Gitim fix #350

Marcello-Sega · 2021-04-19T12:04:11Z

No description provided.

houndci-bot · 2021-04-19T12:04:18Z

pytim/gitim.py

+                   for atomid in simplices[i]:
+                       close = tree_neighs.query_ball_point(_points[atomid],radii[atomid] 2*self.alpha radii[real_neighs])
+                       if len(close)>0:
+                           cond2[i] = False


indentation is not a multiple of four

houndci-bot · 2021-04-19T12:04:18Z

pytim/gitim.py

+                   # if their centers distance d < 2 alpha   r_s   r_n
+                   for atomid in simplices[i]:
+                       close = tree_neighs.query_ball_point(_points[atomid],radii[atomid] 2*self.alpha radii[real_neighs])
+                       if len(close)>0:


indentation is not a multiple of four
missing whitespace around operator

houndci-bot · 2021-04-19T12:04:18Z

pytim/gitim.py

+                   # will be close to a putative surface one 's' (part of the simplex)
+                   # if their centers distance d < 2 alpha   r_s   r_n
+                   for atomid in simplices[i]:
+                       close = tree_neighs.query_ball_point(_points[atomid],radii[atomid] 2*self.alpha radii[real_neighs])


indentation is not a multiple of four
line too long (122 > 79 characters)
missing whitespace after ','

houndci-bot · 2021-04-19T12:04:18Z

pytim/gitim.py

+                   # An atom 'n' in the neighborhood of the kissing sphere's center
+                   # will be close to a putative surface one 's' (part of the simplex)
+                   # if their centers distance d < 2 alpha   r_s   r_n
+                   for atomid in simplices[i]:


indentation is not a multiple of four

houndci-bot · 2021-04-19T12:04:18Z

pytim/gitim.py

+                   # specify a distance that depends on the radius of the particle.
+                   # An atom 'n' in the neighborhood of the kissing sphere's center
+                   # will be close to a putative surface one 's' (part of the simplex)
+                   # if their centers distance d < 2 alpha   r_s   r_n


indentation is not a multiple of four (comment)

houndci-bot · 2021-04-19T12:04:19Z

pytim/gitim.py

+        # we will now search for those which are also close to the simplex
+        for i,neighbors in enumerate(neigborhoods):
+            if len(neighbors) > 0:
+               real_neighs = list(set(neighbors) - set(simplices[i]))


indentation is not a multiple of four

houndci-bot · 2021-04-19T12:04:19Z

pytim/gitim.py

+        # find all atoms within the kissing sphere to each of the simplices
+        neighborhoods = tree.query_ball_point(x=cc[cond],r=cr[cond])
+        # we will now search for those which are also close to the simplex
+        for i,neighbors in enumerate(neigborhoods):


missing whitespace after ','
undefined name 'neigborhoods'

houndci-bot · 2021-04-19T12:04:19Z

pytim/gitim.py

+            tree = cKDTree(extrapoints[:-8])
+        cond2 =  cond | True # all True, will set them false below
+        # find all atoms within the kissing sphere to each of the simplices
+        neighborhoods = tree.query_ball_point(x=cc[cond],r=cr[cond])


local variable 'neighborhoods' is assigned to but never used
missing whitespace after ','

houndci-bot · 2021-04-19T12:04:19Z

pytim/gitim.py

+            tree = cKDTree(extrapoints)
+        else:
+            tree = cKDTree(extrapoints[:-8])
+        cond2 =  cond | True # all True, will set them false below


at least two spaces before inline comment
multiple spaces after operator

houndci-bot · 2021-04-19T12:04:20Z

pytim/gitim.py

+        if self._noextrapoints:
+            tree = cKDTree(extrapoints)
+        else:
+            tree = cKDTree(extrapoints[:-8])


undefined name 'cKDTree'

houndci-bot · 2021-04-19T15:16:01Z

pytim/gitim.py

+            for atomid in real_neighs:
+                d = linalgnorm(_points[simplices[i]]-tree.data[atomid],axis=1)
+                if np.count_nonzero(d-radii[atomid]-radii[simplices[i]] - 2.*self.alpha<0) > 1:
+                        cond2[i] = False


over-indented

houndci-bot · 2021-04-19T15:16:01Z

pytim/gitim.py

+            real_neighs = list(set(neighbors) -set(neighborhoods2[i])- set(simplices[i]))
+            for atomid in real_neighs:
+                d = linalgnorm(_points[simplices[i]]-tree.data[atomid],axis=1)
+                if np.count_nonzero(d-radii[atomid]-radii[simplices[i]] - 2.*self.alpha<0) > 1:


line too long (95 > 79 characters)
missing whitespace around operator

houndci-bot · 2021-04-19T15:16:01Z

pytim/gitim.py

+            # To be sure, we alse remove points belonging to the kissed simplex as well.
+            real_neighs = list(set(neighbors) -set(neighborhoods2[i])- set(simplices[i]))
+            for atomid in real_neighs:
+                d = linalgnorm(_points[simplices[i]]-tree.data[atomid],axis=1)


missing whitespace after ','

houndci-bot · 2021-04-19T15:16:02Z

pytim/gitim.py

+        for i,neighbors in enumerate(neighborhoods1):
+            # we are not interested in points either too far away from the sphere border.
+            # To be sure, we alse remove points belonging to the kissed simplex as well.
+            real_neighs = list(set(neighbors) -set(neighborhoods2[i])- set(simplices[i]))


line too long (89 > 79 characters)
missing whitespace around operator

houndci-bot · 2021-04-19T15:16:02Z

pytim/gitim.py

+        # we will now search for those which are also close to the simplex
+        for i,neighbors in enumerate(neighborhoods1):
+            # we are not interested in points either too far away from the sphere border.
+            # To be sure, we alse remove points belonging to the kissed simplex as well.


line too long (88 > 79 characters)

houndci-bot · 2021-04-19T15:16:03Z

pytim/gitim.py

+        neighborhoods1 = tree.query_ball_point(x=cc[cond],r=cr[cond])
+        radii2 = cr[cond]-2*self.alpha
+        radii2[radii2<0] = 0.0 # query_ball_point treats negative radii as positive...
+        # if they are within the kissing sphere, but further than 2*alpha from its


line too long (82 > 79 characters)

houndci-bot · 2021-04-19T15:16:03Z

pytim/gitim.py

+        # find all atoms within the kissing sphere to each of the simplices
+        neighborhoods1 = tree.query_ball_point(x=cc[cond],r=cr[cond])
+        radii2 = cr[cond]-2*self.alpha
+        radii2[radii2<0] = 0.0 # query_ball_point treats negative radii as positive...


at least two spaces before inline comment
line too long (86 > 79 characters)
missing whitespace around operator

houndci-bot · 2021-04-19T15:16:03Z

pytim/gitim.py

+            tree = cKDTree(extrapoints[:-8])
+        cond2 =  cond | True # all True, will set them false below
+        # find all atoms within the kissing sphere to each of the simplices
+        neighborhoods1 = tree.query_ball_point(x=cc[cond],r=cr[cond])


missing whitespace after ','

houndci-bot · 2021-04-19T15:16:04Z

pytim/gitim.py

@@ -221,10  223,36 @@ def alpha_shape(self, alpha, group, layer):
        except IndexError:
            raise IndexError("alpha_shape called using a wrong layer")

-        cr = circumradius(_points, radii, simplices)
+        # radii and centers of the kissing spheres
+        cr,cc = circumradius(_points, radii, simplices)


missing whitespace after ','

houndci-bot · 2021-04-19T15:16:04Z

pytim/utilities_dbscan.py

    neighborhoods = np.array([
        np.array(neighbors)
        for neighbors in tree.query_ball_point(points, cluster_cut, n_jobs=-1)
-    ])
+    ],dtype=object)


missing whitespace after ','

houndci-bot · 2021-04-21T12:03:47Z

pytim/gitim.py

@@ -279,6  319,8 @@ def _assign_layers(self):
            alpha_ids = self.alpha_shape(self.alpha, alpha_group, layer)

            group = alpha_group[alpha_ids]
+            if self.surface_cluster_cut is not None:
+                group=self._filter_biggest_surface_cluster(group,self.surface_cluster_cut)


line too long (90 > 79 characters)
missing whitespace after ','
missing whitespace around operator

houndci-bot · 2021-04-21T12:03:47Z

pytim/gitim.py

+            for atomid in real_neighs:
+                d = linalgnorm(_points[simplices[sid][0]]-tree.data[atomid],axis=1)
+                if np.count_nonzero(d-radii[atomid]-radii[simplices[sid][0]] - 2.*self.alpha<0) > 1:
+                        cond2[sid] = False


over-indented

houndci-bot · 2021-04-21T12:03:47Z

pytim/gitim.py

+            real_neighs = list(set(neighbors) -set(neighborhoods2[i])- set(simplices[i]))
+            for atomid in real_neighs:
+                d = linalgnorm(_points[simplices[sid][0]]-tree.data[atomid],axis=1)
+                if np.count_nonzero(d-radii[atomid]-radii[simplices[sid][0]] - 2.*self.alpha<0) > 1:


line too long (100 > 79 characters)
missing whitespace around operator

houndci-bot · 2021-04-21T12:03:47Z

pytim/gitim.py

+            # To be sure, we alse remove points belonging to the kissed simplex as well.
+            real_neighs = list(set(neighbors) -set(neighborhoods2[i])- set(simplices[i]))
+            for atomid in real_neighs:
+                d = linalgnorm(_points[simplices[sid][0]]-tree.data[atomid],axis=1)


line too long (83 > 79 characters)
missing whitespace after ','

houndci-bot · 2021-04-21T12:03:48Z

pytim/gitim.py

+                                    to filter out cavitating bubbles.
+        :param float surface_cluster_cut: Filter surface atoms/molecules 
+                                    to include only those in the largest cluster
+                                    of (initially detected) surface ones. Useful


line too long (80 > 79 characters)

houndci-bot · 2021-04-21T12:03:48Z

pytim/gitim.py

@@ -58,6  60,16 @@ class GITIM(Interface):
        :param bool biggest_cluster_only: Tag as surface atoms/molecules only
                                    those in the largest cluster. Need to
                                    specify also a :py:obj:`cluster_cut` value.
+        :param bool biggest_surface_cluster_only: Filter surface atoms/molecules 
+                                    to include only those in the largest cluster


line too long (80 > 79 characters)

houndci-bot · 2021-04-21T12:03:48Z

pytim/gitim.py

@@ -58,6  60,16 @@ class GITIM(Interface):
        :param bool biggest_cluster_only: Tag as surface atoms/molecules only
                                    those in the largest cluster. Need to
                                    specify also a :py:obj:`cluster_cut` value.
+        :param bool biggest_surface_cluster_only: Filter surface atoms/molecules 


line too long (80 > 79 characters)
trailing whitespace

houndci-bot · 2021-04-21T12:03:49Z

pytim/interface.py

+        l,c,n = utilities.do_cluster_analysis_dbscan(
+                group, cut,
+                molecular=False)
+        return group[np.where(l == np.argmax(c))[0]]


ambiguous variable name 'l'

houndci-bot · 2021-04-21T12:03:49Z

pytim/interface.py

@@ -145,6  145,12 @@ def _assign_symmetry(self, symmetry):
                raise ValueError(messages.WRONG_DIRECTION)
            self.symmetry = symmetry

+    def _filter_biggest_surface_cluster(self,group,cut):
+        l,c,n = utilities.do_cluster_analysis_dbscan(


missing whitespace after ','

houndci-bot · 2021-04-21T12:03:49Z

pytim/interface.py

@@ -145,6  145,12 @@ def _assign_symmetry(self, symmetry):
                raise ValueError(messages.WRONG_DIRECTION)
            self.symmetry = symmetry

+    def _filter_biggest_surface_cluster(self,group,cut):


missing whitespace after ','

Fix numpy warning

de818f5

houndci-bot reviewed Apr 19, 2021

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Marcello-Sega force-pushed the gitim-fix branch from 65152a5 to e337670 Compare April 19, 2021 15:15

houndci-bot reviewed Apr 19, 2021

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Marcello-Sega and others added 2 commits April 21, 2021 14:02

GITIM: kissing sphere test fix

4f3fc23

filtering surface-atoms clusters

ffe83f7

Marcello-Sega force-pushed the gitim-fix branch from e337670 to ffe83f7 Compare April 21, 2021 12:03

houndci-bot reviewed Apr 21, 2021

View reviewed changes

Merge branch 'master' into gitim-fix

e64da9f

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Gitim fix #350

Gitim fix #350

Marcello-Sega commented Apr 19, 2021

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Gitim fix #350

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Gitim fix #350

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Marcello-Sega commented Apr 19, 2021

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