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