APBS Sphinx

This is still very much pre-alpha software. Beyond here there be monsters!

Building the Beast

First off, you'll need Python 3.5, built with venv support. Note that currently the Python 3.5 Ubuntu package is broken. You'll also need a C++11 compiler and CMake (3.2.x).

Install Python Virtual Environment, install dependencies and generate JSON schema from PDBx/mmCIF star file

1. cd <sphinx_repo>
2. git submodule init
3. git submodule update
4. python3 bootstrap.py
5. source sphinx-env/bin/activate

Build the Geometric Flow plugin

7. cd <sphinx_repo>/plugins/Geoflow/src
8. mkdir build
9. cd build
10. cmake ..
11. make
12. cp geoflow.so ../..

Build the PBAM plugin

7. cd <sphinx_repo>/plugins/PB_S_AM/src
8. mkdir build
9. cd build
10. cmake -DENABLE_PBAM_SPHINX=ON ..
11. make pbam_sph
12. cp ./pbam/src/pbam_sph.so ../..

Build the TABI-PB plugin

7. cd <sphinx_repo>/plugins/TABIPB/src
8. mkdir build
9. cd build
10. cmake -DENABLE_TABIPB_SPHINX=ON ..
11. make
12. cp tabipb_sph.so ../..

Testing the Beast

We are currently using Nose to run the unit tests. From the prototype directory just run nosetests.

Running the Beast

From <sphinx_repo> try this: python apbs.py example/geoflow.apbs infile=example/imidazole.xyzr outfile=imidazole.txt

Or this: python apbs.py example/pbam/pbam.apbs infile=example/imidazole.xyzr outfile=pbam.txt

Or this: python apbs.py example/tabipb.apbs infile=example/imidazole.xyzr outfile=pbam.txt

It just ran the geometric flow solver on imidazole.xyzr and printed some electrostatic information about the molecule into imidazole.txt.

Oh, there's this crazy io.mc file too, although there's not really much in it that's useful.

It's worth noting that the file geoflow.apbs is Python code, and that it's really just for playing with what's possible using Python to specify pipelines. Whether or not we continue to use the same Python syntax is still up in the air. It may make more sense to create a DSL for specifying pipelines.

###This is important here The main takeaway is that *.apbs files specify plugin pipelines. A typical user can specify, on the command line, a pre-written APBS command file (*.apbs) that takes named parameters and operates on what those parameters specify. In this case, run the Geometric Flow solver on the imidazole.xyzr file and put the results in imidazole.txt.

An atypical user may choose to create their own pipeline files, and thus gain much more control over how the data is processed. We provide different levels of control to suit both typical and power users. ###Thanks for paying extra-special attention

Running Solvers in Parallel

There is a really simple example of running two geoflow jobs in example/dual-geoflow.apbs. It may be run as above. It will solve the imidazole molecule, as well as diet.xyzr. The latter is hardcoded to print it's results to diet.txt. This example shows that two solvers may run concurrently, as well as how it's possible to hardcode information (the input and output files) into a command file (.apbs).

Anatomy of the Beast

There is a work-in-progress white paper on Sphinx that dwells on some of the details.

TODO

7. The Geometric Flow plugin needs a means of taking parameters. I suggest that all the solver plug-ins take a parameter file. Something like the .in files of yore.
8. Remove all the debug junk that's printed in Geoflow.
9. Get the Semantic Databus idea into working shape
10. Validate plug-in pipelines
11. Extend this command line mode with something more user friendly. Hey maybe extend that SillyServer plugin (what's that there for anyway?) to spawn a browser and connect to Sphinx, thus providing the user a GUI? What? That's crazy talk!
12. Moar solvers! ...
13. There are a lot of TODO's in the source code. ...
14. Ad nauseum