Category Archives: How To

How to do things. doh.

How to Install Open Source PyMOL on Windows 10

It is possible to get an installer for the crystallographer’s favourite molecular visualization tool for Windows machines, that is if you are willing to pay a fee. Fortunately, Christoph Gohlke has made available free, pre-compiled Windows versions of the latest PyMOL software, along with all of it’s requirements, it’s just not particularly straightforward to install. The PyMOLWiki offers a three-step guide on how to do this and I will break it down to make it somewhat clearer.

1. Install the latest version of Python 3 for Windows

Download the Windows Installer (x-bit) for Python 3 from their website, x being your Windows architecture – 32 or 64.

Then, follow the instructions on how to install it. You can check if it has installed by running the following in PowerShell:

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Making pwd redundant

I’m going to keep this one brief, because I am mid-confirmation-and-paper-writing madness. I have seen too many people – both beginners and seasoned veterans – wandering around their Linux filesystem blindfolded:

Isn’t it hideous?

Whenever you want to see where you are, you have to execute pwd (present working directory), which will print your absolute location to stdout. If you have many terminals open at the same time, it is easy to lose track of where you are, and every other command becomes pwd; surely, I hear you cry, there has to be a better way!

Well, fear not! With a little tinkering with ~/.bashrc, we can display the working directory as part of the special PS1 environment variable, responsible for how your username and computer are displayed above. Putting the following at the top of ~/.bashrc

me=`id | awk -F\( '{print $2}' | awk -F\) '{print $1}'`
export PS1="`uname -n |  /bin/sed 's/\..*//'`{$me}:\$PWD$ "

… saving, and starting a new termanal window results in:

Much better!

I haven’t used pwd in 3 years.

How to Blopig

Blopig has a wealth of knowledge, with everything from a Bayesian answer to the question “should ketchup be stored in the fridge?“* to the Nobel-Prize-Winner-approved analysis of AlphaFold2. Blopig runs on WordPress and uses blocks, components for adding different types of content to a post. These are blocks like paragraphs, headers, images, image galleries, and videos. Here are some hints and tips for getting the most out of WordPress.

One of the first blocks worth mentioning is the “Read More…” block…

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Python’s Data Classes

When writing code, you have inevitably needed to store data throughout your pipeline. In these cases you store your value, list or data frame as a variable to easily use it elsewhere in your code. However, sometimes your data has an awkward form, consisting of a number of different length lists or data of different types and sizes. While it is still doable to work with, and using tuples or dictionaries can help, accessing different elements in your data quickly becomes messy and it is less intuitive what your code is actually doing.

To solve the above stated problem, data classes were introduced as a new feature in Python 3.7. A data class is a regular Python class, but with certain methods already implemented for you. This makes them easy to create and removes a lot of boilerplate (repeated code) making them simpler, more intuitive and pretty. Further, as data classes are part of the standard library, you can directly import it without needing to install any external dependencies (noice).

With the sales pitch out of the way, let us look at how we can use data classes. 

from dataclasses import dataclass
from typing import Any

@dataclass
class Antibody:
    vgene: str
    jgene: None
    sequence: Any = 'EVQ'
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Solving WORDLE with grep

People seem to have become obsessed with wordle, just like they became obsessed with sudoku. After my initial burst of “oh a new game!” had waned, I was left thinking “my time is precious and this is exactly what we have computers for”. With this in mind, below is my quick and dirty way of solving these. I’m sure the regexp gurus amongst you will have a more elegant solution.

Step 1: Make sure you’ve got /usr/share/dict/words installed. This is just a huge list of words in a specific language and for me, this required installing the British words list.

sudo apt-get install wbritish

Step 2: Go to wordle

Step 3: Pick a random 5-letter word as your starting point. This is where grep and /usr/share/dict/words comes in:

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Simplify your life with SLURM and sync

For my first blog post of the year, we’re talking about SLURM, everyone’s favorite job manager. If like me, you have the joy of running a literal boat-load of jobs with all kinds of parameters and command-line arguments you’ll know there are a few tips and tricks that make the process of managing these tasks and results as painless as possible. Now, I do expect most people reading this will already be aware of these tricks but for those who don’t, I hope this is helpful. After all, it’s impossible to know what you don’t know you need to know, you know? Any alternatives, improvements, or suggestions are welcome!

Array Jobs

Job arrays are perfect for the times you want to run the same job several times with slight differences each time. Imagine you need to repeat a job 10 times with slightly different arguments with each run. Rather than submit 10 (slightly different) batch scripts you can submit 1 script with all the information needed to complete all 10 jobs.

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Packaging with Conda

If you are as happy for the big snake as I am, you have probably wondered how you can create a Conda package with your amazing code. Fear not, in the following text you will learn how to make others go; 

conda install -c coolperson amazingcode

Roughly, the only thing needed to create a Conda package, is a ‘meta.yaml’ file specific for your code. This file contains all the metadata needed to create your package and is highly customizable. While this means the meta.yaml can be written to allow your Conda package to work on any operating system and with any dependencies (doesn’t have to be python) it can be annoying to write from scratch (here is a guide for manually writing this file). Since we just want to create a simple Conda package, we will in this guide avoid fiddling around with the meta.yaml file and instead create the file based on a PyPI package. This will also give you a nice template, if you later need to adapt your meta.yaml file.
Note: Conda packages can also be made from GitHub repositories, which is likely favorable in most cases, but it also requires some manual work on the meta.yaml.

1. Create a PyPI package of your code

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Getting the PDB structures of compounds in ChEMBL

Recently I was dealing with a set of compounds with known target activities from the ChEMBL database, and I wanted to find out which of them also had PDB  crystal structures in complex with that target.

Referencing this manually is very easy for cases where we are interested in 2-3 compounds, but for any larger number, using the ChEMBL and PDB web services greatly reduces the number of clicks.

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Command-Line Interfaces (CLIs), argparse.ArgumentParser and some of my tricks.

Command-Line Interfaces (CLIs) are one of the best ways of providing your programs with useful parameters to customize their execution. If you are not familiar with CLI, in this blog post we will introduce them. Let’s say that you have a program that reads a file, computes something, and then, writes the results into another file. The simplest way of providing those arguments would be:

$ python mycode.py my/inputFile my/outputFile
### mycode.py ###
def doSomething(inputFilename):
    with open(inputFilename) as f:
        return len(f.readlines())

if __name__ == "__main__":
    #Notice that the order of the arguments is important
    inputFilename = sys.argv[1]
    outputFilename = sys.argv[2]

    with open(outputFilename, "w") as f:
        f.write( doSomething(inputFilename))
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