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=60135991&iu=/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 wrote: > 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=60135991&iu=/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=60135991&iu=/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=60135991&iu=/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=60135991&iu=/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 01:15 PM, Fredrik Wallner wrote: > Well, I was referring to the fact that > a += b won't work, but a.OBMol += b.OBMol will. That isn't intuitive to me... Ah. Yes, pybel should override the __add__(). -- 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=60135991&iu=/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
Well, I was referring to the fact that a += b won't work, but a.OBMol += b.OBMol will. That isn't intuitive to me... /Fredrik Skickat från min iPhone > 25 okt 2013 kl. 16:46 skrev Dimitri Maziuk : > >> 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=60135991&iu=/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=60135991&iu=/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 11:55 AM, Dimitri Maziuk wrote: > On 10/25/2013 10:11 AM, Igor Filippov wrote: >> I don't think it does. >> I could be wrong but I think one has to create a bond from somewhere in >> mol1 to somewhere in mol2 explicitly. > > Now if "+" doesn't actually do anything useful unless you first (e.g.) > a.lose( "H12" ), b.lose( "O1H1" ), then I agree: "a + b" is not very > intuitive. Actually, after looking at Noel's example I see that it doesn't join them, it just draws them side-by-side. So forget I said anything. (I would naively expect "CC" + "CCO" to produce "" and H2O, but IANAChemist.) -- 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=60135991&iu=/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 10:11 AM, Igor Filippov wrote: > I don't think it does. > I could be wrong but I think one has to create a bond from somewhere in > mol1 to somewhere in mol2 explicitly. Now if "+" doesn't actually do anything useful unless you first (e.g.) a.lose( "H12" ), b.lose( "O1H1" ), then I agree: "a + b" is not very intuitive. -- 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=60135991&iu=/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 don't think it does. I could be wrong but I think one has to create a bond from somewhere in mol1 to somewhere in mol2 explicitly. Igor On Fri, Oct 25, 2013 at 10:46 AM, Dimitri Maziuk wrote: > 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=60135991&iu=/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=60135991&iu=/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=60135991&iu=/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" :
> 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 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=60135991&iu=/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 >
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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 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=60135991&iu=/4140/ostg.clktrk
> ___
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> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
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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 > 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=60135991&iu=/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=60135991&iu=/4140/ostg.clktrk___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
[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=60135991&iu=/4140/ostg.clktrk ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
