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donerancldonerancl
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remove unnecessary try-except
1 parent a4903a2 commit ed469f2

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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
@@ -945,71 +945,69 @@ def sliceitup_arom(self, molecule, size_threshold=5):
945945
# mol_set contains new set of fragments
946946
mol_set = Chem.GetMolFrags(new_mol, asMols=True)
947947
# check all fragments' size
948-
try:
949-
if all(sum(1 for atom in mol.GetAtoms() if atom.GetAtomicNum() == 6) >= size_threshold for mol in mol_set):
950-
if len(mol_set) == 2:
951-
frag1 = Chem.MolToSmiles(mol_set[0])
952-
frag2 = Chem.MolToSmiles(mol_set[1])
953-
954-
frag1_R = frag1.count("Na")
955-
frag1_L = frag1.count("K")
956-
frag2_R = frag2.count("Na")
957-
frag2_L = frag2.count("K")
958-
959-
# if frag 2 has the least Rs and frag 1 has the
960-
# same or fewer Ls than frag 2 -->
961-
# assign R to frag 2 and L to frag 1
962-
if frag1_R > frag2_R and frag1_L <= frag2_L:
963-
frag1_smi = frag1.replace("*", "L")
964-
frag2_smi = frag2.replace("*", "R")
965-
966-
# if frag 2 has the least Ls and frag 1 has the
967-
# same or fewer Rs than frag 2 -->
968-
# assign R to frag 1 and L to frag 2
969-
elif frag1_L > frag2_L and frag1_R <= frag2_R:
970-
frag1_smi = frag1.replace("*", "R")
971-
frag2_smi = frag2.replace("*", "L")
972-
973-
# if frag 1 has the least Ls and frag 2 has the
974-
# same or fewer Rs than frag 1 -->
975-
# assign R to frag 2 and L to frag 1
976-
elif frag2_L > frag1_L and frag2_R <= frag1_R:
977-
frag1_smi = frag1.replace("*", "L")
978-
frag2_smi = frag2.replace("*", "R")
979-
980-
# if frag 1 has the least Rs and frag 2 has the
981-
# same or fewer Ls than frag 1 -->
982-
# assign R to frag 1 and L to frag 2
983-
elif frag2_R > frag1_R and frag2_L <= frag1_L:
984-
frag1_smi = frag1.replace("*", "R")
985-
frag2_smi = frag2.replace("*", "L")
986-
987-
# else if frag 1 and frag 2 have equal number
988-
# of Rs and Ls or one frag has more Rs and
989-
# more Ls than the other, choose randomly
990-
elif randint(0, 1) == 1:
991-
frag1_smi = frag1.replace("*", "L")
992-
frag2_smi = frag2.replace("*", "R")
948+
949+
if all(sum(1 for atom in mol.GetAtoms() if atom.GetAtomicNum() == 6) >= size_threshold for mol in mol_set):
950+
if len(mol_set) == 2:
951+
frag1 = Chem.MolToSmiles(mol_set[0])
952+
frag2 = Chem.MolToSmiles(mol_set[1])
953+
954+
frag1_R = frag1.count("Na")
955+
frag1_L = frag1.count("K")
956+
frag2_R = frag2.count("Na")
957+
frag2_L = frag2.count("K")
958+
959+
# if frag 2 has the least Rs and frag 1 has the
960+
# same or fewer Ls than frag 2 -->
961+
# assign R to frag 2 and L to frag 1
962+
if frag1_R > frag2_R and frag1_L <= frag2_L:
963+
frag1_smi = frag1.replace("*", "L")
964+
frag2_smi = frag2.replace("*", "R")
965+
966+
# if frag 2 has the least Ls and frag 1 has the
967+
# same or fewer Rs than frag 2 -->
968+
# assign R to frag 1 and L to frag 2
969+
elif frag1_L > frag2_L and frag1_R <= frag2_R:
970+
frag1_smi = frag1.replace("*", "R")
971+
frag2_smi = frag2.replace("*", "L")
972+
973+
# if frag 1 has the least Ls and frag 2 has the
974+
# same or fewer Rs than frag 1 -->
975+
# assign R to frag 2 and L to frag 1
976+
elif frag2_L > frag1_L and frag2_R <= frag1_R:
977+
frag1_smi = frag1.replace("*", "L")
978+
frag2_smi = frag2.replace("*", "R")
979+
980+
# if frag 1 has the least Rs and frag 2 has the
981+
# same or fewer Ls than frag 1 -->
982+
# assign R to frag 1 and L to frag 2
983+
elif frag2_R > frag1_R and frag2_L <= frag1_L:
984+
frag1_smi = frag1.replace("*", "R")
985+
frag2_smi = frag2.replace("*", "L")
986+
987+
# else if frag 1 and frag 2 have equal number
988+
# of Rs and Ls or one frag has more Rs and
989+
# more Ls than the other, choose randomly
990+
elif randint(0, 1) == 1:
991+
frag1_smi = frag1.replace("*", "L")
992+
frag2_smi = frag2.replace("*", "R")
993+
else:
994+
frag1_smi = frag1.replace("*", "R")
995+
frag2_smi = frag2.replace("*", "L")
996+
997+
frag_list = [frag1_smi, frag2_smi]
998+
999+
elif len(mol_set) > 2: # means it cut into 3 fragments
1000+
frag_list = []
1001+
for ind, rdmol in enumerate(mol_set):
1002+
frag = Chem.MolToSmiles(rdmol)
1003+
if frag.count("*") > 1:
1004+
frag_smi = frag.replace("*", "R")
9931005
else:
994-
frag1_smi = frag1.replace("*", "R")
995-
frag2_smi = frag2.replace("*", "L")
996-
997-
frag_list = [frag1_smi, frag2_smi]
998-
999-
elif len(mol_set) > 2: # means it cut into 3 fragments
1000-
frag_list = []
1001-
for ind, rdmol in enumerate(mol_set):
1002-
frag = Chem.MolToSmiles(rdmol)
1003-
if frag.count("*") > 1:
1004-
frag_smi = frag.replace("*", "R")
1005-
else:
1006-
frag_smi = frag.replace("*", "L")
1007-
frag_list.append(frag_smi)
1008-
break
1009-
else:
1010-
# turn to next matched_atom_map
1011-
continue
1012-
except:
1006+
frag_smi = frag.replace("*", "L")
1007+
frag_list.append(frag_smi)
1008+
break
1009+
else:
1010+
# turn to next matched_atom_map
10131011
continue
10141012
else:
10151013
# no match for this pattern
@@ -1111,52 +1109,49 @@ def sliceitup_aliph(self, molecule, size_threshold=5):
11111109
# mol_set contains new set of fragments
11121110
mol_set = Chem.GetMolFrags(new_mol, asMols=True)
11131111
# check all fragments' size
1114-
try:
1115-
if all(sum(1 for atom in mol.GetAtoms() if atom.GetAtomicNum() == 6) >= size_threshold for mol in mol_set):
1116-
if len(mol_set) == 2:
1117-
frag1 = Chem.MolToSmiles(mol_set[0])
1118-
frag2 = Chem.MolToSmiles(mol_set[1])
1119-
1120-
frag1_R = frag1.count("Na")
1121-
frag1_L = frag1.count("K")
1122-
frag2_R = frag2.count("Na")
1123-
frag2_L = frag2.count("K")
1124-
1125-
if frag1_R > frag2_R and frag1_L <= frag2_L:
1126-
frag1_smi = frag1.replace("*", "L")
1127-
frag2_smi = frag2.replace("*", "R")
1128-
elif frag1_L > frag2_L and frag1_R <= frag2_R:
1129-
frag1_smi = frag1.replace("*", "R")
1130-
frag2_smi = frag2.replace("*", "L")
1131-
elif frag2_L > frag1_L and frag2_R <= frag1_R:
1132-
frag1_smi = frag1.replace("*", "L")
1133-
frag2_smi = frag2.replace("*", "R")
1134-
elif frag2_R > frag1_R and frag2_L <= frag1_L:
1135-
frag1_smi = frag1.replace("*", "R")
1136-
frag2_smi = frag2.replace("*", "L")
1137-
elif randint(0,1)==1:
1138-
frag1_smi = frag1.replace("*", "L")
1139-
frag2_smi = frag2.replace("*", "R")
1112+
if all(sum(1 for atom in mol.GetAtoms() if atom.GetAtomicNum() == 6) >= size_threshold for mol in mol_set):
1113+
if len(mol_set) == 2:
1114+
frag1 = Chem.MolToSmiles(mol_set[0])
1115+
frag2 = Chem.MolToSmiles(mol_set[1])
1116+
1117+
frag1_R = frag1.count("Na")
1118+
frag1_L = frag1.count("K")
1119+
frag2_R = frag2.count("Na")
1120+
frag2_L = frag2.count("K")
1121+
1122+
if frag1_R > frag2_R and frag1_L <= frag2_L:
1123+
frag1_smi = frag1.replace("*", "L")
1124+
frag2_smi = frag2.replace("*", "R")
1125+
elif frag1_L > frag2_L and frag1_R <= frag2_R:
1126+
frag1_smi = frag1.replace("*", "R")
1127+
frag2_smi = frag2.replace("*", "L")
1128+
elif frag2_L > frag1_L and frag2_R <= frag1_R:
1129+
frag1_smi = frag1.replace("*", "L")
1130+
frag2_smi = frag2.replace("*", "R")
1131+
elif frag2_R > frag1_R and frag2_L <= frag1_L:
1132+
frag1_smi = frag1.replace("*", "R")
1133+
frag2_smi = frag2.replace("*", "L")
1134+
elif randint(0,1)==1:
1135+
frag1_smi = frag1.replace("*", "L")
1136+
frag2_smi = frag2.replace("*", "R")
1137+
else:
1138+
frag1_smi = frag1.replace("*", "R")
1139+
frag2_smi = frag2.replace("*", "L")
1140+
1141+
frag_list = [frag1_smi, frag2_smi]
1142+
1143+
elif len(mol_set) > 2: # means it cut into 3 fragments
1144+
frag_list = []
1145+
for ind, rdmol in enumerate(mol_set):
1146+
frag = Chem.MolToSmiles(rdmol)
1147+
if frag.count("*") > 1:
1148+
frag_smi = frag.replace("*", "R")
11401149
else:
1141-
frag1_smi = frag1.replace("*", "R")
1142-
frag2_smi = frag2.replace("*", "L")
1143-
1144-
frag_list = [frag1_smi, frag2_smi]
1145-
1146-
elif len(mol_set) > 2: # means it cut into 3 fragments
1147-
frag_list = []
1148-
for ind, rdmol in enumerate(mol_set):
1149-
frag = Chem.MolToSmiles(rdmol)
1150-
if frag.count("*") > 1:
1151-
frag_smi = frag.replace("*", "R")
1152-
else:
1153-
frag_smi = frag.replace("*", "L")
1154-
frag_list.append(frag_smi)
1155-
break
1156-
else:
1157-
# turn to next matched_atom_map
1158-
continue
1159-
except:
1150+
frag_smi = frag.replace("*", "L")
1151+
frag_list.append(frag_smi)
1152+
break
1153+
else:
1154+
# turn to next matched_atom_map
11601155
continue
11611156
else:
11621157
# no match for this pattern

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