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hypnopump / chemnlp_rhea_x_uniprot_parsing.ipynb
Last active April 28, 2023 11:35
Prototype for a Rhea (https://www.rhea-db.org/) parser. The idea is to connect reactions to Uniprot enzymes
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hypnopump / keops_attention.py
Last active December 1, 2022 14:24
Attention comparison between PyTorch and KeOps
"""
Copyright 2021 Eric Alcaide
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
Redistribution and use in source and binary forms, with or without modification, are permitted provided that the
following conditions are met:
1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
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hypnopump / dihedral_angle_from_coordinates.py
Last active February 29, 2024 20:53
Dihedral angles from coordinates. Get dihedral angles from protein backbone coordinates. Calculate Phi, Psi from 3D coordinates of (N-term, C-alpha and C-term)
""" Dihedral angles from coordinates. Get dihedral angles from
protein backbone coordinates.
This script takes 4 vectors representing 4 points as input
and returns the dihedral angle between them.
The script was originally developed to calculate dihedral angles (phi,psi)
from protein backbone atoms' coordinates in 3D (N-term, C-alhpa, Cterm).
"""
import numpy as np
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hypnopump / keybase.md
Created July 21, 2017 21:49

Keybase proof

I hereby claim:

  • I am ericalcaide on github.
  • I am ericalcaide (https://keybase.io/ericalcaide) on keybase.
  • I have a public key ASCgsxWHQ6CsueecShMbhOLE-3nV3KFQVXRPkVaXrYXpQQo

To claim this, I am signing this object: