knn default

Author: Carlos Hernandez

mdentropy/cli/dmutinf.py

@@ -37,7 +37,7 @@ def configure_parser(sub_parsers):
     p.add_argument('-t', '--topology', dest='top',
                    help='File containing topology.', default=None)
     p.add_argument('-b', '--n-bins', dest='nbins',
-                   help='Number of bins', default=30, type=int)
+                   help='Number of bins', default=3, type=int)
     p.add_argument('-n', '--n-threads', dest='n_threads',
                    help='Number of threads to be used.',
                    default=None, type=int)
@@ -49,7 +49,7 @@ def configure_parser(sub_parsers):
                    help='Entropy estimate method.',
                    choices=['chaowangjost', 'grassberger', 'kde',
                             'knn', 'naive'],
-                   default='grassberger')
+                   default='knn')
     p.add_argument('-d', '--dihedrals', dest='dihedrals',
                    help='Dihedral angles to analyze.',
                    nargs='+',

mdentropy/cli/dtent.py

@@ -44,7 +44,7 @@ def configure_parser(sub_parsers):
                    dest='top', help='File containing topology.',
                    default=None)
     p.add_argument('-b', '--n-bins', dest='nbins',
-                   help='Number of bins', default=30, type=int)
+                   help='Number of bins', default=3, type=int)
     p.add_argument('-n', '--n-threads', dest='N',
                    help='Number of threads', default=None, type=int)
     p.add_argument('-o', '--output', dest='out',
@@ -53,7 +53,7 @@ def configure_parser(sub_parsers):
                    help='Entropy estimate method.',
                    choices=['chaowangjost', 'grassberger', 'kde',
                             'knn', 'naive'],
-                   default='grassberger')
+                   default='knn')
     p.add_argument('-d', '--dihedrals', dest='dihedrals',
                    help='Dihedral angles to analyze.',
                    nargs='+',

mdentropy/core/entropy.py

@@ -68,10 +68,9 @@ def entropy(n_bins, rng, method, *args):
     return naive(counts)
 
 
-def centropy(n_bins, x, y, rng=None, method='grassberger'):
+def centropy(n_bins, x, y, rng=None, method='knn'):
     """Conditional entropy calculation
 
-
     Parameters
     ----------
     n_bins : int

mdentropy/core/information.py

@@ -10,7 +10,7 @@
 EPS = finfo(float32).eps
 
 
-def mutinf(n_bins, x, y, rng=None, method='grassberger'):
+def mutinf(n_bins, x, y, rng=None, method='knn'):
     """Mutual information calculation
 
     Parameters
@@ -70,7 +70,7 @@ def knn_mutinf(x, y, k=None, boxsize=None):
     return (-a - b + c + d)
 
 
-def nmutinf(n_bins, x, y, rng=None, method='grassberger'):
+def nmutinf(n_bins, x, y, rng=None, method='knn'):
     """Normalized mutual information calculation
 
     Parameters
@@ -95,7 +95,7 @@ def nmutinf(n_bins, x, y, rng=None, method='grassberger'):
                       entropy(n_bins, [rng], method, y)))
 
 
-def cmutinf(n_bins, x, y, z, rng=None, method='grassberger'):
+def cmutinf(n_bins, x, y, z, rng=None, method='knn'):
     """Conditional mutual information calculation
 
     Parameters
@@ -159,7 +159,7 @@ def knn_cmutinf(x, y, z, k=None, boxsize=None):
     return (-a - b + c + d)
 
 
-def ncmutinf(n_bins, x, y, z, rng=None, method='grassberger'):
+def ncmutinf(n_bins, x, y, z, rng=None, method='knn'):
     """Normalized conditional mutual information calculation
 
     Parameters