search

choderalab / msm-pipeline

A pipeline for MSMs.
GNU Lesser General Public License v3.0
2 stars 5 forks source link

added SASA featurizer #40

Open sonyahanson opened 7 years ago

sonyahanson commented 7 years ago

added SASA featurizer

sonyahanson commented 7 years ago

Changed this to be by residue, since by atom (the default) was estimated to take over 300 hrs.

getting output of FeatureReader:   6% ( 1529/22149) [          ] eta 333:53:34

Not sure if this is the best idea in the end, as it seems like others have just done featurizing for MSMs by other methods, and then look at SASA to determine how to reseed trajectories.

But whatever, this is here now.

sonyahanson commented 7 years ago

This still seems to be quite slow, so may not be worth using ever. Has been running all weekend, and still has a ways to go: getting output of FeatureReader: 20% ( 4452/22149) [## ] eta 283:24:45 |

maxentile commented 7 years ago

Hmm, should be able to speed it up a lot by parallelizing, as we did for contacts here: https://github.com/choderalab/msm-pipeline/blob/master/msmpipeline/contact_features.py#L67-L69 !

sonyahanson commented 7 years ago

Added hmmiter option and coarse grained transition matrix output.