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braceal / molecules

Machine learning for molecular dynamics.
MIT License
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Add point cloud data to datasets #34

Closed braceal closed 4 years ago

braceal commented 4 years ago

Use carbon-alpha atoms

braceal commented 4 years ago

@acadev

braceal commented 4 years ago

The file: https://github.com/braceal/molecules/blob/master/molecules/sim/contact_maps.py

update _save_sparse_contact_maps and sparse_contact_maps_from_traj accordingly.

Add a new h5 dataset at the same level as rmsd, fnc, contact_maps.

Dataset name idea: carbon_alpha_pc

dtype: float32

braceal commented 4 years ago

parallel_traj_to_dset update to have parallel dset generation. Should be very easy. Just add ca_pc variable to the list definitions

braceal commented 4 years ago

For testing use this script. Pass in the pdb file, traj file, reference pdb (usually the same) and the output .h5 file

https://github.com/braceal/molecules/blob/master/scripts/traj_to_sparse_contact_map.py

Once a single traj is working. Try parallel.

For parallel mode, pass in a directory for traj_file and add the -P flag. Verbose mode -v is helpful for debugging. Currently prints every 80th processes output - number of cores on lambda.