Ahh ok… Interesting way to format a file! Got to love ChemAxon...
Best,
Nick
Nicholas C. Firth | PhD Student | Cancer Therapeutics
The Institute of Cancer Research | 15 Cotswold Road | Belmont | Sutton | Surrey
| SM2 5NG
T 020 8722 4033 | E
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
Hello all,
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
On Tue, Apr 28, 2015 at 5:59 AM, Greg Landrum greg.land...@gmail.com wrote:
There's certainly no reason why the java wrappers shouldn't work if they are
dynamically linked; I just tried it on my ubuntu box and they work fine. I
don't normally do it because it would make distributing the
Riccardo Vianello:
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.
Yes, the SD tag data is not a general purpose data field. It's not possible,
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:
On 04/29/2015 01:47 PM, Andrew Dalke wrote:
Postel's Robustness principle is a mistake.
See RFC 3117 for elaboration,
...
Or from
http://cacm.acm.org/magazines/2011/8/114933-the-robustness-principle-reconsidered/fulltext
:
There is a difference between ACM members writing network
On 04/29/2015 07:54 AM, Andrew Dalke wrote:
I don't have a good solution. Were it me, I would have the writer
fail should any unsupported value be present in the output,
including those which are allowed by the SD specification but will
cause problems in practice, like embedded \0 and
On 04/29/2015 05:32 PM, Andrew Dalke wrote:
On Apr 29, 2015, at 9:19 PM, Dimitri Maziuk wrote:
There is a difference between ACM members writing network protocols and
domain people writing junk.
I think that you are saying that the MDL connection table
file formats are junk. I do not
Actually, you want to send your loving thoughts to MDL (now: Biovia).
They defined the SDF format :-).
Cheers
-- Jan
On 2015-04-29 13:26, Nicholas Firth wrote:
Ahh ok… Interesting way to format a file! Got to love ChemAxon...
Best,
Nick
*Nicholas C. Firth*| PhD Student | Cancer Therapeutics
On Wed, Apr 29, 2015 at 9:48 AM, Gianluca Sforna gia...@gmail.com wrote:
On Tue, Apr 28, 2015 at 5:59 AM, Greg Landrum greg.land...@gmail.com
wrote:
There's certainly no reason why the java wrappers shouldn't work if they
are
dynamically linked; I just tried it on my ubuntu box and they
Here are my thoughts on this:
The RDKit is usually strict while parsing molecules from SDF, SMILES, or
other formats. This is done for one simple reason: it tends to be
difficult/impossible to recover from syntax errors in input in a way that
doesn't result in a significant chance of producing a
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