PyMolecule: v. 2.0 ready for publication
All issues for this milestone are closed. You may close this milestone now.
Unstarted Issues (open and unassigned)
Ongoing Issues (open and assigned)
Completed Issues (closed)
- Does GitHub allow non-logged-in users to add issues?
- PIP and Conda repositories
- Scoria zip file is just the python package directory
- Updated demo script?
- Ok to merge latest branch?
- Fix the scoria I broke. :)
- Bonds by distance default should be false.
- Delete frame function
- If not too much trouble, add "hyphens:none;" to css of documentation.
- When loading in MD Analysis files, does the get_filename() work afterwards?
- Windows testing
- README.md needs to be updated.
- If pymolecule not present throw message how to install it.
- Load molecules in class constructor.
- Unit tests?
- Error catching
- Demonstration of PyMolecule
- Markdown tutorial describing how to document python code.
- Ability to change frame default value.
- Add alias functions
- save_pdb() should accept frame
- def copy() should also copy all trajectories
- Description of the main code sections
- Documentation (function-by-function dependency)
- Error handling
- Read and write multi-frame PDBs
- Add trajectory support (just a list of pymolecule objects)
- Make pymolecule MDAnalysis compatible.
- Simple implementation of a few key numpy functions in pure python to enable basic functionality w/o numpy.
- More graceful way to load PDB trajectories
- Degrades gracefully when no numpy/scipy
- Unit tests on all functions.
- MD Analysis integration