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donerancldonerancl
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remove unnecessary try-except
1 parent 3559562 commit 69142c4

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Lines changed: 104 additions & 109 deletions

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‎rmgpy/molecule/fragment.py‎

Lines changed: 104 additions & 109 deletions
Original file line numberDiff line numberDiff line change
@@ -947,71 +947,69 @@ def sliceitup_arom(self, molecule, size_threshold=5):
947947
# mol_set contains new set of fragments
948948
mol_set = Chem.GetMolFrags(new_mol, asMols=True)
949949
# check all fragments' size
950-
try:
951-
if all(sum(1 for atom in mol.GetAtoms() if atom.GetAtomicNum() == 6) >= size_threshold for mol in mol_set):
952-
if len(mol_set) == 2:
953-
frag1 = Chem.MolToSmiles(mol_set[0])
954-
frag2 = Chem.MolToSmiles(mol_set[1])
955-
956-
frag1_R = frag1.count("Na")
957-
frag1_L = frag1.count("K")
958-
frag2_R = frag2.count("Na")
959-
frag2_L = frag2.count("K")
960-
961-
# if frag 2 has the least Rs and frag 1 has the
962-
# same or fewer Ls than frag 2 -->
963-
# assign R to frag 2 and L to frag 1
964-
if frag1_R > frag2_R and frag1_L <= frag2_L:
965-
frag1_smi = frag1.replace("*", "L")
966-
frag2_smi = frag2.replace("*", "R")
967-
968-
# if frag 2 has the least Ls and frag 1 has the
969-
# same or fewer Rs than frag 2 -->
970-
# assign R to frag 1 and L to frag 2
971-
elif frag1_L > frag2_L and frag1_R <= frag2_R:
972-
frag1_smi = frag1.replace("*", "R")
973-
frag2_smi = frag2.replace("*", "L")
974-
975-
# if frag 1 has the least Ls and frag 2 has the
976-
# same or fewer Rs than frag 1 -->
977-
# assign R to frag 2 and L to frag 1
978-
elif frag2_L > frag1_L and frag2_R <= frag1_R:
979-
frag1_smi = frag1.replace("*", "L")
980-
frag2_smi = frag2.replace("*", "R")
981-
982-
# if frag 1 has the least Rs and frag 2 has the
983-
# same or fewer Ls than frag 1 -->
984-
# assign R to frag 1 and L to frag 2
985-
elif frag2_R > frag1_R and frag2_L <= frag1_L:
986-
frag1_smi = frag1.replace("*", "R")
987-
frag2_smi = frag2.replace("*", "L")
988-
989-
# else if frag 1 and frag 2 have equal number
990-
# of Rs and Ls or one frag has more Rs and
991-
# more Ls than the other, choose randomly
992-
elif randint(0, 1) == 1:
993-
frag1_smi = frag1.replace("*", "L")
994-
frag2_smi = frag2.replace("*", "R")
950+
951+
if all(sum(1 for atom in mol.GetAtoms() if atom.GetAtomicNum() == 6) >= size_threshold for mol in mol_set):
952+
if len(mol_set) == 2:
953+
frag1 = Chem.MolToSmiles(mol_set[0])
954+
frag2 = Chem.MolToSmiles(mol_set[1])
955+
956+
frag1_R = frag1.count("Na")
957+
frag1_L = frag1.count("K")
958+
frag2_R = frag2.count("Na")
959+
frag2_L = frag2.count("K")
960+
961+
# if frag 2 has the least Rs and frag 1 has the
962+
# same or fewer Ls than frag 2 -->
963+
# assign R to frag 2 and L to frag 1
964+
if frag1_R > frag2_R and frag1_L <= frag2_L:
965+
frag1_smi = frag1.replace("*", "L")
966+
frag2_smi = frag2.replace("*", "R")
967+
968+
# if frag 2 has the least Ls and frag 1 has the
969+
# same or fewer Rs than frag 2 -->
970+
# assign R to frag 1 and L to frag 2
971+
elif frag1_L > frag2_L and frag1_R <= frag2_R:
972+
frag1_smi = frag1.replace("*", "R")
973+
frag2_smi = frag2.replace("*", "L")
974+
975+
# if frag 1 has the least Ls and frag 2 has the
976+
# same or fewer Rs than frag 1 -->
977+
# assign R to frag 2 and L to frag 1
978+
elif frag2_L > frag1_L and frag2_R <= frag1_R:
979+
frag1_smi = frag1.replace("*", "L")
980+
frag2_smi = frag2.replace("*", "R")
981+
982+
# if frag 1 has the least Rs and frag 2 has the
983+
# same or fewer Ls than frag 1 -->
984+
# assign R to frag 1 and L to frag 2
985+
elif frag2_R > frag1_R and frag2_L <= frag1_L:
986+
frag1_smi = frag1.replace("*", "R")
987+
frag2_smi = frag2.replace("*", "L")
988+
989+
# else if frag 1 and frag 2 have equal number
990+
# of Rs and Ls or one frag has more Rs and
991+
# more Ls than the other, choose randomly
992+
elif randint(0, 1) == 1:
993+
frag1_smi = frag1.replace("*", "L")
994+
frag2_smi = frag2.replace("*", "R")
995+
else:
996+
frag1_smi = frag1.replace("*", "R")
997+
frag2_smi = frag2.replace("*", "L")
998+
999+
frag_list = [frag1_smi, frag2_smi]
1000+
1001+
elif len(mol_set) > 2: # means it cut into 3 fragments
1002+
frag_list = []
1003+
for ind, rdmol in enumerate(mol_set):
1004+
frag = Chem.MolToSmiles(rdmol)
1005+
if frag.count("*") > 1:
1006+
frag_smi = frag.replace("*", "R")
9951007
else:
996-
frag1_smi = frag1.replace("*", "R")
997-
frag2_smi = frag2.replace("*", "L")
998-
999-
frag_list = [frag1_smi, frag2_smi]
1000-
1001-
elif len(mol_set) > 2: # means it cut into 3 fragments
1002-
frag_list = []
1003-
for ind, rdmol in enumerate(mol_set):
1004-
frag = Chem.MolToSmiles(rdmol)
1005-
if frag.count("*") > 1:
1006-
frag_smi = frag.replace("*", "R")
1007-
else:
1008-
frag_smi = frag.replace("*", "L")
1009-
frag_list.append(frag_smi)
1010-
break
1011-
else:
1012-
# turn to next matched_atom_map
1013-
continue
1014-
except:
1008+
frag_smi = frag.replace("*", "L")
1009+
frag_list.append(frag_smi)
1010+
break
1011+
else:
1012+
# turn to next matched_atom_map
10151013
continue
10161014
else:
10171015
# no match for this pattern
@@ -1113,52 +1111,49 @@ def sliceitup_aliph(self, molecule, size_threshold=5):
11131111
# mol_set contains new set of fragments
11141112
mol_set = Chem.GetMolFrags(new_mol, asMols=True)
11151113
# check all fragments' size
1116-
try:
1117-
if all(sum(1 for atom in mol.GetAtoms() if atom.GetAtomicNum() == 6) >= size_threshold for mol in mol_set):
1118-
if len(mol_set) == 2:
1119-
frag1 = Chem.MolToSmiles(mol_set[0])
1120-
frag2 = Chem.MolToSmiles(mol_set[1])
1121-
1122-
frag1_R = frag1.count("Na")
1123-
frag1_L = frag1.count("K")
1124-
frag2_R = frag2.count("Na")
1125-
frag2_L = frag2.count("K")
1126-
1127-
if frag1_R > frag2_R and frag1_L <= frag2_L:
1128-
frag1_smi = frag1.replace("*", "L")
1129-
frag2_smi = frag2.replace("*", "R")
1130-
elif frag1_L > frag2_L and frag1_R <= frag2_R:
1131-
frag1_smi = frag1.replace("*", "R")
1132-
frag2_smi = frag2.replace("*", "L")
1133-
elif frag2_L > frag1_L and frag2_R <= frag1_R:
1134-
frag1_smi = frag1.replace("*", "L")
1135-
frag2_smi = frag2.replace("*", "R")
1136-
elif frag2_R > frag1_R and frag2_L <= frag1_L:
1137-
frag1_smi = frag1.replace("*", "R")
1138-
frag2_smi = frag2.replace("*", "L")
1139-
elif randint(0,1)==1:
1140-
frag1_smi = frag1.replace("*", "L")
1141-
frag2_smi = frag2.replace("*", "R")
1114+
if all(sum(1 for atom in mol.GetAtoms() if atom.GetAtomicNum() == 6) >= size_threshold for mol in mol_set):
1115+
if len(mol_set) == 2:
1116+
frag1 = Chem.MolToSmiles(mol_set[0])
1117+
frag2 = Chem.MolToSmiles(mol_set[1])
1118+
1119+
frag1_R = frag1.count("Na")
1120+
frag1_L = frag1.count("K")
1121+
frag2_R = frag2.count("Na")
1122+
frag2_L = frag2.count("K")
1123+
1124+
if frag1_R > frag2_R and frag1_L <= frag2_L:
1125+
frag1_smi = frag1.replace("*", "L")
1126+
frag2_smi = frag2.replace("*", "R")
1127+
elif frag1_L > frag2_L and frag1_R <= frag2_R:
1128+
frag1_smi = frag1.replace("*", "R")
1129+
frag2_smi = frag2.replace("*", "L")
1130+
elif frag2_L > frag1_L and frag2_R <= frag1_R:
1131+
frag1_smi = frag1.replace("*", "L")
1132+
frag2_smi = frag2.replace("*", "R")
1133+
elif frag2_R > frag1_R and frag2_L <= frag1_L:
1134+
frag1_smi = frag1.replace("*", "R")
1135+
frag2_smi = frag2.replace("*", "L")
1136+
elif randint(0,1)==1:
1137+
frag1_smi = frag1.replace("*", "L")
1138+
frag2_smi = frag2.replace("*", "R")
1139+
else:
1140+
frag1_smi = frag1.replace("*", "R")
1141+
frag2_smi = frag2.replace("*", "L")
1142+
1143+
frag_list = [frag1_smi, frag2_smi]
1144+
1145+
elif len(mol_set) > 2: # means it cut into 3 fragments
1146+
frag_list = []
1147+
for ind, rdmol in enumerate(mol_set):
1148+
frag = Chem.MolToSmiles(rdmol)
1149+
if frag.count("*") > 1:
1150+
frag_smi = frag.replace("*", "R")
11421151
else:
1143-
frag1_smi = frag1.replace("*", "R")
1144-
frag2_smi = frag2.replace("*", "L")
1145-
1146-
frag_list = [frag1_smi, frag2_smi]
1147-
1148-
elif len(mol_set) > 2: # means it cut into 3 fragments
1149-
frag_list = []
1150-
for ind, rdmol in enumerate(mol_set):
1151-
frag = Chem.MolToSmiles(rdmol)
1152-
if frag.count("*") > 1:
1153-
frag_smi = frag.replace("*", "R")
1154-
else:
1155-
frag_smi = frag.replace("*", "L")
1156-
frag_list.append(frag_smi)
1157-
break
1158-
else:
1159-
# turn to next matched_atom_map
1160-
continue
1161-
except:
1152+
frag_smi = frag.replace("*", "L")
1153+
frag_list.append(frag_smi)
1154+
break
1155+
else:
1156+
# turn to next matched_atom_map
11621157
continue
11631158
else:
11641159
# no match for this pattern

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