Pickling in Python can be dangerous.
That’s where Quickle comes in — as long as you’re using Python 3.8 or later…
To Pickle, Or Not To Pickle? — Quickle!
Category Archives: How To
Ten Simple Rules For Solving Any Problem
Welcome! Take three deep breaths, each time expel the air through your nose with force. Now you are ready for this adventure. Let us dive right in and reflect on the premise of this blog post.
I, personally, dislike the word “solve”. What does it even mean? And that is already the second time I have used that word. The word solve implies all kinds of nonsense, such as completion or the existence of a solution. Let us recast it as: new insights, positive reframing or simply “ah-ha!”. These “problems” can be anything too: emotional ones (external or internal), scientific or research ones, artistic ones, writing ones. If you feel like it, just call it a problem.
Whoever is writing this blog post, he certainly does talk a lot … We should really get going or we will run out of time. You know what, let us start again. Welcome to:
Continue readingSeaborn 101
Seaborn is a Python-based data visualization library, which is based on matplotlib (https://seaborn.pydata.org/) . I would like to share some guidance/code to get started with drawing plots using this library! I will be using the dataset ‘flights’ from Seaborn (https://github.com/mwaskom/seaborn-data) to highlight an example.
Continue readingCalculating symmeterised small molecule RMSDs using graph automorphisms in python with GEMMI and NetworkX
When a ring flips, how do we calculate RMSD?
This surprisingly simple question leads to a very interesting problem! If we take a benzene molecule, say, and rotate it 180 degrees, then we have the exact same molecule, but if we have a data structure in which our atoms are labelled, and we apply the same transformation to the atomic positions, the numbering does not reflect that symmetry. If we were then naively to calculate the RMSD it would be huge, despite the fact that the molecule is, chemically speaking, identical.
How can we make our RMSD calculations reflect these symmetries?
Continue readingMaking Pretty Pictures with PyMOL
There’s few things I like more in our field than the opportunity to make a really nice image of a protein structure. Don’t judge me, but I’ve been known to spend the occasional evening in front of the TV with a cup of tea and PyMOL open in front of me! I’ve presented on the subject at a couple of our research group retreats, and have wanted to type it up into a blog post for a while – and this is the last opportunity I will have, since I will be leaving in just a few weeks time, after nearly eight years (!) as an OPIGlet. So, here goes – my tips and tricks for making pretty pictures with PyMOL!
Ray Tracing
set ray_trace_mode, number
I always ray trace my images to make them higher quality. It can take a while for large proteins, but it’s always worth it! My favourite setting is 1, but 3 can be fun to make things a bit more cartoon-ish.
You can also improve the quality of the image by increasing the ‘surface_quality’ and ‘cartoon_sampling’ settings.
BioDataScience101: a fantastic initiative to learn bioinformatics and data science
Last Wednesday, I was fortunate enough to be invited as a guest lecturer to the 3rd BioDataScience101 workshop, an initiative spearheaded by Paolo Marcatili, Professor of Bioinformatics at the Technical University of Denmark (DTU). This session, on amino acid sequence analysis applied to both proteomics and antibody drug discovery, was designed and organised by OPIG’s very own Tobias Olsen.
Continue readingEnhance your presentation by using virtual webcams and scene transitions
If you haven’t checked out Matt’s post on using OBS for recording video, I highly recommend doing so. OBS is a terrific way to present your work online. It can provide (amongst many, many other things) the ability to create live picture-in-picture scenes, so you can move through your powerpoint deck whilst overlaying video of your tiny talking head in the corner.
Continuing on from Matt’s post, I’d like to promote the OBS virtual camera plugin and Touch Portal.
Every company, department or course has its own favourite video conferencing application and whilst they all have their strengths, consistency is not one of them. If you want to consistently display your presentation and your live video regardless of the platform in use, this quickly gets into the “messy” territory. This is where the virtual camera comes in.
Using Python in PyMOL
Decades later, we owe Warren DeLano and his commitment to open source a great debt. Warren wrote PyMOL, an amazingly powerful and popular molecular visualization tool, but it has many hidden talents.
Perhaps its greatest strength is the use of the open source language, Python, as its control language.
Continue readingBuilding More Useful Bash Scripts
If there is some set of keystrokes that you find yourself using day in, day out, you can almost certainly write something that can automate the process. This could be something simple that could be achieved by putting a bash alias somewhere in your ~/.bashrc:
Improving your Python code quality using git pre-commit hooks
Intro
I recently completed an internship during which I spent a considerable amount of time doing software engineering. One of my main take-aways from this experience was that in industry, a lot more attention is spent on ensuring that code committed to a GitHub repo is clean and bug-free.
This is achieved through several means like code review (get other people to read your code), test-driven development (make sure your code works as you are adding functionality) or paired development (have two people work together on the same piece of code). Here, I will instead focus on a useful tool that is easy to integrate into your existing git workflow: Pre-commit hooks.
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