[Open Babel] Which is the function in API doing the same thing as --join
Hello, Thank you all who are helping me with this openbabel. We use --join to join all input molecules into a single output moleculeentry. But which is the right function to do this in the pybel or openbable API? I just can't find it... Regards! -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60135991iu=/4140/ostg.clktrk ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Which is the function in API doing the same thing as --join
Hi, Have you tried mol1 += mol2? I use it for joining proteins with ligands, but should work in any case. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2013/10/25 Zhengyh swanboi...@gmail.com Hello, Thank you all who are helping me with this openbabel. We use --join to join all input molecules into a single output moleculeentry. But which is the right function to do this in the pybel or openbable API? I just can't find it... Regards! -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60135991iu=/4140/ostg.clktrk ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60135991iu=/4140/ostg.clktrk___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Which is the function in API doing the same thing as --join
Maciek hit send before I did :-) a = pybel.readstring(smi, CC) b = pybel.readstring(smi, CCO) a.OBMol += b.OBMol print a.write(smi) ...gives... CC.CCO On 25 October 2013 10:11, Zhengyh swanboi...@gmail.com wrote: Hello, Thank you all who are helping me with this openbabel. We use --join to join all input molecules into a single output moleculeentry. But which is the right function to do this in the pybel or openbable API? I just can't find it... Regards! -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60135991iu=/4140/ostg.clktrk ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60135991iu=/4140/ostg.clktrk ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Which is the function in API doing the same thing as --join
Hi, Wouldn't this be good to have exposed directly in pybel? Seems a bit non-intuitive to have to add the OBMols… Kind regards, Fredrik 25 okt 2013 kl. 11:28 skrev Noel O'Boyle baoille...@gmail.com: Maciek hit send before I did :-) a = pybel.readstring(smi, CC) b = pybel.readstring(smi, CCO) a.OBMol += b.OBMol print a.write(smi) ...gives... CC.CCO On 25 October 2013 10:11, Zhengyh swanboi...@gmail.com wrote: Hello, Thank you all who are helping me with this openbabel. We use --join to join all input molecules into a single output moleculeentry. But which is the right function to do this in the pybel or openbable API? I just can't find it... Regards! -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60135991iu=/4140/ostg.clktrk ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60135991iu=/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 -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60135991iu=/4140/ostg.clktrk___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Which is the function in API doing the same thing as --join
On 2013-10-25 04:33, Fredrik Wallner wrote: Hi, Wouldn't this be good to have exposed directly in pybel? Seems a bit non-intuitive to have to add the OBMols… To a programmer it's plenty intuitive. What's not intuitive to this programmer is if a and b have more than one possible binding site, how does it pick one. Dima -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60135991iu=/4140/ostg.clktrk ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Which is the function in API doing the same thing as --join
(I would naively expect CC + CCO to produce and H2O, but There are obviously multiple possible *chemical* things one could imagine. But there’s no way code can or should make assumptions about chemical transformations. We do have a chemical transformation class for handling reactions/modifications. -Geoff -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60135991iu=/4140/ostg.clktrk ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Which is the function in API doing the same thing as --join
On 10/25/2013 01:48 PM, Geoffrey Hutchison wrote: (I would naively expect CC + CCO to produce and H2O, but There are obviously multiple possible *chemical* things one could imagine. But there’s no way code can or should make assumptions about chemical transformations. It's because my naive idea of a molecule is a thing with atoms and bonds. So if I define molecule + molecule = molecule I expect the result to be a single molecule with a bond where the '+' was. I.e. I'd expect OBMol + OBMol = OBMol to be something that creates a bond whereas OBMol + OBMol = (OBMol, OBMol) is a set of disjoint molecules, no strings attached. -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu signature.asc Description: OpenPGP digital signature -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60135991iu=/4140/ostg.clktrk___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Which is the function in API doing the same thing as --join
a molecule is a thing with atoms and bonds. Hmmm, no salts? No organometalics? On Fri, Oct 25, 2013 at 3:08 PM, Dimitri Maziuk dmaz...@bmrb.wisc.eduwrote: On 10/25/2013 01:48 PM, Geoffrey Hutchison wrote: (I would naively expect CC + CCO to produce and H2O, but There are obviously multiple possible *chemical* things one could imagine. But there’s no way code can or should make assumptions about chemical transformations. It's because my naive idea of a molecule is a thing with atoms and bonds. So if I define molecule + molecule = molecule I expect the result to be a single molecule with a bond where the '+' was. I.e. I'd expect OBMol + OBMol = OBMol to be something that creates a bond whereas OBMol + OBMol = (OBMol, OBMol) is a set of disjoint molecules, no strings attached. -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60135991iu=/4140/ostg.clktrk ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60135991iu=/4140/ostg.clktrk___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Which is the function in API doing the same thing as --join
On 10/25/2013 02:11 PM, Igor Filippov wrote: a molecule is a thing with atoms and bonds. Hmmm, no salts? No organometalics? I didn't say you have to define bond as (e.g.) peptide-only. As long as you know something's holding this carbon and this metal more or less together... -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu signature.asc Description: OpenPGP digital signature -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60135991iu=/4140/ostg.clktrk___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
