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Merge pull request #26 from gruenewald-lab/cg_charges
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have cg charges
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@fgrunewald
fgrunewald authored Oct 16, 2024
2 parents 3465bea + d1616f0 commit e398f3d
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12 changes: 11 additions & 1 deletion cgsmiles/read_cgsmiles.py
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Original file line number Diff line number Diff line change
Expand Up @@ -185,6 +185,16 @@ def read_cgsmiles(pattern):
# the fragname starts at the second character and ends
# one before the last according to the above pattern
fragname = match.group(0)[2:-1]
# check for charge
charge = 0.0
for sign in ["+", "-"]:
if sign in fragname:
fragname, charge = fragname.split(sign)
if len(charge) == 0:
charge = float(sign+"1")
else:
charge = float(sign+charge)

# if this residue is part of a branch we store it in
# the recipe dict together with the anchor residue
# and expansion number
Expand All @@ -194,7 +204,7 @@ def read_cgsmiles(pattern):
# new we add new residue as often as required
connection = []
for _ in range(0, n_mon):
mol_graph.add_node(current, fragname=fragname)
mol_graph.add_node(current, fragname=fragname, charge=charge)

if prev_node is not None:
mol_graph.add_edge(prev_node, current, order=1)
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31 changes: 29 additions & 2 deletions cgsmiles/tests/test_cgsmile_parsing.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,50 +3,65 @@
from cgsmiles import read_cgsmiles
from cgsmiles.read_fragments import strip_bonding_descriptors, fragment_iter

@pytest.mark.parametrize('smile, nodes, edges, orders',(
@pytest.mark.parametrize('smile, nodes, charges, edges, orders',(
# smiple linear sequence
("{[#PMA][#PEO][#PMA]}",
["PMA", "PEO", "PMA"],
None,
[(0, 1), (1, 2)],
[1, 1]),
# smiple charges
("{[#PMA+][#PEO][#PMA-0.25]}",
["PMA", "PEO", "PMA"],
{0: 1.0, 1: 0.0, 2:-0.25},
[(0, 1), (1, 2)],
[1, 1]),
# smiple linear sequenece with multi-edge
("{[#PMA]1[#PEO]1}",
["PMA", "PEO"],
None,
[(0, 1)],
[2]),
# simple branched sequence
("{[#PMA][#PMA]([#PEO][#PEO])[#PMA]}",
["PMA", "PMA", "PEO", "PEO", "PMA"],
None,
[(0, 1), (1, 2), (2, 3), (1, 4)],
[1, 1, 1, 1]),
# simple sequence two branches
("{[#PMA][#PMA][#PMA]([#PEO][#PEO])([#CH3])[#PMA]}",
["PMA", "PMA", "PMA", "PEO", "PEO", "CH3", "PMA"],
None,
[(0, 1), (1, 2), (2, 3), (3, 4), (2, 5), (2, 6)],
[1, 1, 1, 1, 1, 1]),
# simple linear sequence with expansion
("{[#PMA]|3}",
["PMA", "PMA", "PMA"],
None,
[(0, 1), (1, 2)],
[1, 1]),
# smiple cycle sequence
("{[#PMA]1[#PEO][#PMA]1}",
["PMA", "PEO", "PMA"],
None,
[(0, 1), (1, 2), (0, 2)],
[1, 1, 1]),
# smiple cycle sequence with %
("{[#PMA]%123[#PEO][#PMA]%123}",
["PMA", "PEO", "PMA"],
None,
[(0, 1), (1, 2), (0, 2)],
[1, 1, 1]),
# complex cycle
("{[#PMA]1[#PEO]2[#PMA]1[#PEO]2}",
["PMA", "PEO", "PMA", "PEO"],
None,
[(0, 1), (1, 2), (0, 2), (1, 3), (2, 3)],
[1, 1, 1, 1, 1]),
# complex cycle with %
("{[#PMA]%134[#PEO]%256[#PMA]%134[#PEO]%256}",
["PMA", "PEO", "PMA", "PEO"],
None,
[(0, 1), (1, 2), (0, 2), (1, 3), (2, 3)],
[1, 1, 1, 1, 1]),
# # complex cycle with three times same ID
Expand All @@ -59,13 +74,15 @@
# in cycle
("{[#PMA]12[#PMA][#PMA][#PEO]12}",
["PMA", "PMA", "PMA", "PEO"],
None,
[(0, 1), (1, 2), (2, 3), (0, 3)],
[1, 1, 1, 2]),
# simple branch expension
("{[#PMA]([#PEO][#PEO][#OHter])|3}",
["PMA", "PEO", "PEO", "OHter",
"PMA", "PEO", "PEO", "OHter",
"PMA", "PEO", "PEO", "OHter"],
None,
[(0, 1), (1, 2), (2, 3),
(0, 4), (4, 5), (5, 6), (6, 7),
(4, 8), (8, 9), (9, 10), (10, 11)],
Expand All @@ -74,6 +91,7 @@
("{[#PMA]([#PEO]|3)|2}",
["PMA", "PEO", "PEO", "PEO",
"PMA", "PEO", "PEO", "PEO"],
None,
[(0, 1), (1, 2), (2, 3),
(0, 4), (4, 5), (5, 6), (6, 7)],
[1, 1, 1, 1, 1, 1, 1]),
Expand All @@ -82,6 +100,7 @@
("{[#PMA][#PMA]([#PEO][#PEO]([#OH])[#PEO])[#PMA]}",
["PMA", "PMA", "PEO", "PEO", "OH",
"PEO", "PMA"],
None,
[(0, 1), (1, 2), (2, 3),
(3, 4), (3, 5), (1, 6)],
[1, 1, 1, 1, 1, 1]),
Expand All @@ -90,6 +109,7 @@
("{[#PMA][#PMA]([#PEO][#PEO]([#OH]|2)[#PEO])[#PMA]}",
["PMA", "PMA", "PEO", "PEO", "OH", "OH",
"PEO", "PMA"],
None,
[(0, 1), (1, 2), (2, 3),
(3, 4), (4, 5), (3, 6), (1, 7)],
[1, 1, 1, 1, 1, 1, 1]),
Expand All @@ -99,6 +119,7 @@
("{[#PMA][#PMA]([#PEO][#PEO]([#OH])[#PEO])|2[#PMA]}",
["PMA", "PMA", "PEO", "PEO", "OH", "PEO",
"PMA", "PEO", "PEO", "PEO", "OH", "PMA"],
None,
[(0, 1), (1, 2), (2, 3),
(3, 4), (3, 5), (1, 6), (6, 7), (7, 8),
(8, 9), (8, 10), (6, 11)],
Expand All @@ -115,6 +136,7 @@
("{[#PMA][#PMA]([#PEO][#PQ]([#OH])|3[#PEO])[#PMA]}",
["PMA", "PMA", "PEO", "PQ", "OH",
"PQ", "OH", "PQ", "OH", "PEO", "PMA"],
None,
[(0, 1), (1, 2), (1, 10),
(2, 3), (3, 4), (3, 5), (5, 6),
(5, 7), (7, 8), (7, 9)],
Expand All @@ -134,12 +156,13 @@
("{[#PMA][#PMA]([#PEO][#PQ]([#OH])|3[#PEO])[#PMA]([#CH3])|2}",
["PMA", "PMA", "PEO", "PQ", "OH",
"PQ", "OH", "PQ", "OH", "PEO", "PMA", "CH3", "PMA", "CH3"],
None,
[(0, 1), (1, 2), (1, 10),
(2, 3), (3, 4), (3, 5), (5, 6),
(5, 7), (7, 8), (7, 9), (10, 11), (10, 12), (12, 13)],
[1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]),
))
def test_read_cgsmiles(smile, nodes, edges, orders):
def test_read_cgsmiles(smile, nodes, charges, edges, orders):
"""
Test that the meta-molecule is correctly reproduced
from the simplified smile string syntax.
Expand All @@ -153,6 +176,10 @@ def test_read_cgsmiles(smile, nodes, edges, orders):
fragnames = nx.get_node_attributes(meta_mol, 'fragname')
assert nodes == list(fragnames.values())

if charges:
set_charges = nx.get_node_attributes(meta_mol, 'charge')
assert set_charges == charges

@pytest.mark.parametrize('big_smile, smile, bonding, rs, ez',(
# smiple symmetric bonding
("[$]COC[$]",
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