Replace numpy in1d usage with numpy.isin (#503)

Replaced numpy in1d() with isin()

Author: Marcello-Sega

pytim/interface.py

@@ -8,6 +8,10 @@
 from . import utilities
 from scipy.spatial import cKDTree
 
+from .patches import patchNumpy_isin
+
+patchNumpy_isin()
+    
 
 class Interface(object):
     """ The Interface metaclass. Classes for interfacial determination
@@ -670,8 +674,8 @@ def __():
         ...     #interface.writepdb(method.__name__+'.pdb') ; # debug
         ...     cond = (ref_ind == ind )
         ...     if np.all(cond) ==  False:
-        ...         miss1 = (np.in1d(ref_ind,ind)==False).sum()
-        ...         miss2 = (np.in1d(ind,ref_ind)==False).sum()
+        ...         miss1 = (~np.isin(ref_ind, ind)).sum()
+        ...         miss2 = (~np.isin(ind, ref_ind)).sum()
         ...         percent = (miss1 + miss2)*0.5/len(ref_ind) * 100.
         ...         if percent > 2: # this should be 0 for ITIM, and < 5
         ...                         # for GITIM, with this config+alpha
@@ -707,8 +711,8 @@ def __():
         ...     #interface.writepdb(method.__name__+'.pdb') ; # debug
         ...     cond = (ref_ind == ind )
         ...     if np.all(cond) ==  False:
-        ...         miss1 = (np.in1d(ref_ind,ind)==False).sum()
-        ...         miss2 = (np.in1d(ind,ref_ind)==False).sum()
+        ...         miss1 = (~np.isin(ref_ind, ind)).sum()
+        ...         miss2 = (~np.isin(ind, ref_ind)).sum()
         ...         percent = (miss1 + miss2)*0.5/len(ref_ind) * 100.
         ...         if percent > 4 : # should be ~ 4 % for this system
         ...             print (miss1+miss2)

pytim/itim.py

@@ -21,8 +21,9 @@
 from .sanity_check import SanityCheck
 
 from .interface import Interface
-from .patches import patchTrajectory, patchOpenMM, patchMDTRAJ
+from .patches import patchTrajectory, patchOpenMM, patchMDTRAJ, patchNumpy_isin
 
+patchNumpy_isin()
 
 class ITIM(Interface):
     """ Identifies interfacial molecules at macroscopically flat interfaces.
@@ -278,7 +279,7 @@ def _append_layers(self, uplow, layer, layers):
             # NOTE that from MDAnalysis 0.16, .ids runs from 1->N
             # (was 0->N-1 in 0.15), we use now .indices
             indices = np.flatnonzero(
-                np.in1d(self.cluster_group.atoms.indices,
+                np.isin(self.cluster_group.atoms.indices,
                         inlayer_group.atoms.indices))
             # and update the tagged, sorted atoms
             self._seen[uplow][indices] = layer + 1

pytim/patches.py

@@ -1,6 +1,10 @@
 # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding: utf-8 -*-
 # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
 from __future__ import print_function
+import numpy as np
+def patchNumpy_isin():
+    try: np.isin
+    except AttributeError: np.isin = np.in1d
 
 def patchTrajectory(trajectory, interface):
     """ Patch the MDAnalysis trajectory class