<div dir="ltr">Hi Diksha,<div><br></div><div>I can reply for both of these projects since I'm the mentor for either of them.</div><div><br></div><div><b>YAeHMOP project:</b> </div><div>Here we're only talking about the computational part of the tool, the software that's in the tightbind directory in the github repo (<a href="https://github.com/greglandrum/yaehmop/tree/master/tightbind">https://github.com/greglandrum/yaehmop/tree/master/tightbind</a>)</div><div>This is a codebase that is in C (with a bit of fortran or f2c translated C) and that currently assumes that it's going to be run from the command line reading from an input file and writing to an output file. There's a lot of documentation describing what the toolkit does on the sourceforge page (<a href="http://yaehmop.sourceforge.net/" target="_blank">http://yaehmop.sourceforge.ne<wbr>t/</a>). The idea of the project would be to:</div><div>1) Create a library form of the package that exposes the important functions via a public API. We'll need to figure out what the important pieces of functionality are there, but it won't be a huge number of functions.</div><div>2) Write a good set of regression tests for that public API</div><div>3) Replace as much as possible of the legacy fortran (or f2c translated C) code. </div><div> 3a) The first piece of this will be replacing calls to the fortran matrix diagonalization code with calls to similar functionality provided by the eigen library.</div><div> 3b) The second part will be to replace the code that calculates the overlap integrals that are used. This is a fairly hairy bit of code and so we'll have to figure out if there's a sensible way to rewrite it or if we should make sure that the C code no longer calls out to things from the f2c library.</div><div><br></div><div>That's already a reasonable chunk of work and would be really useful, but if there's still time I would suggest that it be spent starting to write a set of unit tests and/or doing a good cross-platform build system based on cmake.</div><div><br></div><div>A good start if you want to do this project would be to get a copy of the yaehmop source, compile a copy of it, and demonstrate some basic knowledge of how it works by writing a couple of regression tests (you can pick a framework for this) using the input files in the yaehmop/examples directory as input and the code's newly added ability to be called from another package (you'll find the commits for this in the changes made last year).</div><div><br></div><div><b>Fingerprint project</b>:</div><div>Here is an brief (and a bit out of date) overview of what chemical fingerprints are and what is currently implemented in the RDKit: <a href="http://www.rdkit.org/UGM/2012/Landrum_RDKit_UGM.Fingerprints.Final.pptx.pdf" target="_blank">http://www.rdkit.org/UG<wbr>M/2012/Landrum_RDKit_UGM.Finge<wbr>rprints.Final.pptx.pdf</a></div><div>Googling for "chemical fingerprint" will turn up a bunch of hits that may also help.</div><div>Here the idea is to create a new fingerprinting function for the RDKit that allows the caller to specify the types of molecular "subgraphs" to be found, the type of features to be mapped onto those, and the hashing approach to be used.</div><div><br></div><div>A good way to start if you want to do this project would be to clone the RDKit github repo and get it building on your own, find the C++ fingerprinting code, write a function that generates an RDKit fingerprint using the connectivity invariant from the Morgan fingerprint, and then write some good tests for that function.</div><div><br></div><div>Best Regards,</div><div>-greg</div><div><br></div><div><br></div><div><br></div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Mar 13, 2017 at 1:20 PM, <span dir="ltr"><<a href="mailto:diksha.godbole@gmail.com" target="_blank">diksha.godbole@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div lang="EN-IN" link="blue" vlink="#954F72"><div class="m_-7403904463823420810WordSection1"><p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal">Respected Sir/Madam,<u></u><u></u></p><div><p class="MsoNormal"> <wbr> My name is Diksha Godbole and I am an undergraduate studying Computer Engineering .With this mail I would like to express my profound interest in the Project: YAeHmop as a library. I have a good C/C++ programming knowledge and would like to discus more about what undertaking this project would mean and what will be expected for me .I have also expressed my interest in a previous mail for the project: <span class="m_-7403904463823420810mw-headline">Create a generalized fingerprinting function, I hope with your guidance I can decide which project would best suit my interests and skill set.</span><span style="font-size:13.5pt"><u></u><u></u></span></p></div><p class="m_-7403904463823420810MsoNoSpacing">Looking forward to your guidance ,</p><p class="m_-7403904463823420810MsoNoSpacing">Thanking You ,</p><p class="m_-7403904463823420810MsoNoSpacing">Diksha Godbole<span style="font-size:13.5pt"><u></u><u></u></span></p><p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal">Sent from <a href="https://go.microsoft.com/fwlink/?LinkId=550986" target="_blank">Mail</a> for Windows 10<u></u><u></u></p><p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal"><u></u> <u></u></p><p class="MsoNormal"><u></u> <u></u></p></div></div><br>______________________________<wbr>_________________<br>
Openchemistry-developers mailing list<br>
<a href="mailto:Openchemistry-developers@public.kitware.com">Openchemistry-developers@<wbr>public.kitware.com</a><br>
<a href="http://public.kitware.com/mailman/listinfo/openchemistry-developers" rel="noreferrer" target="_blank">http://public.kitware.com/<wbr>mailman/listinfo/<wbr>openchemistry-developers</a><br>
<br></blockquote></div><br></div>