This SD file is then used as an input for another program, that program is
having problems reading the sequence numbers.
Thanks,
MAK
On Fri, Dec 16, 2016 at 10:43 PM, Greg Landrum
wrote:
> It's easy enough to make this an option, but given that it is part of the
> SDF spec (as Andrew has pointe
It's easy enough to make this an option, but given that it is part of the SDF
spec (as Andrew has pointed out) the only reason I can think of to do so would
be because it causes problems for some other piece of (likely commonly used)
software.
Are the sequence numbers causing a problem for you?
On Dec 17, 2016, at 1:45 AM, Milinda Samaraweera wrote:
> However at the end of each tag header I noticed there is a number (bolded):
>
> ...
> >(1)
> N1-(2-ethylbutyl)hexane-1,3,6-triamine
...
> What is this number and how you avoid printing this number when SDwriter is
> used? As this n
Hello
In cases like this i know that Greg did the valid implementation according
to the standard. If you check the ctfile definition (
http://c4.cabrillo.edu/404/ctfile.pdf#page41) you will see that the data
header is pretty flexible. The only requirement is that it starts with a >.
Usually we fin
On Wed, Mar 30, 2016 at 2:47 PM, Tim Dudgeon wrote:
> And there's no other way to generate a SDF from Java?
> e.g. can each ROMol be converted to text in SD format and then that text
> written to the Java OutputStream?
>
There's no way to do it in a single step.
You can get the mol block and the
And there's no other way to generate a SDF from Java?
e.g. can each ROMol be converted to text in SD format and then that text
written to the Java OutputStream?
Tim
On 30/03/2016 13:31, Greg Landrum wrote:
Hi Tim,
That constructor is expecting a C++ stream pointer. The takeOwnership
flag te
Hi Tim,
That constructor is expecting a C++ stream pointer. The takeOwnership flag
tells it to take assume ownership of the pointer (i.e. to free up the
memory being used by the stream when the SDWriter itself is free'd). I am
guessing that this will not be useable from Java (and should probably b
Hi Michal,
On Mon, Jan 6, 2014 at 3:30 PM, Michal Krompiec
wrote:
> Hello Greg,
> >>> Chem.MolToSmiles(Chem.MolFromSmiles('O=C1NC=CC1=C1C=C(-c2nccc2)NC1=O'))
> [14:25:55] Can't kekulize mol
>
>
The problem is, once again, in the pyrrole:
In [2]: Chem.MolFromSmiles('O=C1NC=CC1=C1C=C(-c2nccc2)NC1=O
Hello Greg,
>>> Chem.MolToSmiles(Chem.MolFromSmiles('O=C1NC=CC1=C1C=C(-c2nccc2)NC1=O'))
[14:25:55] Can't kekulize mol
This smiles was generated from ChemSketch. OpenBabel converts it to
O=C1NC=CC1=C1C=C(c2[nH]ccc2)NC1=O which is correctly interpreted by
RDKit (no problems with kekulization).
But I
Dear Greg,
It seems that all examples I found are in fact incorrect (due to an
error during conversion of SDF produced by ISIS Draw with OpenBabel)
and contain this bit:
c1(sc(c2c1nsn2)) which was meant to be: c1scc2N=S=Nc12.
By the way, ChemSketch understands c1(sc(c2c1nsn2)) as N1SNc2cscc12.
So i
Hi Michal,
On Thu, Dec 5, 2013 at 11:52 AM, Michal Krompiec
wrote:
> Hello,
> Is it possible to suppress kekulization by SDWriter? I get the
> following error on a call to SDWriter.write:
> ValueError: Sanitization error: Can't kekulize mol
> But some molecules can't be kekulized using RDKit's al
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] 'SDWriter' object has no attribute 'close
Cedric MORETTI wrote:
>
> Hello all,
>
> I have I little problem with RDKIT( I hope :D)
>
> My program don't arrive to close the SDwriter whereas I p
Cedric MORETTI wrote:
>
> Hello all,
>
> I have I little problem with RDKIT( I hope :D)
>
> My program don’t arrive to close the SDwriter whereas I put the
> command “writer.close()” and Chem.SDWriter.close() in the end of programm
>
> I just let the part of the code that is import for understand
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