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utils.py
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33 lines (29 loc) · 791 Bytes
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import os
import numpy as np
import glob
import mdtraj as md
def mkdir(dir_name):
if not os.path.exists(dir_name):
os.mkdir(dir_name)
def get_fns(dir_name,pattern):
return np.sort(glob.glob(os.path.join(dir_name, pattern)))
def load_traj_coords_dir(dir_name,pattern,top):
fns = get_fns(dir_name, pattern)
all_d = []
for fn in fns:
t = md.load(fn, top=top)
d = t.xyz.reshape((len(t), 3*top.n_atoms))
all_d.append(d)
all_d = np.vstack(all_d)
return all_d
def load_npy_dir(dir_name,pattern):
fns = get_fns(dir_name, pattern)
all_d = []
for fn in fns:
d = np.load(fn)
all_d.append(d)
if len(d.shape) == 1:
all_d = np.hstack(all_d)
else:
all_d = np.vstack(all_d)
return all_d