Comments (8)
from adaptivemd.
For basic model building functionality required for adaptive sampling it would be sufficient to slightly extend the options of remote_analysis()
. The minimal functionality includes the following options:
- featurizer selection (e.g. 'add_all', 'add_backbone_torsion')
- transformation (e.g. None or TICA)
- TICA options (lag, kinetic variance or number of dimensions)
- clustering method (k-means or regspace + metric, cutoff or number of clusters)
- MSM lagtime
If these options can be passed most cases will be covered. For everything more complicated a custom function or additional script could be used.
from adaptivemd.
from adaptivemd.
featurizer selection (e.g. 'add_all', 'add_backbone_torsion')
This is in there now.
I think we should cover the usual suspects. If you want something really fancy you can always write your own analysis code. NP. But most people will want to use PyEmma in some standard ways like we teach in the courses (as @nsplattner listed). Features are in there now. TICA is always on but has some options. Clustering should be selectable, but so far we only have n_states. MSM lagtime is in there.
from adaptivemd.
I'm not sure how the function remote_analysis()
is supposed to work. The choice of features seems to be hardcoded (line 44, feat.add_backbone_torsions()
) Is this supposed to be an example or customizable? How can arguments be passed to the featurizer? If its an example it should not be in the main code but rather in the tutorial directory.
from adaptivemd.
This was an example where I hardcoded it. it should be obvious what to change. Unfortunately PyEMMA does not allow to store a feature description in some way. but the upcoming PR #28 will change that.
from adaptivemd.
O.k., thanks for the details!
It is obvious what to change, the problem is that a) its not clear that this is an example since its placed in the package and b) its not convenient to have a custom function placed in the package since its lost when the code is updated.
from adaptivemd.
Sorry for the confusing. It was not planned originally to turn it into a package. I did that to make it easier for you guys. All the additional work including cleanups, documentation is kind of hard to do in 2 weeks time.
PR #28 and #35 will solve that problem and allow much more customization tough.
from adaptivemd.
Related Issues (20)
- Bug with reloading a project? HOT 3
- Modeller Arguments are not passed HOT 3
- Simulation / Model / Analysis Workflow HOT 9
- mongodb file size limitations HOT 3
- MSM analysis worker HOT 1
- Some worker bug HOT 2
- PyEMMA not preserving input file order? HOT 1
- Tutorial part 1
- Tutorial part 2
- Tutorial part 3
- Complete API docs
- Tutorial part 4
- Events not working HOT 2
- mongodb available in Anaconda distribution HOT 1
- Tutorial 5 not working HOT 9
- Additional Features
- Simple test in README.md does not work HOT 2
- Python 3 compatibility
- Local unit tests
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from adaptivemd.