diff --git a/plumed/io/parsers/__init__.py b/plumed/io/parsers/__init__.py index 971ea0d..918ffb8 100644 --- a/plumed/io/parsers/__init__.py +++ b/plumed/io/parsers/__init__.py @@ -1,7 +1,7 @@ -from read_wham import read_wham -from read_colvar import read_colvar -from read_fes import read_fes -from read_hills import read_hills -from read_plumed import read_plumed -from read_str import read_str +from .read_wham import read_wham +from .read_colvar import read_colvar +from .read_fes import read_fes +from .read_hills import read_hills +from .read_plumed import read_plumed +from .read_str import read_str diff --git a/plumed/io/parsers/read_colvar.py b/plumed/io/parsers/read_colvar.py index c9b27d8..af7528d 100644 --- a/plumed/io/parsers/read_colvar.py +++ b/plumed/io/parsers/read_colvar.py @@ -3,17 +3,19 @@ import numpy as np import six + def read_colvar(fname, verbose=False): - if verbose: print(fname) - f = open(fname) if isinstance(fname, six.string_types) else fname + if verbose: + print(fname) + f = open(fname) if isinstance(fname, six.string_types) else fname - with f: - line = f.readline() - assert line[:2] == '#!', 'Missing or incorrect header' - columns = line.split()[2:] - f.seek(0) - df = pd.read_csv(f, delim_whitespace=True, comment="#", skiprows=1, header=None) + with f: + line = f.readline() + assert line[:2] == '#!', 'Missing or incorrect header' + columns = line.split()[2:] + f.seek(0) + df = pd.read_csv(f, delim_whitespace=True, comment="#", skiprows=1, header=None) - df.columns = columns - df.time = map(np.round, df.time) - return df + df.columns = columns + df.time = map(np.round, df.time) + return df diff --git a/plumed/io/parsers/read_fes.py b/plumed/io/parsers/read_fes.py index a1708cd..d171dfb 100644 --- a/plumed/io/parsers/read_fes.py +++ b/plumed/io/parsers/read_fes.py @@ -1,10 +1,11 @@ import pandas as pd + def read_fes(fname): - lines = [l[1:] for l in open(fname).readlines() if l.startswith("#")] - columns = lines[1].split() - data = [map(float, l.split()) for l in lines[2:]] - df = pd.DataFrame(data, columns=columns) - df.Window = map(int, df.Window) - return df + lines = [l[1:] for l in open(fname).readlines() if l.startswith("#")] + columns = lines[1].split() + data = [map(float, l.split()) for l in lines[2:]] + df = pd.DataFrame(data, columns=columns) + df.Window = map(int, df.Window) + return df diff --git a/plumed/io/parsers/read_hills.py b/plumed/io/parsers/read_hills.py index 5e063d8..35d9019 100644 --- a/plumed/io/parsers/read_hills.py +++ b/plumed/io/parsers/read_hills.py @@ -1,9 +1,10 @@ import pandas as pd + def read_hills(f="HILLS"): - lines = open(f).readlines() - columns = lines[0].split()[2:] - data = [map(float, l.split()) for l in lines if not l.startswith("#")] - df = pd.DataFrame(data, columns=columns) - return df + lines = open(f).readlines() + columns = lines[0].split()[2:] + data = [map(float, l.split()) for l in lines if not l.startswith("#")] + df = pd.DataFrame(data, columns=columns) + return df diff --git a/plumed/io/parsers/read_str.py b/plumed/io/parsers/read_str.py index 504c60d..e78dc24 100644 --- a/plumed/io/parsers/read_str.py +++ b/plumed/io/parsers/read_str.py @@ -1,6 +1,7 @@ import pandas as pd + def read_str(filename): columns = ['_Gen_dist_constraint.ID', diff --git a/plumed/io/parsers/read_wham.py b/plumed/io/parsers/read_wham.py index 3e29dec..c51c226 100644 --- a/plumed/io/parsers/read_wham.py +++ b/plumed/io/parsers/read_wham.py @@ -1,8 +1,9 @@ import pandas as pd + def read_wham(fname): - df = pd.read_csv(fname, sep="\t", comment="#", header=None) - columns = "Coor Free FreeErr Prob ProbErr".split() - df.columns = columns - return df + df = pd.read_csv(fname, sep="\t", comment="#", header=None) + columns = "Coor Free FreeErr Prob ProbErr".split() + df.columns = columns + return df