[Debian-med-packaging] Bug#697819: autodocksuite: New upstream version 4.2.5.1

[mdt]

Package: autodock
Version: 4.2.3-1
Severity: wishlist
Tags: upstream

AutoDock 4.2.5.1 Release Notes: http://autodock.scripps.edu/downloads/autodock-4-2-release-notes

=============================================================================
                   AutoDock Release Notes
                  Release 4.2.5.1 (December 2012)
=============================================================================
The changes since the 4.2.5 release (11/02/2012):
#bug fix
4.2.5 incorrectly calculated part of the intermolecular desolvation
energy term; 4.2.5.1 corrects this.  All 4.2.5 users should upgrade
to 4.2.5.1 and re-do any runs.

=============================================================================
                   AutoDock Release Notes
                  Release 4.2.5 (November 12 2012)
=============================================================================

Please note that the previous general release was 4.2.3, 29 January 2010. 
The 4.2.4 release (7 July 2010) was a specialized release for 
"Fight Aids at Home" and other IBM World Community Grid projects.  

Supported computer platforms in 4.2.5:

Linux2 on Intel x86  remains supported, as does Solaris 8 on SPARC.
Supported Macintosh platforms are OS X 10.4-10.5 (Tiger and Leopard) on
Intel x86 and PowerPC, and OS X 10.6-10.8 (Snow Leopard, Lion, and
Mountain Lion) on Intel x86.  The executable binaries for Windows on
Intel x86 have been built on Windows 5 (XP) and have been tested on Windows 6
and Windows 7.  Windows users no longer need to install the CygWin environment,
but they may if they like.

The changes since the 4.2.3 release (1/29/2010):

#new features
-: new support for specifying output verbosity ranging from low (-2) up to high (8)
   with symbolic settings for "outlev" defined in constants.h and used in main.cc
-: new automatic calculation of 'about' as the center of the ligand root group
-: new WIN32 MinGW portability - replacements for times() and getrusage()
-: new desolvation term separate from vdW+Hbond term in epdb 
     "Per-atom Intermolecular Energy Analysis" table 
-: now intelec is on by default; off if "intelec off" in DPF
-: Almost all AutoDock defaults now match defaults supplied by ADT, simplifying PDF files

#code inspection and internal interface self-documentation
-: We thank Steffen Moeller (steffen_moeller at gmx.de) for his enthusiastic
   and expert detailed inspection of all function and method calls,
   in particular identifying "constant" arguments and verifying
   data type compatibiliy.

#improvements
-: improved detailed output of Intermolecular Energy Analysis
-: increased MAX_RUNS from 256 to 2000
-: improved error detection and termination: 
      replaced exit() by EXIT_SUCCESS/EXIT_FAILURE(win32) or stop(msg)
-: increased precision of energy table
-: implemented EnergyComponent structures
-: integrated call_gs into call_glss
-: improved input checking with ga_run/gals_run
[Added checks to "ga_run/gals_run" for missing "set_ga" and missing "set_psw1" errors]
-: simplified logic so more of the FATAL errors are simply handed to "stop()"
-: now set random number seeds at beginning of simanneal execution; output reduced
-: new compile-time option to print energy terms for each atom [for debugging]
-: AutoDock intramolecular energy smoothing now matches that in AutoGrid
-: Consolidated the "side effects" of trilinterp that record per-atom energy components
   and total energy components into two sets of "EnergyComponent" structures instead
   of two Real arrays and two pointers to Real.
-: developed substitutes for WIN32 MinGW "times()" and "getpid()"
-: modified mkTorTree.cc to fill in the root atom information
-: Changed 'tlist' declaration to allow space for root atoms at end 

#bug fixes
-: corrected energy breakdown report when using flexible residues
-: desolvation energy term is included even for distant pairs (r>nbc)
-: corrected eintcal side effects of "outlev" setting
-: removed support for unused DPF tokens

#autogrid
AutoGrid 4.2.5 has no functional changes from AutoGrid 4.2.3. 
The only significant code changes were those required for porting to Windows.o
We added 'copyfilesfromAD', a maintenance script that copies key shared source files 
from AutoDock to AutoGrid.

-- System Information:
Debian Release: 6.0.6
  APT prefers stable-updates
  APT policy: (500, 'stable-updates'), (500, 'proposed-updates'), (500, 'stable')
Architecture: amd64 (x86_64)

Kernel: Linux 3.2.0-0.bpo.4-amd64 (SMP w/4 CPU cores)
Locale: LANG=it_IT.UTF-8, LC_CTYPE=it_IT.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash

Versions of packages autodock depends on:
ii  libc6                         2.11.3-4   Embedded GNU C Library: Shared lib
ii  libgcc1                       1:4.4.5-8  GCC support library
ii  libstdc++6                    4.4.5-8    The GNU Standard C++ Library v3

autodock recommends no packages.

Versions of packages autodock suggests:
pn  autodocktools                 <none>     (no description available)
pn  autogrid                      <none>     (no description available)

-- no debconf information