Commit 15a2fde2 authored by Morten Kjeldgaard's avatar Morten Kjeldgaard Committed by Frédéric-Emmanuel Picca

Imported Debian patch 0.7pre1+svn3470-0ubuntu1~natty1

parent 37ae14ba
The source package uses quilt for the modifications of the upstream source.
If you want to change something it is best to use the quilt approach as
documented in
/usr/share/doc/quilt/README.source
-- Morten Kjeldgaard <mok0@ubuntu.com>, Mon, 31 Jan 2011 13:25:23 +0100
.TH BFACTAN 1 "January, 2011"
.\" Please adjust this date whenever revising the manpage.
.SH NAME
bfactan \- program to...
.SH SYNOPSIS
.B bfactan
.I file
.SH DESCRIPTION
This manual page briefly documents the
.B bfactan
program.
.PP
\fBbfactan\fP is a part of the Coot suite of programs.
.SH SEE ALSO
.BR coot (1),
.BR density-score-by-residue (1),
.BR findligand (1),
.BR findwaters (1),
.BR fix-nomenclature-errors (1),
.BR lidia (1).
.br
.SH AUTHOR
\fBbfactan\fP is written by Paul Emsley.
.PP
This manual page was written by Morten Kjeldgaard <mok@bioxray.dk>
coot (0.7pre1+svn3470-0ubuntu1~natty1) natty; urgency=low
* Build for natty
-- Morten Kjeldgaard <mok0@ubuntu.com> Thu, 14 Apr 2011 12:37:54 +0200
coot (0.7pre1+svn3470-0ubuntu1~lucid1) lucid; urgency=low
* New upstream release
-- Morten Kjeldgaard <mok0@ubuntu.com> Tue, 12 Apr 2011 12:45:50 +0200
coot (0.7pre1+svn3406-0ubuntu3~lucid1) lucid; urgency=low
* Coot's nest now stores working directory and window
position in a config file.
-- Morten Kjeldgaard <mok0@ubuntu.com> Tue, 15 Mar 2011 12:11:45 +0100
coot (0.7pre1+svn3406-0ubuntu2~lucid1) lucid; urgency=low
* Command line parser completely rewritten, now includes a --directory
switch to set cwd, and a --state-script switch that bypasses the
dialog box and runs the state script [patch: optparser.diff]
* Add coots-nest wrapper program to allow Coot to be started from
the desktop menu system. Makes use of the above switch.
* debian/control: add dependency on python-vte.
-- Morten Kjeldgaard <mok0@ubuntu.com> Wed, 09 Mar 2011 13:30:25 +0100
coot (0.7pre1+svn3406-0ubuntu1~lucid1) lucid; urgency=low
* New upstream version svn 3406
* Convenience library patch to include protein_db subdir
* Show svn revision number in splash
* Tentative Python code patch allowing user to short-circuit where Coot
looks for specific programs [application-path.diff]
* Coot man page: detail .coot.py, add sbase section.
* Install desktop entry and custom icons
-- Morten Kjeldgaard <mok0@ubuntu.com> Sun, 20 Feb 2011 11:43:45 +0100
coot (0.7pre1+svn3369-0ubuntu1~lucid2) lucid; urgency=low
* Be careful when editing patches... the configure switch
--with-fftw-library-prefix switch broke...
-- Morten Kjeldgaard <mok0@ubuntu.com> Thu, 10 Feb 2011 11:19:13 +0100
coot (0.7pre1+svn3369-0ubuntu1~lucid1) lucid; urgency=low
* Updated coot manpage again
* Get rid of "Check for Updates" menu item which is confusing
when Coot is installed via apt-get.
* Patches now follow Debian Patch Tagging Guidelines
-- Morten Kjeldgaard <mok0@ubuntu.com> Tue, 08 Feb 2011 10:56:45 +0100
coot (0.7pre1+svn3355-0ubuntu1~lucid3) lucid; urgency=low
* Updated coot manpage
* Consider -c command line arguments Python by default
[patch: command-line.diff]
* Finally define correct path to refmac dictionary
* Use svn revision number in package name
-- Morten Kjeldgaard <mok0@ubuntu.com> Thu, 03 Feb 2011 14:18:14 +0100
coot (0.7pre1+bzr3269-0ubuntu1~lucid2) lucid; urgency=low
* Turn off generation of 0-coot-history.scm [patch:
coot-history.diff]
* Don't distribute guile files in /usr/share/coot
* Use the correct single-precision fftw library [patch:
configure-fftw-prefix.diff]
* include citation.bib file
-- Morten Kjeldgaard <mok0@ubuntu.com> Wed, 02 Feb 2011 12:59:22 +0100
coot (0.7pre1+bzr3269-0ubuntu1~lucid1) lucid; urgency=low
* Initial release (Closes LP: #176211)
-- Morten Kjeldgaard <mok0@ubuntu.com> Fri, 07 Jan 2011 12:29:22 +0100
@article{Emsley:ba5144,
author = {Emsley, P. and Lohkamp, B. and Scott, W. G. and Cowtan, K.},
title = {{Features and development of {\it Coot}}},
journal = {Acta Crystallographica Section D},
year = {2010},
volume = {66},
number = {4},
pages = {486--501},
month = {Apr},
doi = {10.1107/S0907444910007493},
url = {http://dx.doi.org/10.1107/S0907444910007493},
eprint = {http://journals.iucr.org/d/issues/2010/04/00/ba5144/},
}
@article{Emsley:ba5070,
author = {Emsley, Paul and Cowtan, Kevin},
title = {{{\it Coot}: model-building tools for molecular graphics}},
journal = {Acta Crystallographica Section D},
year = {2004},
volume = {60},
number = {12 Part 1},
pages = {2126--2132},
month = {Dec},
doi = {10.1107/S0907444904019158},
url = {http://dx.doi.org/10.1107/S0907444904019158},
eprint = {http://journals.iucr.org/d/issues/2004/12/01/ba5070/}
}
Source: coot
Section: science
Priority: optional
Maintainer: Morten Kjeldgaard <mok0@ubuntu.com>
Build-Depends: debhelper (>= 7), autotools-dev, automake, libtool,
quilt, libmmdb-dev (>=1.23), libclipper-dev, libgpp4-dev, libssm-dev
(>=1.1), libgsl0-dev, libglib2.0-dev, libgtk2.0-dev,
libgtkglext1-dev, freeglut3-dev, libgnomecanvas2-dev,
libgoocanvas-dev, python-dev, python-gtk2-dev, swig (>= 1.3.36), texinfo,
imagemagick, ghostscript, sharutils
Standards-Version: 3.9.1
Homepage: http://www.biop.ox.ac.uk/coot/
Vcs-Bzr: http://bazaar.launchpad.net/~mok0/coot/ubuntu
Package: coot
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}, coot-data, refmac-dict,
python-vte, python
Suggests: coot-docs
Description: model building program for macromolecular crystallography
Coot is a program for constructing atomic models of macromolecules
from x-ray diffraction data. Coot displays electron density maps and
molecular models and allows model manipulations such as idealization,
refinement, manual rotation/translation, rigid-body fitting, ligand
search, solvation, mutations, rotamers. Validation tools such as
Ramachandran and geometry plots are available to the user. This
package provides a Coot build with embedded Python support.
Package: coot-data
Architecture: all
Depends: ${misc:Depends}
Description: various data files needed by Coot
Coot is an interactive program for fitting atomic models to
crystallographic electron density maps. This package contains various
data files needed by Coot.
Package: coot-docs
Architecture: all
Depends: ${misc:Depends}
Description: documentation for Coot
Coot is an interactive program for fitting atomic models to
crystallographic electron density maps. This package contains
documentation source files for Coot.
This diff is collapsed.
/usr/share/coot/reference-structures
debian/tmp/usr/share/coot
debian/pdbget.sh /usr/share/coot
#!/bin/sh
# postinst script for coot-data, see: dh_installdeb(1)
set -e
# summary of how this script can be called:
# * <postinst> `configure' <most-recently-configured-version>
# * <old-postinst> `abort-upgrade' <new version>
# * <conflictor's-postinst> `abort-remove' `in-favour' <package>
# <new-version>
# * <postinst> `abort-remove'
# * <deconfigured's-postinst> `abort-deconfigure' `in-favour'
# <failed-install-package> <version> `removing'
# <conflicting-package> <version>
# for details, see http://www.debian.org/doc/debian-policy/ or
# the debian-policy package
ENTRIES="1c75 1es9 1fye 1gk9 1hvb 1i8o 1jg1 1c7k 1et1 1g2b 1gmx 1hyo
1iqz 1jk3 1ds1 1euw 1g2y 1h4x 1i0d 1ird 1jl1 1dy5 1f4p 1g4i 1h97 1i0v
1j98 1k7c 1e29 1f86 1g61 1hbn 1i12 1j9b 1ka1 1e4m 1f94 1g66 1hdh 1i27
1jbe 1koi 1e9g 1f9v 1g6x 1hdo 1i2t 1jcl 1kth 1eb6 1fn8 1g7a 1heu 1i40
1jf8 1ejg 1fsg 1ga6 1hg7 1i4u 1jfb"
sdir=/usr/share/coot/reference-structures
case "$1" in
configure)
N=`echo $ENTRIES|wc -w`
echo Download $N reference structures from Protein Data Bank:
# $sdir is created by the package, but better make sure
test -d $sdir || mkdir -p $sdir
cd $sdir
sh /usr/share/coot/pdbget.sh $ENTRIES
stat=$?
echo Done.
exit $stat
;;
abort-upgrade|abort-remove|abort-deconfigure)
;;
*)
echo "postinst called with unknown argument \`$1'" >&2
exit 1
;;
esac
# dh_installdeb will replace this with shell code automatically
# generated by other debhelper scripts.
#DEBHELPER#
exit 0
#!/bin/sh
# prerm script for coot-data
#
# see: dh_installdeb(1)
set -e
# summary of how this script can be called:
# * <prerm> `remove'
# * <old-prerm> `upgrade' <new-version>
# * <new-prerm> `failed-upgrade' <old-version>
# * <conflictor's-prerm> `remove' `in-favour' <package> <new-version>
# * <deconfigured's-prerm> `deconfigure' `in-favour'
# <package-being-installed> <version> `removing'
# <conflicting-package> <version>
# for details, see http://www.debian.org/doc/debian-policy/ or
# the debian-policy package
case "$1" in
upgrade)
;;
remove)
;;
deconfigure)
;;
failed-upgrade)
;;
purge)
if [ -d /usr/share/coot/reference-structures ] ; then
rm -f /usr/share/coot/reference-structures/*
fi
;;
*)
echo "prerm called with unknown argument \`$1'" >&2
exit 1
;;
esac
# dh_installdeb will replace this with shell code automatically
# generated by other debhelper scripts.
#DEBHELPER#
exit 0
.TH COOT 1 "March 2011"
.\" Please adjust this date whenever revising the manpage.
.SH NAME
Coot \- model building program for macromolecular crystallography
.SH SYNOPSIS
.B coot
.RI [ options ]
.SH DESCRIPTION
This manual page briefly documents the \fBCoot\fP molecular graphics
program.
.PP
\fBCoot\fP is a program that displays electron density maps and models
and allows certain model manipulations: idealization, refinement,
manual rotation/translation, rigid-body fitting, ligand search,
solvation, mutations, rotamers, Ramachandran plots and other
stuff.
.PP
\fBCoot\fP has an embedded Python interpreter. Thus the full power of
python is available. On startup, \fBCoot\fP will look for an
initialization script (\fI$HOME/.coot.py\fP) and will execute it if
found. This file typically contains Python commands that set personal
preferences.
.PP
On exit \fBCoot\fP saves the current state to a file called
\fI0-coot.state.py\fP. This state file contains information about the
screen centre, the clipping, colour map rotation size, the symmetry
radius, and other molecule related parameters such as filename, column
labels, coordinate filename etc. The next time \fBCoot\fP starts up in
the same directory, the user is prompted to load the state file thus
restoring the previous session.
.SH OPTIONS
These programs follow the usual GNU command line syntax, with long
options starting with two dashes (`-'). A summary of options is
included below.
.TP
.B \-\-help
print command line options and exit.
.TP
.B \-\-detailed-help
print help, including all details and hidden options, and exit.
.TP
.B \-\-full-help
print help, including hidden options, and exit.
.TP
.B \-\-version
print the version and exit.
.TP
.B \-\-version\-full
output detailed version details and exit.
.PP
Experimental data options:
.TP
\fB\-p\fP, \fB\-\-pdb\fP \fI<filename>\fR ...
input PDB, SHELX .ins/.res and CIF files.
.TP
\fB\-\-coords\fP, \fB\-\-xyzin\fP ...
same as \-\-pdb.
.TP
\fB-m\fP, \fB\-\-map\fP \fI<filename>\fR ...
read a CCP4-format electron density map.
.TP
\fB\-d\fP, \fB\-\-data\fP, \fB\-\-hklin\fP \fI<filename>\fR ...
MTZ, PHS or mmCIF reflection data file.
.TP
\fB\-\-hklin\fP
same as \-\-data.
.TP
\fB\-a\fP, \fB\-\-auto\fP \fI<filename>\fR ...
auto\-read MTZ format reflection files (with default MTZ column labels
FWT, PHWT).
.TP
.B \-\-code \fI<PDB ident>\fR ...
on starting Coot, get the PDB file and MTZ file (if it exists) from
the Electron Density Server (EDS).
.TP
.B \-\-dictionary \fI<filename>\fR ...
read in a CIF monomer dictionary.
.PP
Scripting options:
.TP
\fB\-s\fP, \fB\-\-script\fP \fIfilename\fR ...
run a script on startup.
.TP
.B \-c, \fB\-\-command\fP \fIcommand\fR ...
run a Python command on startup.
.TP
.B \-\-python
process \-c arguments as Python rather than Scheme. This option only
has any meaning if \fBCoot\fP is built with Guile support, in which
case \-c arguments are considered to be Scheme by default.
.PP
Environment:
.TP
.B \-\-ccp4\-project \fIdirectory\fB
optionally define CCP4 project directory.
.TP
\fB\-\-directory \fIdirectory\fP
Define working directory. Coot will chdir to this directory before
starting any work.
.PP
Startup options:
.TP
.B \-\-no\-state\-script
don't run the 0\-coot.state.py script on start up. Don't save a state
script on exit either.
.TP
.B \-\-state\-script
run the 0\-coot.state.py script on start up, without popping a dialog
box to prompt the user.
.TP
.B \-\-no-graphics
run \fBCoot\fP without graphics.
.TP
.B \-\-no\-guano
don't leave "Coot droppings" i.e. don't write state and history files on exit.
.TP
.B \-\-no-splash-screen
don't display the pretty splash screen on startup.
.TP
.B \-\-splash\-screen \fIfilename\P
alternate splash screen, should be a .png format file. This option is
currently ignored.
.TP
.B \-\-small-screen
start up on computer with a small screen (e.g. EEE PC and other
notebook computers.
.TP
.B \-\-stereo
start up in hardware stereo mode.
.TP
.B \-\-side\-by\-side
start in side-by-side stereo mode.
.TP
.B \-\-zalman\-stereo
use Zalman stereo hardware.
.PP
Miscellaneous:
.TP
\fB\-\-host\fP, \fB\-\-hostname \fIhost\fP
start listener on \fIhost\fP.
.TP
.B \-\-port \fInumber\fP
port number for listener define by \-\-host.
.PP
Coot maintenance:
.TP
.B \-\-update-self
attempt to update self.
.TP
.B \-\-self-test
run internal self-test and exit.
.SH EXAMPLES
For example, one might use:
.PP
coot \-\-pdb post\-refinement.pdb \-\-auto refmac\-2.mtz \-\-dictionary lig.cif
.SH FILES
.TP
.I $HOME/.coot.py
file containing user Python code, for example global personal startup
settings. If this file is found, it will be executed immediately before
the state file.
.TP
.I $HOME/.coot-preferences/coot_preferences.py
contains global user preferences. Do not edit this file, changes will be
overwritten.
.TP
.I $HOME/.coot-preferences/*.py
All *.py files are loaded in alphabetical order when the program
starts. The user can place various customizations here.
.TP
.I ./0-coot.state.py
contains the state of \fBCoot\fP when it last exited, for example file
names of structures and maps, the colours of the molecules and map,
the screen centre, map size and so on. When restarting a session, this
file should usually be used.
.TP
.I ./0-coot-history.py
The history of coot commands in the last coot session.
.TP
.I ./coot-download/
Directory where the files downloaded by \fBCoot\fP from the network
are saved. (For example files fetched from the European Bioinformatics
Institute (EBI) and the Electron Density Server (EDS))
.TP
.I ./coot-backup/
At each model modification a PDB file containing the current coordinates is
saved in this directory.
.TP
.I ./coot-refmac/
When running \fBRefmac\fP using the \fBCoot\fP interface, the input and
output are saved in this directory.
.TP
.I ./coot-ccp4/
When running CCP4 programs using the \fBCoot\fP interface. Input and
output files are saved in this directory.
.TP
.I ./coot-molprobity/
When running Molprobity's \fBProbe\fP and \fBReduce\fP using the
\fBCoot\fP interface, the input and output are saved in this directory.
.SH ENVIRONMENT VARIABLES
Certain environment variables can optionally be used to modify where
in the file system \fBCoot\fP finds information. Default values are
given in brackets.
.TP
.B COOT_MONOMER_LIB_DIR
\fIDirectory\fP containing the \fBRefmac\fR dictionary files, used
internally by \fBCoot\fP. This environment variable must point to the
monomers directory [/usr/share/refmac/monomers].
.TP
.B COOT_REFMAC_LIB_DIR
\fIDirectory\fP containing the \fBRefmac\fR dictionary files, used when
\fBRefmac\fP or \fBlibcheck\fP is invoked via the \fBCoot\fP interface.
Below the defined directory, the program must find a data/monomers/
hierachy [/usr/share/refmac].
.TP
.B COOT_RESOURCES_FILE
Path to the GTK2 resource \fIfile\fP, for customization of the widgets
[/usr/share/coot/cootrc].
.TP
.B COOT_SBASE_DIR
Path to the \fIdirectory\fP containing the MMDB sbase database files,
that are distributed with the CCP4 package. \fBCoot\fP can optionally
make use of the sbase database.
.SH SEE ALSO
.BR bfactan (1),
.BR density-score-by-residue (1),
.BR findligand (1),
.BR findwaters (1),
.BR fix-nomenclature-errors (1),
.BR lidia (1).
.br
.SH AUTHOR
\fBCoot\fP is written by Paul Emsley, Kevin Cowtan, Bernhard
Lohkamp, and several other contributors.
.PP
This manual page was written for the Ubuntu coot package by Morten
Kjeldgaard <mok0@ubuntu.com>.
[Desktop Entry]
Name=Coot
GenericName=
Comment=
Type=Application
Exec=/usr/bin/coots-nest
Icon=coot
Terminal=false
Categories=Education;Science;
debian/tmp/usr/share/info/*
debian/tmp/usr/bin
debian/tmp/usr/share/icons
debian/coot.desktop /usr/share/applications
debian/coots-nest /usr/bin
debian/bfactan.1
debian/coot.1
debian/density-score-by-residue.1
debian/findligand.1
debian/findwaters.1
debian/fix-nomenclature-errors.1
debian/lidia.1
debian/coots-nest.1
?package(coot):needs="X11|text|vc|wm" section="Apps/see-menu-manual"\
title="coot" command="/usr/bin/coots-nest"
#!/usr/bin/env python
# This is Coot's nest, a wrapper around Coot that allows it to be
# started from the menu system of the desktop. This wrapper first
# asks the user to select the working directory, and then starts
# Coot using the --directory switch. The terminal output from Coot
# is displayed in a terminal window. This terminal cannot be closed
# manually, but exits shortly after Coot exits.
#
# Copyright: (C) 2011 Morten Kjeldgaard <mok@bioxray.dk>
#
# This program is free software: you can redistribute it and/or
# modify it under the terms of the GNU General Public License as
# published by the Free Software Foundation, either version 3 of the
# License, or (at your option) any later version.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
import pygtk
pygtk.require('2.0')
import gtk
import vte
import time
import os
backgroundimage = "/usr/share/coot/pixmaps/coots-nest-background.png"
class CootsNest:
def close_application(self):
pos = self._window.get_position()
self.config.set_window_position(pos)
siz = self._window.get_size()
self.config.set_window_size(siz)
self.config.write()
secs = 1
time.sleep(secs)
gtk.main_quit()
#.
def close_application_not(self, win):
msg = "You cannot close this window like that.\nYou must exit Coot first"
message = gtk.MessageDialog(win,
gtk.DIALOG_MODAL,
gtk.MESSAGE_INFO,
gtk.BUTTONS_NONE, msg)
message.add_button(gtk.STOCK_OK, gtk.RESPONSE_CLOSE)
resp = message.run()
if resp == gtk.RESPONSE_CLOSE:
message.destroy()
#.
return True
#.
def write(self, text):
x, y = self._terminal.get_cursor_position()
self._terminal.feed(text + '\r\n', len(text) + 1)
#.
def __init__(self, config):
self.config = config
window = gtk.Window(gtk.WINDOW_TOPLEVEL)
self._window = window
window.set_resizable(True)
window.connect('delete_event', lambda x, args: self.close_application_not(x))
window.set_title("Coot's nest")
window.set_deletable(False)
pos = config.get_window_position()
if pos:
window.move(pos[0], pos[1])
#.
terminal = vte.Terminal()
self._terminal = terminal
terminal.set_scrollback_lines(500)
if os.path.exists(backgroundimage):
background = gtk.gdk.pixbuf_new_from_file(backgroundimage)
terminal.set_background_image(background)
#.
terminal.connect("child-exited", lambda x: self.close_application())
cwd = config.get_workdir()
if cwd:
argstr = ["dummy", "--state-script", "--directory=" + cwd]
terminal.fork_command(command="/usr/bin/coot", argv=argstr)
#.
else:
argstr = ["dummy", "--state-script"]
terminal.fork_command(command="/usr/bin/coot", argv=argstr)
#.
terminal.feed("Coot's nest starting Coot...\n\n\r")
if cwd:
terminal.feed("INFO:: nesting coot at "+cwd+"\n\n\r")
#.
else:
terminal.feed("WARNING:: no directory specified, nesting coot at "+
os.getcwd()+"\n\n\r")
#.
window.add(terminal)
window.show_all()
#.
#.
from ConfigParser import SafeConfigParser
class NestConfigParser (SafeConfigParser):
filename = ""
def __init__(self, fnam):
self.filename = fnam
SafeConfigParser.__init__(self)
self.workdir = os.getcwd()
self.pos = (0,0)
self.siz = (100,100)
def read(self):
c = SafeConfigParser.read(self,self.filename)
if not c:
self.add_section ("general")
self.add_section("window")
#.
else:
if not self.has_section("general"):
self.add_section("general")
#.
if not self.has_section("window"):