A fairly easy first issue would be to fix the two warnings found when compiling with a recent gcc. Note that a simple loop should be preferred over expressions that involve recent C++ standards (due to portability).
Regards, - Noel On Thu, 13 Feb 2020 at 14:15, Naruki Yoshikawa <naruki.yoshik...@gmail.com> wrote: > 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/ > https://summerofcode.withgoogle.com/archive/2019/projects/5300703310905344/ > Here is our paper based on the GSoC project: > https://jcheminf.biomedcentral.com/articles/10.1186/s13321-019-0372-5 > > I have some works left related to my project. > As I cannot join GSoC anymore, I hope someone would solve the following > problems. > > 1. Stereochemistry: > I found out something is wrong > with OBDistanceGeometry::CheckStereoConstraints(), but I still don't > understand what is wrong. > I posted some problematic cases before. > https://sourceforge.net/p/openbabel/mailman/message/36699127/ > <https://sourceforge.net/p/openbabel/mailman/message/36699127/The> > The function is replaced now, but it is still problematic. > It compares canonical SMILES of input and output, but when I generate > canonical SMILES from generated 3D structures, SMILES sometimes don't > match. > We need to fix this problem. > > If you can list problematic test cases, it would help us to solve the > issue. > I think this is an easy task and a good starting point to start > contribution. You can create an issue to report problematic cases. > > Here are related codes and discussions: > https://github.com/openbabel/openbabel/pull/1875#issuecomment-547242242 > > https://github.com/openbabel/openbabel/blob/6e80d6548e04af1dc13f9ff975f18714c7024617/src/distgeom.cpp#L912 > > https://github.com/openbabel/openbabel/blob/6e80d6548e04af1dc13f9ff975f18714c7024617/test/testdistgeom.py#L24 > > You can use our test dataset at > https://github.com/n-yoshikawa/ob-fragment-generation/tree/master/data > > 2. Improve performance: > I wrote distance geometry last year, but it was so slow compared to > RDKit's. > If you can improve the performance, it is great. > The slowest part was error minimization in my evaluation. > > https://github.com/openbabel/openbabel/blob/6e80d6548e04af1dc13f9ff975f18714c7024617/src/distgeom.cpp#L1171 > I doubt initial geometry is strange due to loose distance constraints, but > I am not so sure. > > 3. Large ring: > The default fragment-based coordinate generation works poorly for unknown > large ring fragments. > Geoff attempted to solve this, but it is not complete yet. > https://github.com/openbabel/openbabel/pull/2019 > Using distance geometry for unknown fragment is another possible solution, > but the performance was poor in my implementation. > > I used a lot of technical terms here. Please let me know if you have any > questions. > > Naruki > > 2020年2月13日(木) 3:17 Hashim Chaudhry <hashimchaudr...@gmail.com>: > >> Hello Devs, >> >> I'm really looking to contribute to Openbabel however, I'm having a hard >> time figuring out where to start. I'd really appreciate if someone could >> point me in the right direction. >> >> *Why I want to contribute?* >> I came across an Openbabel GSOC project idea (Develop a validation and >> standardization filter) at Openchemistry.org and it piqued my interest. >> I'm well aware that the organizations haven't been announced yet, >> nevertheless, I'm looking to contribute to Openbabel to get a start in >> Open-Source work and get familiar with the code-base before GSOC. >> >> *About Me* >> I'm a third-year Computer Science undergrad student. I have completed a >> number of self learning courses for Programming, Data Structures, >> Machine Learning and Data Science(with Python). >> I believe these courses have laid a foundation that would really help me >> to learn and contribute to Openbabel. >> >> Moreover, here's a link to my Kaggle profile >> <https://www.kaggle.com/hashimchaudry>. I'm a beginner finding my way >> into Data Science. It ain't much, but it's honest work. >> >> Regards, >> Hashim >> ReplyReply to allForward >> _______________________________________________ >> OpenBabel-Devel mailing list >> OpenBabel-Devel@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/openbabel-devel >> > _______________________________________________ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-devel >
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