Copy missing ApoA1 benchmarking file into examples/ on install

[jchodera]

@peastman: The apoa1.pdb file (required by benchmark.py for some benchmarks) was not copied into examples on installation. This PR adds that file to the installation.

I notice there are other files in the examples/ directory that are also not installed, such as input-charmm36-tip5p.dms. Should these other files be included as well?

Is there a more robust way to do this with CMakeLists.txt than to list all the files explicitly, especially since we seem to forget to modify this file when new example files are added?

[peastman]

We could switch it to use wildcard patterns. For example, *.pdb rather than listing the PDB files individually.

[tobigithub]

tnx,
just a quick solution as reference for others, command on LINUX to get PDB:

https://raw.githubusercontent.com/pandegroup/openmm/master/examples/apoa1.pdb

[jchodera]

We could switch it to use wildcard patterns. For example, *.pdb rather than listing the PDB files individually.

Sounds great!

I'd still love to see some organization of the structure within the examples directory, along with a clear README.md to describe what is in there, but that would probably have to wait for a more major release.

[peastman]

Should I go ahead and merge this, or wait for you to redo it with wildcards?

[jchodera]

@peastman: I've switched these to wildcards.

I'd still love to introduce some subdirectory structure and READMEs into the examples/ directory at some point, if you'd be OK with it. Vomiting a bunch of unrelated files into a single examples/ directory just seems unkind to our users.

[jchodera]

@peastman: Well, it looks like CMake doesn't understand wildcards:

CMake Error at examples/cmake_install.cmake:68 (file):
  file INSTALL cannot find
  "/Users/travis/build/pandegroup/openmm/examples/*.py".
Call Stack (most recent call first):
  cmake_install.cmake:243 (include)

How about you take this over and open your own PR with whatever solution you prefer?

[peastman]

It doesn't work like that. You have to use file(GLOB ...) to build the list of matching files. https://cmake.org/cmake/help/v3.0/command/file.html.

I'd still love to introduce some subdirectory structure

Sounds very reasonable.

[peastman]

Closing this since the problem has already been fixed.