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...
--
Di
> 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 mult
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 becau
> (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 reactio
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
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 expos
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 f
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 a
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 d
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 s
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")
>
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
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 a
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