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The pyemma documentation
http://pythonhosted.org/pyEMMA/api/generated/pyemma.coordinates.featurizer.html#pyemma.coordinates.data.featurizer.MDFeaturizer.add_distances
documents the keyword `indices2`…
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Hi,
We have another issue of DaskGridSearchCV. The example is XGBRegressor (https://github.com/pinjutien/grid-search/tree/master/grid_search_issue2).
In this case, when DaskGridSearchCV is on, t…
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It pains me to open this, but:
``` python
pyemma.__version__
# '2.2.7'
src
#
isample.shape
# (200, 2)
type(isample)
# numpy.ndarray
pyemma.coordinates.save_traj(src.filenames, isample, None, top=st…
gph82 updated
8 years ago
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Would it be possible for `pyemma.coordinates.featurizer()` to accept a `Topology` object as a substitute for a PDB file? The current API suggests only a filename is permitted right now:
https://gith…
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I'm trying to cluster a very large dataset (1.2M frames) with `pyemma.coordinates.cluster_mini_batch_kmeans`, and find that the clustering code eats up all memory over a few hours without ever startin…
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I'd like to start the bidding on a new title. Currently it's
Nearest neighbors of discrete time-trees
which is fine, though doesn't seem to really capture what the paper is about.
Some suggestions…
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Hello,
I have freshly upgraded to Keras 1.0.0 from 0.3.x and an error message was raised upon loading back a previously saved network. Using theano backend, tried with theano 0.8.0 and 0.8.1 with the…
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I'm not sure if this is a silly mistake on my part or an issue with the chunking, but I've run into an odd error in minRMSD clustering of a large dataset:
```
[chodera@mskcc-ln1 ~]$ cat cluster-CK2.o…
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After getting some weird results using parallel minRMSD clustering with equitemporally selected generators in #759, I modified the script (thanks to @maxentile!) to apply equitemporal minRMSD clusteri…
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There seems to be a bug in featurizer.py when it tries to unpack the values to variables. This error only occurs if you call the add_chi1_torsions() function.
``` python
707 def __init__(self…