Task: Chemistry
Description: Debian Science Chemistry packages
 This metapackage will install Debian Science packages related to
 Chemistry.  You might also be interested in the field::chemistry
 debtag and, depending on your focus, in the 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, \
         viewmol, xdrawchem, xmakemol-gl | xmakemol, v-sim
Why: from the DebianScience/Chemistry wiki page

Depends: rasmol
Registration: http://www.rasmol.org/register.shtml
Published-Title: RasMol: Biomolecular graphics for all
Published-Authors: Roger Sayle and E. James Milner-White
Published-In: Trends in Biochemical Sciences (TIBS)
Published-Year: 1995

Depends: adun.app
Why: 3D viewer and calculation output visualisation

Depends: gdpc

Depends: xbs

Depends: gelemental

Suggests: gdpc-examples

Depends: avogadro

Depends: gamgi

Depends: massxpert

Depends: drawxtl

Depends: chemical-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....

Depends: jmol

Depends: qutemol
Homepage: http://qutemol.sourceforge.net/
License: GPL
Pkg-Description: Interactive and Innovative Molecular Graphics
 QuteMol is an open source (GPL), interactive, high quality molecular
 visualization system. QuteMol exploits the current GPU capabilites through
 OpenGL shaders to offers an array of innovative visual effects. QuteMol
 visualization techniques are aimed at improving clarity and an easier
 understanding of the 3D shape and structure of large molecules or complex
 proteins.
  * Real Time Ambient Occlusion
  * Depth Aware Silhouette Enhancement
  * Ball and Sticks, Space-Fill and Liquorice visualization modes
  * High resolution antialiased snapshots for creating publication quality
    renderings
  * Automatic generation of animated gifs of rotating molecules for web pages
    animations
  * Real-time rendering of large molecules and protein (>100k atoms)
  * Standard PDB input
  * Support as a plugins of the NanoEngineer-1 the modeling and simulation
    program for nano-composites
 This program needs the VCG library http://vcg.sourceforge.net which has
 to be packaged first.

Depends: cp2k
Homepage: http://cp2k.berlios.de/
WNPP: 518984
License: GPL
Responsible: Debichem Project <debichem-devel@lists.alioth.debian.org>
Pkg-Description: CP2K is a program to perform atomistic and molecular
 simulations of solid state, liquid, molecular and biological
 systems. It provides a general framework for different methods such as
 e.g. density functional theory (DFT) using a mixed Gaussian and plane
 waves approach (GPW), and classical pair and many-body potentials.

Depends: pdb2pqr

Depends: openchrom
Homepage: http://www.openchrom.net/
License: EPL
Pkg-Description: process chromatographic and mass spectrometric data
 OpenChrom is an open source software for chromatography based on the
 Eclipse Rich Client Platform (RCP). Its focus is to handle mass
 spectrometry systems (e.g. GC/MS, LC/MS, Py-GC/MS, HPLC-MS) data files
 natively. OpenChrom is able to import binary and textual chromatographic
 data files, such as *.D chromatograms from Agilent Technologies or
 NetCDF. Moreover, it offers a nice graphical user interface and is
 available for various operating systems, e.g. Windows, Linux, Solaris
 and Mac OSX. A basis set of methods to detect baselines, peaks and to
 integrate peaks in a chromatogram are implemented. Preprocessing steps,
 e.g. to remove certain mass fragments (m/z) such as nitrogen (28) or
 water (18), are supported by applying filter on the chromatogram or mass
 spectrum. Extensions are welcome, as OpenChrom is open source and uses a
 flexible approach, which allows others to implement their own methods,
 algorithms, filters, detectors or integrators. Therefore, OpenChrom
 shall be an efficiently system to process chromatographic and mass
 spectrometric data using an extensible and flexible plugin approach.

