Charles,
thank you for your quick answer!
I tested your files but I wasn't able to figure out how to make them work, even
following
your advices.
I'm using Vim 7.0.305 on a Debian system, and I tried all the options I was
aware of:
- copying all $HOME/.vim(/syntax) directories (that weren't there before I
created them)
- copying all to the system-wide /usr/share/vim/vim70(/syntax) location
Surprisingly (at least for me), sourcing manually the file
:source $HOME/.vim/syntax/pdb.vim
doesn't give any error.
Any clue?
Thanks again,
Stefano
Charles Campbell wrote:
> 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 $HOME/.vim (or merge it with whatever's there).
>
> I went by the bar placements rather than the apparent columnar data; its
> easy enough to adjust.
>
> Regards,
> Chip Campbell
>
>
> >
>
>
> ------------------------------------------------------------------------
>
> " filetype.vim:
> " Author: Charles E. Campbell, Jr.
> " Date: Mar 18, 2009
>
> if exists("did_load_myfiletypes")
> finish
> endif
> let did_load_myfiletypes= 1
>
> augroup filetypedetect
> au BufNewFile,BufReadPost *.pdb setf pdb
> augroup END
>
>
> ------------------------------------------------------------------------
>
> " pdb.vim
> " Author: Charles E. Campbell, Jr.
> " Date: Mar 18, 2009
> " Version: 1a NOT RELEASED
> " ---------------------------------------------------------------------
> " Initialization {{{1
> " Remove any old syntax stuff hanging around
> syntax clear
>
> " ---------------------------------------------------------------------
> " Syntax {{{1
> syn match pdbCol1 /^.*\%11v/
> nextgroup=pdbCol2
> syn match pdbCol2 /\%11v.*\%14v/ contained nextgroup=pdbCol3
> syn match pdbCol3 /\%14v.*\%18v/ contained nextgroup=pdbCol4
> syn match pdbCol4 /\%18v.*\%24v/ contained nextgroup=pdbCol5
> syn match pdbCol5 /\%24v.*\%35v/ contained nextgroup=pdbCol6
> syn match pdbCol6 /\%35v.*\%43v/ contained nextgroup=pdbCol7
> syn match pdbCol7 /\%43v.*\%51v/ contained nextgroup=pdbCol8
> syn match pdbCol8 /\%51v.*\%58v/ contained nextgroup=pdbCol9
> syn match pdbCol9 /\%58v.*\%64v/ contained nextgroup=pdbCol10
> syn match pdbCol10 /\%64v.*\%73v/ contained nextgroup=pdbCol11
> syn match pdbCol11 /\%73v.*$/ 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
--
Stefano Forli, PhD
Research Associate
Olson Molecular Graphics Laboratory
Dept. Molecular Biology, MB-5
The Scripps Research Institute
10550 North Torrey Pines Road
La Jolla, CA 92037-1000, USA.
tel: (858) 784-2055
fax: (858) 784-2860
email: [email protected]
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