ljmartin
/ sesmesh_distance_grid_algorithm.ipynb
Created
November 24, 2021 01:51
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ljmartin
/ binding_affinity.ipynb
Created
November 29, 2021 21:42
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ljmartin
/ example_duckdb.ipynb
Created
January 8, 2022 21:48
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ljmartin
/ treetrunk.ipynb
Created
January 10, 2022 08:50
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ljmartin
/ bayesian_IC50_blog.ipynb
Created
March 29, 2022 08:54
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ljmartin
/ dunbrack.aln
Created
June 30, 2022 03:58
This file has been truncated, but you can view the full file.
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| CLUSTAL | |
| 0ANNOTATION/1-2208 B1N---B1N~B1C-------B1C--------B1~B2-------B2---------B2~B3- | |
| AGC_AKT1/150-408 FEYL----------------KLLGKGT----------------FGKVILVKE--ka---- | |
| AGC_AKT2/152-409 FDYL----------------KLLGKGT----------------FGKVILVRE--ka---- | |
| AGC_AKT3/148-405 FDYL----------------KLLGKGT----------------FGKVILVRE--ka---- | |
| AGC_CDC42BPA/77-343 FEIL----------------KVIGRGA----------------FGEVAVVKL--kn---- | |
| AGC_CDC42BPB/76-342 FEII----------------KVIGRGA----------------FGEVAVVKM--kn---- | |
| AGC_CDC42BPG/71-337 FEIL----------------KVIGRGA----------------FGEVTVVRQ--rd---- | |
| AGC_CIT/97-360 FEVR----------------SLVGCGH----------------FAEVQVVRE--ka---- |
ljmartin
/ smooth_one.py
Created
July 4, 2022 03:32
a function that looks like y=x at a distance, but smoothly goes to 1 instead of 0.
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| def f(x): | |
| return (x**3 + x**2 + x + 1) / (x**2 + x + 1) | |
| x = np.linspace(0,10,100) | |
| plt.plot(x, f(x)) | |
| plt.plot(x,x) |
ljmartin
/ rankingGeometric.ipynb
Created
November 8, 2022 22:51
modeling ability to rank with pymc3 using geometric distribution
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ljmartin
/ binary_LogReg_DuckDB.ipynb
Last active
November 25, 2022 06:15
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ljmartin
/ hbonds_like_molstar.py
Created
December 12, 2022 06:28
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| prot_dons = np.array(pocket.GetSubstructMatches(HDonorSmarts)).flatten() | |
| prot_accs = np.array(pocket.GetSubstructMatches(HAcceptorSmarts)).flatten() | |
| lig_dons = np.array(ligand.GetSubstructMatches(HDonorSmarts)).flatten() | |
| lig_accs = np.array(ligand.GetSubstructMatches(HAcceptorSmarts)).flatten() | |
| def unit_vector(vector): | |
| """ Returns the unit vector of the vector. """ | |
| return vector / np.linalg.norm(vector) |