Collin Arnett collinarnett

## keybase.md

      
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                collinarnett
                / keybase.md
            
            
              Created
              August 1, 2022 15:42
            
          
    Keybase proof

I hereby claim:

I am collinarnett on github.
I am collinarnett (https://keybase.io/collinarnett) on keybase.
I have a public key ASDpLh5BV42nb3PqkA5T4p2neVWsovqb3cmx9H_9OraQJQo

To claim this, I am signing this object:

  
## flake.nix
{
  inputs = {
    flake-utils.url = "github:numtide/flake-utils";
    nickel.url = "github:tweag/nickel";
  };
  outputs = { self, nixpkgs, flake-utils, nickel }@inputs:
    flake-utils.lib.eachDefaultSystem (system:
      let pkgs = nixpkgs.legacyPackages.${system};
      in rec {
        devShell =

## pimp_my_zeus.md

      
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                collinarnett
                / pimp_my_zeus.md
            
            
              Created
              November 3, 2021 18:47
            
              
                Making Zeus more user friendly
              
          
    Making Zeus more user friendly

Professors will often instruct students to use zeus without explain much. This is not unusual since their objective is not to teach you about the command line interface (CLI) but rather the content of the course. This guide is meant to simplify the process of using Zeus while also giving a brief glimse into the motivation behind using the CLI.
Logging In

Currently the process of logging into Zeus is as follows:

Enter the ssh command


## pi_camera.py
import io
import picamera
import logging
import socketserver
from threading import Condition
from http import server

PAGE="""\
<html>
<head>

## architectures.py
# 64x64
class Generator64(nn.Module):
    def __init__(self, ngpu):
        super(Generator64, self).__init__()
        self.ngpu = ngpu
        self.main = nn.Sequential(
            nn.ConvTranspose2d(100, 512, kernel_size=4, stride=1, padding=0),
            nn.BatchNorm2d(512),
            nn.LeakyReLU(0.2),
            nn.ConvTranspose2d(512, 256, kernel_size=4, stride=2, padding=1),

## distance_maps.py
def calc_dist_matrix(residues):
    """Returns a matrix of distances between residues of the same chain."""
    size = len(residues)
    answer = np.zeros((size, size), np.float)
    for row, residue_one in enumerate(residues):
        for col, residue_two in enumerate(residues):
            answer[row, col] = residue_one["CA"] - residue_two["CA"]
    return answer

## download_data.py
from pathlib import Path
from urllib import request
from tqdm import tqdm

test_folder = Path("test")
train_folder = Path("train")
test_list = Path('test_ids.txt').read_text().splitlines()
train_list = Path('train_ids.txt').read_text().splitlines()

test_folder.mkdir(exist_ok=True)
	{
	inputs = {
	flake-utils.url = "github:numtide/flake-utils";
	nickel.url = "github:tweag/nickel";
	};
	outputs = { self, nixpkgs, flake-utils, nickel }@inputs:
	flake-utils.lib.eachDefaultSystem (system:
	let pkgs = nixpkgs.legacyPackages.${system};
	in rec {
	devShell =
	import io
	import picamera
	import logging
	import socketserver
	from threading import Condition
	from http import server

	PAGE="""\
	<html>
	<head>
	# 64x64
	class Generator64(nn.Module):
	def __init__(self, ngpu):
	super(Generator64, self).__init__()
	self.ngpu = ngpu
	self.main = nn.Sequential(
	nn.ConvTranspose2d(100, 512, kernel_size=4, stride=1, padding=0),
	nn.BatchNorm2d(512),
	nn.LeakyReLU(0.2),
	nn.ConvTranspose2d(512, 256, kernel_size=4, stride=2, padding=1),
	def calc_dist_matrix(residues):
	"""Returns a matrix of distances between residues of the same chain."""
	size = len(residues)
	answer = np.zeros((size, size), np.float)
	for row, residue_one in enumerate(residues):
	for col, residue_two in enumerate(residues):
	answer[row, col] = residue_one["CA"] - residue_two["CA"]
	return answer
	from pathlib import Path
	from urllib import request
	from tqdm import tqdm

	test_folder = Path("test")
	train_folder = Path("train")
	test_list = Path('test_ids.txt').read_text().splitlines()
	train_list = Path('train_ids.txt').read_text().splitlines()

	test_folder.mkdir(exist_ok=True)