Tim, You are absolutely right. As soon as I removed openbabel rpm which came with my Fedora 12 installation I could compile and link things properly with the svn snapshot libopenbabel.
Thank you, Igor P.S. Chris the fix for atomic aliases works like a charm, thanks once again! On Mon, 2010-08-09 at 12:11 -0400, Tim Vandermeersch wrote: > 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
