Add this on top: DGeomHelpers::EmbedMolecule(*mol); Igor
On Fri, 2008-08-08 at 13:07 +0100, Evgueni Kolossov wrote: > 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 > > > > > > ------------------------------------------------------------------------- > > This SF.Net email is sponsored by the Moblin Your Move > Developer's > > challenge Build the coolest Linux based applications with > Moblin SDK & > > win great prizes Grand prize is a trip for two to an Open > Source event > > anywhere in the world > > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > > _______________________________________________ > > Rdkit-discuss mailing list > > [email protected] > > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > > > > > > > ------------------------------------------------------------------------- > > This SF.Net email is sponsored by the Moblin Your Move > Developer's challenge > > Build the coolest Linux based applications with Moblin SDK & > win great prizes > > Grand prize is a trip for two to an Open Source event > anywhere in the world > > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > > _______________________________________________ > Rdkit-discuss mailing list [email protected] > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > -- > Igor Filippov <[email protected]> > > > > > -- > Dr. Evgueni Kolossov (PhD) > [email protected] > Tel. +44(0)1628 627168 > Mob. +44(0)7812070446 > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge > Build the coolest Linux based applications with Moblin SDK & win great prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ Rdkit-discuss mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Igor Filippov <[email protected]>
