Task: Chemistry
Description: Debian Science Chemistry packages
 This metapackage will install Debian Science packages related to Chemistry.
 You might be interested as well in field::chemistry debtag and, depending on 
 your focus, in education-chemistry metapackage.

Why: To be handled by debichem once they have metapackages (like \
     science-geography / Debian GIS and science-biology / Debian Med)

Depends: apbs, bkchem, bodr, libcdk-java, chemeq, \
         chemical-mime-data, chemtool, easychem, gabedit, galculator, \
         garlic, gausssum, gchempaint, gdis, ghemical, gcrystal, gcu-bin, \
         gcu-plugin, gperiodic, \
         gromacs | gromacs-lam | gromacs-mpich | gromacs-openmpi, \
         kalzium, katomic, mopac7-bin, mpqc, mpqc-support, \
         openbabel, python-openbabel, polyxmass, psi3, pymol, rasmol, \
         viewmol, xdrawchem, xmakemol-gl | xmakemol
Why: from the DebianScience/Chemistry wiki page

Depends: gdpc

Depends: xbs

Depends: gelemental

Suggests: gdpc-examples

Depends: avogadro
Homepage: http://avogadro.openmolecules.net/wiki/Main_Page
WNPP: 450814
License: GPL
Responsible: Debichem Team <debichem-devel@lists.alioth.debian.org>
Pkg-URL: http://packages.debian.org/experimental/avogadro
Pkg-Description: advanced molecular editor
 Avogadro is an advanced molecular editor designed for cross-platform use in
 computational chemistry, molecular modeling, bioinformatics, materials
 science, and related areas. It offers flexible rendering and a powerful plugin 
 architecture.

Depends: drawxtl
Homepage: http://home.att.net/~larry.finger/drawxtl/
WNPP: 428750
License: LGPL/Public Domain/GL2PS LICENSE
Responsible: Daniel Leidert <daniel.leidert@wgdd.de>
Pkg-Description: display crystal structures on ordinary computer hardware
 DRAWxtl reads a basic description of the crystal structure, which includes
 unit-cell parameters, space group, atomic coordinates, thermal parameters or
 a Fourier map, and outputs a geometry object that contains polyhedra, planes,
 lone-pair cones, spheres or ellipsoids, bonds, iso-surface Fourier contours
 and the unit-cell boundary.
 .
 Four forms of graphics are produced:
 .
  (1) an openGL window for immediate viewing
  (2) the Persistence of Vision Ray Tracer (POV-RAY) scene language for
      publication-quality drawings
  (3) the Virtual Reality Modeling Language (VRML) for dissemination
      across the Internet
  (4) a Postscript rendering of the OpenGL window for those that want
      high-quality output but do not have
      POV-RAY installed.

Depends: gamgi
Homepage: http://www.gamgi.org/
WNPP: 465994
License: GPL
Responsible: Steffen Moeller <steffen_moeller@gmx.de>
Pkg-Description: general atomistic modelling graphic interface
 Graphical interface to build or analyse atomic structures.

Depends: libegad
Homepage: http://egad.ucsd.edu/egad/
WNPP: 429693
License: LGPL
Responsible: LI Daobing <lidaobing@gmail.com>
Pkg-Description: rational protein design library
 The EGAD Library is a modular, object oriented approach to rational protein
 design. It is platform-independent, written in C++ and, most importantly,
 free. Its raison d'etre is to serve as a tool for building protein design
 applications. It can also be used as a test-bed for the comparison of
 different energy functions and minimization algorithms under the same physical
 model.
 .
 Citations of EGAD Library should reference the paper in the Journal of
 Computational Chemistry. doi:10.1002/jcc.20727

Depends: libint
Homepage: http://www.chem.vt.edu/chem-dept/valeev/software/libint/libint.html
WNPP: 425039
License: GPL
Responsible: Daniel Leidert <daniel.leidert@wgdd.de>
Pkg-Description: Evaluate the integrals in modern atomic and molecular theory
 Libint library is used to evaluate the traditional (electron repulsion)
 and certain novel two-body matrix elements (integrals) over Cartesian
 Gaussian functions used in modern atomic and molecular theory. The idea
 of the library is to let computer write optimized code for computing
 such integrals. There are two primary advantages to this: much less
 human effort is required to write code for computing new integrals, and
 code can be optimized specifically for a particular computer
 architecture (e.g., vector processor).
 .
 Libint has been utilized to implement methods such as Hartree-Fock (HF)
 and Kohn-Sham density functional theory (KS DFT), second-order
 Moller-Plesset perturbation theory (MP2), coupled cluster singles and
 doubles (CCSD) method, as well as explicitly correlated R12 methods.
 The following software packages use Libint: 
 .
 .
 Improves mpqc (#409025) and psi3.

Depends: molden
Homepage: http://www.cmbi.ru.nl/molden/
License: non-free
Responsible: Debichem Team <debichem-devel@lists.alioth.debian.org>
Pkg-URL: http://svn.debian.org/wsvn/debichem/wnpp/molden/?rev=0&sc=1
Pkg-Description: processing program of molecular and electronic structure
 MOLDEN is a package for displaying Molecular Density from the Ab
 Initio packages GAMESS-UK , GAMESS-US and GAUSSIAN and the
 Semi-Empirical packages Mopac/Ampac, it also supports a number of
 other programs via the MOLDEN Format. MOLDEN reads all the required
 information from the GAMESS / GAUSSIAN outputfile. MOLDEN is capable
 of displaying Molecular Orbitals, the electron density and the
 Molecular minus Atomic density. Either the spherically averaged
 atomic density or the oriented ground state atomic density can be
 subtracted for a number of standard basis sets. MOLDEN supports
 contour plots, 3-d grid plots with hidden lines and a combination of
 both. It can write a variety of graphics instructions; postscript, X,
 VRML, povray, OpenGL, tekronix4014, hpgl, hp2392 and Figure. The X
 version of MOLDEN is also capable of importing and displaying of
 chemx, PDB, and a variety of mopac/ampac files and lots of other
 formats. It also can animate reaction paths and molecular
 vibrations. It can calculate and display the true or Multipole
 Derived Electrostatic Potential and atomic charges can be fitted to
 the Electrostatic Potential calculated on a Connolly surface. MOLDEN
 has a powerful Z-matrix editor which give full control over the
 geometry and allows you to build molecules from scratch, including
 polypeptides. MOLDEN was also submitted to the QCPE (QCPE619),
 allthough the X version is considerably running behind on the current
 one.

Depends: molekel
Homepage: http://bioinformatics.org/molekel/
License: GPL-2+
Responsible: Michael Banck <mbanck@debian.org>
Pkg-URL: http://svn.debian.org/wsvn/debichem/wnpp/molekel/?rev=0&sc=1
Pkg-Description: Advanced Interactive 3D-Graphics for Molecular Sciences

Depends: tinker
Homepage: http://dasher.wustl.edu/tinker/
License: non-free
Responsible: LI Daobing <lidaobing@gmail.com>
Pkg-URL: http://svn.debian.org/wsvn/debichem/wnpp/tinker/?rev=0&sc=1
Pkg-Description: Software Tools for Molecular Design
 The TINKER molecular modeling software is a complete and general
 package for molecular mechanics and dynamics, with some special
 features for biopolymers. TINKER has the ability to use any of
 several common parameter sets, such as Amber (ff94, ff96, ff98 and
 ff99), CHARMM (19 and 27), Allinger MM (MM2-1991 and MM3-2000), OPLS
 (OPLS-UA, OPLS-AA and OPLS-AA/L), Liam Dang's polarizable potentials,
 and our own AMOEBA polarizable atomic multipole force
 field. Parameter sets for other standard force fields such as GROMOS,
 UFF, ENCAD and MM4 are under consideration for future releases.
 .
 The TINKER package includes a variety of novel algorithms such as a
 new distance geometry metrization method that has greater speed and
 better sampling than standard methods, Elber's reaction path methods,
 several of our Potential Smoothing and Search (PSS) methods for
 global optimization, an efficient potential surface scanning
 procedure, a flexible implementation of atomic multipole-based
 electrostatics with explicit dipole polarizability, a selection of
 continuum solvation treatments including several variants of the
 generalized Born (GB/SA) model, an efficient truncated Newton (TNCG)
 local optimizer, surface areas and volumes with derivatives, a simple
 free energy perturbation facility, normal mode analysis, minimization
 in Cartesian, torsional or rigid body space, velocity Verlet
 stochastic dynamics, an improved spherical energy cutoff method,
 Particle Mesh Ewald summation for partial charges and regular Ewald
 for polarizable multipoles, a novel reaction field treatment of long
 range electrostatics, and more....
