First Post!
Alright,I've tried it numerous times before. This time, I'll try it again.This blog will contain blog posts on using python in chemistry related fields such as: Theoretical And Computational...
View ArticleUsing OpenBabel to Make Input Files for GAMESS
One thing that people tend to hate to do, is to make repetitive tasks. One such thing could be to prepare 100 different geometry optimizations using DFT[1] and a happy mixture of basis sets[2] and...
View ArticleCut'n'Frag: Fragment smart using SMARTS
In our research group, part of the research we do is method development. To facilitate these new methods, tools are often required to setup various calculations or treat output files. Some of this...
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Obtaining Contact Numbers using SMARTS
Because I'm on a roll with blogging right now and I am looking for excuses to not write the next paper, here is a post about how to utilize SMARTS[1] for something cheminformatically-vant such as the...
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Adding Hydrogen Atoms Is No Mean Feat
I've had a problem since Monday. Hydrogen atoms. You take an MD from say GROMACS or Tinker and make a 16 Angstrom extract of the entire system (this is Chorismate Mutase, PDB: 2CHT) in pymol via the...
View ArticleGreat resources are often hidden (and forgotten)
You know the problem. You found a resource that you thought was awesome, but where did you find it? how did you find it? and most importantly - how do you find it again after you closed the browser...
View ArticleThe Wonders of Numpy
I originally envisioned this post to be somewhat of a wall of code which would show just how ugly you can actually write code that works (see the public gist for that) but without the checks to see...
View ArticleProgramming the Ideal Gas
You've heard about it before. Many times. It's a model system used a lot in chemistry. The Ideal Gas law: A system where the particles can be treated as non-interacting. How do you program such a...
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Adding a PyQt GUI to your program
I am all in for command line interface (CLI) programs. I'll admit that. They work in terminals. You can run them without an X Server and usually option flags are easy to use and obvious*. But sometimes...
View ArticleA Threaded PyQt GUI and Particles
I wrote a post about adding a GUI to your command line interface program. Sometimes people just want to click stuff. If you tried it / implemented it yourself, you'd have seen that the program would...
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Fun and a little disappointment with amino acids
So you have Open Babel, you have the Python bindings to Open Babel and you think: "I just want to have fun!".I wrote a small script to generate the 3D structures of the amino acids because I wan't to...
View ArticleOne way to safe guard imports of external libraries
Say you have some code that is dependent on some 3rd party library, for instance users can download FragIt that requires Open Babel, but what happens if the user 'forgot' to install Open Babel or...
View ArticleHowto figure out whether two lists have any elements in common
While working with FragIt I had to figure out whether two lists had some elements in common (it does not matter which!) and I came up with the following piece of code (with the help of Google and Stack...
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