Hello Hashim and other future GSoC candidates,
I am a former GSoC student. I worked on the 3D structure generation of Open
Babel in GSoC 2018 and 2019.
https://summerofcode.withgoogle.com/archive/2018/projects/5957928301363200/
Hi all,
I've been developing a new distance geometry method these days.
https://github.com/openbabel/openbabel/pull/1875
I generated SMILES from experimental structures and predict a 3D
structure from the SMILES.
I compare InChIKey of experimental structure and predicted structure
to evaluate
s expected to be faster than current RDKit and
more accurate in stereochemistry than current Open Babel. Implementing
a better prediction method could be beneficial for a wide range of
applications such as drug design.
Thanks,
Naruki
---
Naruki Yoshikawa
Department of Computational Biology and Medica
) !=
mol2.GetAtom(idx2)->GetAtomicNum());
}
Thanks,
Naruki
2018年10月14日(日) 21:33 Koes, David :
>
> Try using OBIsomorphismMapper to find tge right mapping of atoms which will
> implicitly give you the right matching for bonds. For example:
> https://github.com/dkoes/openbabe
Hi everyone,
I'm evaluating my fragment-based coordinate generation method.
I want to measure the error of bond lengths and angles, but I have a
problem in getting corresponding ones from two molecules.
What I want to do is like this:
// mol1: ground truth loaded from SDF
// mol2:
Hi Noel,
I updated the fragmentation code.
My code is available at https://github.com/n-yoshikawa/contributed/blob/
master/c%2B%2B/fragments/obfragment.cpp
I enumerated ten most frequent fragments from our data by using this code.
The result was as follows:
SMILES percent
[C]1=CC=[C]C=C1
ion method is beneficial for chemistry and
leads to new discoveries in the field of drug design.
Thanks,
Naruki
---
Naruki Yoshikawa
Department of Computational Biology and Medical Sciences,
Graduate School of Frontier Sciences
The Universit
