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sssr fixed. memory usage decreased.
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stsouko committed Feb 26, 2019
1 parent c006de2 commit 4b1ffbb
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Showing 3 changed files with 217 additions and 21 deletions.
41 changes: 21 additions & 20 deletions CGRtools/algorithms/sssr.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -69,8 +69,8 @@ def sssr(self):
if n in next_stack:
next_stack[n].extend(next_broom)
else:
next_broom.extend(stack[n])
terminated[n] = next_stack[n] = next_broom
stack[n].extend(next_broom) # not visited
terminated[n] = stack[n]
elif n in next_stack: # even rings
next_stack[n].extend(next_broom)
if n not in terminated:
Expand All @@ -89,8 +89,8 @@ def sssr(self):
if n in next_stack:
next_stack[n].extend(next_broom)
else:
next_broom.extend(stack[n])
terminated[n] = next_stack[n] = next_broom
stack[n].extend(next_broom) # not visited
terminated[n] = stack[n]
elif n in next_stack: # even rings
next_stack[n].extend(next_broom)
if n not in terminated:
Expand Down Expand Up @@ -145,29 +145,30 @@ def sssr(self):

c_set.append((c_num, p1ij, p2ij))

n_ringidx, c_sssr = 0, {}
c_sssr = {}
for c_num, p1ij, p2ij in sorted(c_set):
if c_num % 2:
if c_num % 2: # odd rings
c1 = p1ij[0]
c11 = c1[1]
c12 = c1[-2]
for c2 in p2ij:
if c11 != c2[1]:
c = c1 + c2[-2:0:-1]
ck = tuple(sorted(c))
if ck not in c_sssr:
c_sssr[ck] = c
n_ringidx += 1
if n_ringidx == n_sssr:
if c11 == c2[1] or c12 == c2[-2]:
continue
c = c1 + c2[-2:0:-1]
ck = tuple(sorted(c))
if ck not in c_sssr:
c_sssr[ck] = c
if len(c_sssr) == n_sssr:
return list(c_sssr.values())
else:
for c1, c2 in zip(p1ij, p1ij[1:]):
if c1[1] != c2[1]:
c = c1 + c2[-2:0:-1]
ck = tuple(sorted(c))
if ck not in c_sssr:
c_sssr[ck] = c
n_ringidx += 1
if n_ringidx == n_sssr:
if c1[1] == c2[1] or c1[-2] == c2[-2]:
continue
c = c1 + c2[-2:0:-1]
ck = tuple(sorted(c))
if ck not in c_sssr:
c_sssr[ck] = c
if len(c_sssr) == n_sssr:
return list(c_sssr.values())


Expand Down
2 changes: 1 addition & 1 deletion setup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@

setup(
name='CGRtools',
version='3.1.1',
version='3.1.2',
packages=['CGRtools', 'CGRtools.algorithms', 'CGRtools.attributes', 'CGRtools.containers', 'CGRtools.files',
'CGRtools.files.dll', 'CGRtools.periodictable', 'CGRtools.utils'],
url='https://github.com/cimm-kzn/CGRtools',
Expand Down
195 changes: 195 additions & 0 deletions test/cycle.sdf
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Original file line number Diff line number Diff line change
Expand Up @@ -325,4 +325,199 @@ $$$$
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$$$$

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