Re: [Open Babel] cmake errors regarding perl bindings
Final update: The perl bindings also work fine with this build. I only had to update PERL5LIB to get going. Thanks, AK On Tuesday, November 5, 2013 11:40 PM, Anil Kumar wrote: Dear Dr. Hutchsison, I was able to compile .../master.zip which you pointed out. Thank you. Further, this is what worked for me -- As mentioned in the compile page I had to explicitly use: -DPERL_LIBRARY=/usr/lib/libperl.so.5.10 -DPERL_INCLUDE_PATH=/usr/lib/perl/5.10.1/CORE. -DSWIG=ON Finally, I had to turn off GUI ( even though I did have wxWidget pre-reqs). I did not pursue that too much since I do not need the GUI functionality, maybe its an easy fix. Again, I appreciate your response, Anil Kumar On Monday, November 4, 2013 10:17 PM, Geoffrey Hutchison wrote: My suggestion would be to compile from the development "master". You can download the source code through GitHub from here: https://github.com/openbabel/openbabel/archive/master.zip I believe this has been fixed. It would be helpful to know as we move towards a 2.3.3. bug-fix release. Thanks very much, -Geoff-- November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
[Open Babel] bonds in pybel
Hi guys, one for the next release wishlist: is it possible to expose bonds as an iterable, similar to atoms? -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu signature.asc Description: OpenPGP digital signature -- November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] bonds in pybel
Hi, Since pybel doesn’t have a ”bond-concept” at the moment, I suppose it needs to be defined first. But if you will settle for OBBonds, the following short generator could work: def pybelbonditer(pybmol): for i in range(pybmol.OBMol.NumBonds()): yield pybmol.OBMol.GetBond(i) It’s now possible to iterate over the bonds with for bond in pybelbonditer(pybelmolecule): print bond.GetBeginAtomIdx(), bond.GetEndAtomIdx(), bond.GetBondOrder() Kind regards, Fredrik 12 nov 2013 kl. 01:01 skrev Dimitri Maziuk : > Hi guys, > > one for the next release wishlist: is it possible to expose bonds as an > iterable, similar to atoms? > > -- > Dimitri Maziuk > Programmer/sysadmin > BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu > > -- > November Webinars for C, C++, Fortran Developers > Accelerate application performance with scalable programming models. Explore > techniques for threading, error checking, porting, and tuning. Get the most > from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss signature.asc Description: Message signed with OpenPGP using GPGMail -- November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] bonds in pybel
Or, if you import openbabel you can directly do: for bond in openbabel.OBMolBondIter(obmol): print bond.GetBeginAtomIdx(), bond.GetEndAtomIdx(), bond.GetBondOrder() 12 nov 2013 kl. 07:55 skrev Fredrik Wallner : > Hi, > > Since pybel doesn’t have a ”bond-concept” at the moment, I suppose it needs > to be defined first. But if you will settle for OBBonds, the following short > generator could work: > > def pybelbonditer(pybmol): > for i in range(pybmol.OBMol.NumBonds()): > yield pybmol.OBMol.GetBond(i) > > It’s now possible to iterate over the bonds with > > for bond in pybelbonditer(pybelmolecule): > print bond.GetBeginAtomIdx(), bond.GetEndAtomIdx(), bond.GetBondOrder() > > Kind regards, > Fredrik > 12 nov 2013 kl. 01:01 skrev Dimitri Maziuk : > >> Hi guys, >> >> one for the next release wishlist: is it possible to expose bonds as an >> iterable, similar to atoms? >> >> -- >> Dimitri Maziuk >> Programmer/sysadmin >> BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu >> >> -- >> November Webinars for C, C++, Fortran Developers >> Accelerate application performance with scalable programming models. Explore >> techniques for threading, error checking, porting, and tuning. Get the most >> from the latest Intel processors and coprocessors. See abstracts and register >> http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk___ >> OpenBabel-discuss mailing list >> OpenBabel-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > -- > November Webinars for C, C++, Fortran Developers > Accelerate application performance with scalable programming models. Explore > techniques for threading, error checking, porting, and tuning. Get the most > from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss signature.asc Description: Message signed with OpenPGP using GPGMail -- November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
