ljmartin
/ addCaps-start-to-finish.ipynb
Created
November 26, 2023 04:17
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
ljmartin
/ hbond_w_rdkit_example.ipynb
Created
November 26, 2023 04:09
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
ljmartin
/ methane.xml
Created
September 16, 2023 09:31
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| <ForceField> | |
| <AtomTypes> | |
| <Type name="metha-C" class="O" element="C" mass="16.04"/> | |
| </AtomTypes> | |
| <Residues> | |
| <Residue name="UME"> | |
| <Atom name="C" type="metha-C"/> | |
| </Residue> | |
| </Residues> | |
| <NonbondedForce coulomb14scale="0.833333" lj14scale="0.5"> |
ljmartin
/ twoD_vDW_surfaces.ipynb
Last active
August 25, 2023 08:47
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
ljmartin
/ super-gaussians.ipynb
Created
January 27, 2023 03:24
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
ljmartin
/ hbonds_like_molstar.py
Created
December 12, 2022 06:28
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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) |
ljmartin
/ binary_LogReg_DuckDB.ipynb
Last active
November 25, 2022 06:15
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
ljmartin
/ rankingGeometric.ipynb
Created
November 8, 2022 22:51
modeling ability to rank with pymc3 using geometric distribution
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
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.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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
/ dunbrack.aln
Created
June 30, 2022 03:58
This file has been truncated, but you can view the full file.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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---- |