mmml kernel-fit¶
Kernel fitting utilities.
Usage¶
mmml kernel-fit --help
Options¶
usage: mmml kernel-fit [-h] [--out-dir OUT_DIR] [--natmk NATMK]
[--out-h5 OUT_H5] [--out-mdcm OUT_MDCM]
[--out-kmdcm OUT_KMDCM] [--residue-name RESIDUE_NAME]
[--nkfr NKFR] [--optimize] [--train-frames TRAIN_FRAMES]
[--lam LAM] [--sigma SIGMA] [--base-name BASE_NAME]
h5
Fit kernel ridge: distance matrix -> (AQ,BQ,CQ). Write CHARMM kernel files and
optional H5.
positional arguments:
h5 charmm_ml_comparison.h5 or similar
Input & configuration:
--residue-name RESIDUE_NAME
Residue name for mdcm header and default filenames
Output & artifacts:
--out-dir, -o OUT_DIR
Directory for x_fit.txt, coefs*.txt
--out-h5 OUT_H5 If set, evaluate and write H5 for GUI
--out-mdcm OUT_MDCM Write .mdcm file (default: out_dir/RESIDUE.mdcm)
--out-kmdcm OUT_KMDCM
Write .kmdcm kernel file (default:
out_dir/RESIDUE.kmdcm)
Diagnostics & safety:
-h, --help show this help message and exit
Other options:
--natmk NATMK Number of atoms for distance matrix (default: from H5)
--nkfr NKFR NKFR for kmdcm (default: number of frames)
--optimize Optimize (AQ,BQ,CQ) per frame before fitting
--train-frames TRAIN_FRAMES
Comma-separated frame indices for training (default:
all)
--lam LAM Kernel ridge regularization
--sigma SIGMA RBF kernel width
--base-name BASE_NAME
Prefix for x_fit/coefs filenames