I don't see any option to display the presence of specific isotopes when
creating graphics from openbabel (i.e. converting to PNG or SVG). For
instance, glucose and 13C6-glucose give me the same PNG image.
Is this capability not available or am I missing something simple?
Thanks.
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On 11/18/2013 03:20 PM, Dimitri Maziuk wrote:
> On 11/18/2013 03:07 PM, Geoffrey Hutchison wrote:
>>> In the meantime, here's the patch -- feel free to rename "Prevalent" if
>>
>> I think my big question is why you do the loop in the
> GetPrevalentIsotope() method? Why not just round the mass to an
On 11/18/2013 03:07 PM, Geoffrey Hutchison wrote:
>> In the meantime, here's the patch -- feel free to rename "Prevalent" if
>
> I think my big question is why you do the loop in the
GetPrevalentIsotope() method? Why not just round the mass to an integer?
There should be no perceptible difference
> In the meantime, here's the patch -- feel free to rename "Prevalent" if
I think my big question is why you do the loop in the GetPrevalentIsotope()
method? Why not just round the mass to an integer? I mean, if it's Uranium 235,
it's within 0.5 amu of 235.0.
-Geoff
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On 11/18/2013 01:32 PM, Geoffrey Hutchison wrote:
>> make an isotope/mass vector a member of OBElement instead of its "mass
>> Atomic mass (in amu)", but that's just me.)
>
> The problem is that the full isotope table is fairly huge and rarely
used. Checking memory use, I see that in my programs,
> make an isotope/mass vector a member of OBElement instead of its "mass
> Atomic mass (in amu)", but that's just me.)
The problem is that the full isotope table is fairly huge and rarely used.
Checking memory use, I see that in my programs, it's usually never even
initialized, while the element
On 11/14/2013 09:54 AM, Dimitri Maziuk wrote:
> Yeah well. I saw that OBIsotopeTable looks like there must be one per
> element and I saw one "isotab" extern global and grep didn't show when
> or where it's initialized. Those things put together didn't make sense.
And now that I looked again w
On 2013-11-14 06:43, David Hall wrote:
> I'm unsure why you make comments saying that you doubt isotope.txt is
> not where information about isotopes lives for openbabel.
I was confused by 31.9988 and the fact that setting carbon isotope to 7
didn't throw an (e.g.) ArrayOutOfBounds. I then reali
It seems you want a list of the isotopes for a particular element? Looking
at the C++ code for openbabel, it seems like this might be easy to expose,
but for now, if you have a guess about the range of the function you can
get something in python fairly quickly:
In [1]: import openbabel
In [2]: f
PS. just to make sure I'm not reading some stale garbage from the heap:
>>> for i in (9, 8, 7, 6, 5, 4) :
... mol = pybel.readstring("smi","C(=O)=O")
... mol.OBMol.BeginModify()
... for atom in mol.atoms :
... if atom.OBAtom.IsCarbon() : atom.OBAtom.SetIsotope( i )
...
On 11/13/2013 05:08 PM, Geoffrey Hutchison wrote:
... I mean, do you want
> something which says carbon-11 is basically nonexistent? If so, no you
> can't use Open Babel for that since we don't store or tabulate the
> abundance of isotopes, only the isotopic masses and the mass for the most
> comm
I'm really not sure I understand your use case. I interpreted your question
as "I want to use the OBIsotopeTable to find the integer associated with
the most common isotope". In code, that shows up something like:
int atomicNum = 6; // carbon
double exactMass = isotab.GetExactMass(atomicNum);
int
On 11/13/2013 04:34 PM, Geoffrey Hutchison wrote:
> I'm not sure what you want. You want to know that the most common isotope
> (0) is, in fact, carbon 13 or something? I mean, you can round the exact
> mass and this will give you the isotope. I can't think of a
> counter-example. Can you?
No, but
I'm not sure what you want. You want to know that the most common isotope
(0) is, in fact, carbon 13 or something? I mean, you can round the exact
mass and this will give you the isotope. I can't think of a
counter-example. Can you?
-Geoff
On Wed, Nov 13, 2013 at 4:42 PM, Dimitri Maziuk wrote:
Hi all,
is there a way to find the number of "isotope 0"? I'm not seeing
anything suitable in isotope table.
TIA
--
Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
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