[Debichem-commits] r1156 - in /unstable/openbabel/debian: TODO changelog man/ man/obenergy.1 man/obminimize.1 man/obrotamer.1 rules

Thu Feb 28 12:43:47 UTC 2008

Author: dleidert-guest
Date: Thu Feb 28 12:43:46 2008
New Revision: 1156

URL: http://svn.debian.org/wsvn/debichem/?sc=1&rev=1156
Log:
* debian/rules: Added DEB_INSTALL_MANPAGES_openbabel to install missing
  man-pages (retrieved from SVN).
* debian/man/*.1: Added man-pages already in openbabels SVN but not shipped
  with the source.

Added:
    unstable/openbabel/debian/man/
    unstable/openbabel/debian/man/obenergy.1
    unstable/openbabel/debian/man/obminimize.1
    unstable/openbabel/debian/man/obrotamer.1
Modified:
    unstable/openbabel/debian/TODO
    unstable/openbabel/debian/changelog
    unstable/openbabel/debian/rules

Modified: unstable/openbabel/debian/TODO
URL: http://svn.debian.org/wsvn/debichem/unstable/openbabel/debian/TODO?rev=1156&op=diff
==============================================================================

--- unstable/openbabel/debian/TODO (original)
+++ unstable/openbabel/debian/TODO Thu Feb 28 12:43:46 2008
@@ -6,9 +6,5 @@
   
   + solve libinchi-packaging question
   
-  + fix GCC 4.3 FTBFS! (must fix this upstream ... Jean told me, he prepared
-    a patch for upstream in the past)
-    http://bugs.debian.org/455170
-  
   + package the wx-gui of openbabel
 

Modified: unstable/openbabel/debian/changelog
URL: http://svn.debian.org/wsvn/debichem/unstable/openbabel/debian/changelog?rev=1156&op=diff
==============================================================================
--- unstable/openbabel/debian/changelog (original)
+++ unstable/openbabel/debian/changelog Thu Feb 28 12:43:46 2008
@@ -21,7 +21,10 @@
     Added READMEs regarding povray.
   * debian/openbabel.examples: Added example for the newly added READMEs.
   * debian/rules: Added DEB_INSTALL_DOCS_ALL for docs to install in all
-    packages.
+    packages. Added DEB_INSTALL_MANPAGES_openbabel to install missing
+    man-pages (retrieved from SVN).
+  * debian/man/*.1: Added man-pages already in openbabels SVN but not shipped
+    with the source.
   * debian/patches/fix_ftbfs_with_gcc_43.patch: Added.
     - Add missing includes to fix an FTBFS with GCC 4.3 (closes: #455170).
   * debian/patches/fix_467498_pedantic_issues: Added.

Added: unstable/openbabel/debian/man/obenergy.1
URL: http://svn.debian.org/wsvn/debichem/unstable/openbabel/debian/man/obenergy.1?rev=1156&op=file
==============================================================================
--- unstable/openbabel/debian/man/obenergy.1 (added)
+++ unstable/openbabel/debian/man/obenergy.1 Thu Feb 28 12:43:46 2008
@@ -1,0 +1,70 @@
+.Dd April 7, 2007
+.Os "Open Babel" 2.1
+.Dt obenergy 1 URM
+.Sh NAME
+.Nm obenergy
+.Nd "calculate the energy for a molecule"
+.Sh SYNOPSIS
+.Nm
+.Op Ar OPTIONS
+.Ar filename
+.Sh DESCRIPTION
+The obenergy tool can be used to calculate the energy for molecules 
+inside (multi-)molecule files (e.g., MOL2, etc.)
+.Sh OPTIONS
+If no filename is given, obenergy will give all options including the
+available forcefields.
+.Bl -tag -width flag
+.It Fl v
+Verbose: print out all individual energy interactions
+.It Fl ff Ar forcefield
+Select the forcefield
+.El
+.Sh EXAMPLES
+.Pp
+View the possible options, including available forcefields: 
+.Dl "obenergy"
+.Pp
+Calculate the energy for the molecule(s) in file test.mol2:
+.Dl "obenergy test.mol2"
+.Pp
+Calculate the energy for the molecule(s) in file test.mol2 using the 
+Ghemical forcefield:
+.Dl "obenergy -ff Ghemical test.mol2"
+.Pp
+Calculate the energy for the molecule(s) in file test.mol2 and print
+out all individual energy interactions:
+.Dl "obenergy -v test.mol2"
+.Sh SEE ALSO
+.Xr babel 1 ,
+.Xr obminimize 1 ,
+.Xr obrotamer 1 .
+.Pp
+The web pages for Open Babel can be found at:
+<\fBhttp://openbabel.sourceforge.net/\fR> 
+.Pp
+The web pages for Open Babel Molecular Mechanics can be found at: 
+<\fBhttp://openbabel.sourceforge.net/wiki/Molecular_mechanics\fR>
+.Sh AUTHORS
+The obenergy program was contributed by
+.An Tim Vandermeersch.
+.Pp
+.An -nosplit
+Open Babel is developed by a cast of many, including currrent maintainers
+.An Geoff Hutchison ,
+.An Chris Morley ,
+.An Michael Banck , 
+and innumerable others who have contributed fixes and additions. 
+For more contributors to Open Babel, see 
+<\fBhttp://openbabel.sourceforge.net/wiki/THANKS\fR>
+.Sh COPYRIGHT
+Copyright (C) 2007 by Tim Vandermeersch.
+.Pp
+ 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 version 2 of the License.
+.Pp
+ 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.

Added: unstable/openbabel/debian/man/obminimize.1
URL: http://svn.debian.org/wsvn/debichem/unstable/openbabel/debian/man/obminimize.1?rev=1156&op=file
==============================================================================
--- unstable/openbabel/debian/man/obminimize.1 (added)
+++ unstable/openbabel/debian/man/obminimize.1 Thu Feb 28 12:43:46 2008
@@ -1,0 +1,80 @@
+.Dd April 7, 2007
+.Os "Open Babel" 2.1
+.Dt obminimize 1 URM
+.Sh NAME
+.Nm obminimize
+.Nd "optimize the geometry, minimize the energy for a molecule"
+.Sh SYNOPSIS
+.Nm
+.Op Ar OPTIONS
+.Ar filename
+.Sh DESCRIPTION
+The obminimize tool can be used to minimize the energy for molecules 
+inside (multi-)molecule files (e.g., MOL2, etc.)
+.Sh OPTIONS
+If no filename is given, obminimize will give all options including the
+available forcefields.
+.Bl -tag -width flag
+.It Fl n Ar steps
+Specify the maximum number of steps (default=2500)
+.It Fl cg
+Use conjugate gradients algorithm (default)
+.It Fl sd
+Use steepest descent algorithm
+.It Fl c Ar criteria
+Set convergence criteria (default=1e-6)
+.It Fl ff Ar forcefield
+Select the forcefield
+.El
+.Sh EXAMPLES
+.Pp
+View the possible options, including available forcefields: 
+.Dl "obminimize"
+.Pp
+Minimize the energy for the molecule(s) in file test.mol2:
+.Dl "obminimize test.mol2"
+.Pp
+Minimize the energy for the molecule(s) in file test.mol2 using the 
+Ghemical forcefield:
+.Dl "obminimize -ff Ghemical test.mol2"
+.Pp
+Minimize the energy for the molecule(s) in file test.mol2 by taking
+at most 300 geometry optimization steps
+.Dl "obminimize -n 300 test.mol2"
+.Pp
+Minimize the energy for the molecule(s) in file test.mol2 using the 
+steepest descent algorithm and convergence criteria 1e-5:
+.Dl "obminimize -sd -c 1e-5 test.mol2"
+.Sh SEE ALSO
+.Xr babel 1 ,
+.Xr obenergy 1 ,
+.Xr obrotamer 1 .
+.Pp
+The web pages for Open Babel can be found at:
+<\fBhttp://openbabel.sourceforge.net/\fR> 
+.Pp
+The web pages for Open Babel Molecular Mechanics can be found at: 
+<\fBhttp://openbabel.sourceforge.net/wiki/Molecular_mechanics\fR>
+.Sh AUTHORS
+The minimize program was contributed by
+.An Tim Vandermeersch.
+.Pp
+.An -nosplit
+Open Babel is developed by a cast of many, including currrent maintainers
+.An Geoff Hutchison ,
+.An Chris Morley ,
+.An Michael Banck , 
+and innumerable others who have contributed fixes and additions. 
+For more contributors to Open Babel, see 
+<\fBhttp://openbabel.sourceforge.net/wiki/THANKS\fR>
+.Sh COPYRIGHT
+Copyright (C) 2007 by Tim Vandermeersch.
+.Pp
+ 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 version 2 of the License.
+.Pp
+ 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.

Added: unstable/openbabel/debian/man/obrotamer.1
URL: http://svn.debian.org/wsvn/debichem/unstable/openbabel/debian/man/obrotamer.1?rev=1156&op=file
==============================================================================
--- unstable/openbabel/debian/man/obrotamer.1 (added)
+++ unstable/openbabel/debian/man/obrotamer.1 Thu Feb 28 12:43:46 2008
@@ -1,0 +1,53 @@
+.Dd April 7, 2007
+.Os "Open Babel" 2.1
+.Dt obrotamer 1 URM
+.Sh NAME
+.Nm obrotamer
+.Nd "generate conformer/rotamer coordinates"
+.Sh SYNOPSIS
+.Nm
+.Ar filename
+.Sh DESCRIPTION
+The obrotamer tool can be used as part of a conformational search 
+by generating random isomers based on rotating dihedral angles. These
+rotamers are not conformers -- that is, obrotamer does not perform geometry
+optimization after generating the rotamer structure. The obminimize tool
+can do geometry optimization using molecular mechanics.
+.Sh EXAMPLES
+.Dl "obrotamer baseconformer.sdf >rotamer1.sdf"
+.Pp
+Generate a random rotational isomer of baseconformer.sdf and write
+it to rotamer1.sdf
+.Sh SEE ALSO
+.Xr babel 1 ,
+.Xr obenergy 1 ,
+.Xr obfit 1 ,
+.Xr obgrep 1 ,
+.Xr obminimize 1 ,
+.Xr obrotate 1 .
+.Pp
+The web pages for Open Babel can be found at:
+<\fBhttp://openbabel.sourceforge.net/\fR>
+.Sh AUTHORS
+.An -nosplit
+Open Babel is developed by a cast of many, including currrent maintainers
+.An Geoff Hutchison ,
+.An Chris Morley ,
+.An Michael Banck , 
+and innumerable others who have contributed fixes and additions. 
+For more contributors to Open Babel, see 
+<\fBhttp://openbabel.sourceforge.net/wiki/THANKS\fR>
+.Sh COPYRIGHT
+Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc. 
+.br
+Some portions Copyright (C) 2001-2007 by Geoffrey R. Hutchison and
+other contributors.
+.Pp
+ 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 version 2 of the License.
+.Pp
+ 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.

Modified: unstable/openbabel/debian/rules
URL: http://svn.debian.org/wsvn/debichem/unstable/openbabel/debian/rules?rev=1156&op=diff
==============================================================================
--- unstable/openbabel/debian/rules (original)
+++ unstable/openbabel/debian/rules Thu Feb 28 12:43:46 2008
@@ -8,7 +8,7 @@
 DEB_CONFIGURE_EXTRA_FLAGS := --with-pkglibdir=/usr/lib/openbabel/2.1
 DEB_INSTALL_DOCS_ALL := AUTHORS README THANKS
 PYVERS=$(shell pyversions -vs)
-
+DEB_INSTALL_MANPAGES_openbabel := debian/man/obenergy.1  debian/man/obminimize.1  debian/man/obrotamer.1
 
 build/python-openbabel:: $(PYVERS:%=build-python-openbabel%)
 


