Adden new reader for energy files

This commit is contained in:
sebastiankloth 2022-04-27 14:16:04 +02:00
parent 68b8e1a305
commit 36a5d02b8c
2 changed files with 47 additions and 0 deletions

View File

@ -73,3 +73,12 @@ def open(directory='', topology='*.tpr', trajectory='*.xtc', cached=False,
except reader.NojumpError:
reader.generate_nojump_matrixes(coords)
return coords
def open_energy(file, energies=None):
"""Reads an gromacs energy file and output the data in a pandas DataFrame.
Args:
file: Filename of the energy file
energies (opt.): Specify energies to extract from the energy file
"""
df = reader.energy_reader(file, energies=energies)
return df

View File

@ -181,6 +181,44 @@ def correct_nojump_matrixes_for_whole(trajectory):
for d in range(3):
reader.nojump_matrixes[d][0] = cor[:, d]
save_nojump_matrixes(reader)
def energy_reader(file, energies=None):
read_energy(file, energies=None):
"""Reads an gromacs energy file and output the data in a pandas DataFrame.
Args:
file: Filename of the energy file
energies (opt.): Specify energies to extract from the energy file
"""
if energies is None:
energies = np.arange(1, 100).astype('str')
directory = file.rsplit("/", 1)[0]
ps = subprocess.Popen(("echo", *energies), stdout=subprocess.PIPE)
try:
subprocess.run(("gmx", "energy", "-f", file, "-o", f"{directory}/tmp.xvg", "-quiet"), stdin=ps.stdout)
except FileNotFoundError:
print("No GROMACS found!")
ps.wait()
labels = []
is_legend = False
with open(f"{directory}/tmp.xvg") as f:
for i, line in enumerate(f):
if line.split(" ")[0] == "@":
if re.search("s\d+", line.split()[1]):
is_legend = True
labels.append(line.split('"')[1])
elif is_legend:
header = i
break
data = np.genfromtxt(f"{directory}/tmp.xvg", skip_header=header)
df = pd.DataFrame({"Time":data[:,0]})
for i, label in enumerate(labels):
tmp_df = pd.DataFrame({label:data[:,i+1]})
df = pd.concat([df, tmp_df], axis=1)
subprocess.run(("rm", f"{directory}/tmp.xvg"))
return df
class BaseReader: