This PR fixes #63

• [x] Added tutorial for membrane-only systems.

I would appreciate some feedback for this tutorial while I finish the other two notebooks. @lilyminium @orbeckst @richardjgowers @IAlibay

Thanks!
Edit: I forgot to mention I couldn't manage to make the NGLwidget render, so I ended up adding the png files of the widgets. Hope that works as an alternative.

After fixing #70 , the tutorial of the membrane-only system needed some updates. This version should close #74.

Changes in this PR:

• [x] Updated interpretation of mean curvature plots.
• [x] Changed units in H and K plots (from nm to Å).
• [x] Added ticks to color bars in curvature plots.

I'm tagging @lilyminium and @orbeckst who usually review my PRs, but more reviewers are welcome. :) Thanks.

This PR is an initial suggestion to fix #41

• Methods included in the initial analysis base:

• [x] __init__

• [x] _prepare

• [x] _single_frame

• [x] _conclude

• Some additional comments

This first AnalysisBase was build under the following assumptions:

1. The atoms of reference in AtomGroup remain the same during the n_frames of the trajectory.
2. lipid translocation does not occur during the trajectory. (Although I am not considering bilayers, this reinforces 1)
3. By introducing a grid of bigger size than the simulation box, the calculation of H and K may be jeopardized by the introduction of np.nans. This selection will certainly generate np.nans in the calculation of the gradient, which ultimately will affect the averaged grids. Hence, the attempt of warning the user (in __init__).
4. The overall result is the averaged np.array of surface, K, and H over frames. (in _conclude)
5. The calculation of surface, H, and K, is performed in every frame (in _single_frame).
6. The respective values of surface, H and K and their normalized grids are initialized (in _prepare). They are a tuple of np.arrays where the first element contains the respective values, and the second element counts the elements when defined.
7. To sum and normalize values, the _output function was introduced. (But I am not sure this is something people would agree with)

As discussed in #21 with @lilyminium, this analysis base will potentially replace core.py.

Periodic Boundary Conditions (PBC) are not applied when mapping coordinates to grid (grid_map).

To fix this issue:

• [ ] Add PBC conditions to map coordinates.
• [ ] Add test using dummy coordinates to map values that exceed by defect or excess the boundaries of the grid.

For example:

• System with 9 beads with coordinates of x -1, 0, 1 and y -1, 0 ,1
• System with 16 beads with coordinates of x -2, -1, 0, 1, and y -2, -1, 0 ,1, 2.

In this PR I added PBC conditions. Changes in this PR fix #36 and possibly #22

• [x] self.ag.wrap() added to__init__ and _single_frame.
• [x] Added tests for coordinate wrapping, including negative coordinates in x, y, and z, as suggested in #22
• [x] Since PBC has an effect on the overall results, respective tests for results.z_surface and results.mean were updated.
• [x] I am not sure mentors would be interested in keeping previous tests, so I didn't delete but marked them as xfail(reason="PBC conditions not applied.") (See line 276 is tests_membrane_curvature.py.

@orbeckst @lilyminium @IAlibay are there any other relevant tests I am missing here? Thanks

Changes here included fixes #66

While I was here I changed other minor things

• [x] Added pip in README.
• [x] Fixed installation instructions for MDATests and added link.
• [x] Fixed typos in Usage page in docs.

This PR fixes #46

• [x] In setup.py, three packages were added to install requires:

• 'numpy>=1.20.2',

• 'mdanalysis>=2.0.0',

• 'mdanalysistests>=2.0.0'.

• [x] For NumPy:

• Check if installed.

• Check Python>=3.6

@IAlibay, would you please confirm no more changes are needed here at the moment?

Changes in this PR fixes #58

Changes include:

• [x] Updated algorithm page.
• [x] Update Usage page for three cases
• Membrane-only
• Membrane-protein with posres.
• Membrane-protein with no posres.
• [x] Updated visualization page.

Pending:

• [x] Add real data file to the test suite.
• [x] Add real plots to the Visualization page.

Question: I left the usage page as if I were going to use a different test data file for each case.

• Is it a good idea to add a dataset for each one of the cases I have or better to reuse some MDA tests?

Happy to receive any other suggestions. Thanks!

@lilyminium @orbeckst @IAlibay @fiona-naughton

Description

As discussed here is my solution (assuming CI doesn't complain) to the CI issues in PR #49

To do

• [ ] Remove extra branch in PR (currently used to test)

Status

• [ ] Ready to go

Function core_fast_leaflets split into three functions:

• [x] get positions for each atom in the atom group for each frame.
• [x] identify the grid cell for each coordinate.
• [x] calculate the average z for the atom group.

Tests added:

• [x] test_get_positions using dummy coordinates for beads 0 to 8, all of them with z=10:

o ______ o _____ o _______ |
|   (6)  |  (7)   |   (8)  |
o ______ o _____ o _______ |
|   (3)  |  (4)   |   (5)  |
o _______o ______ o ______ |
|   (0)  |  (1)   |   (2)  |
o ______ o ______ o ______ |

Using the same number of beads in grids,

• [x] test_avg_unit_cell added for two systems.

1. z values of z=10
2. z values as below:

o ______ o _____ o _______ |
| (z=10) | (z=20) | (z=30) |
o ______ o _____ o _______ |
| (z=10) | (z=20) | (z=30) |
o _______o ______ o ______ |
| (z=10) | (z=20) | (z=30) |
o ______ o ______ o ______ |

3. z values of z=10 and number of beads per unit cell as shown below:

o ____ o ____ o ___ |
|   2  |  1   |  1  |
o ____ o ____ o ___ |
|   1  |  2   |  1  |
o ____ o ____ o ___ |
|   1  |  1   |  2  |
o ____ o ____ o ___ |

• [x] test_derive_surface added for same dummy_coordinates as in test_get_positions.

This PR fixes #33.

Changes included:

• [x] pytest.mark.xfail test of negative coordinates in grid_map.
• [x] 9- and 25-grid combined into one function with pytest.parametrize.
• [x] Test_mapper changed by adding assertion of dummy coordinates.
• [x] Test with grid_map using 6 unit cells in grid of 9 lipids as shown below:

^   o ___ o ___ o ___ o ___ o ___ o ___ |
|   | (6) |     | (7) |     | (8) |     |
|   o ___ o ___ o ___ o ___ o ___ o ___ |
|   |     |     |     |     |     |     |
|   o ___ o ___ o ___ o ___ o ___ o ___ |
y   | (3) |     | (4) |     | (5) |     | 
|   o ___ o ___ o ___ o ___ o ___ o ___ |
|   |     |     |     |     |     |     |
|   o ___ o ___ o ___ o ___ o ___ o ___ |
|   | (0) |     | (1) |     | (2) |
v   o ___ o ___ o ___ o ___ o ___ o ___ |
    0.   0.5    1.   1.5.   2.   2.5.   3.
    <----------------- x --------------->

For grid with 9 lipid types: Bead 0 mapped to [ 0 0 ], with Coordinates ( 0 , 0 ) Bead 1 mapped to [ 2 0 ], with Coordinates ( 1 , 0 ) Bead 2 mapped to [ 4 0 ], with Coordinates ( 2 , 0 ) Bead 3 mapped to [ 0 2 ], with Coordinates ( 0 , 1 ) Bead 4 mapped to [ 2 2 ], with Coordinates ( 1 , 1 ) Bead 5 mapped to [ 2 2 ], with Coordinates ( 1 , 1 ) Bead 6 mapped to [ 0 4 ], with Coordinates ( 0 , 2 ) Bead 7 mapped to [ 2 4 ], with Coordinates ( 1 , 2 ) Bead 8 mapped to [ 4 4 ], with Coordinates ( 2 , 2 )

and the equivalent to the grid of 25 lipids.

This PR may also fix: #27 since function def_all_beads was deleted after replacing MDtraj by MDAnalysis. #28 since function core_fast was deleted after refactoring. #32 since function def_all_beads was deleted after refactoring and replaced by direct selection using MDAnalysis. and #16

Questions: (possible minor change)

• In line 172 and 177, I could simplify to factor = 1 and then in lines 174 and 179, respectively. assert grid_map(dummy_coord, 1) == dummy_coord assert grid_map(dummy_coord, 2) == (dummy_coord[0]*2, dummy_coord[1]*2)

@ojeda-e with the amazing new release of membrane-curvature perhaps we can think about putting up a package on conda-forge?

I would be happy to help you set it up, let me know. :)

Although still functional, installation with setup.py is deprecated. According to PEP518:

The build system dependencies will be stored in a file named pyproject.toml that is written in the TOML format [6].

Additionally, there are two files that can be deleted in the root directory: .lgtm.yml and _config.yml

To fix this issue:

• [ ] Add pyproject.toml.
• [ ] If necessary, modify setup.cfg.
• [ ] Remove .lgtm.yml and _config.yml in root.

Now that MDAKits are live to roll we should work towards registering membrane-curvature as an MDAKit!

See the blog post for more info.

AFAIK membrane-curvature already meets all the requirements listed in the white paper.

Description

This PR fixes #84 by adding AVS benchmarks to the project.

Changes

• [x] Addedn config json file
• [x] Added benchmarks/__init__.py
• [x] Added membranecurvature.py benchmark file.

Status

• [ ] Ready to go

Currently, there is no information about the performance of membrane curvature. It would be nice to have a page in the documentation that addresses this matter. Although the idea is not very well defined yet, some guidelines for an initial version of the benchmark are:

• Performance over number of lipids in single-frame systems.
• Performance over number of frames with a fixed number of lipids.
• Keep the list of assumptions regardless of the approach.
• Consider dummy Universes.
• MDAnalysis uses ASV (Check code here)

Thanks @hmacdope, @lilyminium and @richardjgowers for the suggestions.