PlethoraChutney

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• I am plethorachutney on github.
• I am plethorachutney (https://keybase.io/plethorachutney) on keybase.
• I have a public key ASCNhMxyDzdrBvmhlN1W1u8lln0lwMH4G38UAhsueU3WJgo

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PlethoraChutney

#!/usr/bin/env python3
import sys
if len(sys.argv) == 1:
    diam = input('Particle diameter (A): ')
    defocus = input('Mean defocus (um): ')
    res = input('Target resolution (A): ')
    ps = input('Pixel size (a/pix): ')
elif len(sys.argv) != 5:
    print('Usage: box-sizer.py {diameter in A} {defocus in um} {resolution in A} {apix in A/pix}')
    sys.exit(1)

PlethoraChutney

#!/usr/bin/env python3
import re
import sys

char_pattern = re.compile('color:#7f7f7f[^>]*>([^<]*)')

with open(sys.argv[1], 'r') as f:
    lines = [x.rstrip() for x in f]

line = ''.join(lines)

PlethoraChutney

library(tidyverse)

data <- read_csv('~/Downloads/data-precs.csv')

counted <- data |> 
  filter(!is.na(res_id)) |> 
  select(pdb_id, name, secondary) |> 
  group_by(pdb_id) |> 
  mutate(
    previous = lag(secondary)

PlethoraChutney

conda create --name blender python==3.10 biotite==0.35.0 mdanalysis==2.2.0 -c conda-forge -y
CONDAENV=$(conda info --envs | grep blender | awk -F ' ' '{print $2}')
pushd /Applications/Blender.app/Contents/Resources/3.4/ > /dev/null
mv python old_python
ln -s $CONDAENV python
popd > /dev/null

PlethoraChutney

#!/bin/bash

# Test to make sure csparc2star.py is in PATH and installed correctly:
csparc2star.py -h &> /dev/null
if [ $? -ne 0 ]; then
        echo Failed to run csparc2star.py. Are you in the correct virtual environment? Did you check your path?
        exit
fi

# Change this to your csparc scratch directory. This should be where all your P* dirs are

PlethoraChutney

#!/usr/bin/env python
import numpy as np
import pandas as pd
import umap
import sys
import matplotlib.pyplot as plt
import seaborn as sns
from sklearn.preprocessing import StandardScaler
from cryosparc.dataset import Dataset

PlethoraChutney

return {
    Span = function (elem)
        if quarto.doc.is_format('docx') then
            if elem.classes:includes('aside') then
                return ""
            else
                return elem
            end
        end
    end

PlethoraChutney

from cryosparc.tools import CryoSPARC
import numpy as np

cs = CryoSPARC(
  # you'll need env variables here, or just set stuff directly
)
cs.test_connection()

# we will filter fullsize_particles so that only the intersection with
# downsampled particles are retained. ctf, alignments, etc. will all

PlethoraChutney