Commit 0eaee679 authored by Nicholas Breen's avatar Nicholas Breen

Updating packaging for 4.0 release (first part - debian/rules, debian/control, local man pages)

parent 575aadb9
TODO for gromacs
----------------
* 40_missing_cpp.dpatch, 10_manpages.dpatch: Can these be applied upstream?
What about 04_autoconf_mpisuffix.dpatch? Can we talk to upstream to apply
this one as well? Probably other packagers will benefit from it too.
-> 40_missing_cpp becomes obsolete with next major upstream release
("when it's ready")
-> 10_manpages needs an update against CVS HEAD for inclusion
* 04_autoconf_mpisuffix.dpatch:
-> comment the configure.ac stuff? (it is.)
2 suggestion for upstream:
1) ask upstream to add the AM_MAINTAINER_MODE macro (avoids the toolchain
if configure.ac or Makefile.am are changed)
2) preserve LIBSUFFIX if set via ./configure (we don't need the patch then)
http://paste.debian.net/49064 (patch)
* TODO: manpage errors - triggered by leading points followed by a space and a
word - should be fixed upstream too
\&. works if if you want to have a leading dot
* Resolve alpha + fortran + openmpi linking problems in conjunction with
openmpi team (currently fortran is disabled for that build)
* Implement debian/rules get-orig-source target.
The Debian Policy speaks about an optional target, but it says: "fetches
[..] the original source package [..] does any necessary rearrangement [..]".
At leat to my interpretation, this target should be reserved for repackaging.
gromacs (4.0-1) unstable; urgency=low
* New upstream release.
- debian/man: remove g_nmtraj.1, g_sdf.1, g_spatial.1 (incorporated
upstream).
- debian/patches: remove 05_autoconf_gsl.dpatch (fixed upstream) and
40_missing_cpp.dpatch (preprocessor functionality now built in).
- debian/rules: remove g_ffscan renaming (no longer shipped).
* debian/control: Drop versioned dependency on base-files.
-- Nicholas Breen <nbreen@ofb.net> Sun, 12 Oct 2008 14:47:37 -0700
gromacs (3.3.3-3) unstable; urgency=low
[ Daniel Leidert ]
......
......@@ -13,7 +13,7 @@ Vcs-Svn: svn+ssh://svn.debian.org/svn/debichem/unstable/gromacs/
Package: gromacs
Architecture: any
Section: science
Depends: gromacs-data (= ${source:Version}), ${shlibs:Depends}, base-files (>= 4.0.1)
Depends: gromacs-data (= ${source:Version}), ${shlibs:Depends}
Recommends: cpp
Conflicts: radiance (<= 3R8+20070924.dfsg-1)
Description: Molecular dynamics simulator, with building and analysis tools
......@@ -76,7 +76,7 @@ Description: GROMACS molecular dynamics sim, development kit
Package: gromacs-mpich
Architecture: any
Section: science
Depends: ${shlibs:Depends}, mpich-bin, base-files (>= 4.0.1)
Depends: ${shlibs:Depends}, mpich-bin
Recommends: gromacs
Suggests: gromacs-data
Description: Molecular dynamics sim, binaries for MPICH parallelization
......@@ -97,7 +97,7 @@ Description: Molecular dynamics sim, binaries for MPICH parallelization
Package: gromacs-lam
Architecture: any
Section: science
Depends: ${shlibs:Depends}, lam-runtime (>= 7.0), base-files (>= 4.0.1)
Depends: ${shlibs:Depends}, lam-runtime (>= 7.0)
Recommends: gromacs
Suggests: gromacs-data
Description: Molecular dynamics sim, binaries for LAM-MPI parallelization
......@@ -118,7 +118,7 @@ Description: Molecular dynamics sim, binaries for LAM-MPI parallelization
Package: gromacs-openmpi
Architecture: alpha amd64 i386 ia64 powerpc kfreebsd-i386 kfreebsd-amd64 hurd-i386
Section: science
Depends: ${shlibs:Depends}, openmpi-bin (>= 1.2.3), base-files (>= 4.0.1)
Depends: ${shlibs:Depends}, openmpi-bin (>= 1.2.3)
Recommends: gromacs
Suggests: gromacs-data
Description: Molecular dynamics sim, binaries for OpenMPI parallelization
......
.TH "G_NMTRAJ" "1" "15 Feb 2008" "GROMACS suite, Version 3.3"
.SH NAME
g_nmtraj \- generate a virtual trajectory from an eigenvector
.SH SYNOPSIS
.B g_nmtraj
.BI "\-s " topol.tpr
.BI "\-v " eigenvec.trr
.BI "\-o " nmtraj.xtc
.B \-[no]h
.B \-[no]X
.BI "\-nice " int
.BI "\-eignr " int
.BI "\-temp " real
.BI "\-amplitude " real
.BI "\-nframes " int
.SH DESCRIPTION
.B g_nmtraj
generates a virtual trajectory from an eigenvector, corresponding
to a harmonic Cartesian oscillation around the average structure. The
eigenvectors should normally be mass-weighted, but you can use non-weighted
eigenvectors to generate orthogonal motions. The output frames are written as
a trajectory file covering an entire period, and the first frame is the
average structure. If you write the trajectory in (or convert to) PDB format
you can view it directly in
.BR pymol (1)
and also render a photorealistic movie.
Motion amplitudes are calculated from the eigenvalues and a preset
temperature, assuming equipartition of the energy over all modes. To make the
motion clearly visible in PyMol you might want to amplify it by setting an
unrealistic high temperature. However, be aware that both the linear
Cartesian displacements and mass weighting will lead to serious structure
deformation for high amplitudes \- this is is simply a limitation of the
Cartesian normal mode model. By default the selected eigenvector is set to 7,
since the first six normal modes are the translational and rotational
degrees of freedom.
.SH OPTIONS
.TP
.BI "\-s " topol.tpr
Structure+mass(db) (\fIInput\fP): tpr tpb tpa gro g96 pdb xml
.TP
.BI "\-v " eigenvec.trr
Full precision trajectory (\fIInput\fP): trr trj
.TP
.BI "\-o " nmtraj.xtc
Generic trajectory (\fIOutput\fP): xtc trr trj gro g96 pdb
.TP
.BI "\-[no]h
Print help info and quit (default: \fIno\fP).
.TP
.BI "\-[no]X
Use dialog box GUI to edit command line options (default: \fIno\fP).
.TP
.BI "\-nice " int
Set the nicelevel (default: \fI19\fP).
.TP
.BI "\-eignr " int
Eigenvector to use (default: \fI7\fP). The first is 1.
.TP
.BI "\-temp " real
Temperature, in Kelvin (default: \fI300\fP).
.TP
.BI "\-amplitude " real
Amplitude for modes with eigenvalue <= 0 (default: \fI0\.25\fP).
.TP
.BI "\-nframes " int
Number of frames to generate (default: \fI30\fP).
.SH SEE ALSO
.BR gromacs (7),
.BR pymol (1)
.PP
More information about the \fBGROMACS\fR suite is available in
\fI/usr/share/doc/gromacs\fR or at \fI\%http://www.gromacs.org/\fR.
.TH "G_SDF" "1" "3 Mar 2008" "GROMACS suite, Version 3.3"
.SH NAME
g_sdf \- calculate spatial distribution function
.SH SYNOPSIS
.B g_sdf
.BI "\-s " topol.tpr
.BI "\-f " traj.xtc
.BI "\-n " index.ndx
.BI "\-o " gom_plt.dat
.BI "\-r " refmol.gro
.B \-[no]h
.BI "\-nice " int
.BI "\-b " time
.BI "\-e " time
.BI "\-dt " time
.BI "\-mode " int
.BI "\-triangle " vector
.BI "\-dtri " vector
.BI "\-bin " real
.BI "\-grid " vector
.SH DESCRIPTION
.B g_sdf
calculates the spatial distribution function (SDF) of a set of atoms within a coordinate system defined by three atoms. There is single body, two body and three body SDF implemented (select with option -mode). In the single body case the local coordinate system is defined by using a triple of atoms from one single molecule, for the two and three body case the configurations are dynamically searched complexes of two or three molecules (or residues) meeting certain distance consitions (see below).
.SH OPTIONS
.TP
.BI "\-s " topol.tpr
Structure+mass(db) (\fIInput, optional\fP): tpr tpb tpa gro g96 pdb xml
.TP
.BI "\-f " traj.xtc
Generic trajectory (\fIInput\fP): xtc trr trj gro g96 pdb
.TP
.BI "\-n " index.ndx
Index file (\fIInput, Output\fP)
.TP
.BI "\-o " gom_plt.dat
Generic data file (\fIOutput\fP)
.TP
.BI "\-r " refmol.gro
Generic structure (\fIOutput, optional\fP): gro g96 pdb xml
.TP
.BI "\-[no]h
Print help info and quit (default: \fIno\fP).
.TP
.BI "\-nice " int
Set the nicelevel (default: \fI19\fP).
.TP
.BI "\-b " time
First frame (ps) to read from trajectory (default: \fI0\fP).
.TP
.BI "\-e" time
Last frame (ps) to read from trajectory (default: \fIend of file\fP).
.TP
.BI "\-mode " int
SDF in [1,2,3] particle mode (default: \fI1\fP).
.TP
.BI "\-triangle " vector
r(1,3), r(2,3), r(1,2) (default: \fI0 0 0\fP).
.TP
.BI "\-dtri " vector
dr(1,3), dr(2,3), dr(1,2) (default: \fI0.03 0.03 0.03\fP).
.TP
.BI "\-bin" real
Binwidth for the 3D-grid (nm) (default: \fI0.05\fP).
.TP
.BI "\-grid " vector
Size of the 3D-grid (nm,nm,nm) (default: \fI1 1 1\fP).
.SH USAGE
The program needs a trajectory, a GROMACS run input file and an index file to work. You have to setup 4 groups in the index file before using g_sdf:
The first three groups are used to define the SDF coordinate system. The programm will dynamically generate the atom tripels according to the selected -mode: In -mode 1 the triples will be just the 1st, 2nd, 3rd, ... atoms from groups 1, 2 and 3. Hence the nth entries in groups 1, 2 and 3 must be from the same residue. In -mode 2 the triples will be 1st, 2nd, 3rd, ... atoms from groups 1 and 2 (with the nth entries in groups 1 and 2 having the same res-id). For each pair from groups 1 and 2 group 3 is searched for an atom meeting the distance conditions set with -triangle and -dtri relative to atoms 1 and 2. In -mode 3 for each atom in group 1 group 2 is searched for an atom meeting the distance condition and if a pair is found group 3 is searched for an atom meeting the further conditions. The triple will only be used if all three atoms have different res-id's.
The local coordinate system is always defined using the following scheme: Atom 1 will be used as the point of origin for the SDF. Atom 1 and 2 will define the principle axis (Z) of the coordinate system. The other two axis will be defined inplane (Y) and normal (X) to the plane through Atoms 1, 2 and 3. The fourth group contains the atoms for which the SDF will be evaluated.
For -mode 2 and 3 you have to define the distance conditions for the 2 resp. 3 molecule complexes to be searched for using -triangle and -dtri.
The SDF will be sampled in cartesian coordinates. Use '-grid x y z' to define the size of the SDF grid around the reference molecule. The Volume of the SDF grid will be V=x*y*z (nm^3). Use -bin to set the binwidth for grid.
The output will be a binary 3D-grid file (gom_plt.dat) in the .plt format that can be be read directly by gOpenMol. The option -r will generate a .gro file with the reference molecule(s) transfered to the SDF coordinate system. Load this file into gOpenMol and display the SDF as a contour plot (see http://www.csc.fi/gopenmol/index.phtml for further documentation).
For further information about SDF's have a look at: A. Vishnyakov, JPC A, 105, 2001, 1702 and the references cited within.
.SH ALTERNATIVES
g_spatial also produces spatial distribution functions. g_spatial differs from g_sdf in that g_spatial gives the user full control of the alignment procedure. The downside is that g_spatial requires more time and more disk space.
.SH SEE ALSO
.BR gromacs (7),
.BR g_spatial (1)
.PP
More information about the \fBGROMACS\fR suite is available in
\fI/usr/share/doc/gromacs\fR or at \fI\%http://www.gromacs.org/\fR.
.PP
Further information about SDFs is published in A. Vishnyakov, JPC A, 105, 2001, 1702 and the references cited within.
.TH "G_SPATIAL" "1" "3 Mar 2008" "GROMACS suite, Version 3.3"
.SH NAME
g_spatial \- calculate spatial distribution function
.SH SYNOPSIS
.B g_spatial
.BI "\-s " topol.tpr
.BI "\-f " traj.xtc
.BI "\-n " index.ndx
.B \-[no]h
.BI "\-nice " int
.BI "\-b " time
.BI "\-e " time
.BI "\-dt " time
.B \-[no]w
.B \-[no]pbc
.B \-[no]div
.BI "\-ign " int
.BI "\-bin " real
.BI "\-nab " int
.SH DESCRIPTION
.B g_nmtraj
calculates the spatial distribution function (SDF) and outputs it in a form
that can be read by VMD as Gaussian98 cube format. This was developed from
template.c (gromacs-3.3). For a system of 32K atoms and a 50ns trajectory, the
SDF can be generated in about 30 minutes, with most of the time dedicated to
the two runs through
.BR trjconv (1)
that are required to center everything properly.
This also takes a whole bunch of space (3 copies of the xtc file). Still, the
pictures are pretty and very informative when the fitted selection is properly
made. 3-4 atoms in a widely mobile group like a free amino acid in solution
works well, or select the protein backbone in a stable folded structure to get
the SDF of solvent and look at the time-averaged solvation shell. It is also
possible using this program to generate the SDF based on some arbitrary
Cartesian coordinate. To do that, simply omit the preliminary trjconv steps.
.SH OPTIONS
.TP
.BI "\-s " topol.tpr
Structure+mass(db) (\fIInput\fP): tpr tpb tpa gro g96 pdb xml
.TP
.BI "\-f " traj.xtc
Generic trajectory (\fIInput\fP): xtc trr trj gro g96 pdb
.TP
.BI "\-n " index.ndx
Index file (\fIInput, Output\fP)
.TP
.BI "\-[no]h
Print help info and quit (default: \fIno\fP).
.TP
.BI "\-nice " int
Set the nicelevel (default: \fI19\fP).
.TP
.BI "\-b " time
First frame (ps) to read from trajectory (default: \fI0\fP).
.TP
.BI "\-e" time
Last frame (ps) to read from trajectory (default: \fIend of file\fP).
.TP
.BI "\-[no]w
View outpot xvg, xpm, eps, and pdb files (default: \fIno\fP).
.TP
.BI "\-[no]pbc
Use periodic boundary conditions for computing distances (default: \fIno\fP).
.TP
.BI "\-[no]div
Calculate and apply the divisor for bin occupancies based on atoms/minimal cube size. Set as TRUE for visualization and as FALSE (-nodiv) to get accurate counts per frame (default: \fITRUE\fP).
.TP
.BI "\-ign " int
Do not display this number of outer cubes. Positive values may reduce boundary speckles; -1 ensures outer surface is visible (default: \fI-1\fP).
.TP
.BI "\-bin " real
Width of the bins in nm (default: \fI0.05\fP).
.TP
.BI "\-nab " int
Number of additional bins to ensure proper memory allocation (default: \fI4\fP).
.SH USAGE
1. Use make_ndx to create a group containing the atoms around which you want the SDF
2. trjconv -s a.tpr -f a.xtc -o b.xtc -center tric -ur compact -pbc none
3. trjconv -s a.tpr -f b.xtc -o c.xtc -fit rot+trans
4. run g_spatial on the xtc output of step #3.
5. Load grid.cube into VMD and view as an isosurface.
Note: Systems such as micelles will require micelle clustering between steps 1 and 2.
.SH WARNINGS
The SDF will be generated for a cube that contains all bins that have some non-zero occupancy. However, the preparatory -fit rot+trans option to trjconv implies that your system will be rotating and translating in space (in order that the selected group does not). Therefore the values that are returned will only be valid for some region around your central group/coordinate that has full overlap with system volume throughout the entire translated/rotated system over the course of the trajectory. It is up to the user to ensure that this is the case.
To reduce the amount of space and time required, you can output only the coordinates that are going to be used in the first and subsequent run through trjconv. However, be sure to set the -nab option to a sufficiently high value since memory is allocated for cube bins based on the initial coordinates and the -nab (Number of Additional Bins) option value.
.SH BUGS
When the allocated memory is not large enough, a segmentation fault may occur. This is usually detected and the program is halted prior to the fault while displaying a warning message suggesting the use of the -nab option. However, the program does not detect all such events. If you encounter a segmentation fault, run it again with an increased -nab value.
.SH ALTERNATIVES
g_sdf also produces spatial distribution functions. g_spatial differs from g_sdf in that g_spatial gives the user full control of the alignment procedure. The downside is that g_spatial requires more time and more disk space.
.SH SEE ALSO
.BR gromacs (7),
.BR g_sdf (1)
.PP
More information about the \fBGROMACS\fR suite is available in
\fI/usr/share/doc/gromacs\fR or at \fI\%http://www.gromacs.org/\fR.
04_autoconf_mpisuffix.dpatch
05_autoconf_gsl.dpatch
10_manpages.dpatch
#10_manpages.dpatch
11_readme.dpatch
40_missing_cpp.dpatch
......@@ -35,7 +35,6 @@ COMMON_CONFIG_PARAMS = \
--datadir=\$${prefix}/share \
--mandir=\$${prefix}/share/man \
--infodir=\$${prefix}/share/info \
--program-transform-name="s/^ffscan/g_ffscan/" \
--enable-shared \
--with-gsl
......@@ -84,7 +83,7 @@ configure-stamp: patch-stamp
cp -f /usr/share/misc/config.sub config.sub
-test -r /usr/share/misc/config.guess && \
cp -f /usr/share/misc/config.guess config.guess
# patches 04_autoconf_mpisuffix & 05_autoconf_gsl change configure.ac, requiring a fresh autotools pass
# patch 04_autoconf_mpisuffix changes configure.ac, requiring a fresh autotools pass
aclocal && \
autoconf && \
automake-1.10 || automake
......@@ -203,17 +202,8 @@ install-basic: build
dh_installdirs -pgromacs
$(MAKE) -C build/basic install DESTDIR=$(CURDIR)/debian/gromacs
$(MAKE) -C build/basic-dp install DESTDIR=$(CURDIR)/debian/gromacs
# extraneous man page, no longer associated with a binary
# (and it needs to be removed lest it conflict with mono-mcs)
rm -f $(CURDIR)/debian/gromacs/usr/share/man/man1/disco.1
# rename ffscan to avoid a namespace conflict with fortools package
#mv $(CURDIR)/debian/gromacs/usr/bin/ffscan $(CURDIR)/debian/gromacs/usr/bin/g_ffscan
#sed -e 's/ffscan/g_ffscan/g' $(CURDIR)/debian/gromacs/usr/share/man/man1/ffscan.1 > $(CURDIR)/debian/gromacs/usr/share/man/man1/g_ffscan.1 && \
#rm $(CURDIR)/debian/gromacs/usr/share/man/man1/ffscan.1
sed -i -e 's/ffscan/g_ffscan/g' $(CURDIR)/debian/gromacs/usr/share/man/man1/g_ffscan.1
rm -f $(CURDIR)/debian/gromacs/usr/share/man/man1/*_d.1
dh_installman -pgromacs debian/man/luck.1 debian/man/average.1 debian/man/g_nmtraj.1 \
debian/man/g_kinetics.1 debian/man/g_spatial.1 debian/man/g_sdf.1 debian/man/gromacs.7
dh_installman -pgromacs debian/man/luck.1 debian/man/average.1 debian/man/g_kinetics.1 debian/man/gromacs.7
for manpage in $(CURDIR)/debian/gromacs/usr/share/man/man1/*.1; do \
dh_link -pgromacs usr/share/man/man1/`basename $${manpage}` usr/share/man/man1/`basename $${manpage} .1`_d.1 ; \
done
......@@ -266,7 +256,7 @@ binary-indep: build install
dh_testdir
dh_testroot
dh_installchangelogs -i
dh_installdocs -pgromacs-data -XTODO
dh_installdocs -pgromacs-data
dh_compress -i
dh_fixperms -i
dh_installdeb -i
......@@ -278,7 +268,7 @@ binary-arch: build install
dh_testdir -s
dh_testroot -s
dh_installchangelogs -s
dh_installdocs -s -XTODO
dh_installdocs -s
dh_strip -A
dh_link -s
dh_compress -s
......
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