msmbuilder

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change readme

3

@msmbuilder/developers and any others: should we change the readme to indicate the no-longer-developed status here? happy to draft/PR this. i do have an environment in which i still run MSMBuilder...

brookehus

Question about HierarchyParser

1

Hi, I've got a results directory with the following structure: ``` S1P/ ├── [ 714] run01 │   ├── [ 102] 0350-0400 │   ├── [ 102] 0400-0450 │   ├── [ 102]...

jeiros

msmb fails to load dll on clean install

1

I've just installed anaconda and msmbuilder but I cannot get it to run successfully. I get the following error (in an Administrator anaconda prompt in windows 10): (base) D:\programs>msmb -h...

orthonalmatrix

Getting the mapping for a HMM

1

I know these is no hard mapping for HMM, but is there a simple way to get the "highest probability" mapping for each frame? I know I can get some...

orthonalmatrix

- [x] Implement feature / fix bug - [ ] Add tests - [ ] Update changelog Included cosine distance metrics in libdistance, as it is quite a common distance...

koileee

ImportError after installation

9

After installation on MacOS 10.14.1, with miniconda, using the command `conda install -c omnia msmbuilder`, I am getting an `ImportError: No module named grid_search`. Here is the full traceback from...

vikshiv

Traceback (most recent call last): File "/misc/home/marzouk/anaconda3/envs/msmbuilder/bin/msmb", line 6, in sys.exit(msmbuilder.scripts.msmb.main()) File "/misc/home/marzouk/anaconda3/envs/msmbuilder/lib/python3.6/site-packages/msmbuilder/scripts/msmb.py", line 28, in main app.start() File "/misc/home/marzouk/anaconda3/envs/msmbuilder/lib/python3.6/site-packages/msmbuilder/cmdline.py", line 464, in start instance.start() File "/misc/home/marzouk/anaconda3/envs/msmbuilder/lib/python3.6/site-packages/msmbuilder/commands/fit_transform.py", line 70, in...

mohamedmarzouk22

During run the tICA vs. PCA example, I found that I need this library but I couldn't get by Conda or pip ModuleNotFoundError: No module named 'simtk'

mohamedmarzouk22

mohamedmarzouk22

New release/build?

1

My problem: OpenPathSampling allows users to define stable states and order parameters in terms of MSMBuilder featurizers, and to perform sampling using OpenMM for the dynamics. This combination is currently...

dwhswenson