Added bugfix for a project builder issue when pdb filename does not exist. The builder actually assumed that the error was a corrupt xtc file, and so it was stuck in an infinite loop trying to throw away the last frame in the xtc.
first attempts at getting the project builder to update the file. This is harder than I thought it would be ...
Merge branch 'proj_builder' of github.com:schwancr/msmbuilder into proj_builder
small fix in ProjectBuilder docstring
added logger prints as well as added the error checking that was originally in the builder.
bugfix in builder
bugfix in updating project that was giving new trajectories the wrong index to save to. Also some other minor changes
fixed typo in comment
Added bugfix for a project builder issue when pdb filename does not exist. The builder actually assumed that the error was a corrupt xtc file, and so it was stuck in an infinite loop trying to throw away the last frame in the xtc.
first attempts at getting the project builder to update the file. This is harder than I thought it would be ...
small fix in ProjectBuilder docstring
added logger prints as well as added the error checking that was originally in the builder.
bugfix in builder
bugfix in updating project that was giving new trajectories the wrong index to save to. Also some other minor changes
fixed typo in comment
Merge branch 'proj_builder' of github.com:schwancr/msmbuilder into proj_builder
cleaned up a little bit.
bugfixes and got things to work.
removed import IPython from builder.py
If all XTCs are corrupt then their is a bad error raised due to trying to read the first file in an empty list. I added a check in the while corrupted loop that will break when there are no files left. This results in a RuntimeError, which is caught by both _update_traj and _load_new_files and correctly just does not add a trajectory to the project. Before the entire script would crash because this error was not caught correctly. I did change it from ValueError, but I have no idea what would be raising that error. This is at the very least more transparent, but some xtc error may still cause a crash.