def fit_protein_pca(yaml_file):
mdl_dir = yaml_file["mdl_dir"]
mdl_params = yaml_file["mdl_params"]
current_mdl_params={}
for i in mdl_params.keys():
if i.startswith("pca__"):
current_mdl_params[i.split("pca__")[1]] = mdl_params[i]
protein_pca_mdl = PCA(**current_mdl_params)
for protein in yaml_file["protein_list"]:
print("Fitting to protein %s" % protein)
with enter_protein_data_dir(yaml_file, protein):
featurized_traj = sorted(glob.glob("./%s/*.jl" %
yaml_file["feature_dir"]), key=keynat)
for f in featurized_traj:
featurized_path = verboseload(f)
try:
protein_pca_mdl.partial_fit(featurized_path)
except:
pass
print("Done partial fitting to protein %s" % protein)
# dumping the pca_mdl
pca_mdl_path = os.path.join(mdl_dir, "pca_mdl.pkl")
verbosedump(protein_pca_mdl, pca_mdl_path)
return
