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Open Source Science

https://github.com/kull-centre/pdbwords

Printing text using protein structures

https://github.com/kull-centre/pdbwords

Science Score: 18.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ✓
    Academic publication links
    Links to: nature.com
  • ○
    Academic email domains
  • ✓
    Institutional organization owner
    Organization kull-centre has institutional domain (www1.bio.ku.dk)
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.9%) to scientific vocabulary
Last synced: 4 months ago · JSON representation

Repository

Printing text using protein structures

Basic Info
  • Host: GitHub
  • Owner: KULL-Centre
  • License: gpl-3.0
  • Language: Python
  • Default Branch: main
  • Size: 1010 KB
Statistics
  • Stars: 10
  • Watchers: 3
  • Forks: 3
  • Open Issues: 1
  • Releases: 0
Created about 6 years ago · Last pushed over 4 years ago
Metadata Files
Readme License

README.md

ABOUT

pdbwords was written by Kresten Lindorff-Larsen, University of Copenhagen, in 2015.

I cannot guarantee that your eyes will not start to bleed if you read the code.

The main ingredient of pdbwords is a protein alphabet, developed by Mark Howarth: http://www.bioch.ox.ac.uk/howarth/alphabet.htm

The python code is distributed under GNU General Public License v3.0

THIS IS HOW YOU RUN PDB WORDS

./pdbwords.py Just write your text here to set it in PDBWORDS

Requirements

The code is essentially a wrapper for ImageMagick, which needs to be installed separately; see http://www.imagemagick.org

I have only tested the code under macOS

More information

Currently the letters A-Z can be used, and it is also possible to use . , ! ? :

All letters will be set as uppercase letters, but you can input as either lower or upper.

Every unknown characters will be set as a space.

Lines will be broken up so that there are no more than MAXCHARS (hardcoded in script) characters on each line. If you want to force a line break, just write xLBx as a (case sensitive) word (again, hardcoded in LINEBREAK in script).

The two last features makes the following hack work to insert blank lines xLBx @ xLBx (which forces a line break, then the @ is converted to a space (it is unknown) and then a new linebreak. Not elegant, but it works.

Background

The letters were mostly discovered by Mark Howarth and are described in a paper: http://www.nature.com/nsmb/journal/v22/n5/full/nsmb.3011.html and a website: http://www.bioch.ox.ac.uk/howarth/alphabet.htm

Owner

  • Name: Linderstrøm-Lang Centre for Protein Science, University of Copenhagen
  • Login: KULL-Centre
  • Kind: organization
  • Location: Copenhagen, Denmark

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