Dear all,
Indeed, as Riccardo mentions, according to the specifications in
CTfile.pdf a property should be truncated after the first blank line.
This is also what other SDF parsers I have tried actually do. What I
noticed is that other SDF parsers are tolerant of spurious lines not
starting with a ">", either blank or containing characters. Currently
the RDKit isn't on read, while it is on write.
I think the easiest solution is to make the SDF parser more tolerant in
such cases, printing a warning rather than throwing an exception. I have
just submitted a pull request about it - feel free to ignore it if you
do not agree with me!
Cheers,
Paolo
On 04/29/15 11:27, Tuomo Kalliokoski wrote:
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
<mailto: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 <mailto:riccardo.viane...@gmail.com>
Date: Wed, 29 Apr 2015 11:33:14 +0200
Subject: Re: [Rdkit-discuss] SDF tags and "->"
To: tkall...@live.com <mailto:tkall...@live.com>
Hi Tuomo,
On Wed, Apr 29, 2015 at 10:47 AM, Tuomo Kalliokoski
<tkall...@live.com <mailto: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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