Stefano Forli wrote:
> Dear list,
>
> as far as I can tell from my searches in the tips and the mailing list
> archives, no one
> already asked about this issue.
>
> I would be interested in creating a syntax scheme for the Proten Data Bank
> files format
> for atomic coordinates of proteins.
>
> In particular, it would be very useful to have different colors for columns
> (even
> alternate ones), since the format is sensitive to the position.
>
>
> 1234567890123456789012345678901234567890123456789012345678901234567890123456789
> | | | | | | | | | | |
> ATOM 1428 N ASP 207 -26.467 -19.015 -22.737 0.00 0.00 -0.337 N
> ATOM 1429 CA ASP 207 -25.440 -18.835 -23.814 0.00 0.00 0.170 C
> ATOM 1430 C ASP 207 -26.043 -19.413 -25.145 0.00 0.00 0.251 C
> ATOM 1431 O ASP 207 -26.005 -18.729 -26.180 0.00 0.00 -0.271
> OA
> ATOM 1432 CB ASP 207 -24.127 -19.567 -23.531 0.00 0.00 0.129 C
>
> The keywords should be pretty few.
> The |usr_44.txt| help file states that "parts can be specific keywords or
> text matching a
> pattern". I found no mention to positional keys to be used, so I wonder if
> there is any
> way for doing that.
>
Hello!
I've attached a syntax highlighting file; put it in
$HOME/.vim/syntax. I've also attached a filetype.vim file;
put it in $HOME/.vim (or merge it with whatever's there).
I went by the bar placements rather than the apparent columnar data; its
easy enough to adjust.
Regards,
Chip Campbell
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" filetype.vim:
" Author: Charles E. Campbell, Jr.
" Date: Mar 18, 2009
if exists("did_load_myfiletypes")
finish
endif
let did_load_myfiletypes= 1
augroup filetypedetect
au BufNewFile,BufReadPost *.pdb setf pdb
augroup END
" pdb.vim
" Author: Charles E. Campbell, Jr.
" Date: Mar 18, 2009
" Version: 1a NOT RELEASED
" ---------------------------------------------------------------------
" Initialization {{{1
" Remove any old syntax stuff hanging around
syntax clear
" ---------------------------------------------------------------------
" Syntax {{{1
syn match pdbCol1 /^.*\%11v/
nextgroup=pdbCol2
syn match pdbCol2 /\%11v.*\%14v/ contained nextgroup=pdbCol3
syn match pdbCol3 /\%14v.*\%18v/ contained nextgroup=pdbCol4
syn match pdbCol4 /\%18v.*\%24v/ contained nextgroup=pdbCol5
syn match pdbCol5 /\%24v.*\%35v/ contained nextgroup=pdbCol6
syn match pdbCol6 /\%35v.*\%43v/ contained nextgroup=pdbCol7
syn match pdbCol7 /\%43v.*\%51v/ contained nextgroup=pdbCol8
syn match pdbCol8 /\%51v.*\%58v/ contained nextgroup=pdbCol9
syn match pdbCol9 /\%58v.*\%64v/ contained nextgroup=pdbCol10
syn match pdbCol10 /\%64v.*\%73v/ contained nextgroup=pdbCol11
syn match pdbCol11 /\%73v.*$/ contained
" ---------------------------------------------------------------------
" Highlighting {{{1
if !exists("b:did_pdb_syntax_inits")
let b:did_pdb_syntax_inits = 1
hi def link pdbCol1 Red
hi def link pdbCol2 Yellow
hi def link pdbCol3 Green
hi def link pdbCol4 Magenta
hi def link pdbCol5 Cyan
hi def link pdbCol6 White
hi def link pdbCol7 Red
hi def link pdbCol8 Yellow
hi def link pdbCol9 Green
hi def link pdbCol10 Magenta
hi def link pdbCol11 Cyan
endif
" ---------------------------------------------------------------------
" vim: ts=4 fdm=marker
