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ENH: hydroxyisobutyryl@K smiles #223

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Sep 30, 2024
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ENH: hydroxyisobutyryl@K smiles #223

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2 changes: 1 addition & 1 deletion alphabase/constants/const_files/modification.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -2440,7 +2440,7 @@ PhosphoCytidine@S 305.041287 305.1812 H(12)C(9)N(3)O(7)P(1) 0.0 Post-translatio
AzidoF@F 41.001397 41.0122 H(-1)N(3) 0.0 Chemical derivative 1845 0.0
Dimethylaminoethyl@C 71.073499 71.121 H(9)C(4)N(1) 0.0 Chemical derivative 1846 0.0
Gluratylation@K 114.031694 114.0993 H(6)C(5)O(3) 0.0 Post-translational 1848 0.0
hydroxyisobutyryl@K 86.036779 86.0892 H(6)C(4)O(2) 0.0 Post-translational 1849 0.0
hydroxyisobutyryl@K 86.036779 86.0892 H(6)C(4)O(2) 0.0 Post-translational 1849 CC(C)(O)C(=O)NCCCCC(N([Xe])[Xe])C([Rn])=O 0.0
MeMePhosphorothioate@S 107.979873 108.0993 H(5)C(2)O(1)P(1)S(1) 0.0 Chemical derivative 1868 0.0
Cation:Fe[III]@D 52.911464 52.8212 H(-3)Fe(1) 0.0 Artefact 1870 0.0
Cation:Fe[III]@E 52.911464 52.8212 H(-3)Fe(1) 0.0 Artefact 1870 0.0
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75 changes: 19 additions & 56 deletions docs/nbs/adding_smiles.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -49,46 +49,6 @@
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"defaultdict(int, {'O': -1, 'H': 2, 'C': 1})"
]
},
"execution_count": 2,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"(ChemicalCompositonFormula(\"C(1)H(4)\") - ChemicalCompositonFormula(\"H(2)O(1)\")).elements"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"ChemicalCompositonFormula('C(1)H(2)O(-1)')"
]
},
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ChemicalCompositonFormula(\"C(1)H(2)O(-1)\")"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [],
"source": [
"n_term_modifications = {'mTRAQ@Any_N-term': 'C(=O)CN1CCN(CC1)C',\n",
Expand Down Expand Up @@ -153,7 +113,8 @@
" 'Pro->(1S,3S,5S)-2-Azabicyclo[3.1.0]hexane-3-carboxylic_acid@P': '[C@H]12N([Xe])[C@@H](C[C@@H]2C1)C(=O)[Rn]',\n",
" 'Pro->(1R,3S,5R)-2-Azabicyclo[3.1.0]hexane-3-carboxylic_acid@P': '[C@@H]12N([Xe])[C@@H](C[C@H]2C1)C(=O)[Rn]',\n",
" 'Pro->(2S,3aS,7aS)-Octahydro-1H-indole-2-carboxylic_acid@P': 'N1([Xe])[C@@H](C[C@@H]2CCCC[C@H]12)C(=O)[Rn]',\n",
" 'Pro->(DL)-5-trifluoromethylproline@P': 'FC(C1CCC(N1([Xe]))C(=O)[Rn])(F)F'}"
" 'Pro->(DL)-5-trifluoromethylproline@P': 'FC(C1CCC(N1([Xe]))C(=O)[Rn])(F)F',\n",
" 'hydroxyisobutyryl@K': 'CC(C)(O)C(=O)NCCCCC(N([Xe])[Xe])C([Rn])=O',}\n"
]
},
{
Expand All @@ -170,7 +131,7 @@
},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": 3,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -195,7 +156,7 @@
},
{
"cell_type": "code",
"execution_count": 6,
"execution_count": 4,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -222,7 +183,7 @@
},
{
"cell_type": "code",
"execution_count": 7,
"execution_count": 5,
"metadata": {},
"outputs": [
{
Expand Down Expand Up @@ -299,10 +260,12 @@
" 'Pro->(2S,3aS,7aS)-Octahydro-1H-indole-2-carboxylic_acid@P': {'composition': 'C(4)H(6)',\n",
" 'smiles': 'N1([Xe])[C@@H](C[C@@H]2CCCC[C@H]12)C(=O)[Rn]'},\n",
" 'Pro->(DL)-5-trifluoromethylproline@P': {'composition': 'C(1)F(3)H(-1)',\n",
" 'smiles': 'FC(C1CCC(N1([Xe]))C(=O)[Rn])(F)F'}}"
" 'smiles': 'FC(C1CCC(N1([Xe]))C(=O)[Rn])(F)F'},\n",
" 'hydroxyisobutyryl@K': {'composition': 'C(4)H(6)O(2)',\n",
" 'smiles': 'CC(C)(O)C(=O)NCCCCC(N([Xe])[Xe])C([Rn])=O'}}"
]
},
"execution_count": 7,
"execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
Expand Down Expand Up @@ -331,7 +294,7 @@
},
{
"cell_type": "code",
"execution_count": 8,
"execution_count": 6,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -350,7 +313,7 @@
},
{
"cell_type": "code",
"execution_count": 9,
"execution_count": 7,
"metadata": {},
"outputs": [
{
Expand Down Expand Up @@ -411,7 +374,7 @@
" 'smiles': '[13C]([2H])([2H])([1H])'}}"
]
},
"execution_count": 9,
"execution_count": 7,
"metadata": {},
"output_type": "execute_result"
}
Expand All @@ -434,7 +397,7 @@
},
{
"cell_type": "code",
"execution_count": 10,
"execution_count": 8,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -453,7 +416,7 @@
},
{
"cell_type": "code",
"execution_count": 11,
"execution_count": 9,
"metadata": {},
"outputs": [
{
Expand All @@ -478,7 +441,7 @@
" 'Cation:Li@Protein_C-term': {'composition': 'H(-1)Li(1)', 'smiles': 'O[Li]'}}"
]
},
"execution_count": 11,
"execution_count": 9,
"metadata": {},
"output_type": "execute_result"
}
Expand All @@ -502,7 +465,7 @@
},
{
"cell_type": "code",
"execution_count": 12,
"execution_count": 10,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -521,7 +484,7 @@
},
{
"cell_type": "code",
"execution_count": 13,
"execution_count": 11,
"metadata": {},
"outputs": [
{
Expand Down Expand Up @@ -832,7 +795,7 @@
"[2796 rows x 13 columns]"
]
},
"execution_count": 13,
"execution_count": 11,
"metadata": {},
"output_type": "execute_result"
}
Expand All @@ -852,7 +815,7 @@
},
{
"cell_type": "code",
"execution_count": 14,
"execution_count": 12,
"metadata": {},
"outputs": [],
"source": [
Expand Down
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