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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Do you want to try writing a patch for the mol2 reader to ignore
these? This could be implemented as an option for the mol2 file
reader.
- Noel
On 8 November 2013 13:08, Maciek Wójcikowski wrote:
> Hi,
>
> Currently I'm working on GOLD docking results, and try to process them
> through OB. Unfor
The manual is here:
http://openbabel.org/docs/current/UseTheLibrary/CppExamples.html
Does this not work for you? Did you run "make install" when compiling
Open Babel?
- Noel
On 12 November 2013 19:56, Nicolas Cheron
wrote:
> Dear all,
>
> I am trying to use the OpenBabel library in one of my pr
OBOp should be in Chemistry::OpenBabel just like OBConversion. If not,
there's a problem at our end.
- Noel
On 13 November 2013 17:18, Wallace Chan wrote:
> Thanks for the reply, Noel. I apologize for being a complete novice, but do
> you have to open OBOp as a separate package? I usually use th
Thanks for the reply, Noel. I apologize for being a complete novice, but do
you have to open OBOp as a separate package? I usually use the line "use
Chemistry::OpenBabel" at the top, but do I have to do this separately for
OBOp? I don't have to do this for OBMol or OBConversion, so I was just
wonde
Dear all,
I am trying to use the OpenBabel library in one of my projects. I first
copied the code on this page
http://openbabel.org/wiki/Developer:Cpp_Tutorial in an example.cpp file, and
tried to compile it for tests purpose. And it doesn't compile.
I tried the Makefile of the manual, and also "
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