at 11.42a EDT on 2003 December 16 Tuesday Jan Reichert said:I never argument because of regex against ^ because escaping won't be a problem. I thought, that
timothy driscoll wrote:
at 10.40a EDT on 2003 December 16 Tuesday Jan Reichert said:that is the point, it will identify old scripts as subject to convertSlangStrict in chime2jmol.pl
sub convertSlangStrict { my $text= shift; $text=~ s/(\d+)([a-z])(?!\])\b/$1:$2/ig; return $text; }
and if it is an old script, that is no #!rasmol -version 2.7.2.2 header (this use of version parameter has to be implemented in RasMol). Regards, Jan
this ignores Chime scripts, and hand-coded scripts, that do not use a shebang and are around in great numbers.
Regards, Jan
ah; I understand what you're saying now.
I have yet to see a convincing argument for this approach, though.
essentially we would be converting a huge number of existing scripts to fit
in a format that we know is already in widespread use for chain selection.
why not use the carat for insertion codes, and escape it for regex searches?
select 3A
was more natural, especial if we look at residue identifiers as symbols,
I don't believe that this slang is used very often in existing scripts because you have to be aware that a chain id could be a number,
and we save an escape character for using it elsewhere.
But we have a problem, because the column 27 of e.g. 1bit 5tra 1g0u 1hzp
and these cases, which were not really an insertion code, format failure in sequence number
1bn9
1c5n
1gp8
contains numbers and this argues strongly to use escape characters (e.g. ^), though I informed RCSB and they hopefully will correct all these files.
Regards, Jan
I understand how it can be done, but please explain why it is necessary. I promise I will shut up, even if we have to agree to disagree... :-)
supporting a symbol (^) for icodes seems easier than dealing with an external conversion routine. for example, one has to assume that the routine won't work in all cases, especially in early stage of implementation, and someone will have to deal with those issues.
regards,
:tim
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