EmbedMolecule. I recommend you read the PDF supplied with RDKit.
2008/8/8 Evgueni Kolossov <[email protected]>:
> Thanks - this is kind of works.
> Unfortunately there is no atomic coordinates generated - how we can do this?
> Otherwise it will display just single dot.
>
> Regards,
> Evgueni
>
>
> 2008/8/8 Igor Filippov <[email protected]>
>>
>> The following works for me:
>>
>> std::stringstream ss;
>> SDWriter *writer = new SDWriter(&ss);
>> writer->setProps(propNames);
>> writer->write(*mol);
>> writer->flush();
>> delete mol;
>> delete writer;
>> std::string sdf=ss.str();
>>
>> Igor
>>
>> On Fri, 2008-08-08 at 12:05 +0100, Evgueni Kolossov wrote:
>> >
>> > Dear Greg,
>> >
>> > Can you please show how to extract text from stringstream (which in
>> > your case actually ostream) into string?
>> > ROMol *mol;
>> > mol = SmilesToMol(strSmile);
>> > ostream *ss = new stringstream();
>> > SDWriter *writer = new SDWriter(ss, false);
>> > writer->write(*mol);
>> >
>> > string strMolStructure;
>> > //Now we want to put MDLMol into the string. For stringstream
>> > ss->str() will do the job but ss is ostream....)
>> >
>> > Regards,
>> > Evgueni
>> >
>> >
>> > -----Original Message-----
>> > From: [email protected]
>> > [mailto:[email protected]] On Behalf Of Greg
>> > Landrum
>> > Sent: 05 August 2008 19:07
>> > To: Igor Filippov [Contr]
>> > Cc: [email protected]
>> > Subject: Re: [Rdkit-discuss] SD File output
>> >
>> >
>> > Dear Igor,
>> >
>> > This is a good one for the mailing list, so I'm cross-posting my
>> > reply.
>> >
>> > On Tue, Aug 5, 2008 at 6:47 PM, Igor Filippov [Contr]
>> > <[email protected]> wrote:
>> > >
>> > > Is there any way to convert a mol object into an SD file (i.e. CTAB
>> > > plus user-defined properties) and have the result in a string?
>> > > MolToMolBlock() only outputs CTAB portion without the properties.
>> >
>> > Indeed there is. You can construct an SDWriter (defined in
>> > $RDBASE/GraphMol/FileParsers/MolWriters.h) using a pointer to a
>> > stringstream, then use the SDWriter's write() method. It's probably
>> > safest to call the flush() method before reading your text out of the
>> > stringstream.
>> >
>> > An example for using this with a SmilesWriter is in the function
>> > testSmilesWriter2() in testMolWriter.cpp. Using an SDWriter is exactly
>> > equivalent.
>> >
>> > -greg
>> >
>> >
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>> --
>> Igor Filippov <[email protected]>
>>
>
>
>
> --
> Dr. Evgueni Kolossov (PhD)
> [email protected]
> Tel. +44(0)1628 627168
> Mob. +44(0)7812070446
>
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