Re: [Rdkit-discuss] SDwriter

2016-12-16 Thread Milinda Samaraweera
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

Re: [Rdkit-discuss] SDwriter

2016-12-16 Thread Greg Landrum
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?

Re: [Rdkit-discuss] SDWriter from Java

2016-03-30 Thread Greg Landrum
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

Re: [Rdkit-discuss] SDWriter from Java

2016-03-30 Thread Tim Dudgeon
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

Re: [Rdkit-discuss] SDWriter from Java

2016-03-30 Thread Greg Landrum
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

Re: [Rdkit-discuss] SDWriter kekulizes by default

2014-01-06 Thread Greg Landrum
Hi Michal, On Mon, Jan 6, 2014 at 3:30 PM, Michal Krompiec michal.kromp...@gmail.comwrote: 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]:

Re: [Rdkit-discuss] SDWriter kekulizes by default

2013-12-06 Thread Michal Krompiec
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

Re: [Rdkit-discuss] SDWriter kekulizes by default

2013-12-05 Thread Greg Landrum
Hi Michal, On Thu, Dec 5, 2013 at 11:52 AM, Michal Krompiec michal.kromp...@gmail.comwrote: 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

Re: [Rdkit-discuss] 'SDWriter' object has no attribute 'close

2010-06-10 Thread markus kossner
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 the

Re: [Rdkit-discuss] 'SDWriter' object has no attribute 'close

2010-06-10 Thread Cedric MORETTI
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 put the command writer.close