GPLv3/L8R - Planning
13 years, 6 months
The XEmacs Package Smoketest
The XEmacs Package Smoketest
Hi,
So we need to have a plan. As you might have seen I have started with
a discussion about how the license should look. If we have that fixed
it will make it easier to change the files.
After that I have been thinking of something like this:
1. Fix the easy parts. Substitute the license in files easily
identified as GPLv2 or later (If nobody objects I have a
substitution script that is more or less ready that does that.)
2. Update files that are GPLv2 or later but that the script didn't
take care of. As input to that, and most of the remaining work, we
have the "GPL version 3 source survey" work by Jerry James. Found
here:
"http://sourceforge.net/apps/mediawiki/xemacs/index.php?title=GPLv3"
3. Take care of the rest. ;-)
4. Merge it all back to trunk with a Changelog saying "Move license
to GPLv3 or later".
Comments, suggestions (and not to mention helping hands) are of course
welcome!
Yours
--
%% Mats
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- 2 participants
- 8 comments
xemacs beta list and gmane archive?
13 years, 6 months
Raymond Toy
Raymond Toy
OT, but I'm asking here anyway. :-)
I often use gmane to read xemacs beta mail (especially since stupid
gmail never sends me my messages to the xemacs-beta list). This works
quite nicely, but today I wanted to look up some older messages. The
articles have been expired from gmane and are no longer available, but
it does show the author and subject lines. Just no body.
Is that something that some xemacs person did? If so, can that be
changed so the messages aren't expired? Or is that a gmane problem?
Ray
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ftp://ftp.xemacs.org doesn't do "PASV" correctly -- makes it tricky to update XEmacs packages from behind a NAT
13 years, 6 months
Samuel Bronson
Samuel Bronson
I can't access ftp://ftp.xemacs.org from behind a NAT. It's not just
an EFS problem, either -- I tried it with Chrome, too, and that didn't
work either.
It also isn't a problem with my connection/NAT: I can access
ftp://ftp.gnu.org just fine with EFS and with Chrome.
It seems to understand the PASV command well enough, but the data
connection itself doesn't seem to go through, so I suspect that the
ftp server and firewall configurations have gotten out of sync, so
that PASV returns connection parameters containing ports that get
filtered. Wireshark didn't really show much except the connections
seeming to time out. (My cable modem drops all ICMP packets -- it told
me so! -- so I can't say whether there were any or not.)
(Strangely, sometimes EFS seems to get a whole lot of NULs in the FTP
process buffer, but I don't know where they come from.)
All of this wouldn't be much of a problem -- I could still access the
files by http -- except that package installation doesn't support
that.
It seems that ftp://ftp.ca.xemacs.org is working today, though.
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[COMMIT] Don't share a counter when checking for circularity, list_merge().
13 years, 6 months
Aidan Kehoe
Aidan Kehoe
Ar an dara lá déag de mí Deireadh Fómhair, scríobh Robert Pluim:
> On Tue, Oct 12, 2010 at 7:37 PM, Aidan Kehoe <kehoea(a)parhasard.net> wrote:
> >
> > From eyeballing the code, the bug seems to be that my circularity
> > checking in list_merge() wasn’t done correctly. The below fixes a
> > related error that I can reproduce easily; could I ask you to apply it
> > locally and tell me if it fixes your error, too?
>
> Yes. Commit away :)
>
OK.
APPROVE COMMIT
NOTE: This patch has been committed.
[...]
--
“Apart from the nine-banded armadillo, man is the only natural host of
Mycobacterium leprae, although it can be grown in the footpads of mice.”
-- Kumar & Clark, Clinical Medicine, summarising improbable leprosy research
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circular list errors being signaled in gnus
13 years, 6 months
Robert Pluim
Robert Pluim
Aidan, the following changeset
changeset: 5253:b6a398dbb403
user: Aidan Kehoe <kehoea(a)parhasard.net>
date: Wed Sep 01 12:51:32 2010 +0100
causes gnus to signal circular list errors that to my eye are
incorrect (and go away when I revert to revision 5252)
Debugger entered--Lisp error: (circular-list ((1213 nil nil nil) (1214
nil nil nil) (1215 nil nil nil)
(1216 nil nil nil) (1217 nil nil nil) (1218 nil nil nil) (1219 nil nil
nil) (1220 nil nil nil) (1221 nil nil
nil) (1222 nil nil nil) (1223 nil nil nil) (1224 nil nil nil) (1225
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(1231 nil nil nil) (1232 nil nil nil) (1233
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sort(((19620 nil nil 21871)) #<compiled-function (from
"/cygdrive/c/Documents and
Settings/RPluim/.xemacs/gnus/lisp/gnus-agent.elc") (a b) "...(38)" [a
b t 2 3] 4 0x2974>)
gnus-agent-expire-group-1("nnimap+myserver:mygroup" #<buffer "
*expire overview*"> (1 . 19620)
(19620) force)
gnus-agent-expire-group("nnimap+myserver:mygroup" (19620) force)
gnus-agent-expire((19620) "nnimap+myserver:mygroup" force)
gnus-request-expire-articles((19620) "nnimap+myserver:mygroup" force)
gnus-summary-delete-article(nil)
call-interactively(gnus-summary-delete-article)
(dispatch-event "[internal]")
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- 2 comments
Re: molecular weight of proteins
13 years, 6 months
Aidan Kehoe
Aidan Kehoe
Ar an t-aonú lá déag de mí Deireadh Fómhair, scríobh Samuel Bronson:
> It looks to me as though you need to start learning elisp in earnest
> -- that is, you must learn defun, how to figure out what lisp call
> corresponds with the way you would do a thing interactively, some
> control structures, etc. rather than just these keyboard macros.
> (Which I didn't even know you could *do*, actually. Wonder what its
> actually good for? Testing that you did't break some keybindings?)
It’s how you can name a keyboard macro; make it the function binding of the
symbol with that string name.
Sirano, it’s great (and very inventive) that you’ve got XEmacs to do what
you want in that way. It’s a whole lot more useful in the medium term,
though, to write Lisp programs in the way everyone else does, since that
makes it much easier to learn from them. Here’s how your 2expressions macro
would usually be written:
(defun 2expressions ()
(interactive)
(goto-char (point-min))
(replace-string "." " ")
(goto-char (point-min))
(flush-lines "^.+ [0-9][0-9][0-9][A-Z][0-9][0-9] e.+$")
(goto-char (point-min))
(replace-regexp "\\(^.+\\) \\(....-....\\) \\([0-9][0-9][0-9][A-Z][0-9][0-9]\\) .+\\(p.+\\) .+$"
"\3 \\1\.\\2 \\4")
(goto-char (point-min))
(vectors_2bhformat)
....)
It’s incomplete, but I hope it gives a flavour of how to go about it. F1 k
will give information about the function called by a sequence, and you
normally call that function from your Lisp code as above (M-< for
beginning-of-buffer is an exception, but that’s described in its doc string.)
--
“Apart from the nine-banded armadillo, man is the only natural host of
Mycobacterium leprae, although it can be grown in the footpads of mice.”
-- Kumar & Clark, Clinical Medicine, summarising improbable leprosy research
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Re: molecular weight of proteins
13 years, 6 months
Aidan Kehoe
Aidan Kehoe
Ar an t-aonú lá déag de mí Deireadh Fómhair, scríobh Sirano Dhe-Paganon:
> Wow; thank you! I've been looking for this for over a year.
>
> I can make it work for one line of protein sequence, but what would be
> spectacular is if I can apply it to automatically calculate countless
> lines of protein sequences. For example, I normally need to calculate 10
> to 100 proteins. Normally these protein sequences are associated with a
> tag or a name: the name is followed by a tab and then the protein
> sequence (see below). So I would paste them into the scratch buffer, then
> execute a command to replace just the protein sequence with the molecular
> weight value, leaving the tag intact. for example:
Ah, okay, you should have said so in the first place :-) . Some more USMLE
procrastination from me, then:
(defun protein-weight-region (start end &optional buffer)
(interactive "*r")
(goto-char start)
;; The regular expression describes a line comprising a series of non-tab
;; characters (the tag), followed by a tab, followed by a series of
;; uppercase Roman-alphabet characters (the protein's amino acids),
;; followed by optional trailing whitespace. The backslashed parentheses
;; delimit the protein, and the protein text is accessed using
;; (match-string 1).
(while (re-search-forward "^[^\t]+\t\\([A-Z]+\\)[ \t]*$" end t)
(goto-char (match-end 1))
(insert (format "%S" (protein-weight-string (match-string 1))))
(delete-region (match-beginning 1) (match-end 1))))
--
“Apart from the nine-banded armadillo, man is the only natural host of
Mycobacterium leprae, although it can be grown in the footpads of mice.”
-- Kumar & Clark, Clinical Medicine, summarising improbable leprosy research
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bug report
13 years, 6 months
William Estrada
William Estrada
Bug report does not send!
> To: XEmacs Beta <xemacs-beta(a)xemacs.org>
> Subject: [Bug: 21.5-b29] line number not displayed
> --text follows this line--
> ================================================================
> Dear Bug Team!
> line number and colunms are not displayed even with:
>
> (setq column-number-mode t)
> (setq line-number-mode t)
> in my init.el file
>
> ================================================================
>
> System Info to help track down your bug:
> ---------------------------------------
>
> uname -a: Linux x86-13.phx2.fedoraproject.org 2.6.32-37.el6.x86_64 #1
> SMP Sun Jun 20 19:29:35 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux
>
> ./configure '--build=x86_64-redhat-linux-gnu'
> '--host=x86_64-redhat-linux-gnu' '--program-prefix='
> '--disable-dependency-tracking' '--prefix=/usr' '--exec-prefix=/usr'
> '--bindir=/usr/bin' '--sbindir=/usr/sbin' '--sysconfdir=/etc'
> '--datadir=/usr/share' '--includedir=/usr/include'
> '--libdir=/usr/lib64' '--libexecdir=/usr/libexec'
> '--localstatedir=/var' '--sharedstatedir=/var/lib'
> '--mandir=/usr/share/man' '--infodir=/usr/share/info'
> '--mandir=/usr/share/man/man1'
> '--with-archlibdir=/usr/lib64/xemacs-21.5-b29/x86_64-redhat-linux'
> '--with-moduledir=/usr/lib64/xemacs-21.5-b29/x86_64-redhat-linux/modules'
> '--with-lispdir=/usr/share/xemacs-21.5-b29/lisp'
> '--with-etcdir=/usr/share/xemacs-21.5-b29/etc'
> '--with-system-packages=/usr/share/xemacs' '--without-msw'
> '--with-mule' '--with-clash-detection' '--with-database=berkdb'
> '--without-ldap' '--without-postgresql' '--with-mail-locking=lockf'
> '--with-pop' '--without-hesiod' '--with-pdump' '--with-debug'
> '--with-error-checking=none' '--enable-bignum=gmp'
> '--with-docdir=/usr/lib64/xemacs-21.5-b29/doc'
> '--with-sound=nonative,alsa' '--with-athena=next'
> '--with-menubars=lucid' '--with-widgets=athena'
> '--with-dialogs=athena' '--with-scrollbars=lucid' '--with-xim=xlib'
> '--without-wnn' 'build_alias=x86_64-redhat-linux-gnu'
> 'host_alias=x86_64-redhat-linux-gnu' 'CFLAGS=-O2 -g -pipe -Wall
> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
> --param=ssp-buffer-size=4 -m64 -mtune=generic -fno-strict-aliasing'
>
>
> XEmacs 21.5-b29 "garbanzo" configured for `x86_64-redhat-linux'.
>
> Compilation Environment and Installation Defaults:
> Source code location: /builddir/build/BUILD/xemacs-21.5.29
> Installation prefix: /usr
> Operating system description file: `s/linux.h'
> Not using any machine description file
> Compiler version: gcc (GCC) 4.4.4 20100630 (Red Hat
> 4.4.4-10)
> - GCC specs file: specs.
> - Compiler command: gcc -Wall -Wno-switch -Wundef
> -Wsign-compare -Wno-char-subscripts -Wpacked -Wunused-parameter -g
> -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
> -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
> -fno-strict-aliasing
> libc version: glibc-2.12-2.x86_64
> Relocating allocator for buffers: no
> GNU version of malloc: yes
> - Using Doug Lea's new malloc from the GNU C Library.
>
> Window System:
> Compiling in support for the X window system:
> - X Windows headers location:
> - X Windows libraries location:
> - Handling WM_COMMAND properly.
> Compiling in support for the Athena widget set:
> - Athena headers location: X11/neXtaw
> - Athena library to link: neXtaw
> Using Lucid menubars.
> Using Lucid scrollbars.
> Using Athena dialog boxes.
> Using Athena native widgets.
>
> TTY:
> Compiling in support for ncurses.
> Compiling in support for GPM (General Purpose Mouse).
>
> Images:
> Compiling in support for GIF images (builtin).
> Compiling in support for XPM images.
> Compiling in support for PNG images.
> Compiling in support for JPEG images.
> Compiling in support for TIFF images.
> Compiling in support for X-Face message headers.
>
> Sound:
> Compiling in support for ALSA (Advanced Linux Sound Architecture).
>
> Databases:
> Compiling in support for Berkeley database.
>
> Internationalization:
> Compiling in support for Mule (multi-lingual Emacs).
> Compiling in support for XIM (X11R5+ I18N input method).
> - Using raw Xlib to provide XIM support.
> Compiling in support for Canna on Mule.
>
> Mail:
> Compiling in support for POP mail retrieval.
> Compiling in support for "lockf" mail spool file locking method.
>
> Other Features:
> Inhibiting IPv6 canonicalization at startup.
> Compiling in support for dynamic shared object modules.
> Compiling in support for more number types using the GNU MP library.
> Using the new GC mark algorithms (KKCC).
> WARNING: ---------------------------------------------------------
> WARNING: The new algorithms are experimental. They are enabled by
> WARNING: default for this release. Use `--disable-kkcc' to
> WARNING: turn it off.
> WARNING: ---------------------------------------------------------
> Using the new portable dumper.
> Dumping into executable.
> Compiling in support for extra debugging code.
>
>
>
> Load-Path Lisp Shadows:
> ----------------------
> (/usr/share/xemacs/site-packages/lisp/pmd/pmd
> /usr/share/xemacs/site-packages/lisp/pmd/pmd
> /usr/share/xemacs/site-packages/lisp/pmd/pmd
> /usr/share/xemacs/site-packages/lisp/site-start.d/pmd
> /usr/share/xemacs/site-packages/lisp/anthy/leim-list
> /usr/share/xemacs/mule-packages/lisp/leim/leim-list
> /usr/share/xemacs/xemacs-packages/lisp/ecrypto/sha1
> /usr/share/xemacs/xemacs-packages/lisp/flim/sha1
> /usr/share/xemacs/xemacs-packages/lisp/ecrypto/md5
> /usr/share/xemacs/xemacs-packages/lisp/flim/md5
> /usr/share/xemacs/xemacs-packages/lisp/ecrypto/hex-util
> /usr/share/xemacs/xemacs-packages/lisp/flim/hex-util
> /usr/share/xemacs/xemacs-packages/lisp/apel/std11
> /usr/share/xemacs/xemacs-packages/lisp/flim/std11
> /usr/share/xemacs/xemacs-packages/lisp/ecrypto/md4
> /usr/share/xemacs/xemacs-packages/lisp/flim/md4
> /usr/share/xemacs/site-packages/lisp/tuareg/camldebug
> /usr/share/xemacs/xemacs-packages/lisp/ocaml/camldebug
> /usr/share/xemacs/xemacs-packages/lisp/flim/hmac-md5
> /usr/share/xemacs/xemacs-packages/lisp/sasl/hmac-md5
> /usr/share/xemacs/xemacs-packages/lisp/flim/sasl-ntlm
> /usr/share/xemacs/xemacs-packages/lisp/sasl/sasl-ntlm
> /usr/share/xemacs/xemacs-packages/lisp/flim/sasl-scram
> /usr/share/xemacs/xemacs-packages/lisp/sasl/sasl-scram
> /usr/share/xemacs/xemacs-packages/lisp/flim/sasl-cram
> /usr/share/xemacs/xemacs-packages/lisp/sasl/sasl-cram
> /usr/share/xemacs/xemacs-packages/lisp/flim/ntlm
> /usr/share/xemacs/xemacs-packages/lisp/sasl/ntlm
> /usr/share/xemacs/xemacs-packages/lisp/flim/sasl
> /usr/share/xemacs/xemacs-packages/lisp/sasl/sasl
> /usr/share/xemacs/xemacs-packages/lisp/flim/hmac-def
> /usr/share/xemacs/xemacs-packages/lisp/sasl/hmac-def
> /usr/share/xemacs/xemacs-packages/lisp/flim/hmac-sha1
> /usr/share/xemacs/xemacs-packages/lisp/sasl/hmac-sha1
> /usr/share/xemacs/xemacs-packages/lisp/flim/sasl-digest
> /usr/share/xemacs/xemacs-packages/lisp/sasl/sasl-digest
> /usr/share/xemacs/xemacs-packages/lisp/cedet-common/sformat
> /usr/share/xemacs/xemacs-packages/lisp/semantic/sformat
> /usr/share/xemacs/xemacs-packages/lisp/cedet-common/working
> /usr/share/xemacs/xemacs-packages/lisp/semantic/working
> /usr/share/xemacs/xemacs-packages/lisp/flim/mel
> /usr/share/xemacs/xemacs-packages/lisp/tm/mel
> /usr/share/xemacs/xemacs-packages/lisp/flim/mel-u
> /usr/share/xemacs/xemacs-packages/lisp/tm/mel-u
> /usr/share/xemacs/xemacs-packages/lisp/flim/mel-q
> /usr/share/xemacs/xemacs-packages/lisp/tm/mel-q
> /usr/share/xemacs/xemacs-packages/lisp/flim/mel-g
> /usr/share/xemacs/xemacs-packages/lisp/tm/mel-g
> /usr/share/xemacs/mule-packages/lisp/mule-base/korea-util
> /usr/share/xemacs-21.5-b29/lisp/mule/korea-util
> /usr/share/xemacs/mule-packages/lisp/mule-base/ethio-util
> /usr/share/xemacs-21.5-b29/lisp/mule/ethio-util
> /usr/share/xemacs/mule-packages/lisp/mule-base/japan-util
> /usr/share/xemacs-21.5-b29/lisp/mule/japan-util
> /usr/share/xemacs/mule-packages/lisp/mule-base/china-util
> /usr/share/xemacs-21.5-b29/lisp/mule/china-util
> /usr/share/xemacs/mule-packages/lisp/mule-base/viet-util
> /usr/share/xemacs-21.5-b29/lisp/mule/viet-util
> /usr/share/xemacs/xemacs-packages/lisp/xemacs-base/regexp-opt
> /usr/share/xemacs-21.5-b29/lisp/regexp-opt
> /usr/share/xemacs/xemacs-packages/lisp/apel/alist
> /usr/share/xemacs-21.5-b29/lisp/alist
> /usr/share/xemacs/xemacs-packages/lisp/build/build-report
> /usr/share/xemacs-21.5-b29/lisp/build-report
> /usr/share/xemacs/xemacs-packages/lisp/xemacs-base/easy-mmode
> /usr/share/xemacs-21.5-b29/lisp/easy-mmode
> /usr/share/xemacs/site-packages/lisp/proofgeneral/generic/pg-response
> /usr/share/xemacs/site-packages/lisp/proofgeneral/generic/pg-response
> /usr/share/xemacs/site-packages/lisp/proofgeneral/generic/proof-x-symbol
> /usr/share/xemacs/site-packages/lisp/proofgeneral/generic/proof-x-symbol
> /usr/share/xemacs/site-packages/lisp/proofgeneral/generic/proof-toolbar
> /usr/share/xemacs/site-packages/lisp/proofgeneral/generic/proof-toolbar
> /usr/share/xemacs/site-packages/lisp/proofgeneral/generic/pg-display-table
> /usr/share/xemacs/site-packages/lisp/proofgeneral/generic/pg-display-table
> /usr/share/xemacs/site-packages/lisp/proofgeneral/generic/pg-autotest
> /usr/share/xemacs/site-packages/lisp/proofgeneral/generic/pg-autotest
> /usr/share/xemacs/site-packages/lisp/proofgeneral/generic/proof-mmm
> /usr/share/xemacs/site-packages/lisp/proofgeneral/generic/proof-mmm
> /usr/share/xemacs/site-packages/lisp/proofgeneral/generic/proof-unicode-tokens
> /usr/share/xemacs/site-packages/lisp/proofgeneral/generic/proof-unicode-tokens
> /usr/share/xemacs/site-packages/lisp/proofgeneral/generic/proof-utils
> /usr/share/xemacs/site-packages/lisp/proofgeneral/generic/proof-utils
> /usr/share/xemacs/site-packages/lisp/proofgeneral/generic/proof-config
> /usr/share/xemacs/site-packages/lisp/proofgeneral/generic/proof-config
> /usr/share/xemacs/site-packages/lisp/proofgeneral/generic/proof-easy-config
> /usr/share/xemacs/site-packages/lisp/proofgeneral/generic/proof-easy-config
> /usr/share/xemacs/site-packages/lisp/proofgeneral/generic/pg-assoc
> /usr/share/xemacs/site-packages/lisp/proofgeneral/generic/pg-assoc
> /usr/share/xemacs/site-packages/lisp/proofgeneral/generic/proof-site
> /usr/share/xemacs/site-packages/lisp/proofgeneral/generic/proof-site
> /usr/share/xemacs/site-packages/lisp/proofgeneral/generic/proof-auxmodes
> /usr/share/xemacs/site-packages/lisp/proofgeneral/generic/proof-auxmodes
> /usr/share/xemacs/site-packages/lisp/proofgeneral/generic/proof-indent
> /usr/share/xemacs/site-packages/lisp/proofgeneral/generic/proof-indent
> /usr/share/xemacs/site-packages/lisp/proofgeneral/generic/pg-goals
> /usr/share/xemacs/site-packages/lisp/proofgeneral/generic/pg-goals
> /usr/share/xemacs/site-packages/lisp/proofgeneral/generic/proof-depends
> /usr/share/xemacs/site-packages/lisp/proofgeneral/generic/proof-depends
> /usr/share/xemacs/site-packages/lisp/proofgeneral/generic/pg-thymodes
> /usr/share/xemacs/site-packages/lisp/proofgeneral/generic/pg-thymodes
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> /usr/share/xemacs/site-packages/lisp/proofgeneral/generic/pg-xml
> /usr/share/xemacs/site-packages/lisp/proofgeneral/generic/pg-xml)
>
> Internationalization Settings:
> -------------------------
>
> Environment:
>
> Value of LC_ALL : nil
> Value of LC_COLLATE : nil
> Value of LC_CTYPE : C
> Value of LC_MESSAGES : nil
> Value of LC_MONETARY : nil
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> (current-locale) => "C"
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> 'mswindows-multibyte-system-default is not a coding system alias
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>
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>
> Features:
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>
>
> Recent keystrokes:
> -----------------
>
> left left left left left left left left left left left
> left left left left left left left left left left left
> left left M-RET M-RET up button2 button2up home DEL
> button1 button1up misc-user C-x button4 5 2 button1
> button1up RET RET RET RET RET RET RET RET DEL DEL C-x
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> e BS BS button1 button1up M-x button2 button2up RE
> T
>
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> Paren mode is paren
> Fontifying custom.el... (regexps).................
> Fontifying custom.el... (regexps)................
> Fontifying custom.el... (regexps)................
> Fontifying custom.el... (regexps)................
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--
William Estrada
Mt Umunhum, CA, USA
HTTP://64.124.13.3 ( Mt-Umunhum-Wireless.net )
Skype: MrUmunhum
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- 5 participants
- 14 comments
Re: molecular weight of proteins
13 years, 6 months
Aidan Kehoe
Aidan Kehoe
Ar an t-aonú lá déag de mí Deireadh Fómhair, scríobh Aidan Kehoe:
> [...]
> (defun protein-weight-region (start end &optional buffer)
> [...]
Actually, here’s a version of that last function that’s much closer to what
you asked for:
(defun protein-weight-region (start end &optional buffer)
(interactive "r")
(let ((weight
(protein-weight-string (replace-in-string
(buffer-substring start end buffer)
"[^A-Z]" ""))))
(delete-region start end buffer)
(goto-char start)
(insert (format "%S\n" weight))
(message "Protein weight is %S" weight)
weight))
--
“Apart from the nine-banded armadillo, man is the only natural host of
Mycobacterium leprae, although it can be grown in the footpads of mice.”
-- Kumar & Clark, Clinical Medicine, summarising improbable leprosy research
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- 1 participants
- 0 comments
molecular weight of proteins
13 years, 6 months
Sirano Dhe-Paganon
Sirano Dhe-Paganon
Hi,
In xemacs, I would like to calculate the molecular weight of proteins, each
of which is listed in a separate line, as shown below for example in the
input section (note the email truncated the lines to 256 characters i
think). I would like to replace the protein sequence with the molecular
weight of the protein. To calculate the molecular weight of each protein,
the molecular weight of all residues of that protein are added (the
molecular weights of each residue is predefined in the table below).
Can someone point me in the right direction or provide lisp code for
analogous examples?
Thank you.
Sirano
input:
MTAITHGSPVGGNDSQGQVLDGQSQHLFQQNQTSSPDSSNENSVATPPPEEQGQGDAPPQHEDEEPAFPHTELANL
DDMINRPRWVVPVLPKGELEVLLEAAIDLSVKGLDVKSEACQRFFRDGLTISFTKILMDEAVSGWKFEIHRCIINN
THRLVELCVAKLSQDWFPLLELLAMALNPHCKFHIYNGTRPCELISSNAQLPEEELFARSSDPRSPKGWLVDLINK
FGTLNGFQILHDRFFNGSALNIQIIAALIKPFGQCYEFLSQHTLKKYFIPVIEIVPHLLENLTDEELKKEAKNEAK
NDALSMIIKSLKNLASRISGQDETIKNLEIFRLKMILRLLQISSFNGKMNALNEINKVISSVSYYTHRHSNPEEEE
WLTAERMAEWIQQNNILSIVLQDSLHQPQYVEKLEKILRFVIKEKALTLQDLDNIWAAQAGKHEAIVKNVHDLLAK
LAWDFSPGQLDHLFDCFKASWTNASKKQREKLLELIRRLAEDDKDGVMAHKVLNLLWNLAQSDDVPVDIMDLALSA
HIKILDYSCSQDRDAQKIQWIDHFIEELRTNDKWVIPALKQIREICSLFGEASQNLSQTQRSPHIFYRHDLINQLQ
QNHALVTLVAENLATYMNSIRLYAGDHEDYDPQTVRLGSRYSHVQEVQERLNFLRFLLKDGQLWLCAPQAKQIWKC
LAENAVYLCDREACFKWYSKLMGDEPDLDPDINKDFFESNVLQLDPSLLTENGMKCFERFFKAVNCRERKLIAKRR
SYMMDDLELIGLDYLWRVVIQSSDEIANRAIDLLKEIYTNLGPRLKANQVVIHEDFIQSCFDRLKASYDTLCVFDG
DKNSINCARQEAIRMVRVLTVIKEYINECDSDYHKERMILPMSRAFCGKHLSLIVRFPNQGRQVDELDIWFHTNDT
IGSVRRCIVNRIKANVAHKKIELFVGGELIDSENDRKLIGQLNLKDKSLITAKLTQINFNMPSSPDSSSDSSTASP
GNHRNHYNDGPNLKVESCLPGVIMSVHPKYISFLWQFANLGSNLNMPPLKNGARVLMKLMPPDRTAVEKLRTVCLD
HANLGEGKLSPPLDSLFFGPSASQVLYLTEVVYALLMPAGVPLTDGSSDFQVHFLKSGGLPLVLSMLIRNNFLPNT
DMETRRGAYLNALKIAKLLLTAIGYGHVRAVAEACQPVVDGTDPITQINQVTHDQAVVLQSALQSIPNPSSECVLR
NESILLAQEISNEASRYMPDICVIRAIQKIIWASACGALGLFFSPNEEITKIYQMTTNGSNKLEVEDEQVCCEALE
VMTLCFALLPTALDALSKEKAWQTFIIDLLLHCPSKTVRQLAQEQFFLMCTRCCMGHRPLLFFITLLFTILGSTAR
EKGKYSGDYFTLLRHLLNYAYNGNINIPNAEVLLVSEIDWLKRIRDNVKNTGETGVEEPILEGHLGVTKELLAFQT
SEKKYHFGCEKGGANLIKELIDDFIFPASKVYLQYLRSGELPAEQAIPVCSSPVTINAGFELLVALAIGCVRNLKQ
IVDCLTEMYYMGTAITTCEALTEWEYLPPVGPRPPKGFVGLKNAGATCYMNSVIQQLYMIPSIRNSILAIEGTGSD
LHDDMFGDEKQDSESNVDPRDDVFGYPHQFEDKPALSKTEDRKEYNIGVLRHLQVIFGHLAASQLQYYVPRGFWKQ
FRLWGEPVNLREQHDALEFFNSLVDSLDEALKALGHPAILSKVLGGSFADQKICQGCPHRFECEESFTTLNVDIRN
HQNLLDSLEQYIKGDLLEGANAYHCEKCDKKVDTVKRLLIKKLPRVLAIQLKRFDYDWERECAIKFNDYFEFPREL
DMGPYTVAGVANLERDNVNSENELIEQKEQSDNETAGGTKYRLVGVLVHSGQASGGHYYSYIIQRNGKDDQTDHWY
KFDDGDVTECKMDDDEEMKNQCFGGEYMGEVFDHMMKRMSYRRQKRWWNAYIPFYEQMDMIDEDDEMIRYISELTI
ARPHQIIMSPAIERSVRKQNVKFMHNRLQYSLEYFQFVKKLLTCNGVYLNPAPGQDYLLPEAEEITMISIQLAARF
LFTTGFHTKKIVRGPASDWYDALCVLLRHSKNVRFWFTHNVLFNVSNRFSEYLLECPSAEVRGAFAKLIVFIAHFS
LQDGSCPSPFASPGPSSQACDNLSLSDHLLRATLNLLRREVSEHGHHLQQYFNLFVMYANLGVAEKTQLLKLNVPA
TFMLVSLDEGPGPPIKYQYAELGKLYSVVSQLIRCCNVSSTMQSSINGNPPLPNPFGDLNLSQPIMPIQQNVLDIL
FVRTSYVKKIIEDCSNSEDTIKLLRFCSWENPQFSSTVLSELLWQVAYSYTYELRPYLDLLFQILLIEDSWQTHRI
HNALKGIPDDRDGLFDTIQRSKNHYQKRAYQCIKCMVALFSSCPVAYQILQGNGDLKRKWTWAVEWLGDELERRPY
TGNPQYSYNNWSPPVQSNETANGYFLERSHSARMTLAKACELCPEEEPDDQDAPDEHEPSPSEDAPLYPHSPASQY
QQNNHVHGQPYTGPAAHHLNNPQKTGQRTQENYEGNEEVSSPQMKDQ
MRRKNSYYVWQKIFQIQFPLYTAYKHNTHPTIEDISTQESNILGAFCDMNDVEVPLHLLRYVCLFCGKNGLSLMKD
CFEYGTPETLPFLIAHAFITVVSNIRIWLHIPAVMQHIIPFRTYVIRYLCKLSDQELRQSAARNMADLMWSTVKEP
LDTTLCFDKESLDLAFKYFMSPTLTMRLAGLSQITNQLHTFNDVCNNESLVSDTETSIAKELADWLISNNVVEHIF
GPNLHIEIIKQCQVILNFLAAEGRLSTQHIDCIWAAAQLKHCSRYIHDLFPSLIKNLDPVPLRHLLNLVSALEPSV
HTEQTLYLASMLIKALWNNALAAKAQLSKQSSFASLLNTNIPIGNKKEEEELRRTAPSPWSPAASPQSSDNSDTHQ
SGGSDIEMDEQLINRTKHVQQRLSDTEESMQGSSDETANSGEDGSSGPGSSSGHSDGSSNEVNSSHASQSAGSPGS
EVQSEDIADIEALKEEDEDDDHGHNPPKSSCGTDLRNRKLESQAGICLGDSQGTSERNGTSSGTGKDLVFNTESLP
SVDNRMRMLDACSHSEDPEHDISGEMNATHIAQGSQESCITRTGDFLGETIGNELFNCRQFIGPQHHHHHHHHHHH
HDGHMVDDMLSADDVSCSSSQVSAKSEKNMADFDGEESGCEEELVQINSHAELTSHLQQHLPNLASIYHEHLSQGP
VVHKHQFNSNAVTDINLDNVCKKGNTLLWDIVQDEDAVNLSEGLINEAEKLLCSLVCWFTDRQIRMRFIEGCLENL
GNNRSVVISLRLLPKLFGTFQQFGSSYDTHWITMWAEKELNMMKLFFDNLVYYIQTVREGRQKHALYSHSAEVQVR
LQFLTCVFSTLGSPDHFRLSLEQVDILWHCLVEDSECYDDALHWFLNQVRSKDQHAMGMETYKHLFLEKMPQLKPE
TISMTGLNLFQHLCNLARLATSAYDGCSNSELCGMDQFWGIALRAQSGDVSRAAIQYINSYYINGKTGLEKEQEFI
SKCMESLMIASSSLEQESHSSLMVIERGLLMLKTHLEAFRRRFAYHLRQWQIEGTGISSHLKALSDKQSLPLRVVC
QPAGLPDKMTIEMYPSDQVADLRAEVTHWYENLQKEQINQQAQLQEFGQSNRKGEFPGGLMGPVRMISSGHELTTD
YDEKALHELGFKDMQMVFVSLGAPRRERKGEGVQLPASCLPPPQKDNIPMLLLLQEPHLTTLFDLLEMLASFKPPS
GKVAVDDSESLRCEELHLHAENLSRRVWELLMLLPTCPNMLMAFQNISDEQSNDGFNWKELLKIKSAHKLLYALEI
IEALGKPNRRIRRESTGSYSDLYPDSDDSSEDQVENSKNSWSCKFVAAGGLQQLLEIFNSGILEPKEQESWTVWQL
DCLACLLKLICQFAVDPSDLDLAYHDVFAWSGIAESHRKRTWPGKSRKAAGDHAKGLHIPRLTEVFLVLVQGTSLI
QRLMSVAYTYDNLAPRVLKAQSDHRSRHEVSHYSMWLLVSWAHCCSLVKSSLADSDHLQDWLKKLTLLIPETAVRH
ESCSGLYKLSLSGLDGGDSINRSFLLLAASTLLKFLPDAQALKPIRIDDYEEEPILKPGCKEYFWLLCKLVDNIHI
KDASQTTLLDLDALARHLADCIRSREILDHQDGNVEDDGLTGLLRLATSVVKHKPPFKFSREGQEFLRDIFNLLFL
LPSLKDRQQPKCKSHSSRAAAYDLLVEMVKGSVENYRLIHNWVMAQHMQSHAPYKWDYWPHEDVRAECRFVGLTNL
GATCYLASTIQQLYMIPEARQAVFTAKYSEDMKHKTTLLELQKMFTYLMESECKAYNPRPFCKTYTMDKQPLNTGE
QKDMTEFFTDLITKIEEMSPELKNTVKSLFGGVITNNVVSLDCEHVSQTAEEFYTVRCQVADMKNIYESLDEVTIK
DTLEGDNMYTCSHCGKKVRAEKRACFKKLPRILSFNTMRYTFNMVTMMKEKVNTHFSFPLRLDMTPYTEDFLMGKS
ERKEGFKEVSDHSKDSESYEYDLIGVTVHTGTADGGHYYSFIRDIVNPHAYKNNKWYLFNDAEVKPFDSAQLASEC
FGGEMTTKTYDSVTDKFMDFSFEKTHSAYMLFYKRMEPEEENGREYKFDVSSELLEWIWHDNMQFLQDKNIFEHTY
FGFMWQLCSCIPSTLPDPKAVSLMTAKLSTSFVLETFIHSKEKPTMLQWIELLTKQFNNSQAACEWFLDRMADDDW
WPMQILIKCPNQIVRQMFQRLCIHVIQRLRPVHAHLYLQPGMEDGSDDMDTSVEDIGGRSCVTRFVRTLLLIMEHG
VKPHSKHLTEYFAFLYEFAKMGEEESQFLLSLQAISTMVHFYMGTKGPENPQVEVLSEEEGEEEEEEEDILSLAEE
KYRPAALEKMIALVALLVEQSRSERHLTLSQTDMAALTGGKGFPFLFQHIRDGINIRQTCNLIFSLCRYNNRLAEH
IVSMLFTSIAKLTPEAANPFFKLLTMLMEFAGGPPGMPPFASYILQRIWEVIEYNPSQCLDWLAVQTPRNKLAHSW
VLQNMENWVERFLLAHNYPRVRTSAAYLLVSLIPSNSFRQMFRSTRSLHIPTRDLPLSPDTTVVLHQVYNVLLGLL
SRAKLYVDAAVHGTTKLVPYFSFMTYCLISKTEKLMFSTYFMDLWNLFQPKLSEPAIATNHNKQALLSFWYNVCAD
CPENIRLIVQNPVVTKNIAFNYILADHDDQDVVLFNRGMLPAYYGILRLCCEQSPAFTRQLASHQNIQWAFKNLTP
HASQYPGAVEELFNLMQLFIAQRPDMREEELEDIKQFKKTTISCYLRCLDGRSCWTTLISAFRILLESDEDRLLVV
FNRGLILMTESFNTLHMMYHEATACHVTGDLVELLSIFLSVLKSTRPYLQRKDVKQALIQWQERIEFAHKLLTLLN
SYSPPELRNACIDVLKELVLLSPHDFLHTLVPFLQHNHCTYHHSNIPMSLGPYFPCRENIKLIGGKSNIRPPRPEL
NMCLLPTMVETSKGKDDVYDRMLLDYFFSYHQFIHLLCRVAINCEKFTETLVKLSVLVAYEGLPLHLALFPKLWTE
LCQTQSAMSKNCIKLLCEDPVFAEYIKCILMDERTFLNNNIVYTFMTHFLLKVQSQVFSEANCANLISTLITNLIS
QYQNLQSDFSNRVEISKASASLNGDLRALALLLSVHTPKQLNPALIPTLQELLSKCRTCLQQRNSLQEQEAKERKT
KDDEGATPIKRRRVSSDEEHTVDSCISDMKTETREVLTPTSTSDNETRDSSIIDPGTEQDLPSPENSSVKEYRMEV
PSSFSEDMSNIRSQHAEEQSNNGRYDDCKEFKDLHCSKDSTLAEEESEFPSTSISAVLSDLADLRSCDGQALPSQD
PEVALSLSCGHSRGLFSHMQQHDILDTLCRTIESTIHVVTRISGKGNQAAS
MDGVVRNLSNDDSVTDSQMLTAISRMIDWVSWPLGKNIDKWIIALLKGLAAVKKFSILIEVSLTKIEKVFSKLLYP
IVRGAALSVLKYMLLTFQHSHEAFHLLLPHIPPMVASLVKEDSNSGTSCLEQLAELVHCMVFRFPGFPDLYEPVME
AIKDLHVPNEDRIKQLLGQDAWTSQKSELAGFYPRLMAKSDTGKIGLINLGNTCYVNSILQALFMASDFRHCVLRL
TENNSQPLMTKLQWLFGFLEHSQRPAISPENFLSASWTPWFSPGTQQDCSEYLKYLLDRLHEEEKTGTRICQKLKQ
SSSPSPPEEPPAPSSTSVEKMFGGKIVTRICCLCCLNVSSREEAFTDLSLAFPPPERCRRRRLGSVMRPTEDITAR
ELPPPTSAQGPGRVGPRRQRKHCITEDTPPTSLYIEGLDSKEAGGQSSQEERIEREEEGKEERTEKEEVGEEEEST
RGEGEREKEEEVEEEEEKVEKETEKEAEQEKEEDSLGAGTHPDAAIPSGERTCGSEGSRSVLDLVNYFLSPEKLTA
ENRYYCESCASLQDAEKVVELSQGPCYLILTLLRFSFDLRTMRRRKILDDVSIPLLLRLPLAGGRGQAYDLCSVVV
HSGVSSESGHYYCYAREGAARPAASLGTADRPEPENQWYLFNDTRVSFSSFESVSNVTSFFPKDTAYVLFYRQRPR
EGPEAELGSSRVRTEPTLHKDLMEAISKDNILYLQEQEKEARSRAAYISALPTSPHWGRGFDEDKDEDEGSPGGCN
PAGGNGGDFHRLVF
MVAEEGGVPADEVILVELYPSGFQRSFFDEEDLNTIAEGDNVYAFQVPPSPSQGTLSAHPLGLSASPRLAAREGQR
FSLSLHSESKVLILFCNLVGSGQQASRFGPPFLIREDRAVSWAQLQQSILSKVRHLMKSEAPVQNLGSLFSIRVVG
LSVACSYLSPKDSRPLCHWAVDRVLHLRRPGGPPHVKLAVEWDSSVKERLFGSLQEERAQDADSVWQQQQAHQQHS
CTLDECFQFYTKEEQLAQDDAWKCPHCQVLQQGMVKLSLWTLPDILIIHLKRFCQVGERRNKLSTLVKFPLSGLNM
APHRPEKHQP
MAPRLQLEKAAWRWAETVRPEEVSQEHIETAYRIWLEPCIRGVCRRNCKGNPNCLVGIGEHIWLGEIDENSFHNID
DPNCERRKKNSFVGLTNLGATCYVNTFLQVWFLNLELRQALYLCPSTCSDYMLGDGIQEEKDYEPQTICEHLQYLF
ALLQNSNRRYIDPSGFVKALGLDTGQQQDAQEFSKLFMSLLEDTLSKQKNPDVRNIVQQQFCGEYAYVTVCNQCGR
ESKLLSKFYELELNIQGHKQLTDCISEFLKEEKLEGDNRYFCENCQSKQNATRKIRLLSLPCTLNLQLMRFVFDRQ
TGHKKKLNTYIGFSEILDMEPYVEHKGGSYVYELSAVLIHRGVSAYSGHYIAHVKDPQSGEWYKFNDEDIEKMEGK
KLQLGIEEDLAEPSKSQTRKPKCGKGTHCSRNAYMLVYRLQTQEKPNTTVQVPAFLQELVDRDNSKFEEWCIEMAE
MRKQSVDKGKAKHEEVKELYQRLPAGAEPYEFVSLEWLQKWLDESTPTKPIDNHACLCSHDKLHPDKISIMKRISE
YAADIFYSRYGGGPRLTVKALCKECVVERCRILRLKNQLNEDYKTVNNLLKAAVKGDGFWVGKSSLRSWRQLALEQ
LDEQDGDAEQSNGKMNGSTLNKDESKEERKEEEELNFNEDILCPHGELCISENERRLVSKEAWSKLQQYFPKAPEF
PSYKECCSQCKILEREGEENEALHKMIANEQKTSLPNLFQDKNRPCLSNWPEDTDVLYIVSQFFVEEWRKFVRKPT
RCSPVSSVGNSALLCPHGGLMFTFASMTKEDSKLIALIWPSEWQMIQKLFVVDHVIKITRIEVGDVNPSETQYISE
PKLCPECREGLLCQQQRDLREYTQATIYVHKVVDNKKVMKDSAPELNVSSSETEEDKEEAKPDGEKDPDFNQIMHA
FSVAPFDQNLSIDGKILSDDCATLGTLGVIPESVILLKADEPIADYAAMDDVMQVCMPEEGFKGTGLLGH
MPIVDKLKEALKPGRKDSADDGELGKLLASSAKKVLLQKIEFEPASKSFSYQLEALKSKYVLLNPKTEGASRHKSG
DDPPARRQGSEHTYESCGDGVPAPQKVLFPTERLSLRWERVFRVGAGLHNLGNTCFLNATIQCLTYTPPLANYLLS
KEHARSCHQGSFCMLCVMQNHIVQAFANSGNAIKPVSFIRDLKKIARHFRFGNQEDAHEFLRYTIDAMQKACLNGC
AKLDRQTQATTLVHQIFGGYLRSRVKCSVCKSVSDTYDPYLDVALEIRQAANIVRALELFVKADVLSGENAYMCAK
CKKKVPASKRFTIHRTSNVLTLSLKRFANFSGGKITKDVGYPEFLNIRPYMSQNNGDPVMYGLYAVLVHSGYSCHA
GHYYCYVKASNGQWYQMNDSLVHSSNVKVVLNQQAYVLFYLRIPGSKKSPEGLISRTGSSSLPGRPSVIPDHSKKN
IGNGIISSPLTGKRQDSGTMKKPHTTEEIGVPISRNGSTLGLKSQNGCIPPKLPSGSPSPKLSQTPTHMPTILDDP
GKKVKKPAPPQHFSPRTAQGLPGTSNSNSSRSGSQRQGSWDSRDVVLSTSPKLLATATANGHGLKGNDESAGLDRR
GSSSSSPEHSASSDSTKAPQTPRSGAAHLCDSQETNCSTAGHSKTPPSGADSKTVKLKSPVLSNTTTEPASTMSPP
PAKKLALSAKKASTLWRATGNDLRPPPPSPSSDLTHPMKTSHPVVASTWPVHRARAVSPAPQSSSRLQPPFSPHPT
LLSSTPKPPGTSEPRSCSSISTALPQVNEDLVSLPHQLPEASEPPRSPSEKRKKTFVGEPQRLGSETCLPQHIREA
TAAPHGKRKRKKKKRPEDTAASALQEGQTQRQPGSPMYRREGQAQLPAVRRQEDGTQPQVNGQQVGCVTDGHHASS
RKRRRKGAEGLGEEGGLHQDPLRHSCSPMGDGDPEAMEESPRKKKKRKQETQRAVEEDGHLKCPRSAKPQDAVVPE
SSSCAPSANGWCPGDRMGLSQAPPVSWNGERESDVVQELLKYSSDKAYGRKVLTWDGKMSAVSQDAIEDSRQARTE
TVVDDWDEEFDRGKEKKIKKFKREKRRNFNAFQKLQTRRNFWSVTHPAKAASLSYRR
output:
291118.08
387123.71
86895.98
35250.21
112872.11
122626.59
Table: molecular weight of individual residues:
A 071.0788
R 156.1875
N 114.1038
D 115.0886
C 103.1388
E 129.1155
Q 128.1307
G 057.0519
H 137.1411
I 113.1594
L 113.1594
K 128.1741
M 131.1926
F 147.1766
P 097.1167
S 087.0782
T 101.1051
W 186.2132
Y 163.1760
V 099.1326
Sirano
<http://www.sgc.utoronto.ca/pmwiki/pmwiki.php?n=ubiquitinbiology.HomePage>
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