]"
]
},
- "execution_count": 38,
+ "execution_count": 46,
"metadata": {},
"output_type": "execute_result"
}
@@ -1241,20 +1271,20 @@
},
{
"cell_type": "code",
- "execution_count": 43,
+ "execution_count": 47,
"id": "d1a27b3f-e2e3-4501-b1cc-e475ccc6a24b",
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
- "AlchemicalNetwork-391c0eb68025cf4b83e4d706f189f745-ddotson-tyk2-demo \n",
+ "AlchemicalNetwork-6f22642592f789c4e7f918412ca947c5-ddotson-tyk2-demo \n",
"┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓\n",
"┃ status ┃ count ┃\n",
"┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩\n",
"│ complete │ 0 │\n",
- "│ running │ 15 │\n",
- "│ waiting │ 9 │\n",
+ "│ running │ 0 │\n",
+ "│ waiting │ 24 │\n",
"│ error │ 0 │\n",
"│ invalid │ 0 │\n",
"│ deleted │ 0 │\n",
@@ -1262,13 +1292,13 @@
"\n"
],
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- "\u001b[3mAlchemicalNetwork-391c0eb68025cf4b83e4d706f189f745-ddotson-tyk2-demo \u001b[0m\n",
+ "\u001b[3mAlchemicalNetwork-6f22642592f789c4e7f918412ca947c5-ddotson-tyk2-demo \u001b[0m\n",
"┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓\n",
"┃\u001b[1m \u001b[0m\u001b[1mstatus \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1m count\u001b[0m\u001b[1m \u001b[0m┃\n",
"┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩\n",
"│\u001b[32m \u001b[0m\u001b[32mcomplete \u001b[0m\u001b[32m \u001b[0m│\u001b[32m \u001b[0m\u001b[32m 0\u001b[0m\u001b[32m \u001b[0m│\n",
- "│\u001b[38;5;172m \u001b[0m\u001b[38;5;172mrunning \u001b[0m\u001b[38;5;172m \u001b[0m│\u001b[38;5;172m \u001b[0m\u001b[38;5;172m 15\u001b[0m\u001b[38;5;172m \u001b[0m│\n",
- "│\u001b[38;2;23;147;208m \u001b[0m\u001b[38;2;23;147;208mwaiting \u001b[0m\u001b[38;2;23;147;208m \u001b[0m│\u001b[38;2;23;147;208m \u001b[0m\u001b[38;2;23;147;208m 9\u001b[0m\u001b[38;2;23;147;208m \u001b[0m│\n",
+ "│\u001b[38;5;172m \u001b[0m\u001b[38;5;172mrunning \u001b[0m\u001b[38;5;172m \u001b[0m│\u001b[38;5;172m \u001b[0m\u001b[38;5;172m 0\u001b[0m\u001b[38;5;172m \u001b[0m│\n",
+ "│\u001b[38;2;23;147;208m \u001b[0m\u001b[38;2;23;147;208mwaiting \u001b[0m\u001b[38;2;23;147;208m \u001b[0m│\u001b[38;2;23;147;208m \u001b[0m\u001b[38;2;23;147;208m 24\u001b[0m\u001b[38;2;23;147;208m \u001b[0m│\n",
"│\u001b[38;2;255;7;58m \u001b[0m\u001b[38;2;255;7;58merror \u001b[0m\u001b[38;2;255;7;58m \u001b[0m│\u001b[38;2;255;7;58m \u001b[0m\u001b[38;2;255;7;58m 0\u001b[0m\u001b[38;2;255;7;58m \u001b[0m│\n",
"│\u001b[38;5;201m \u001b[0m\u001b[38;5;201minvalid \u001b[0m\u001b[38;5;201m \u001b[0m│\u001b[38;5;201m \u001b[0m\u001b[38;5;201m 0\u001b[0m\u001b[38;5;201m \u001b[0m│\n",
"│\u001b[38;5;129m \u001b[0m\u001b[38;5;129mdeleted \u001b[0m\u001b[38;5;129m \u001b[0m│\u001b[38;5;129m \u001b[0m\u001b[38;5;129m 0\u001b[0m\u001b[38;5;129m \u001b[0m│\n",
@@ -1281,10 +1311,10 @@
{
"data": {
"text/plain": [
- "{'waiting': 9, 'running': 15}"
+ "{'waiting': 24}"
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},
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+ "execution_count": 47,
"metadata": {},
"output_type": "execute_result"
}
@@ -1303,20 +1333,20 @@
},
{
"cell_type": "code",
- "execution_count": 52,
+ "execution_count": 53,
"id": "67f5edd1-9775-45e1-a161-85cf12c67265",
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
- "AlchemicalNetwork-391c0eb68025cf4b83e4d706f189f745-ddotson-tyk2-demo \n",
+ "AlchemicalNetwork-6f22642592f789c4e7f918412ca947c5-ddotson-tyk2-demo \n",
"┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓\n",
"┃ status ┃ count ┃\n",
"┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩\n",
- "│ complete │ 0 │\n",
- "│ running │ 24 │\n",
- "│ waiting │ 0 │\n",
+ "│ complete │ 4 │\n",
+ "│ running │ 12 │\n",
+ "│ waiting │ 8 │\n",
"│ error │ 0 │\n",
"│ invalid │ 0 │\n",
"│ deleted │ 0 │\n",
@@ -1324,13 +1354,13 @@
"\n"
],
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- "\u001b[3mAlchemicalNetwork-391c0eb68025cf4b83e4d706f189f745-ddotson-tyk2-demo \u001b[0m\n",
+ "\u001b[3mAlchemicalNetwork-6f22642592f789c4e7f918412ca947c5-ddotson-tyk2-demo \u001b[0m\n",
"┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓\n",
"┃\u001b[1m \u001b[0m\u001b[1mstatus \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1m count\u001b[0m\u001b[1m \u001b[0m┃\n",
"┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩\n",
- "│\u001b[32m \u001b[0m\u001b[32mcomplete \u001b[0m\u001b[32m \u001b[0m│\u001b[32m \u001b[0m\u001b[32m 0\u001b[0m\u001b[32m \u001b[0m│\n",
- "│\u001b[38;5;172m \u001b[0m\u001b[38;5;172mrunning \u001b[0m\u001b[38;5;172m \u001b[0m│\u001b[38;5;172m \u001b[0m\u001b[38;5;172m 24\u001b[0m\u001b[38;5;172m \u001b[0m│\n",
- "│\u001b[38;2;23;147;208m \u001b[0m\u001b[38;2;23;147;208mwaiting \u001b[0m\u001b[38;2;23;147;208m \u001b[0m│\u001b[38;2;23;147;208m \u001b[0m\u001b[38;2;23;147;208m 0\u001b[0m\u001b[38;2;23;147;208m \u001b[0m│\n",
+ "│\u001b[32m \u001b[0m\u001b[32mcomplete \u001b[0m\u001b[32m \u001b[0m│\u001b[32m \u001b[0m\u001b[32m 4\u001b[0m\u001b[32m \u001b[0m│\n",
+ "│\u001b[38;5;172m \u001b[0m\u001b[38;5;172mrunning \u001b[0m\u001b[38;5;172m \u001b[0m│\u001b[38;5;172m \u001b[0m\u001b[38;5;172m 12\u001b[0m\u001b[38;5;172m \u001b[0m│\n",
+ "│\u001b[38;2;23;147;208m \u001b[0m\u001b[38;2;23;147;208mwaiting \u001b[0m\u001b[38;2;23;147;208m \u001b[0m│\u001b[38;2;23;147;208m \u001b[0m\u001b[38;2;23;147;208m 8\u001b[0m\u001b[38;2;23;147;208m \u001b[0m│\n",
"│\u001b[38;2;255;7;58m \u001b[0m\u001b[38;2;255;7;58merror \u001b[0m\u001b[38;2;255;7;58m \u001b[0m│\u001b[38;2;255;7;58m \u001b[0m\u001b[38;2;255;7;58m 0\u001b[0m\u001b[38;2;255;7;58m \u001b[0m│\n",
"│\u001b[38;5;201m \u001b[0m\u001b[38;5;201minvalid \u001b[0m\u001b[38;5;201m \u001b[0m│\u001b[38;5;201m \u001b[0m\u001b[38;5;201m 0\u001b[0m\u001b[38;5;201m \u001b[0m│\n",
"│\u001b[38;5;129m \u001b[0m\u001b[38;5;129mdeleted \u001b[0m\u001b[38;5;129m \u001b[0m│\u001b[38;5;129m \u001b[0m\u001b[38;5;129m 0\u001b[0m\u001b[38;5;129m \u001b[0m│\n",
@@ -1343,10 +1373,10 @@
{
"data": {
"text/plain": [
- "{'running': 24}"
+ "{'waiting': 8, 'complete': 4, 'running': 12}"
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},
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+ "execution_count": 53,
"metadata": {},
"output_type": "execute_result"
}
@@ -1355,37 +1385,45 @@
"asc.get_network_status(an_sk)"
]
},
+ {
+ "cell_type": "markdown",
+ "id": "a30d40aa-ee2a-4811-a21e-baa143b15686",
+ "metadata": {},
+ "source": [
+ "...and some might have errored:"
+ ]
+ },
{
"cell_type": "code",
- "execution_count": 171,
+ "execution_count": 54,
"id": "d78652a8-ecee-491e-aedc-c9312682c418",
"metadata": {},
"outputs": [
{
"data": {
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- "AlchemicalNetwork-391c0eb68025cf4b83e4d706f189f745-ddotson-tyk2-demo \n",
+ "AlchemicalNetwork-6f22642592f789c4e7f918412ca947c5-ddotson-tyk2-demo \n",
"┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓\n",
"┃ status ┃ count ┃\n",
"┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩\n",
- "│ complete │ 12 │\n",
- "│ running │ 12 │\n",
+ "│ complete │ 14 │\n",
+ "│ running │ 9 │\n",
"│ waiting │ 0 │\n",
- "│ error │ 0 │\n",
+ "│ error │ 1 │\n",
"│ invalid │ 0 │\n",
"│ deleted │ 0 │\n",
"└──────────────────────────────────────────────────────────────────┴──────────────────────────────────────────────┘\n",
"\n"
],
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- "\u001b[3mAlchemicalNetwork-391c0eb68025cf4b83e4d706f189f745-ddotson-tyk2-demo \u001b[0m\n",
+ "\u001b[3mAlchemicalNetwork-6f22642592f789c4e7f918412ca947c5-ddotson-tyk2-demo \u001b[0m\n",
"┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓\n",
"┃\u001b[1m \u001b[0m\u001b[1mstatus \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1m count\u001b[0m\u001b[1m \u001b[0m┃\n",
"┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩\n",
- "│\u001b[32m \u001b[0m\u001b[32mcomplete \u001b[0m\u001b[32m \u001b[0m│\u001b[32m \u001b[0m\u001b[32m 12\u001b[0m\u001b[32m \u001b[0m│\n",
- "│\u001b[38;5;172m \u001b[0m\u001b[38;5;172mrunning \u001b[0m\u001b[38;5;172m \u001b[0m│\u001b[38;5;172m \u001b[0m\u001b[38;5;172m 12\u001b[0m\u001b[38;5;172m \u001b[0m│\n",
+ "│\u001b[32m \u001b[0m\u001b[32mcomplete \u001b[0m\u001b[32m \u001b[0m│\u001b[32m \u001b[0m\u001b[32m 14\u001b[0m\u001b[32m \u001b[0m│\n",
+ "│\u001b[38;5;172m \u001b[0m\u001b[38;5;172mrunning \u001b[0m\u001b[38;5;172m \u001b[0m│\u001b[38;5;172m \u001b[0m\u001b[38;5;172m 9\u001b[0m\u001b[38;5;172m \u001b[0m│\n",
"│\u001b[38;2;23;147;208m \u001b[0m\u001b[38;2;23;147;208mwaiting \u001b[0m\u001b[38;2;23;147;208m \u001b[0m│\u001b[38;2;23;147;208m \u001b[0m\u001b[38;2;23;147;208m 0\u001b[0m\u001b[38;2;23;147;208m \u001b[0m│\n",
- "│\u001b[38;2;255;7;58m \u001b[0m\u001b[38;2;255;7;58merror \u001b[0m\u001b[38;2;255;7;58m \u001b[0m│\u001b[38;2;255;7;58m \u001b[0m\u001b[38;2;255;7;58m 0\u001b[0m\u001b[38;2;255;7;58m \u001b[0m│\n",
+ "│\u001b[38;2;255;7;58m \u001b[0m\u001b[38;2;255;7;58merror \u001b[0m\u001b[38;2;255;7;58m \u001b[0m│\u001b[38;2;255;7;58m \u001b[0m\u001b[38;2;255;7;58m 1\u001b[0m\u001b[38;2;255;7;58m \u001b[0m│\n",
"│\u001b[38;5;201m \u001b[0m\u001b[38;5;201minvalid \u001b[0m\u001b[38;5;201m \u001b[0m│\u001b[38;5;201m \u001b[0m\u001b[38;5;201m 0\u001b[0m\u001b[38;5;201m \u001b[0m│\n",
"│\u001b[38;5;129m \u001b[0m\u001b[38;5;129mdeleted \u001b[0m\u001b[38;5;129m \u001b[0m│\u001b[38;5;129m \u001b[0m\u001b[38;5;129m 0\u001b[0m\u001b[38;5;129m \u001b[0m│\n",
"└──────────────────────────────────────────────────────────────────┴──────────────────────────────────────────────┘\n"
@@ -1397,10 +1435,10 @@
{
"data": {
"text/plain": [
- "{'complete': 12, 'running': 12}"
+ "{'error': 1, 'running': 9, 'complete': 14}"
]
},
- "execution_count": 171,
+ "execution_count": 54,
"metadata": {},
"output_type": "execute_result"
}
@@ -1411,50 +1449,80 @@
},
{
"cell_type": "markdown",
- "id": "9dd5fce4-fc5d-4bc4-add2-1ecd6d0c893f",
- "metadata": {},
- "source": [
- "### Dealing with errors"
- ]
- },
- {
- "cell_type": "markdown",
- "id": "b0901744-073e-4ea4-9b5f-b9a49eeb3186",
- "metadata": {},
- "source": [
- "Inevitably, some of your `Task`s will encounter problems in execution, either random or systematic errors. When this happens, the `Task` status will be set to `'error'`. To illustrate this, we'll look at an `AlchemicalNetwork` with some failures:"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 40,
- "id": "2ae49ee5-05ff-4834-9dce-59ff2255b9e2",
+ "id": "ce6a0d3c-7276-47c4-a7a5-949e25a49fd9",
"metadata": {},
- "outputs": [],
"source": [
- "failed_tasks = asc.query_tasks(scope=Scope('ddotson'), status='error')"
+ "...and at some point, none are `waiting` or `running`; they are either `complete` or `errored`:"
]
},
{
"cell_type": "code",
- "execution_count": 41,
- "id": "0f8670fb-efd6-414b-858c-be30d3af742e",
+ "execution_count": 67,
+ "id": "033a8832-e89b-42c7-85ce-e691be138c26",
"metadata": {},
"outputs": [
+ {
+ "data": {
+ "text/html": [
+ "AlchemicalNetwork-6f22642592f789c4e7f918412ca947c5-ddotson-tyk2-demo \n",
+ "┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓\n",
+ "┃ status ┃ count ┃\n",
+ "┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩\n",
+ "│ complete │ 21 │\n",
+ "│ running │ 0 │\n",
+ "│ waiting │ 0 │\n",
+ "│ error │ 3 │\n",
+ "│ invalid │ 0 │\n",
+ "│ deleted │ 0 │\n",
+ "└──────────────────────────────────────────────────────────────────┴──────────────────────────────────────────────┘\n",
+ "
\n"
+ ],
+ "text/plain": [
+ "\u001b[3mAlchemicalNetwork-6f22642592f789c4e7f918412ca947c5-ddotson-tyk2-demo \u001b[0m\n",
+ "┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓\n",
+ "┃\u001b[1m \u001b[0m\u001b[1mstatus \u001b[0m\u001b[1m \u001b[0m┃\u001b[1m \u001b[0m\u001b[1m count\u001b[0m\u001b[1m \u001b[0m┃\n",
+ "┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩\n",
+ "│\u001b[32m \u001b[0m\u001b[32mcomplete \u001b[0m\u001b[32m \u001b[0m│\u001b[32m \u001b[0m\u001b[32m 21\u001b[0m\u001b[32m \u001b[0m│\n",
+ "│\u001b[38;5;172m \u001b[0m\u001b[38;5;172mrunning \u001b[0m\u001b[38;5;172m \u001b[0m│\u001b[38;5;172m \u001b[0m\u001b[38;5;172m 0\u001b[0m\u001b[38;5;172m \u001b[0m│\n",
+ "│\u001b[38;2;23;147;208m \u001b[0m\u001b[38;2;23;147;208mwaiting \u001b[0m\u001b[38;2;23;147;208m \u001b[0m│\u001b[38;2;23;147;208m \u001b[0m\u001b[38;2;23;147;208m 0\u001b[0m\u001b[38;2;23;147;208m \u001b[0m│\n",
+ "│\u001b[38;2;255;7;58m \u001b[0m\u001b[38;2;255;7;58merror \u001b[0m\u001b[38;2;255;7;58m \u001b[0m│\u001b[38;2;255;7;58m \u001b[0m\u001b[38;2;255;7;58m 3\u001b[0m\u001b[38;2;255;7;58m \u001b[0m│\n",
+ "│\u001b[38;5;201m \u001b[0m\u001b[38;5;201minvalid \u001b[0m\u001b[38;5;201m \u001b[0m│\u001b[38;5;201m \u001b[0m\u001b[38;5;201m 0\u001b[0m\u001b[38;5;201m \u001b[0m│\n",
+ "│\u001b[38;5;129m \u001b[0m\u001b[38;5;129mdeleted \u001b[0m\u001b[38;5;129m \u001b[0m│\u001b[38;5;129m \u001b[0m\u001b[38;5;129m 0\u001b[0m\u001b[38;5;129m \u001b[0m│\n",
+ "└──────────────────────────────────────────────────────────────────┴──────────────────────────────────────────────┘\n"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
{
"data": {
"text/plain": [
- ""
+ "{'error': 3, 'complete': 21}"
]
},
- "execution_count": 41,
+ "execution_count": 67,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
- "an2_sk = asc.get_task_networks(failed_tasks[0])[0]\n",
- "an2_sk"
+ "asc.get_network_status(an_sk)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "9dd5fce4-fc5d-4bc4-add2-1ecd6d0c893f",
+ "metadata": {},
+ "source": [
+ "### Dealing with errors"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "id": "b0901744-073e-4ea4-9b5f-b9a49eeb3186",
+ "metadata": {},
+ "source": [
+ "Inevitably, some of your `Task`s will encounter problems in execution, either random or systematic errors. When this happens, the `Task` status will be set to `'error'`."
]
},
{
@@ -1467,27 +1535,25 @@
},
{
"cell_type": "code",
- "execution_count": 42,
+ "execution_count": 68,
"id": "2a75797f-4289-4b49-9165-dd7252d055fd",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
- "[,\n",
- " ,\n",
- " ,\n",
- " ,\n",
- " ]"
+ "[,\n",
+ " ,\n",
+ " ]"
]
},
- "execution_count": 42,
+ "execution_count": 68,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
- "failed_tasks = asc.get_network_tasks(an2_sk, status='error')\n",
+ "failed_tasks = asc.get_network_tasks(an_sk, status='error')\n",
"failed_tasks"
]
},
@@ -1501,14 +1567,14 @@
},
{
"cell_type": "code",
- "execution_count": 43,
+ "execution_count": 69,
"id": "10bb091c-99f4-4dc6-9e57-bd2e6a780761",
"metadata": {},
"outputs": [
{
"data": {
"application/vnd.jupyter.widget-view+json": {
- "model_id": "16504c50b6444cceb90ddd1514b3caad",
+ "model_id": "8bb66e693c9d492186fa5869476610ab",
"version_major": 2,
"version_minor": 0
},
@@ -1520,24 +1586,18 @@
"output_type": "display_data"
},
{
- "data": {
- "text/html": [
- "\n"
- ],
- "text/plain": []
- },
- "metadata": {},
- "output_type": "display_data"
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "INFO:\tHTTP Request: GET https://api.alchemiscale.org/transformations/Transformation-15fdd9ff3f68cde67e706ffa87f6a9b7-ddotson-tyk2-demo/failures/ProtocolDAGResultRef-2bc722e46be751f9ec1a770028f393f7-ddotson-tyk2-demo \"HTTP/1.1 200 OK\"\n"
+ ]
},
{
"data": {
"text/html": [
- "\n",
- "
\n"
+ "\n"
],
- "text/plain": [
- "\n"
- ]
+ "text/plain": []
},
"metadata": {},
"output_type": "display_data"
@@ -1545,10 +1605,10 @@
{
"data": {
"text/plain": [
- "[]"
+ "[]"
]
},
- "execution_count": 43,
+ "execution_count": 69,
"metadata": {},
"output_type": "execute_result"
}
@@ -1568,17 +1628,17 @@
},
{
"cell_type": "code",
- "execution_count": 44,
+ "execution_count": 70,
"id": "b37bc64d-8fc1-42c5-8b88-4383c53f91da",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
- ""
+ ""
]
},
- "execution_count": 44,
+ "execution_count": 70,
"metadata": {},
"output_type": "execute_result"
}
@@ -1589,17 +1649,20 @@
},
{
"cell_type": "code",
- "execution_count": 45,
+ "execution_count": 71,
"id": "4ffe5d77-f42f-4157-b8d1-d8c85c241bbf",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
- "[ProtocolUnitFailure(lig_ejm_55 to lig_ejm_43 repeat 0 generation 0)]"
+ "[ProtocolUnitFailure(lig_jmc_27 to lig_jmc_28 repeat 0 generation 0),\n",
+ " ProtocolUnitFailure(lig_jmc_27 to lig_jmc_28 repeat 0 generation 0),\n",
+ " ProtocolUnitFailure(lig_jmc_27 to lig_jmc_28 repeat 0 generation 0),\n",
+ " ProtocolUnitFailure(lig_jmc_27 to lig_jmc_28 repeat 0 generation 0)]"
]
},
- "execution_count": 45,
+ "execution_count": 71,
"metadata": {},
"output_type": "execute_result"
}
@@ -1618,7 +1681,7 @@
},
{
"cell_type": "code",
- "execution_count": 46,
+ "execution_count": 72,
"id": "8bba1453-7a1b-4f6d-8f20-05009d22ba76",
"metadata": {},
"outputs": [
@@ -1627,23 +1690,29 @@
"output_type": "stream",
"text": [
"Traceback (most recent call last):\n",
- " File \"/opt/conda/lib/python3.10/site-packages/gufe/protocols/protocolunit.py\", line 319, in execute\n",
+ " File \"/lila/home/dotson/mambaforge/envs/alchemiscalemiscale-compute-ddotson-v0.5.0-2024.08.15/lib/python3.12/site-packages/gufe/protocols/protocolunit.py\", line 320, in execute\n",
" outputs = self._execute(context, **inputs)\n",
- " File \"/opt/conda/lib/python3.10/site-packages/openfe/protocols/openmm_rfe/equil_rfe_methods.py\", line 684, in _execute\n",
+ " ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
+ " File \"/lila/home/dotson/mambaforge/envs/alchemiscalemiscale-compute-ddotson-v0.5.0-2024.08.15/lib/python3.12/site-packages/openfe/protocols/openmm_rfe/equil_rfe_methods.py\", line 1129, in _execute\n",
" outputs = self.run(scratch_basepath=ctx.scratch,\n",
- " File \"/opt/conda/lib/python3.10/site-packages/openfe/protocols/openmm_rfe/equil_rfe_methods.py\", line 593, in run\n",
+ " ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
+ " File \"/lila/home/dotson/mambaforge/envs/alchemiscalemiscale-compute-ddotson-v0.5.0-2024.08.15/lib/python3.12/site-packages/openfe/protocols/openmm_rfe/equil_rfe_methods.py\", line 998, in run\n",
" sampler.setup(\n",
- " File \"/opt/conda/lib/python3.10/site-packages/openfe/protocols/openmm_rfe/_rfe_utils/multistate.py\", line 121, in setup\n",
+ " File \"/lila/home/dotson/mambaforge/envs/alchemiscalemiscale-compute-ddotson-v0.5.0-2024.08.15/lib/python3.12/site-packages/openfe/protocols/openmm_rfe/_rfe_utils/multistate.py\", line 121, in setup\n",
" minimize(compound_thermostate_copy, sampler_state,\n",
- " File \"/opt/conda/lib/python3.10/site-packages/openfe/protocols/openmm_rfe/_rfe_utils/multistate.py\", line 295, in minimize\n",
+ " File \"/lila/home/dotson/mambaforge/envs/alchemiscalemiscale-compute-ddotson-v0.5.0-2024.08.15/lib/python3.12/site-packages/openfe/protocols/openmm_rfe/_rfe_utils/multistate.py\", line 295, in minimize\n",
" context, integrator = dummy_cache.get_context(\n",
- " File \"/opt/conda/lib/python3.10/site-packages/openmmtools/cache.py\", line 770, in get_context\n",
+ " ^^^^^^^^^^^^^^^^^^^^^^^^\n",
+ " File \"/lila/home/dotson/mambaforge/envs/alchemiscalemiscale-compute-ddotson-v0.5.0-2024.08.15/lib/python3.12/site-packages/openmmtools/cache.py\", line 770, in get_context\n",
" context = thermodynamic_state.create_context(integrator, self.platform)\n",
- " File \"/opt/conda/lib/python3.10/site-packages/openmmtools/states.py\", line 1179, in create_context\n",
+ " ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
+ " File \"/lila/home/dotson/mambaforge/envs/alchemiscalemiscale-compute-ddotson-v0.5.0-2024.08.15/lib/python3.12/site-packages/openmmtools/states.py\", line 1179, in create_context\n",
" return openmm.Context(system, integrator, platform)\n",
- " File \"/opt/conda/lib/python3.10/site-packages/openmm/openmm.py\", line 3749, in __init__\n",
+ " ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
+ " File \"/lila/home/dotson/mambaforge/envs/alchemiscalemiscale-compute-ddotson-v0.5.0-2024.08.15/lib/python3.12/site-packages/openmm/openmm.py\", line 8037, in __init__\n",
" _openmm.Context_swiginit(self, _openmm.new_Context(*args))\n",
- "openmm.OpenMMException: Error initializing CUDA: CUDA_ERROR_UNKNOWN (999) at /home/conda/feedstock_root/build_artifacts/openmm_1682500546897/work/platforms/cuda/src/CudaContext.cpp:140\n",
+ " ^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
+ "openmm.OpenMMException: Error initializing CUDA: CUDA_ERROR_MPS_CONNECTION_FAILED (805) at /home/conda/feedstock_root/build_artifacts/openmm_1721257909416/work/platforms/cuda/src/CudaContext.cpp:91\n",
"\n"
]
}
@@ -1670,17 +1739,24 @@
},
{
"cell_type": "code",
- "execution_count": 58,
+ "execution_count": 73,
"id": "4c661612-7cfa-4b55-95d0-713d8fcbee22",
"metadata": {},
"outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "INFO:\tHTTP Request: POST https://api.alchemiscale.org/bulk/tasks/status/set \"HTTP/1.1 200 OK\"\n"
+ ]
+ },
{
"data": {
"text/plain": [
- "[]"
+ "[]"
]
},
- "execution_count": 58,
+ "execution_count": 73,
"metadata": {},
"output_type": "execute_result"
}
@@ -1707,52 +1783,80 @@
},
{
"cell_type": "code",
- "execution_count": 63,
+ "execution_count": 74,
"id": "704c9ddd-be00-43c3-9bc1-2ce99fb3fe02",
"metadata": {},
- "outputs": [],
- "source": [
- "results = dict()\n",
- "for tf_sk in asc.get_network_transformations(an_sk):\n",
- " results[str(tf_sk)] = asc.get_transformation_results(tf_sk, visualize=False)"
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "INFO:\tHTTP Request: GET https://api.alchemiscale.org/transformations/Transformation-82e90d15b483a813a6501073e3964930-ddotson-tyk2-demo/results/ProtocolDAGResultRef-01a2e46b4c33a9c52aab71b8c01ba5cd-ddotson-tyk2-demo \"HTTP/1.1 200 OK\"\n",
+ "INFO:\tHTTP Request: GET https://api.alchemiscale.org/transformations/Transformation-73164716e2ad3c2e410fce413fa41be4-ddotson-tyk2-demo/results/ProtocolDAGResultRef-caabc7fbbe8e9bae4ad0da4f5db7cb61-ddotson-tyk2-demo \"HTTP/1.1 200 OK\"\n",
+ "INFO:\tHTTP Request: GET https://api.alchemiscale.org/transformations/Transformation-e3022bfd607e772136f5c262875a8e78-ddotson-tyk2-demo/results/ProtocolDAGResultRef-b6b00c75b4f66e546623a98d42b165c8-ddotson-tyk2-demo \"HTTP/1.1 200 OK\"\n",
+ "INFO:\tHTTP Request: GET https://api.alchemiscale.org/transformations/Transformation-6064e55fed6e90b90b727b299462cbad-ddotson-tyk2-demo/results/ProtocolDAGResultRef-f87f2f38715e0e03c30b574fe3c0e01d-ddotson-tyk2-demo \"HTTP/1.1 200 OK\"\n",
+ "INFO:\tHTTP Request: GET https://api.alchemiscale.org/transformations/Transformation-28453f83bb03486a08afc096a8dc5298-ddotson-tyk2-demo/results/ProtocolDAGResultRef-d206475f1ae25c4818964579eabca7b0-ddotson-tyk2-demo \"HTTP/1.1 200 OK\"\n",
+ "INFO:\tHTTP Request: GET https://api.alchemiscale.org/transformations/Transformation-eebbe29feefc097086749081844d8adc-ddotson-tyk2-demo/results/ProtocolDAGResultRef-2a9f4953c83460388614a4cb872bc601-ddotson-tyk2-demo \"HTTP/1.1 200 OK\"\n",
+ "INFO:\tHTTP Request: GET https://api.alchemiscale.org/transformations/Transformation-2a345646fa5b3900aba8b74935fc4ec6-ddotson-tyk2-demo/results/ProtocolDAGResultRef-821c1a7ccc7740a28f4dd3d553b2f035-ddotson-tyk2-demo \"HTTP/1.1 200 OK\"\n",
+ "INFO:\tHTTP Request: GET https://api.alchemiscale.org/transformations/Transformation-f8fb4a09881bce886dcb55a88be49016-ddotson-tyk2-demo/results/ProtocolDAGResultRef-8295104d5c32f10bdd86b69675bb7494-ddotson-tyk2-demo \"HTTP/1.1 200 OK\"\n",
+ "INFO:\tHTTP Request: GET https://api.alchemiscale.org/transformations/Transformation-874c39cca17041ceb7a91f142104e8eb-ddotson-tyk2-demo/results/ProtocolDAGResultRef-2d7d1eed2ee1b96e67c95385c14b220c-ddotson-tyk2-demo \"HTTP/1.1 200 OK\"\n",
+ "INFO:\tHTTP Request: GET https://api.alchemiscale.org/transformations/Transformation-b4857c06e9564cf3c2451f436f7af410-ddotson-tyk2-demo/results/ProtocolDAGResultRef-fdea668674894a4ebc21cd51a9ca8e02-ddotson-tyk2-demo \"HTTP/1.1 200 OK\"\n",
+ "INFO:\tHTTP Request: GET https://api.alchemiscale.org/transformations/Transformation-958a3d55d581ec276b72394435df4bd0-ddotson-tyk2-demo/results/ProtocolDAGResultRef-19825c22d09bf2a8d70e47e5cac34829-ddotson-tyk2-demo \"HTTP/1.1 200 OK\"\n",
+ "INFO:\tHTTP Request: GET https://api.alchemiscale.org/transformations/Transformation-22a2847c2a28584956e90d549fc6bcc6-ddotson-tyk2-demo/results/ProtocolDAGResultRef-83f986401353591db65c9ed401af260b-ddotson-tyk2-demo \"HTTP/1.1 200 OK\"\n",
+ "INFO:\tHTTP Request: GET https://api.alchemiscale.org/transformations/Transformation-d5cdd9f4f4edd380361129082a01360b-ddotson-tyk2-demo/results/ProtocolDAGResultRef-57a8c3097273d30ff5b0350943883824-ddotson-tyk2-demo \"HTTP/1.1 200 OK\"\n",
+ "INFO:\tHTTP Request: GET https://api.alchemiscale.org/transformations/Transformation-20fd18a057e4affd5c78cad41a81d3b4-ddotson-tyk2-demo/results/ProtocolDAGResultRef-2798447525f7139b158919d08faadb95-ddotson-tyk2-demo \"HTTP/1.1 200 OK\"\n",
+ "INFO:\tHTTP Request: GET https://api.alchemiscale.org/transformations/Transformation-44cf523e9d0e53674fadc59c9b9110b7-ddotson-tyk2-demo/results/ProtocolDAGResultRef-f56c970e363dbe075f2dda74386055a8-ddotson-tyk2-demo \"HTTP/1.1 200 OK\"\n",
+ "INFO:\tHTTP Request: GET https://api.alchemiscale.org/transformations/Transformation-856f85d23d9b8b84916d5b83ebfa1773-ddotson-tyk2-demo/results/ProtocolDAGResultRef-f94dec1b5cc13aff45aba30eb1647c3c-ddotson-tyk2-demo \"HTTP/1.1 200 OK\"\n",
+ "INFO:\tHTTP Request: GET https://api.alchemiscale.org/transformations/Transformation-ef57a778259ba88b9fb4c23cc2bd78f4-ddotson-tyk2-demo/results/ProtocolDAGResultRef-474df4f73b5bdb270a43361d8651dfa4-ddotson-tyk2-demo \"HTTP/1.1 200 OK\"\n",
+ "INFO:\tHTTP Request: GET https://api.alchemiscale.org/transformations/Transformation-c33480c9f0dfd80852541205f46914a7-ddotson-tyk2-demo/results/ProtocolDAGResultRef-943e801e0c7774f3c962ca8127150ace-ddotson-tyk2-demo \"HTTP/1.1 200 OK\"\n",
+ "INFO:\tHTTP Request: GET https://api.alchemiscale.org/transformations/Transformation-4bfeb3edd7f0d47ec52f533a5cf435a0-ddotson-tyk2-demo/results/ProtocolDAGResultRef-0d56400cc2c06fe557f170b872c9a465-ddotson-tyk2-demo \"HTTP/1.1 200 OK\"\n",
+ "INFO:\tHTTP Request: GET https://api.alchemiscale.org/transformations/Transformation-06eac733376ab1ff566248040fe37e01-ddotson-tyk2-demo/results/ProtocolDAGResultRef-cc1df82df45efd8fba44f029a28094b6-ddotson-tyk2-demo \"HTTP/1.1 200 OK\"\n",
+ "INFO:\tHTTP Request: GET https://api.alchemiscale.org/transformations/Transformation-76de739d87d53981abfff4ab9ce071e4-ddotson-tyk2-demo/results/ProtocolDAGResultRef-810f1f48475da9a8cbb7ed364848cdf2-ddotson-tyk2-demo \"HTTP/1.1 200 OK\"\n"
+ ]
+ }
+ ],
+ "source": [
+ "results = dict()\n",
+ "for tf_sk in asc.get_network_transformations(an_sk):\n",
+ " results[str(tf_sk)] = asc.get_transformation_results(tf_sk, visualize=False)"
]
},
{
"cell_type": "code",
- "execution_count": 64,
+ "execution_count": 75,
"id": "816d46a2-178b-459a-80a5-357b5438462a",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
- "{'Transformation-3bde3c547da7c4db25af92e94f34efce-ddotson-tyk2-demo': ,\n",
- " 'Transformation-3d1c7ab3c70341bc88fc91112689a648-ddotson-tyk2-demo': ,\n",
- " 'Transformation-333a2629c325b4f257b416c2431d9132-ddotson-tyk2-demo': ,\n",
- " 'Transformation-086a259a37b0f93979cc23dc31344aa8-ddotson-tyk2-demo': ,\n",
- " 'Transformation-553107db824ee8a99f30fb42cbe5798c-ddotson-tyk2-demo': ,\n",
- " 'Transformation-08f4c68a8e178d698e59cc1a366e3415-ddotson-tyk2-demo': ,\n",
- " 'Transformation-c244dffbafa7e4e95ff4c0a03a54888b-ddotson-tyk2-demo': ,\n",
- " 'Transformation-7080ba2b294fbb443f7c8fd0432523b8-ddotson-tyk2-demo': ,\n",
- " 'Transformation-2168cd5e6257debd9e31a7dea8f865db-ddotson-tyk2-demo': ,\n",
- " 'Transformation-6fedaff17af81e8f8cd903ff54f4fa43-ddotson-tyk2-demo': ,\n",
- " 'Transformation-058b41226978833e875145eca60fa44d-ddotson-tyk2-demo': ,\n",
- " 'Transformation-a34291c782001508c20b0f8fbd8e8768-ddotson-tyk2-demo': ,\n",
- " 'Transformation-be3971fa5275fae3d0767ef387e4f673-ddotson-tyk2-demo': ,\n",
- " 'Transformation-c824272678b20bb10b0b3ed82a75cba7-ddotson-tyk2-demo': ,\n",
- " 'Transformation-72f58e6ef2cc85e52de765b797fb935b-ddotson-tyk2-demo': ,\n",
- " 'Transformation-d5634110bde446e3c0135a213ca126be-ddotson-tyk2-demo': ,\n",
- " 'Transformation-cfc64db96341e6c6fe78b31bc45086fe-ddotson-tyk2-demo': ,\n",
- " 'Transformation-f549eb13fa5c5aa43a4b0581509ec17b-ddotson-tyk2-demo': ,\n",
- " 'Transformation-22f055e336144e1192a54fc36b008761-ddotson-tyk2-demo': ,\n",
- " 'Transformation-954a54426ba12cd7f97b163692de84b3-ddotson-tyk2-demo': ,\n",
- " 'Transformation-43fcc3ea77628d04acffbfafaf7289f3-ddotson-tyk2-demo': ,\n",
- " 'Transformation-1ed12e0907b854bd0810ebb8bce91bbd-ddotson-tyk2-demo': ,\n",
- " 'Transformation-e85c3cfe5386d9e53c4593acf52df560-ddotson-tyk2-demo': ,\n",
- " 'Transformation-1d104d98ba12a95e13d2e086f1839b51-ddotson-tyk2-demo': }"
- ]
- },
- "execution_count": 64,
+ "{'Transformation-15fdd9ff3f68cde67e706ffa87f6a9b7-ddotson-tyk2-demo': None,\n",
+ " 'Transformation-152928d4d69298dcedf2dd622073a95b-ddotson-tyk2-demo': None,\n",
+ " 'Transformation-82e90d15b483a813a6501073e3964930-ddotson-tyk2-demo': ,\n",
+ " 'Transformation-73164716e2ad3c2e410fce413fa41be4-ddotson-tyk2-demo': ,\n",
+ " 'Transformation-e3022bfd607e772136f5c262875a8e78-ddotson-tyk2-demo': ,\n",
+ " 'Transformation-6064e55fed6e90b90b727b299462cbad-ddotson-tyk2-demo': ,\n",
+ " 'Transformation-28453f83bb03486a08afc096a8dc5298-ddotson-tyk2-demo': ,\n",
+ " 'Transformation-eebbe29feefc097086749081844d8adc-ddotson-tyk2-demo': ,\n",
+ " 'Transformation-2a345646fa5b3900aba8b74935fc4ec6-ddotson-tyk2-demo': ,\n",
+ " 'Transformation-f8fb4a09881bce886dcb55a88be49016-ddotson-tyk2-demo': ,\n",
+ " 'Transformation-874c39cca17041ceb7a91f142104e8eb-ddotson-tyk2-demo': ,\n",
+ " 'Transformation-b4857c06e9564cf3c2451f436f7af410-ddotson-tyk2-demo': ,\n",
+ " 'Transformation-958a3d55d581ec276b72394435df4bd0-ddotson-tyk2-demo': ,\n",
+ " 'Transformation-22a2847c2a28584956e90d549fc6bcc6-ddotson-tyk2-demo': ,\n",
+ " 'Transformation-d5cdd9f4f4edd380361129082a01360b-ddotson-tyk2-demo': ,\n",
+ " 'Transformation-20fd18a057e4affd5c78cad41a81d3b4-ddotson-tyk2-demo': ,\n",
+ " 'Transformation-44cf523e9d0e53674fadc59c9b9110b7-ddotson-tyk2-demo': ,\n",
+ " 'Transformation-856f85d23d9b8b84916d5b83ebfa1773-ddotson-tyk2-demo': ,\n",
+ " 'Transformation-ef57a778259ba88b9fb4c23cc2bd78f4-ddotson-tyk2-demo': ,\n",
+ " 'Transformation-c33480c9f0dfd80852541205f46914a7-ddotson-tyk2-demo': ,\n",
+ " 'Transformation-4bfeb3edd7f0d47ec52f533a5cf435a0-ddotson-tyk2-demo': ,\n",
+ " 'Transformation-8e74110792d4c68bb5a772733d490401-ddotson-tyk2-demo': None,\n",
+ " 'Transformation-06eac733376ab1ff566248040fe37e01-ddotson-tyk2-demo': ,\n",
+ " 'Transformation-76de739d87d53981abfff4ab9ce071e4-ddotson-tyk2-demo': }"
+ ]
+ },
+ "execution_count": 75,
"metadata": {},
"output_type": "execute_result"
}
@@ -1763,56 +1867,56 @@
},
{
"cell_type": "code",
- "execution_count": 68,
+ "execution_count": 76,
"id": "35d41826-c6fa-44fe-aec9-45e85bd5d30c",
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
- "39.7580051742956 kilocalorie/mole"
+ "20.937595533249475 kilocalorie_per_mole"
],
"text/latex": [
- "$39.7580051742956\\ \\frac{\\mathrm{kilocalorie}}{\\mathrm{mole}}$"
+ "$20.937595533249475\\ \\mathrm{kilocalorie\\_per\\_mole}$"
],
"text/plain": [
- "39.7580051742956 "
+ "20.937595533249475 "
]
},
- "execution_count": 68,
+ "execution_count": 76,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
- "results['Transformation-08f4c68a8e178d698e59cc1a366e3415-ddotson-tyk2-demo'].get_estimate()"
+ "results['Transformation-82e90d15b483a813a6501073e3964930-ddotson-tyk2-demo'].get_estimate()"
]
},
{
"cell_type": "code",
- "execution_count": 69,
+ "execution_count": 77,
"id": "88efaebb-a47b-4a53-b6b9-382bcfc2b1ec",
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
- "0.0 kilocalorie/mole"
+ "0.0 kilocalorie_per_mole"
],
"text/latex": [
- "$0.0\\ \\frac{\\mathrm{kilocalorie}}{\\mathrm{mole}}$"
+ "$0.0\\ \\mathrm{kilocalorie\\_per\\_mole}$"
],
"text/plain": [
- "0.0 "
+ "0.0 "
]
},
- "execution_count": 69,
+ "execution_count": 77,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
- "results['Transformation-08f4c68a8e178d698e59cc1a366e3415-ddotson-tyk2-demo'].get_uncertainty()"
+ "results['Transformation-82e90d15b483a813a6501073e3964930-ddotson-tyk2-demo'].get_uncertainty()"
]
},
{
@@ -1822,7 +1926,7 @@
"source": [
"In this case, we have only a single `ProtocolDAGResult` for each `Transformation` (since we created and actioned only 1 `Task` for each), and so the uncertainty (standard deviation between replicate simulations) given for this `ProtocolResult` is 0.0. The `RelativeHybridTopologyProtocol` combines `ProtocolDAGResult` values statistically, reducing the uncertainty but not increasing convergence with additional `Task`s\n",
"\n",
- "By contrast other `Protocol`s, such as the `perses` `NonEquilibriumCyclingProtocol`, will improve convergence with more `Task`s on a given `Transformation`; in the case of the `NonEquilibriumCyclingProtocol`, the non-equilibrium work values for each `ProtocolDAGResult` are combined together and fed to `BAR` to produce a single estimate with its own uncertainty."
+ "By contrast other `Protocol`s, such as the `feflow` `NonEquilibriumCyclingProtocol`, will improve convergence with more `Task`s on a given `Transformation`; in the case of the `NonEquilibriumCyclingProtocol`, the non-equilibrium work values for each `ProtocolDAGResult` are combined together and fed to `BAR` to produce a single estimate with its own uncertainty."
]
},
{
@@ -1835,64 +1939,64 @@
},
{
"cell_type": "code",
- "execution_count": 58,
+ "execution_count": 78,
"id": "78a17d4c-da4d-4879-a7d1-ae81f158fc00",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
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