On Mon, Aug 9, 2010 at 5:50 PM, Igor Filippov [Contr] <filipp...@mail.nih.gov> wrote: > Chris, > > Thank you. I'm trying to test it with the latest trunk (r3955) but even > though OB itself compiled fine I'm getting the following error when > trying to link libopenbabel to my program: > > undefined reference to `OpenBabel::AliasData::GetAlias(bool) const' > collect2: ld returned 1 exit status > > Was there some significant change in how libopenbabel should be linked? > It was working fine with 2.2.3 release.
No, the API and "linking method" is unchanged. However, the ABI will be changed for the 2.3 release and the GetAlias function changed from: std::string GetAlias() const; to: std::string GetAlias(bool rightAligned = false) const; Since the linker complains about this symbol being undefined you are probably using the new headers but link to the old library. Tim > Igor > > On Thu, 2010-07-22 at 12:05 -0400, Chris Morley wrote: >> Thanks. Corrected in r3897. >> Chris >> >> On 21/07/2010 15:46, Igor Filippov [Contr] wrote: >> > I've run into a problem with an SD file generated by OB with atomic >> > aliases. This file could not be opened by CambridgeSoft ChemBioDraw, or >> > displayed correctly by ChemAxxon MarvinSketch. >> > CamridgeSoft support tells me the atom numbers should be >> > right-justified, where they are left-justified in OB output. Akos Papp >> > from ChemAxxon says that there is not enough white space between "A" and >> > the atom number. Here is an example of OB output and what Akos >> > corrected: >> > OB output - >> > >> > A 8 >> > R5 >> > A 10 >> > R4 >> > A 11 >> > R3 >> > A 14 >> > R2 >> > A 16 >> > R1 >> > >> > Corrected - >> > >> > A 8 >> > R5 >> > A 10 >> > R4 >> > A 11 >> > R3 >> > A 14 >> > R2 >> > A 16 >> > R1 >> > >> > the corrected file can be opened by ChemDraw, MarvinSketch, as well as >> > Symyx Draw and CACTVS csbr. Could we correct the output of atomic >> > aliases in the next OB release? >> > >> > Igor >> > >> > >> > On Mon, 2010-07-12 at 13:07 -0400, Geoffrey Hutchison wrote: >> >> On Jul 12, 2010, at 12:45 PM, Tim Vandermeersch wrote: >> >> >> >>>> So far I see only SetAtomicNum to specify atom type, but nothing to >> > set >> >>>> the atomic label to something like "R1". >> >>> >> >>> You can use AliasData for this. >> >> >> >> See src/formats/mdlformat.cpp for an exact example. >> >> >> >> Hope that helps, >> >> -Geoff >> > >> > >> > >> > ------------------------------------------------------------------------------ >> > This SF.net email is sponsored by Sprint >> > What will you do first with EVO, the first 4G phone? >> > Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first >> > _______________________________________________ >> > OpenBabel-discuss mailing list >> > OpenBabel-discuss@lists.sourceforge.net >> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >> > >> > >> > >> > >> > No virus found in this incoming message. >> > Checked by AVG - www.avg.com >> > Version: 9.0.851 / Virus Database: 271.1.1/3020 - Release Date: 07/21/10 >> > 19:36:00 >> > >> >> >> ------------------------------------------------------------------------------ >> This SF.net email is sponsored by Sprint >> What will you do first with EVO, the first 4G phone? >> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first >> _______________________________________________ >> OpenBabel-discuss mailing list >> OpenBabel-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by > > Make an app they can't live without > Enter the BlackBerry Developer Challenge > http://p.sf.net/sfu/RIM-dev2dev > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > ------------------------------------------------------------------------------ This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
