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Stephen Royle quantixed

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quantixed / snapshotModel.sh
Created January 17, 2024 10:24
shell script to open each pdb file in a file tree, colour by chain and take a raytraced image
#!/bin/zsh
# Find all *.pdb files recursively
find . -name "*.pdb" | while read -r file; do
# Extract the filename without extension
filename=$(basename "$file" .pdb)
# Extract the name of the directory
dirname=$(dirname "$file")
# Concatenate the directory name and the filename, separated by an underscore
output="${dirname}_${filename}"
@quantixed
quantixed / cue_to_flac.py
Last active November 25, 2023 17:03 — forked from mervick/cue_to_flac.py
CUE splitter using ffmpeg (to flac)
#!/usr/bin/python3
import argparse
import os
import subprocess
def main():
parser = argparse.ArgumentParser(description='Split flac file using cue')
parser.add_argument('cue', type=str, help='path to cue file')
parser.add_argument('--cover', type=str, help='path to cover image')
@quantixed
quantixed / discogsGenresStyles.csv
Created August 26, 2022 06:02
Discogs database Styles with parent Genre
Genre Style
Blues Boogie Woogie
Blues Chicago Blues
Blues Country Blues
Blues Delta Blues
Blues East Coast Blues
Blues Electric Blues
Blues Harmonica Blues
Blues Hill Country Blues
Blues Jump Blues
@quantixed
quantixed / optimal-grant-proposals.csl
Created August 8, 2022 08:11
An alternative citation style layout for UKRI grant proposals, for when you have a bit more space
<?xml version="1.0" encoding="UTF-8"?>
<style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" version="1.0" demote-non-dropping-particle="sort-only" default-locale="en-GB">
<info>
<title>Optimal style for grant proposals</title>
<!--<id>http://csl.mendeley.com/styles/20448741/minimal-grant-proposals</id>-->
<id>http://www.zotero.org/styles/optimal-grant-proposals</id>
<link href="http://www.zotero.org/styles/optimal-grant-proposals" rel="self"/>
<author>
<name>Anton Crombach</name>
<email>anton.crombach@gmail.com</email>
@quantixed
quantixed / minimal-grant-proposals.csl
Last active June 8, 2022 08:08 — forked from antoncrombach/minimal-grant-proposals.csl
Updated to match my preferred UKRI application style
<?xml version="1.0" encoding="UTF-8"?>
<style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" version="1.0" demote-non-dropping-particle="sort-only" default-locale="en-GB">
<info>
<title>Minimal style for grant proposals</title>
<!--<id>http://csl.mendeley.com/styles/20448741/minimal-grant-proposals</id>-->
<id>http://www.zotero.org/styles/minimal-grant-proposals</id>
<link href="http://www.zotero.org/styles/minimal-grant-proposals" rel="self"/>
<author>
<name>Anton Crombach</name>
<email>anton.crombach@gmail.com</email>
@quantixed
quantixed / FitCircleTo2DCoords.ipf
Created May 24, 2022 09:08
Igor function to fit a circle to 2D coords (sparse, irregular, arc). Returns the radius in units of xy
Function FitCircleTo2DCoords(w)
Wave w
// requires 2D numeric wave with two columnns corresponding to xy coords
if(Dimsize(w,1) != 2)
return -1
endif
// make two 1D waves for x and y coords
SplitWave/O/NAME="xW;yW;" w
Wave xW,yW
// solve in terms of u and v coordinates
@quantixed
quantixed / pngSizeForOverleaf.ijm
Created April 22, 2021 15:22
Deduce the page width size needed for a 300 dpi png
/*
* Figure out the width of png images for Overleaf
* png are 300 dpi and page width is 170 mm
*/
#@ File (label = "Input directory", style = "directory") input
#@ String (label = "File suffix", value = ".png") suffix
setBatchMode(true);
processFolder(input);
@quantixed
quantixed / config.ini
Created August 29, 2020 08:31
TexStudio v3.0.0 excerpt of config.ini file before [texmaker] - puts back zenburn coloring on macOS in dark mode
[General]
IniMode=true
[formats]
data\align-ampersand\bold=true
data\align-ampersand\fontFamily=
data\align-ampersand\foreground=#dc8cc3
data\align-ampersand\italic=false
data\align-ampersand\overline=false
data\align-ampersand\pointSize=0
@quantixed
quantixed / ExportDocsAsPNG.jsx
Last active August 29, 2020 07:05
Export ai files to PNG with our preferred settings for manuscript figures
/****************************************************************
* Script to save a directory of ai files to PNG
* Options are: white bakcground, 300 dpi and clipped to artboard
*****************************************************************/
var folder = Folder.selectDialog();
if (folder) {
var files = folder.getFiles("*.ai");
for (var i = 0; i < files.length; i++) {
var currentFile = files[i];
app.open(currentFile);
@quantixed
quantixed / r_project_setup.R
Created June 10, 2020 08:59
Preferred directory structure for R projects
## Setup preferred directory structure in wd
ifelse(!dir.exists("Data"), dir.create("Data"), "Folder exists already")
ifelse(!dir.exists("Output"), dir.create("Output"), "Folder exists already")
ifelse(!dir.exists("Output/Data"), dir.create("Output/Data"), "Folder exists already")
ifelse(!dir.exists("Output/Plots"), dir.create("Output/Plots"), "Folder exists already")
ifelse(!dir.exists("Script"), dir.create("Script"), "Folder exists already")