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Task: Chemistry
Install: false
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)
Recommends: 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-mpich | gromacs-openmpi, \
kalzium, katomic, mopac7-bin, mpqc, mpqc-support, \
openbabel, psi3, pymol, \
viewmol, xdrawchem, xmakemol-gl | xmakemol, v-sim
Why: from the DebianScience/Chemistry wiki page
Recommends: python3-openbabel
Recommends: rasmol
Recommends: adun.app
Why: 3D viewer and calculation output visualisation
Recommends: gdpc
Recommends: xbs
Recommends: gelemental
Suggests: gdpc-examples
Recommends: avogadro
Recommends: gamgi
Recommends: msxpertsuite
Recommends: drawxtl
Recommends: chemical-structures
Recommends: openfoam
Recommends: pyfai
Recommends: python3-mpiplus
Suggests: refmac-dictionary
Suggests: libcoordgen-dev, libmaeparser-dev
Recommends: 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
Recommends: 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.
Recommends: molden
Recommends: molekel
Recommends: tinker
Recommends: jmol
Recommends: qutemol
Recommends: cp2k
Recommends: pdb2pqr
Recommends: mmass, mmass-modules
Recommends: python3-pymzml
Suggests: python-pymzml-doc
Recommends: tandem-mass
Suggests: python3-periodictable
Suggests: libschroedinger-coordgenlibs-dev
Suggests: python3-amp
Recommends: feff85exafs
Recommends: 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.
Recommends: fdmnes
Pkg-URL: http://people.debian.org/~tille/packages/fdmnes/
Recommends: atomes
|
