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Rework smiles parsing in alphabase #460

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058282d
Suggested refactor of smiles parsing with RDKit Atom-map numbers
lucas-diedrich Oct 20, 2026
730335a
Add docstrings
lucas-diedrich Oct 20, 2026
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44 changes: 22 additions & 22 deletions alphabase/constants/const_files/amino_acid.tsv
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Original file line number Diff line number Diff line change
@@ -1,29 +1,29 @@
formula smiles
A C(3)H(5)N(1)O(1)S(0) N([Fl])([Fl])[C@@]([H])(C)C(=O)[Ts]
A C(3)H(5)N(1)O(1)S(0) [NH2:1][C@@H](C)C(=O)[OH:2]
B C(1000000)
C C(3)H(5)N(1)O(1)S(1) N([Fl])([Fl])[C@@]([H])(CS)C(=O)[Ts]
D C(4)H(5)N(1)O(3)S(0) N([Fl])([Fl])[C@@]([H])(CC(=O)O)C(=O)[Ts]
E C(5)H(7)N(1)O(3)S(0) N([Fl])([Fl])[C@@]([H])(CCC(=O)O)C(=O)[Ts]
F C(9)H(9)N(1)O(1)S(0) N([Fl])([Fl])[C@@]([H])(Cc1ccccc1)C(=O)[Ts]
G C(2)H(3)N(1)O(1)S(0) N([Fl])([Fl])CC(=O)[Ts]
H C(6)H(7)N(3)O(1)S(0) N([Fl])([Fl])[C@@]([H])(CC1=CN=C-N1)C(=O)[Ts]
I C(6)H(11)N(1)O(1)S(0) N([Fl])([Fl])[C@@]([H])([C@]([H])(CC)C)C(=O)[Ts]
C C(3)H(5)N(1)O(1)S(1) [NH2:1][C@@H](CS)C(=O)[OH:2]
D C(4)H(5)N(1)O(3)S(0) [NH2:1][C@@H](CC(=O)O)C(=O)[OH:2]
E C(5)H(7)N(1)O(3)S(0) [NH2:1][C@@H](CCC(=O)O)C(=O)[OH:2]
F C(9)H(9)N(1)O(1)S(0) [NH2:1][C@@H](Cc1ccccc1)C(=O)[OH:2]
G C(2)H(3)N(1)O(1)S(0) [NH2:1]CC(=O)[OH:2]
H C(6)H(7)N(3)O(1)S(0) [NH2:1][C@@H](Cc1cnc[nH]1)C(=O)[OH:2]
I C(6)H(11)N(1)O(1)S(0) [NH2:1][C@H](C(=O)[OH:2])[C@@H](C)CC
J C(6)H(11)N(1)O(1)S(0)
K C(6)H(12)N(2)O(1)S(0) N([Fl])([Fl])[C@@]([H])(CCCCN)C(=O)[Ts]
L C(6)H(11)N(1)O(1)S(0) N([Fl])([Fl])[C@@]([H])(CC(C)C)C(=O)[Ts]
M C(5)H(9)N(1)O(1)S(1) N([Fl])([Fl])[C@@]([H])(CCSC)C(=O)[Ts]
N C(4)H(6)N(2)O(2)S(0) N([Fl])([Fl])[C@@]([H])(CC(=O)N)C(=O)[Ts]
O C(12)H(19)N(3)O(2) C[C@@H]1CC=N[C@H]1C(=O)NCCCC[C@@H](C(=O)[Ts])N([Fl])([Fl])
P C(5)H(7)N(1)O(1)S(0) N1([Fl])[C@@]([H])(CCC1)C(=O)[Ts]
Q C(5)H(8)N(2)O(2)S(0) N([Fl])([Fl])[C@@]([H])(CCC(=O)N)C(=O)[Ts]
R C(6)H(12)N(4)O(1)S(0) N([Fl])([Fl])[C@@]([H])(CCCNC(=N)N)C(=O)[Ts]
S C(3)H(5)N(1)O(2)S(0) N([Fl])([Fl])[C@@]([H])(CO)C(=O)[Ts]
T C(4)H(7)N(1)O(2)S(0) N([Fl])([Fl])[C@@]([H])([C@]([H])(O)C)C(=O)[Ts]
U C(3)H(5)N(1)O(1)Se(1) N([Fl])([Fl])[C@@]([H])(C[Se][H])C(=O)[Ts]
V C(5)H(9)N(1)O(1)S(0) N([Fl])([Fl])[C@@]([H])(C(C)C)C(=O)[Ts]
W C(11)H(10)N(2)O(1)S(0) N([Fl])([Fl])[C@@]([H])(CC(=CN2)C1=C2C=CC=C1)C(=O)[Ts]
K C(6)H(12)N(2)O(1)S(0) [NH2:1][C@@H](CCCCN)C(=O)[OH:2]
L C(6)H(11)N(1)O(1)S(0) [NH2:1][C@@H](CC(C)C)C(=O)[OH:2]
M C(5)H(9)N(1)O(1)S(1) [NH2:1][C@@H](CCSC)C(=O)[OH:2]
N C(4)H(6)N(2)O(2)S(0) [NH2:1][C@@H](CC(N)=O)C(=O)[OH:2]
O C(12)H(19)N(3)O(2) [NH2:1][C@@H](CCCCNC(=O)[C@@H]1N=CC[C@H]1C)C(=O)[OH:2]
P C(5)H(7)N(1)O(1)S(0) [NH:1]1CCC[C@H]1C(=O)[OH:2]
Q C(5)H(8)N(2)O(2)S(0) [NH2:1][C@@H](CCC(N)=O)C(=O)[OH:2]
R C(6)H(12)N(4)O(1)S(0) [NH2:1][C@@H](CCCNC(=N)N)C(=O)[OH:2]
S C(3)H(5)N(1)O(2)S(0) [NH2:1][C@@H](CO)C(=O)[OH:2]
T C(4)H(7)N(1)O(2)S(0) [NH2:1][C@H](C(=O)[OH:2])[C@@H](C)O
U C(3)H(5)N(1)O(1)Se(1) [NH2:1][C@@H](C[SeH])C(=O)[OH:2]
V C(5)H(9)N(1)O(1)S(0) [NH2:1][C@H](C(=O)[OH:2])C(C)C
W C(11)H(10)N(2)O(1)S(0) [NH2:1][C@@H](Cc1c[nH]c2ccccc12)C(=O)[OH:2]
X C(1000000)
Y C(9)H(9)N(1)O(2)S(0) N([Fl])([Fl])[C@@]([H])(Cc1ccc(O)cc1)C(=O)[Ts]
Y C(9)H(9)N(1)O(2)S(0) [NH2:1][C@@H](Cc1ccc(O)cc1)C(=O)[OH:2]
Z C(1000000)
s C(3)H(5)N(1)O(2)S(0)
t C(4)H(8)N(1)O(5)P(1)
Expand Down
984 changes: 492 additions & 492 deletions alphabase/constants/const_files/modification.tsv
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151 changes: 76 additions & 75 deletions alphabase/smiles/adding_smiles.py
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Original file line number Diff line number Diff line change
Expand Up @@ -110,89 +110,89 @@ def process_modifications(


n_term_modifications = {
"mTRAQ@Any_N-term": "C(=O)CN1CCN(CC1)C",
"mTRAQ:13C(3)15N(1)@Any_N-term": "C(=O)[13C]([H])([H])[15N]1[13C]([H])([H])[13C]([H])([H])N(CC1)C",
"mTRAQ:13C(6)15N(2)@Any_N-term": "C(=O)[13C]([H])([H])[15N]1[13C]([H])([H])[13C]([H])([H])[15N]([13C]([H])([H])[13C]1([H])([H]))[13C]([H])([H])([H])",
"Acetyl@Any_N-term": "CC(=O)[Lv]",
"Acetyl@Protein_N-term": "CC(=O)[Lv]",
"Propionyl@Any_N-term": "C(=O)CC",
"Biotin@Any_N-term": "C(=O)CCCCC1SCC2NC(=O)NC21",
"Carbamidomethyl@Any_N-term": "C(=O)NC",
"Carbamyl@Any_N-term": "C(=O)N",
"Propionamide@Any_N-term": "CCC(N)=O",
"Pyridylacetyl@Any_N-term": "C(=O)Cc1ccccn1",
"Methyl@Any_N-term": "C",
"Dimethyl@Any_N-term": "C[Lv]C",
"Dimethyl:2H(6)13C(2)@Any_N-term": "[13C]([2H])([2H])([2H])",
"Dimethyl:2H(4)@Any_N-term": "C([2H])([2H])([1H])",
"Dimethyl:2H(4)13C(2)@Any_N-term": "[13C]([2H])([2H])([1H])",
"GG@Protein_N-term": "C(=O)CNC(=O)CN",
"SATA@Any_N-term": "C(=O)CSC(=O)C",
"SATP@Any_N-term": "C(=O)CCSC(=O)C",
"Succinamide@Any_N-term": "C(=O)CCC(=O)NO",
"SATA-Glc@Any_N-term": "C(=O)CS[C@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O",
"mTRAQ@Any_N-term": "[NH2:1]C(=O)CN1CCN(C)CC1",
"mTRAQ:13C(3)15N(1)@Any_N-term": "[NH2:1]C(=O)[13CH2][15N]1CCN(C)[13CH2][13CH2]1",
"mTRAQ:13C(6)15N(2)@Any_N-term": "[NH2:1]C(=O)[13CH2][15N]1[13CH2][13CH2][15N]([13CH3])[13CH2][13CH2]1",
"Acetyl@Any_N-term": "[NH2:1]C(C)=O",
"Acetyl@Protein_N-term": "[NH2:1]C(C)=O",
"Propionyl@Any_N-term": "[NH2:1]C(=O)CC",
"Biotin@Any_N-term": "[NH2:1]C(=O)CCCCC1SCC2NC(=O)NC21",
"Carbamidomethyl@Any_N-term": "[NH2:1]C(=O)NC",
"Carbamyl@Any_N-term": "[NH2:1]C(N)=O",
"Propionamide@Any_N-term": "[NH2:1]CCC(N)=O",
"Pyridylacetyl@Any_N-term": "[NH2:1]C(=O)Cc1ccccn1",
"Methyl@Any_N-term": "[NH2:1]C",
"Dimethyl@Any_N-term": "[NH:1](C)C",
"Dimethyl:2H(6)13C(2)@Any_N-term": "[NH:1]([13C]([2H])([2H])[2H])[13C]([2H])([2H])[2H]",
"Dimethyl:2H(4)@Any_N-term": "[NH:1](C([2H])[2H])C([2H])[2H]",
"Dimethyl:2H(4)13C(2)@Any_N-term": "[NH:1]([13C]([1H])([2H])[2H])[13C]([1H])([2H])[2H]",
"GG@Protein_N-term": "[NH2:1]C(=O)CNC(=O)CN",
"SATA@Any_N-term": "[NH2:1]C(=O)CSC(C)=O",
"SATP@Any_N-term": "[NH2:1]C(=O)CCSC(C)=O",
"Succinamide@Any_N-term": "[NH2:1]C(=O)CCC(=O)NO",
"SATA-Glc@Any_N-term": "[NH2:1]C(=O)CS[C@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O",
}


c_term_modifications = {
"Methyl@Any_C-term": "OC",
"Ethyl@Any_C-term": "OCC",
"Propyl@Any_C-term": "OCCC",
"Amidated@Any_C-term": "N",
"Cation:Na@Any_C-term": "O[Na]",
"Cation:K@Any_C-term": "O[K]",
"Cation:Cu[I]@Any_C-term": "O[Cu]",
"Cation:Li@Any_C-term": "O[Li]",
"Methyl@Any_C-term": "[OH:2]C",
"Ethyl@Any_C-term": "[OH:2]CC",
"Propyl@Any_C-term": "[OH:2]CCC",
"Amidated@Any_C-term": "[NH3:2]",
"Cation:Na@Any_C-term": "[OH:2][Na]",
"Cation:K@Any_C-term": "[OH:2][K]",
"Cation:Cu[I]@Any_C-term": "[OH:2][Cu]",
"Cation:Li@Any_C-term": "[OH:2][Li]",
}


ptm_dict = {
"Carbamidomethyl@C": "C(C(C(=O)[Ts])N([Fl])([Fl]))SCC(=O)N",
"Oxidation@M": "O=C([Ts])C(N([Fl])([Fl]))CCS(=O)C",
"Deamidated@N": "C([C@@H](C(=O)[Ts])N([Fl])([Fl]))C(=O)O",
"Propionyl@K": "CCC(=O)NCCCCC(C(=O)[Ts])N([Fl])([Fl])",
"Deamidated@Q": "C(CC(=O)O)[C@@H](C(=O)[Ts])N([Fl])([Fl])",
"Gln->pyro-Glu@Q^Any_N-term": "O=C([Ts])[C@H]1N([Fl])C(=O)CC1",
"Glu->pyro-Glu@E^Any_N-term": "O=C([Ts])[C@H]1N([Fl])C(=O)CC1",
"Phospho@S": "O=P(O)(O)OC[C@@H](C(=O)[Ts])N([Fl])([Fl])",
"Nitro@Y": "O=[N+]([O-])c1cc(ccc1O)C[C@@H](C(=O)[Ts])N([Fl])([Fl])",
"Acetyl@K": "CC(=O)NCCCC[C@H](N([Fl])([Fl]))C(=O)[Ts]",
"Dimethyl@K": "CN(C)CCCC[C@H](N([Fl])([Fl]))C(=O)[Ts]",
"mTRAQ@K": "[H]N(CCCC[C@H](N([Fl])([Fl]))C(=O)[Ts])C(=O)CN1CCN(C)CC1",
"mTRAQ:13C(3)15N(1)@K": "[H]N(CCCC[C@H](N([Fl])([Fl]))C(=O)[Ts])C(=O)[13CH2][15N]1CCN(C)[13CH2][13CH2]1",
"mTRAQ:13C(6)15N(2)@K": "[H]N(CCCC[C@H](N([Fl])([Fl]))C(=O)[Ts])C(=O)[13CH2][15N]1[13CH2][13CH2][15N]([13CH3])[13CH2][13CH2]1",
"Pyridylethyl@C": "C1=CN=CC=C1CCSCC(C(=O)[Ts])N([Fl])([Fl])",
"Butyryl@K": "CCCC(=O)NCCCCC(C(=O)[Ts])N([Fl])([Fl])",
"Phospho@T": "CC(C(C(=O)[Ts])N([Fl])([Fl]))OP(=O)(O)O",
"Methylthio@C": "CSSC[C@H](N([Fl])([Fl]))C([Ts])=O",
"Carbamidomethyl@M": "CS(CCC(N([Fl])([Fl]))C([Ts])=O)=CC(N)=O",
"Succinyl@K": "C(CCN)CC(C(=O)[Ts])N([Fl])C(=O)CCC(=O)O",
"Crotonyl@K": "CC=CC(=O)NCCCCC(C(=O)[Ts])N([Fl])([Fl])",
"Phospho@Y": "C1=CC(=CC=C1CC(C(=O)[Ts])N([Fl])([Fl]))OP(=O)(O)O",
"Malonyl@K": "N([Fl])([Fl])[C@@H](CCCC(NC(=O)CC(=O)O))C(=O)[Ts]",
"Met->Hse@M^Any_C-term": "N([Fl])([Fl])[C@H](C(=O)[Ts])CCO",
"Pro->(2S,4R)-4-fluoroproline@P": "F[C@@H]1C[C@H](N([Fl])C1)C(=O)[Ts]",
"Pro->(2S,4S)-4fluoroproline@P": "F[C@H]1C[C@H](N([Fl])C1)C(=O)[Ts]",
"Pro->(2S)-1,3-thiazolidine-2-carboxylic_acid@P": "S1[C@H](N([Fl])CC1)C(=O)[Ts]",
"Pro->(4R)-1,3-Thiazolidine-4-carboxylic_acid@P": "S1CN([Fl])[C@@H](C1)C(=O)[Ts]",
"Pro->(2S,4R)-4-hydroxyproline@P": "O[C@@H]1C[C@H](N([Fl])C1)C(=O)[Ts]",
"Pro->(DL)-pipecolic_acid@P": "C1CCN([Fl])C(C1)C(=O)[Ts]",
"Pro->3,4-Dehydro-L-proline@P": "C1C=CC(N1([Fl]))C(=O)[Ts]",
"Pro->(1S,3S,5S)-2-Azabicyclo[3.1.0]hexane-3-carboxylic_acid@P": "[C@H]12N([Fl])[C@@H](C[C@@H]2C1)C(=O)[Ts]",
"Pro->(1R,3S,5R)-2-Azabicyclo[3.1.0]hexane-3-carboxylic_acid@P": "[C@@H]12N([Fl])[C@@H](C[C@H]2C1)C(=O)[Ts]",
"Pro->(2S,3aS,7aS)-Octahydro-1H-indole-2-carboxylic_acid@P": "N1([Fl])[C@@H](C[C@@H]2CCCC[C@H]12)C(=O)[Ts]",
"Pro->(DL)-5-trifluoromethylproline@P": "FC(C1CCC(N1([Fl]))C(=O)[Ts])(F)F",
"hydroxyisobutyryl@K": "CC(C)(O)C(=O)NCCCCC(N([Fl])[Fl])C([Ts])=O",
"GG@K": "NCC(=O)NCC(=O)NCCCC[C@H](N([Fl])([Fl]))C([Ts])=O",
"Phospho@H": "O=P(O)(O)n1cc(nc1)C[C@@H](C(=O)[Ts])N([Fl])([Fl])",
"Phospho@D": "O=P(O)(O)OC(=O)C[C@@H](C(=O)[Ts])N([Fl])([Fl])",
"Cysteinyl@C": "N([Fl])([Fl])[C@@H](C(=O)[Ts])CSSC[C@@H](N)C(=O)O",
"SATA@K": "CC(=O)SCC(=O)NCCCC[C@H](N([Fl])([Fl]))C([Ts])=O",
"SATP@K": "CC(=O)SCCC(=O)NCCCC[C@H](N([Fl])([Fl]))C([Ts])=O",
"Succinamide@K": "ONC(=O)CCC(=O)NCCCC[C@H](N([Fl])([Fl]))C([Ts])=O",
"SATA-Glc@K": "[C@@H]1(O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O)SCC(=O)NCCCC[C@H](N([Fl])[Fl])C([Ts])=O",
"Methyl@H": "Cn1cc(nc1)C[C@@H](C(=O)[Ts])N([Fl])([Fl])",
"Oxidation@P": "O[C@@H]1C[C@H](N([Fl])C1)C(=O)[Ts]",
"Carbamidomethyl@C": "[NH2:1]C(CSCC(N)=O)C(=O)[OH:2]",
"Oxidation@M": "[NH2:1]C(CCS(C)=O)C(=O)[OH:2]",
"Deamidated@N": "[NH2:1][C@@H](CC(=O)O)C(=O)[OH:2]",
"Propionyl@K": "[NH2:1]C(CCCCNC(=O)CC)C(=O)[OH:2]",
"Deamidated@Q": "[NH2:1][C@@H](CCC(=O)O)C(=O)[OH:2]",
"Gln->pyro-Glu@Q^Any_N-term": "[NH:1]1C(=O)CC[C@H]1C(=O)[OH:2]",
"Glu->pyro-Glu@E^Any_N-term": "[NH:1]1C(=O)CC[C@H]1C(=O)[OH:2]",
"Phospho@S": "[NH2:1][C@@H](COP(=O)(O)O)C(=O)[OH:2]",
"Nitro@Y": "[NH2:1][C@@H](Cc1ccc(O)c([N+](=O)[O-])c1)C(=O)[OH:2]",
"Acetyl@K": "[NH2:1][C@@H](CCCCNC(C)=O)C(=O)[OH:2]",
"Dimethyl@K": "[NH2:1][C@@H](CCCCN(C)C)C(=O)[OH:2]",
"mTRAQ@K": "[NH2:1][C@@H](CCCCNC(=O)CN1CCN(C)CC1)C(=O)[OH:2]",
"mTRAQ:13C(3)15N(1)@K": "[NH2:1][C@@H](CCCCNC(=O)[13CH2][15N]1CCN(C)[13CH2][13CH2]1)C(=O)[OH:2]",
"mTRAQ:13C(6)15N(2)@K": "[NH2:1][C@@H](CCCCNC(=O)[13CH2][15N]1[13CH2][13CH2][15N]([13CH3])[13CH2][13CH2]1)C(=O)[OH:2]",
"Pyridylethyl@C": "[NH2:1]C(CSCCc1ccncc1)C(=O)[OH:2]",
"Butyryl@K": "[NH2:1]C(CCCCNC(=O)CCC)C(=O)[OH:2]",
"Phospho@T": "[NH2:1]C(C(=O)[OH:2])C(C)OP(=O)(O)O",
"Methylthio@C": "[NH2:1][C@@H](CSSC)C(=O)[OH:2]",
"Carbamidomethyl@M": "[NH2:1]C(CCS(C)=CC(N)=O)C(=O)[OH:2]",
"Succinyl@K": "[NH:1](C(=O)CCC(=O)O)C(CCCCN)C(=O)[OH:2]",
"Crotonyl@K": "[NH2:1]C(CCCCNC(=O)C=CC)C(=O)[OH:2]",
"Phospho@Y": "[NH2:1]C(Cc1ccc(OP(=O)(O)O)cc1)C(=O)[OH:2]",
"Malonyl@K": "[NH2:1][C@@H](CCCCNC(=O)CC(=O)O)C(=O)[OH:2]",
"Met->Hse@M^Any_C-term": "[NH2:1][C@@H](CCO)C(=O)[OH:2]",
"Pro->(2S,4R)-4-fluoroproline@P": "[NH:1]1C[C@H](F)C[C@H]1C(=O)[OH:2]",
"Pro->(2S,4S)-4fluoroproline@P": "[NH:1]1C[C@@H](F)C[C@H]1C(=O)[OH:2]",
"Pro->(2S)-1,3-thiazolidine-2-carboxylic_acid@P": "[NH:1]1CCS[C@H]1C(=O)[OH:2]",
"Pro->(4R)-1,3-Thiazolidine-4-carboxylic_acid@P": "[NH:1]1CSC[C@H]1C(=O)[OH:2]",
"Pro->(2S,4R)-4-hydroxyproline@P": "[NH:1]1C[C@H](O)C[C@H]1C(=O)[OH:2]",
"Pro->(DL)-pipecolic_acid@P": "[NH:1]1CCCCC1C(=O)[OH:2]",
"Pro->3,4-Dehydro-L-proline@P": "[NH:1]1CC=CC1C(=O)[OH:2]",
"Pro->(1S,3S,5S)-2-Azabicyclo[3.1.0]hexane-3-carboxylic_acid@P": "[NH:1]1[C@H](C(=O)[OH:2])C[C@@H]2C[C@@H]21",
"Pro->(1R,3S,5R)-2-Azabicyclo[3.1.0]hexane-3-carboxylic_acid@P": "[NH:1]1[C@@H]2C[C@@H]2C[C@H]1C(=O)[OH:2]",
"Pro->(2S,3aS,7aS)-Octahydro-1H-indole-2-carboxylic_acid@P": "[NH:1]1[C@H](C(=O)[OH:2])C[C@@H]2CCCC[C@@H]21",
"Pro->(DL)-5-trifluoromethylproline@P": "[NH:1]1C(C(=O)[OH:2])CCC1C(F)(F)F",
"hydroxyisobutyryl@K": "[NH2:1]C(CCCCNC(=O)C(C)(C)O)C(=O)[OH:2]",
"GG@K": "[NH2:1][C@@H](CCCCNC(=O)CNC(=O)CN)C(=O)[OH:2]",
"Phospho@H": "[NH2:1][C@@H](Cc1cn(P(=O)(O)O)cn1)C(=O)[OH:2]",
"Phospho@D": "[NH2:1][C@@H](CC(=O)OP(=O)(O)O)C(=O)[OH:2]",
"Cysteinyl@C": "[NH2:1][C@H](CSSC[C@@H](N)C(=O)O)C(=O)[OH:2]",
"SATA@K": "[NH2:1][C@@H](CCCCNC(=O)CSC(C)=O)C(=O)[OH:2]",
"SATP@K": "[NH2:1][C@@H](CCCCNC(=O)CCSC(C)=O)C(=O)[OH:2]",
"Succinamide@K": "[NH2:1][C@@H](CCCCNC(=O)CCC(=O)NO)C(=O)[OH:2]",
"SATA-Glc@K": "[NH2:1][C@@H](CCCCNC(=O)CS[C@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O)C(=O)[OH:2]",
"Methyl@H": "[NH2:1][C@@H](Cc1cn(C)cn1)C(=O)[OH:2]",
"Oxidation@P": "[NH:1]1C[C@H](O)C[C@H]1C(=O)[OH:2]",
}

for i in n_term_modifications:
Expand All @@ -206,6 +206,7 @@ def process_modifications(


def main():
"""Compute the compositions of all dictionaries above and write them to modification.tsv."""
ptms_to_add = process_modifications(ptm_dict, mod_type="ptm")
add_new_modifications(ptms_to_add)

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