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Merged
ChristineSchulz merged 2 commits into from
Aug 4, 2026
Merged

[pre-commit.ci] pre-commit autoupdate #45

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6b03d93
[pre-commit.ci] pre-commit autoupdate
pre-commit-ci[bot] Aug 3, 2026
0e02e7b
fix: ruff checks
ChristineSchulz Aug 4, 2026
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2 changes: 1 addition & 1 deletion .pre-commit-config.yaml
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@@ -1,7 +1,7 @@
repos:
- repo: https://github.com/astral-sh/ruff-pre-commit
# Ruff version.
rev: v0.16.0
rev: v0.16.1
hooks:
# Run the linter.
- id: ruff-check
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2 changes: 1 addition & 1 deletion notebooks/AFold_Alignment_CPU.ipynb
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Expand Up @@ -24,8 +24,8 @@
"metadata": {},
"outputs": [],
"source": [
"from pathlib import Path\n",
"import os\n",
"from pathlib import Path\n",
"\n",
"ALPHAFOLD_MODEL_DIR = Path.cwd() / \"af3models\""
]
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9 changes: 5 additions & 4 deletions notebooks/AFold_Confidence_Levels.ipynb
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Expand Up @@ -18,13 +18,14 @@
"metadata": {},
"outputs": [],
"source": [
"from Bio.PDB.MMCIF2Dict import MMCIF2Dict\n",
"import json\n",
"import pandas as pd\n",
"import numpy as np\n",
"from pathlib import Path\n",
"\n",
"import matplotlib.pyplot as plt\n",
"import numpy as np\n",
"import pandas as pd\n",
"import seaborn as sns\n",
"from pathlib import Path"
"from Bio.PDB.MMCIF2Dict import MMCIF2Dict"
]
},
{
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10 changes: 5 additions & 5 deletions notebooks/AFold_Diffusion_GPU.ipynb
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Expand Up @@ -15,8 +15,8 @@
"metadata": {},
"outputs": [],
"source": [
"from pathlib import Path\n",
"import os"
"import os\n",
"from pathlib import Path"
]
},
{
Expand Down Expand Up @@ -104,10 +104,10 @@
"\n",
"# Run with option --norun_data_pipeline for featurisation and model inference\n",
"python $ALPHAFOLD_BIN_DIR/run_alphafold.py \\\\\n",
" --json_path={str(ALPHAFOLD_JSON_PATH_PART2)} \\\\\n",
" --json_path={ALPHAFOLD_JSON_PATH_PART2!s} \\\\\n",
" --db_dir=$ALPHAFOLD_DATABASES \\\\\n",
" --model_dir={str(ALPHAFOLD_MODEL_DIR)} \\\\\n",
" --output_dir={str(ALPHAFOLD_RESULTS_DIR_PART2)} \\\\\n",
" --model_dir={ALPHAFOLD_MODEL_DIR!s} \\\\\n",
" --output_dir={ALPHAFOLD_RESULTS_DIR_PART2!s} \\\\\n",
" --norun_data_pipeline\n",
"\n",
"\"\"\"\n",
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6 changes: 3 additions & 3 deletions notebooks/Boltz_w_mmseqs.ipynb
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Expand Up @@ -7,9 +7,9 @@
"metadata": {},
"outputs": [],
"source": [
"from pathlib import Path\n",
"import os\n",
"import re"
"import re\n",
"from pathlib import Path"
]
},
{
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"module load devel/cuda/12.8\n",
"conda activate /mnt/sds-hd/sd25g005/boltz\n",
"\n",
"boltz predict {str(INPUT_FILE)} \\\\\n",
"boltz predict {INPUT_FILE!s} \\\\\n",
" --write_full_pae \\\\\n",
" --out_dir {BOLTZ_WORKING_DIR}\n",
"\"\"\"\n",
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6 changes: 3 additions & 3 deletions notebooks/bindcraft.ipynb
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Expand Up @@ -7,10 +7,10 @@
"metadata": {},
"outputs": [],
"source": [
"from pathlib import Path\n",
"import json\n",
"import subprocess\n",
"import sys\n",
"import subprocess"
"from pathlib import Path"
]
},
{
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}
],
"source": [
"subprocess.run(subprocess_command)"
"subprocess.run(subprocess_command, check=False)"
]
},
{
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5 changes: 3 additions & 2 deletions notebooks/boltz_confidence_levels.ipynb
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Expand Up @@ -14,9 +14,10 @@
"source": [
"import json\n",
"from pathlib import Path\n",
"import pandas as pd\n",
"import numpy as np\n",
"\n",
"import matplotlib.pyplot as plt\n",
"import numpy as np\n",
"import pandas as pd\n",
"import seaborn as sns"
]
},
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8 changes: 4 additions & 4 deletions notebooks/boltzgen.ipynb
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Expand Up @@ -7,8 +7,8 @@
"metadata": {},
"outputs": [],
"source": [
"from pathlib import Path\n",
"import os"
"import os\n",
"from pathlib import Path"
]
},
{
Expand Down Expand Up @@ -128,8 +128,8 @@
"conda activate /mnt/sds-hd/sd25g005/boltzgen\n",
"\n",
"\n",
"boltzgen run {str(BOLTZGEN_YAML_PATH)} \\\\\n",
" --output {str(RESULTS_DIR)} \\\\\n",
"boltzgen run {BOLTZGEN_YAML_PATH!s} \\\\\n",
" --output {RESULTS_DIR!s} \\\\\n",
" --protocol protein-anything \\\\\n",
" --num_designs 10 \\\\\n",
" --budget 2 \\\\\n",
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101 changes: 101 additions & 0 deletions notebooks/output/G3_smol_model_0_log.txt
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#"Step","Potential Energy (kJ/mole)","Temperature (K)"
100,-81080.58720808476,121.31874120383213
200,-78313.7057307288,185.32396860376724
300,-76481.71139936894,222.82389004569384
400,-75192.7838633582,249.57350582339248
500,-74760.0232584998,275.2175138159008
600,-73913.4253199622,272.1033746816618
700,-73410.06711988896,279.82156893470335
800,-73219.50578718632,290.92226920809645
900,-73337.76031523198,291.43830015630317
1000,-73069.85076551884,288.9139028217889
1100,-72761.8388331458,290.34052810131897
1200,-72712.72887068242,296.39741008170915
1300,-72779.40636854619,299.73433139791416
1400,-72424.32328443974,290.80775757192606
1500,-72504.57073622197,298.68291387320204
1600,-72551.92991667241,307.9075478787154
1700,-72335.59952955693,300.3021881406422
1800,-72602.98579054326,299.2159084899603
1900,-72645.23365431279,305.4544144483917
2000,-72561.47773390263,303.1927752667898
2100,-72394.57427626103,307.5467468699607
2200,-72460.05600004643,306.0321414618004
2300,-72389.21426802129,305.9075670984179
2400,-72380.62618666142,295.32509727644737
2500,-72440.75621443242,299.3691038889378
2600,-72795.96334104985,306.5323359868537
2700,-72524.70404844731,300.56453388670155
2800,-72585.37475996464,306.6681553104267
2900,-72328.19083815068,299.7429094604556
3000,-72153.89075117558,294.2909183581887
3100,-72533.38107328862,297.14334410354286
3200,-72479.74862699956,292.1639162671813
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3500,-72760.6135142371,312.77254656027725
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3900,-73093.92625074834,302.3504755103157
4000,-72820.89785414189,295.7159489978873
4100,-72964.53731947392,310.0887952177814
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4400,-73039.0674193427,300.10269319897304
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5000,-72847.03686218709,298.14112124358076
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5800,-72867.73728971928,298.90822548386615
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6000,-72850.32148390263,300.07382471926627
6100,-72737.50778608769,298.5724163304005
6200,-72779.8195841834,298.05457079204075
6300,-72642.34109144658,301.70255685053417
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6900,-72604.8387291953,305.2812860515214
7000,-72357.47517042607,306.13271374634087
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9800,-72662.3186076209,298.1290789634745
9900,-72767.03103189915,306.64489556392004
10000,-72676.8577998206,303.147025599902
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