still get an identical partial charge as the
carboxylic acid group is recognized as such:
print(pybel.readstring('smi','O=CO').write('mol2'))
David Koes
Associate Professor
Computational & Systems Biology
University of Pittsburgh
On 7/26/21 5:36 AM, David van der Spoel wrote:
Hi,
m
That sounds great. I for one will never complain about inconveniences induced by adding additional testing. You should
be able to gzip the files and read the gz version directly with obabel to save on space.
David Koes
Associate Professor
Computational & Systems Biology
Univer
to the
correct_output file.
This would make it much easier to add tests if it is appropriate to compare
file outputs exactly.
Thanks,
David Koes
Associate Professor
Computational & Systems Biology
University of Pittsburgh
On 6/8/21 11:22 AM, David van der Spoel wrote:
On 2021-06-08 15:42, David
Hi Madeleine,
It sounds like you have a really excellent set of test structures. It would be fantastic if you could contribute these
to the testing framework.
David Koes
Associate Professor
Computational & Systems Biology
University of Pittsburgh
On 6/8/21 8:15 AM, Marie-Madeleine
.
David Koes
Associate Professor
Computational & Systems Biology
University of Pittsburgh
On 6/7/21 8:22 AM, Marie-Madeleine Walz wrote:
Hi David,
thank you for your reply. I tested your code that assigns a sp2
hybridisation to a N as e.g. in azete (in mol.cpp), and it solves the
incorrect
else if(atom->GetAtomicNum() == OBElements::Nitrogen
&& atom->GetExplicitDegree() == 2
&& atom->IsInRing()) //azete
atom->SetHyb(2);
and this particular problem is fixed. It isn't clear to me if a less
string
but I lack the expertise to correct it.
David Koes
Associate Professor
Computational & Systems Biology
University of Pittsburgh
On 5/14/21 5:44 PM, Stefano Forli wrote:
Hi all,
I agree about the impractical task of fixing the task in more than a
handful of files.
Besides, there's an
would typically assume that the formal charge
should be specified in the input file. Also, I'm not sure bondtyping is
the right place for Kekulization fixes.
David Koes
Associate Professor
Computational & Systems Biology
University of Pittsburgh
On 5/13/21 10:50 AM, Ghahremanpour, Moha
. If the problem is the source code
has bad bond typing, update to a version with the pull request and rebuild.
Thanks,
David Koes
Associate Professor
Computational & Systems Biology
University of Pittsburgh
On 5/11/21 2:51 PM, David van der Spoel wrote:
Hi,
is anyone working on bondtyper
important).
Thanks,
David Koes
Assistant Professor
Computational & Systems Biology
University of Pittsburgh
On 7/29/19 4:11 PM, Geoffrey Hutchison wrote:
David Koes has contributed a pull request that fixes a bunch of file handling
errors via round-trip testing.
One thing he's impleme
(a helper function that passes the contents of its first argument as
stdin to the commandline specified as the second argument).
Definitely want to know how to add input/output files and properly reference
them from all three test scenarios.
David Koes
Assistant Professor
Computational
antics as IsSingle did.
My two cents.
David Koes
Assistant Professor
Computational & Systems Biology
University of Pittsburgh
--
Check out the vibrant tech community on one of the world's most
engaging
is not
updated with new formats (as happened with exyzformat and orcaformat),
then static builds start to fail.
Is there any reason why formats/CMakeLists.txt couldn't include
formats.cmake? Or, alternatively, src/CMakeLists.txt could include
src/formats/CMakeLists.txt directly?
Thanks,
David Koes
x.mol2 x.sdf.gz # previously x.sdf.gz was text output
In my perfect world compression state would be embedded within the
OBFormat class, but since these are singletons that doesn't work.
David Koes
Assistant Professor
Computational and Systems Biology
University of Pittsburgh
On 06/16/2015 05:28
with a newer version of zlib.
Are the build failures due to the commit, or to other changes?
Thanks,
David Koes
Assistant Professor
Computational and Systems Biology
University of Pittsburgh
On 06/16/2015 06:21 AM, Noel O'Boyle wrote:
I think we need to embrace a certain amount of backwards
Eh. Most changes seem to be syntactic sugar (e.g., NULL-nullptr). What
are the changes that bring actual value to the users/developers and why
can't they be implemented without breaking compatibility?
You can have a great library written in C. Or Python. Or Haskel. I
don't see the fact that
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