sjdv1982

Nucleotide Repositories

This document describes the planned repository split for nucleotide-fragment generation, library construction, rotaconformer generation, and downstream analysis. The plan originated in professional-TODO/ and is still to be finalized.

Repository Dependency Diagram

sjdv1982

Hello world!

sjdv1982

(continuing the same chat, ChatGPT 5.4 Thinking)

Prompt

(your question verbatim)

Tu peux me confirmer ou non que l'ordre des atomes dans les npy est toujours le meme?

Response

sjdv1982

Prompt

Hello, can you explain to me how to get the coordinates corresponding to my conformer indices? I was given the indices before, and now I would like to know how to get the corresponding coordinates. I was given a link to the GitHub repo of the coordinates:

https://github.com/sjdv1982/nucleotide-library (it contains a README)

and the following explanation:

Your conformer indices should correspond to the conformer array that you get when you concatenate the primary .npy and the extension .npy

sjdv1982

import numpy as np
import jax
from jax import numpy as jnp

def _run_argsort_numpy(args) -> jnp.ndarray:
    jax.debug.print("Run argsort using Numpy")
    arr, axis = args
    return np.argsort(arr, axis=axis).astype(np.int32)

def run_argsort_numpy(arr:jnp.ndarray, axis=None) -> jnp.ndarray:

sjdv1982

# Author: Sjoerd de Vries, CNRS
# license: public domain

import sys
import os
import h5py
import numpy as np

active_paper_file = sys.argv[1]
target_directory = sys.argv[2]

sjdv1982

"""
11 cards, 55 points in total

S = current score
K = cards remaining

score increase = (chance to draw a non-joker * average value of non-joker) - (chance to draw a joker * S)
= (K-1)/K * (55-S)/(K-1) - 1/K * S
= (55-S)/K - S/K
= (55 - 2S)/K

sjdv1982

"""
Parses the biological assemblies of a mmCIF file
For each assembly.
 a list of 4x4 transformation matrices is computed, and returned together
 with a list of chains
Each transformation matrix is to be applied to each chain in the list

Biological assemblies may contain non-protein or fantasy chains; it is possible
 to pass in a list of interesting chains, and the returned chain lists will
 then be filtered accordingly

sjdv1982

"""fivethirtyeight.com Riddler Classic, Dec 11
https://fivethirtyeight.com/features/how-high-can-you-count-with-menorah-math/


'''
From Alex van den Brandhof comes a matter of life and death:

The Potentate of Puzzles decides to give five unlucky citizens a test. The potentate has countless red hats, green hats and blue hats. She says to the citizens, “Tomorrow, you will all be blindfolded as I place one of these hats on each of your heads. Once all the hats are placed, your blindfolds will be removed. At this point, there will be no communication between any of you! As soon as I give a signal, everyone must guess — at the same time — the color of the hat atop their own head. If at least one of you guesses correctly, all of you will survive! Otherwise …”

The potentate continues: “The good news is that there’s a little more information you’ll have. I will be arranging you into two rows facing each other, with two of you in one row and three of you in the other. Citizens in the same row cannot see each other,

sjdv1982