The default method of RDKit uses valence considerations to detect the hybridisation state of an atom, since geometries are optional for the molecular structures. While there are geometry criteria for hybridisation states, they are not implemented in rdkit. Here is an example how to use these criteria (number of bonded […]
programming
62 posts
Ever wondered how relevant the R^2 value of any data series actually is? Sometimes, you see reasonably good coefficients of determination (depending on your scientific discipline and research question, “reasonably good” means something between .2 and .99) for comparably small data sets. This is not how this works.
Whenever you run calculations on a large machine (e.g. ARCHER), your jobs are subject to queuing policies. Since the waiting time should be fair (whatever this means), these queueing policies are complex and often consist of several hundred rules. However, from a user perspective, the only interesting question is
If you have the following symptom: You use Django and Phusion Passenger in at least version 4. A specific request is waiting forever. Restarting apache has no effect.
Sometimes, you want to present code output in a way that is more appealing to the eye than just unstructured output. In ipython, there are markdown cells available but you cannot execute any code there. So what if you want to show the markdown output generated by a code cell […]
A few days ago, I came across a challenge put up by the British Library (here, German and here, English). They have a sword (not too far from UCL where I work) with an inscription that seems to be strange at the first glance.
When parsing a CASTEP formatted grid with python, you may be tempted to use numpy.loadtxt – in particular, as it allows for fast access to the numerical data afterwards. However, you need to know the number of grid points in each dimension in order to work out the proper arguments […]
Calculating the hydrogen bond occupancy is a frequent task in the analysis of molecular dynamics simulations. Therefore, it has been implemented in packages like VMD hbonds or MDAnalysis.analysis.hbonds. However, these implementations do not fully treat periodic boundary conditions, as hydrogen bonds crossing the simulation box boundary are not incorporated into […]
I made a short tutorial on installing and using ipython parallel in a ipython notebook. As it is an ipython notebook itself, please follow this link.
When transferring pen-and-paper calculations into computer code, issues related to floating point precision tend to arise. For my preferred rapid prototyping language, python, this is the case as well. Of course, you can work with the decimal module, but this does not help you out in each and every case. […]