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News and Updates

Version 0.2, documentation, and website [2020-03-03]

Thus far geomm has really been an internal project used in the Dickson lab for sharing tricky pieces of code related to managing periodic boundary conditions and superimposing molecules. These use cases are deceptively not-simple and handled in a very sloppy manner by all the other packages available.

While not a particularly exciting release we were motivated to make something official to support some domain specific computations in doing simulations for ligand-unbinding simulations using wepy and the upcoming paper describing it.

At this point geomm is lacking a lot of discrete features, but we wanted to publish this and get the idea out there so that others can hopefully design better libraries (and potentially collaborate on this one). See the Motivations section of the Introduction page for a longer statement of these design ideas.

One common question people new to the geomm and wepy way of dealing with molecular data is how to actually get data for it. This comes from a common pattern in the field of always having a reader for such and such file formats (usually a PDB file). Our goal is to let PDB (or otherwise) be PDB readers and let us focus on the computation. As this is pretty foreign to those used to walled gardens and not accustomed to open data formats we have provided some extensive @@rst::any:`examples<examples/format_conversion>`@@ of converting a PDB file to a variety of other data formats using common Python ecosystem libraries like pandas. These examples are using mdtraj but could easily apply to any other package you are using.

~salotz