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Implementation of Water Bridge Interaction Calculation #225

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Implementation of Water Bridge Interaction Calculation #225

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bd61970
Update fingerprint.py
talagayev Nov 10, 2024
df3c1ba
Update fingerprint.py
talagayev Nov 14, 2024
0583aac
Update fingerprint.py
talagayev Nov 15, 2024
f8bb5af
fix and refactor merged data
cbouy Nov 16, 2024
8844af7
chore: allow WaterBridge in interactions list
cbouy Nov 18, 2024
57665be
fix: include WaterBridge in list of interactions
cbouy Nov 22, 2024
f377538
tests: add files and basic unit tests
cbouy Nov 22, 2024
0478d95
docs: fix list instead of dict
cbouy Nov 24, 2024
fd128d5
chore: update converter cache size conditionally
cbouy Nov 24, 2024
56eb85f
tests: improve coverage
cbouy Nov 24, 2024
53f420e
docs: add docstring for bridged analysis and rename with underscore
cbouy Nov 24, 2024
40763d0
chore: add count support
cbouy Nov 24, 2024
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9 changes: 3 additions & 6 deletions docs/notebooks/docking.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -609,7 +609,7 @@
"ref_mol = plf.Molecule.from_mda(ref)\n",
"\n",
"# generate IFP for the reference\n",
"fp_ref = plf.Fingerprint(fp.interactions)\n",
"fp_ref = plf.Fingerprint(list(fp.interactions))\n",
"fp_ref.run_from_iterable([ref_mol], protein_mol)\n",
"df_ref = fp_ref.to_dataframe(index_col=\"Pose\")\n",
"\n",
Expand Down Expand Up @@ -853,11 +853,8 @@
}
],
"metadata": {
"interpreter": {
"hash": "8787e9fc73b27535744a25d17e74686c0add9df598b8e27ca04412fce7f0c7ae"
},
"kernelspec": {
"display_name": "Python 3.8.5 ('prolif')",
"display_name": "prolif",
"language": "python",
"name": "python3"
},
Expand All @@ -871,7 +868,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.13"
"version": "3.11.9"
}
},
"nbformat": 4,
Expand Down
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