PythonScript for protein colorizing

Mark Olson

I thought it would be fun to make a lexer for colorizing protein sequences according to amino acid properties, and the current UDL system doesn’t seem well-suited for this. So I used PythonScript!

See https://github.com/molsonkiko/NPP_protein_lexer and maybe submit a pull request if you have an idea of how to improve it.

Michael Vincent

@Mark-Olson said in PythonScript for protein colorizing:

colorizing protein sequences according to amino acid properties,

I have an idea what you’re talking about but no experience in that field whatsoever. But between this and your JSONTools plugin, I’m happy to see a new talented developer contributing to the Notepad++ ecosystem.

Keep up the good work!

Cheers.

Alan Kilborn

@Mark-Olson

Just asking, I didn’t look at it: Does it absolutely need its own custom script, or could the EnhanceAnyLexer plugin have been used to do the same thing? This is typically the goto plugin when the UDL system falls short.

Mark Olson

@Alan-Kilborn
I wasn’t really familiar with EnhanceAnyLexer prior to making this script, but now that I’ve tried it out this is actually really simple!

Just need to create a lexer called protein with white text background, install the plugin and add this to EnhanceAnyLexerConfig.ini

[protein]
; default (black)
0x000000 = [^DEPHKRNQSTILMFWVACGY]
; acidic (blue)
0xbe0000 = [DE]
; cyclic (green)
0x00f600 = P
; basic (red)
0x0000be = [HKR]
; hydrophilic (cyan)
0xb0d000 = [NQST]
; amphiphilic (orange)
0x00b0d0 = [ACGY]
; lipophilic
0x848484 = [ILMFWV]
; check in the respective styler xml if the following IDs are valid
excluded_styles = 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,20,21,22,23

and you get the same result, except better because amphiphilic amino acids are now orange.

David Brigden52

@Mark-Olson And now I have to look up “amphophilic”

Neat