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Refactor pyenzyme.py and SAHH_kinetics.ipynb
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@haeussma
haeussma committed Sep 27, 2024
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73 changes: 31 additions & 42 deletions docs/examples/SAHH_kinetics.ipynb
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"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"from mtphandler.molecule import Protein\n",
"\n",
"my_variant = Protein(\n",
" id=\"L191G\",\n",
" name=\"L191G\",\n",
")"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"data": {
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},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": 4,
"metadata": {},
"outputs": [],
"source": [
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},
{
"cell_type": "code",
"execution_count": 4,
"execution_count": 5,
"metadata": {},
"outputs": [],
"source": [
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},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": 6,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">📍 Assigned <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">228</span> initial concentration coditions for <span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">[</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'TmSAHH'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">, </span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'SIH'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">, </span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'McSAHH'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">, </span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'BUFFER'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">, </span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'MhSAHH'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">, </span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'SAH'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">, </span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'Hyc'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">, </span>\n",
"<span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'MtSAHH'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">, </span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'DTNB'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">, </span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'TNB'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">]</span> from data/plate_map_SAHH_kinetics.xlsx to the plate.\n",
"<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">📍 Assigned <span style=\"color: #008080; text-decoration-color: #008080; font-weight: bold\">228</span> initial concentration coditions for <span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">[</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'SAH'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">, </span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'MhSAHH'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">, </span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'SIH'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">, </span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'Hyc'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">, </span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'MtSAHH'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">, </span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'BUFFER'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">, </span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'McSAHH'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">, </span>\n",
"<span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'TmSAHH'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">, </span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'DTNB'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">, </span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">'TNB'</span><span style=\"color: #800080; text-decoration-color: #800080; font-weight: bold\">]</span> from data/plate_map_SAHH_kinetics.xlsx to the plate.\n",
"</pre>\n"
],
"text/plain": [
"📍 Assigned \u001b[1;36m228\u001b[0m initial concentration coditions for \u001b[1;35m[\u001b[0m\u001b[1;35m'TmSAHH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'SIH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'McSAHH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'BUFFER'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'MhSAHH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'SAH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'Hyc'\u001b[0m\u001b[1;35m, \u001b[0m\n",
"\u001b[1;35m'MtSAHH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'DTNB'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'TNB'\u001b[0m\u001b[1;35m]\u001b[0m from data/plate_map_SAHH_kinetics.xlsx to the plate.\n"
"📍 Assigned \u001b[1;36m228\u001b[0m initial concentration coditions for \u001b[1;35m[\u001b[0m\u001b[1;35m'SAH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'MhSAHH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'SIH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'Hyc'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'MtSAHH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'BUFFER'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'McSAHH'\u001b[0m\u001b[1;35m, \u001b[0m\n",
"\u001b[1;35m'TmSAHH'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'DTNB'\u001b[0m\u001b[1;35m, \u001b[0m\u001b[1;35m'TNB'\u001b[0m\u001b[1;35m]\u001b[0m from data/plate_map_SAHH_kinetics.xlsx to the plate.\n"
]
},
"metadata": {},
Expand Down Expand Up @@ -144620,7 +144634,7 @@
},
{
"cell_type": "code",
"execution_count": 6,
"execution_count": 7,
"metadata": {},
"outputs": [
{
Expand Down Expand Up @@ -144837,7 +144851,9 @@
"plate.blank_species(BUFFER)\n",
"\n",
"# Then the all other species\n",
"plate.blank_species(SAH)\n",
"plate.blank_species(\n",
" SAH,\n",
")\n",
"plate.blank_species(SIH)\n",
"plate.blank_species(McSAHH)\n",
"plate.blank_species(MtSAHH)\n",
Expand All @@ -144858,7 +144874,7 @@
},
{
"cell_type": "code",
"execution_count": 7,
"execution_count": 8,
"metadata": {},
"outputs": [
{
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},
{
"cell_type": "code",
"execution_count": 8,
"execution_count": 9,
"metadata": {},
"outputs": [
{
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},
{
"cell_type": "code",
"execution_count": 9,
"execution_count": 10,
"metadata": {},
"outputs": [],
"source": [
Expand Down Expand Up @@ -147701,40 +147717,13 @@
},
{
"cell_type": "code",
"execution_count": 10,
"execution_count": 11,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"added temp unit s\n",
"added temp unit s\n",
"added temp unit s\n",
"added temp unit s\n",
"added temp unit s\n",
"added temp unit s\n",
"added temp unit s\n",
"added temp unit s\n",
"added temp unit s\n",
"added temp unit s\n",
"added temp unit s\n",
"added temp unit s\n",
"added temp unit s\n",
"added temp unit s\n",
"added temp unit s\n",
"added temp unit s\n",
"added temp unit s\n",
"added temp unit s\n",
"added temp unit s\n",
"added temp unit s\n",
"added temp unit s\n",
"added temp unit s\n",
"added temp unit s\n",
"added temp unit s\n",
"added temp unit s\n",
"added temp unit s\n",
"added temp unit s\n",
"✅ Added measurements from 6 wells with concentration values to EnzymeMLDocument\n"
]
}
Expand All @@ -147759,7 +147748,7 @@
},
{
"cell_type": "code",
"execution_count": 11,
"execution_count": 12,
"metadata": {},
"outputs": [
{
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},
{
"cell_type": "code",
"execution_count": 12,
"execution_count": 13,
"metadata": {},
"outputs": [],
"source": [
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