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Concepts to cover
Lily Wang edited this page Aug 31, 2019
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These notes are gathered from every post in mdnalysis-discussion from October 1st 2018 to August 21st 2019 (UTC). Release 0.19.0 came out on October 10th, 2018.
Out of 133 posts, these were the broad topics:
- Analysis (42)
- Universe I/O (20)
- Irrelevant, i.e. not about MDAnalysis (14) (Not covered here)
- Google Summer of Code (11) (Not covered here)
- Topology (10)
- AtomGroup/ResidueGroup (5)
- Selection (9)
- Package stuff, i.e. dependencies / failing tests / bugs (5) (Not covered here)
- Installation issues (4) (Not covered here)
- Universe (3)
- Trajectory (2)
- PMDA/large data (2)
- Questions due to updates (2) (not covered)
- Development (2) (not covered)
- Units (1)
Understandably, questions about analysis were the largest proportion. These loosely fell into several subcategories.
Category | # | Notes | Solution | Links |
---|---|---|---|---|
Format (general) | 4 | How to use formats that MDAnalysis has defined. | Notebooks | |
Format behaviour | 3 | How MDA treats formats | Notes on MD format pages about their behaviour | |
Other formats | 3 | I/O with custom formats, e.g. Numpy or GridData | Cover this in I/O page | |
Incompatible format | 2 | How formats work | Notes on MD format pages about their behaviour | |
Write trajectory | 2 | How to write a trajectory | Notebook and in Quickstart guide | |
Memory | 2 | Problems with large data | Notes on how memory works in MDAnalysis, and pointer to PMDA | |
Paths | 2 | Python/path issue | Add a note in a notebook "Change this for your file" | |
General MD | 1 | Mismatch between TPR and GRO | Perhaps mention this as a possibility? | |
Trajectory slicing | 1 | Loading in a trajectory in steps | Note that this isn't possible. |
Category | # | Notes | Solution | Links |
---|---|---|---|---|
Adding TopologyAttr | 4 | How to add topology attributes -- especially bfactor vs tempfactor. | Describe this in a Topology Manipulation section, as well as having examples in notebooks as a way to visualise analysis. | |
Guessing topology information | 3 | Guessing bonds or elements. | Be clear about what is/can be guessed. | |
Modifying bonds | 2 | How to add, remove, or modify bonds. | Topology manipulation section | |
Adding segment | 1 | How to add new segments. | Document this with other Group editing. |
Category | # | Notes | Solution | Links |
---|---|---|---|---|
Selection command | 4 | Which string to use to get desired atom groups. | A comprehensive page on atom selection language -- this is as much MD knowledge as MDAnalysis. | |
Proper selection group | 2 | How to select the right AtomGroup for the analysis. | Notes on selection on the specific analysis pages. | |
Using GROMACS index | 1 | Can we use .ndx files to select? | No, but awesome idea. | |
Dynamic evaluation | 1 | Does the selection update over the analysis? | Yes, needs a note on the analysis page. | |
Ranked selection | 1 | Selecting the 10 nearest atoms. | The solution is neat and could be a notebook. |
Category | # | Notes | Solution | Links |
---|---|---|---|---|
Transformation | 2 | How to transform molecules. | A notebook on transformations | |
Attributes | 2 | Getting/setting attributes | A concise API reference | |
Group behaviour | 1 | OOP behaviour | Describe clearly how Groups work in docs. |
Category | # | Notes | Solution | Links |
---|---|---|---|---|
System building | 2 | Building molecules from coordinates by assigning TopologyAttrs | Include this in system building documentation | |
Universe dimensions | 1 | Universe attributes | Concise API reference |
Category | # | Notes | Solution | Links |
---|---|---|---|---|
Trajectory | 2 | Dealing with dynamic positions | Point out positions changes and detail consequences. |
|
PMDA | 2 | Dealing with large data | Outside the scope of this guide. Link to PMDA docs. | |
Unit transformation | 1 | Transforming LJ units to conventional units | Possibly include this in the Units page. |
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