diff --git a/alphabase/constants/const_files/modification.tsv b/alphabase/constants/const_files/modification.tsv index 705c5886..47c455ff 100644 --- a/alphabase/constants/const_files/modification.tsv +++ b/alphabase/constants/const_files/modification.tsv @@ -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 diff --git a/docs/nbs/adding_smiles.ipynb b/docs/nbs/adding_smiles.ipynb index e0899474..66d4c1dd 100644 --- a/docs/nbs/adding_smiles.ipynb +++ b/docs/nbs/adding_smiles.ipynb @@ -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", @@ -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" ] }, { @@ -170,7 +131,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 3, "metadata": {}, "outputs": [], "source": [ @@ -195,7 +156,7 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 4, "metadata": {}, "outputs": [], "source": [ @@ -222,7 +183,7 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": 5, "metadata": {}, "outputs": [ { @@ -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" } @@ -331,7 +294,7 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": 6, "metadata": {}, "outputs": [], "source": [ @@ -350,7 +313,7 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": 7, "metadata": {}, "outputs": [ { @@ -411,7 +374,7 @@ " 'smiles': '[13C]([2H])([2H])([1H])'}}" ] }, - "execution_count": 9, + "execution_count": 7, "metadata": {}, "output_type": "execute_result" } @@ -434,7 +397,7 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": 8, "metadata": {}, "outputs": [], "source": [ @@ -453,7 +416,7 @@ }, { "cell_type": "code", - "execution_count": 11, + "execution_count": 9, "metadata": {}, "outputs": [ { @@ -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" } @@ -502,7 +465,7 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": 10, "metadata": {}, "outputs": [], "source": [ @@ -521,7 +484,7 @@ }, { "cell_type": "code", - "execution_count": 13, + "execution_count": 11, "metadata": {}, "outputs": [ { @@ -832,7 +795,7 @@ "[2796 rows x 13 columns]" ] }, - "execution_count": 13, + "execution_count": 11, "metadata": {}, "output_type": "execute_result" } @@ -852,7 +815,7 @@ }, { "cell_type": "code", - "execution_count": 14, + "execution_count": 12, "metadata": {}, "outputs": [], "source": [