writer, consisting in raising an error if blank lines are present inside
the data item.
[but once again, I didn't notice the defailt reply-to settings of rdkit-discuss
and accidentally brought the thread off-list, sorry.]
Regards,
Riccardo
On Wed, Apr 29, 2015 at 11:46 AM, Tuomo Kalliokoski <tkall...@live.com> wrote:
Hello Riccardo,
Thanks for the swift reply! Indeed, it is the extra line-feed, not the "->". It
was just around the same line where I had the issue, so it got me confused.
I suppose the current functionality of RDKit, irrespective to the SDF file
format specifications, is a bit odd: SDWriter produces file that SDMolSupplier
can't handle.
Best regards,
Tuomo
From: riccardo.viane...@gmail.com
Date: Wed, 29 Apr 2015 11:33:14 +0200
Subject: Re: [Rdkit-discuss] SDF tags and "->"
To: tkall...@live.com
Hi Tuomo,
On Wed, Apr 29, 2015 at 10:47 AM, Tuomo Kalliokoski <tkall...@live.com> wrote:
I have got a bunch of SDF-files with molecules and some long descriptions in
SDF-tags on them that include stuff like "->" inside.
These files have been produced by ChemAxon's software and are handled fine by
their software.
Such files can be written out also from RDKit 2014_09_02, but they fail when
you try to read them in.
I suspect the parse error could be independent from the "->", but due to the
blank line ("\n\n") that appears inside the "TESTFIELD" data:
mol.SetProp("TESTFIELD","This should not work -> Let's see\n\nI guess this is
not visible\n")
and that is interpreted as the data item terminator. Iirc this interpretation
is compliant with the specifications for the SDF file format, but I could be
mistaken.
Best regards,
Riccardo
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