These are prospective packages for the Debichem project, for which an ITP bug report has already been filed. Just because a project is listed here does not mean it needs to be packaged eventually, just that it was deemed interest in a person, who wants to package it.
* Package name : libccp4 Version : Upstream Author : * URL : http://www.ccp4.ac.uk/html * License : Programming Lang: Description :
Collaborative Computational Project, Number 4. 1994. “The CCP4 Suite: Programs for Protein Crystallography”. Acta Cryst. D50, 760-763
* Package name : coot Version : 0.8.9.1 Upstream Author : Paul Emsley <email@example.com> * URL : https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/ * License : GPL-3+ Programming Lang: C++ Description : model building program for macromolecular crystallography
Coot is a molecular-graphics application for model building and validation of biological macromolecules. The program displays electron-density maps and atomic models and allows model manipulations such as idealization, real-space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers and Ramachandran idealization. Furthermore, tools are provided for model validation as well as interfaces to external programs for refinement, validation and graphics.
* Package name : dl-poly-classic Version : 4.09.1 Upstream Author : * URL : https://www.ccp5.ac.uk/DL_POLY_CLASSIC/ * License : BSD Programming Lang: Fortran/Java Description : general purpose molecular dynamics simulation package
DL_POLY Classic is a general purpose (parallel and serial) molecular dynamics simulation package.
It can be executed as a serial or parallel application. The code achieves parallelisation using the Replicated Data strategy, which is suitable for homogeneous, distributed-memory, parallel computers. The code is useful for simulations of up to 30,000 atoms with good parallel performance on up to 100 processors, though in some circumstances it can exceed or fail to reach these limits.
* Package name : exciting Version : 13 (nitrogen) Upstream Author : Claudia Ambrosch-Draxl <firstname.lastname@example.org> * URL : http://exciting-code.org * License : GPL Programming Lang: Fortran 90 Description : All-electron full-potential electronic-structure code
exciting is a full-potential all-electron density-functional-theory (DFT) package based on the linearized augmented plane-wave (LAPW) method. It can be applied to all kinds of materials, irrespective of the atomic species involved, and also allows for the investigation of the atomic-core region.
Its particular focus is on excited state properties, within the framework of time-dependent DFT (TDDFT) as well as within many-body perturbation theory (MBPT).
High precision all-electron DFT code based on the FP-LAPW method including local-orbitals Various xc functionals available Calculation of forces and structural optimization Treatment of magnetism in the most general way, including spin-orbit coupling and non-collinear magnetism Plotting of band structure, Fermi surface, charge density, potential etc. (1D, 2D and 3D) Visualization with xmgrace and XCrySDen supported MPI k-point parallelization, as well as optimization for multithreaded numeric libraries (BLAS LAPACK)
Excited states features:
Macroscopic dielectric function within time-dependent DFT and the Bethe-Salpeter equation Available exchange-correlation kernels: RPA, ALDA, long-range contribution model-kernels, BSE-derived kernel RPA and ALDA loss function for finite momentum transfer q-vectors
This package will be part of the Debian Science nanoscale-physics metapackage.
* Package name : inchi Version : 1.04 Upstream Author : IUPAC and InChI Trust Limited * URL : https://www.inchi-trust.org * License : IUPAC-InChI Trust License 1.0 (more permissive then LGPL-2.1+) Programming Lang: C Description : International Chemical Identifier generator
Library to generate Standard/non-Standard InChI/InChIKey.
Many chemistry related softwares (at least OpenBABEL which has been already packaged in debian) carry private copies of this library. This library should be packaged for better compliance to debian policy which discourages inclusions of 3rd party codes.
* Package name : python-nmoldyn Version : 3.0.11 Upstream Author : * URL : http://dirac.cnrs-orleans.fr/nMOLDYN.html * License : CeCILL Free Software License Programming Lang: Description :
nMOLDYN is an interactive analysis program for Molecular Dynamics simulations. It is especially designed for the computation and decomposition of neutron scattering spectra, but also computes other quantities.
Quantities related to neutron scattering:
coherent intermediate scattering function memory function for coherent scattering function dynamic structure factor incoherent intermediate scattering function elastic incoherent structure factor
mean-square displacement velocity autocorrelation function memory function for velocity autocorrelation function density of states angular velocity autocorrelation function (and its spectrum) reorientational correlation function
* Package name : openmm Version : 7.3.1 Upstream Author : Stanford University and the Authors * URL : http://openmm.org * License : MIT, LGPL, other Programming Lang: C Description : high performance toolkit for molecular simulation
The OpenMM Software suite encompasses several essential software tools for molecular simulations:
OpenMM: a library providing tools for modern molecular modeling simulation. It can be easily hooked into any code, and has a strong emphasis on hardware acceleration, thus providing not just a consistent API, but superior performance. PyOpenMM: a python API that wraps the OpenMM library, for those preferring to code in python. AMBER-compatible front end to OpenMM, designed for AMBER users that would like to enjoy the speed of OpenMM. MSMBuilder: analyze and combine data generated by molecular dynamics runs. MSM Builder provides a means to parallelize OpenMM runs across multiple GPUs OpenMM Zephyr: a user-friendly, easy to use, molecular simulation application, with OpenMM accelerated Gromacs inside, for studying molecular dynamics of proteins, RNA, and other molecules.
* Package name : osra Version : 2.0.0 Upstream Author : Igor Filippov <email@example.com> * URL : https://sourceforge.net/projects/osra/ * License : GPL-2+ Programming Lang: C++, Java Description : optical structure recognition application
OSRA is a utility designed to convert graphical representations of chemical structures, as they appear in journal articles, patent documents, textbooks, trade magazines etc., into SMILES or SD files - a computer recognizable molecular structure format. OSRA can read a document in any of the over 90 graphical formats parseable by ImageMagick - including GIF, JPEG, PNG, TIFF, PDF, PS etc., and generate the SMILES or SDF representation of the molecular structure images encountered within that document.
* Package name : wannier90 Version : 3.0.0 Upstream Author : Arash Mostofi <firstname.lastname@example.org> * URL : http://www.wannier.org/ * License : GPL Programming Lang: Fortran 90 Description : Maximally Localized Wannier Functions
Wannier90 is an electronic-structure software computing maximally-localized Wannier functions (MLWF). It works on top of other electronic-structure software, such as Abinit, FLEUR, and PwSCF.
* Package name : xtalopt Version : r12.0 Upstream Author : David Lonie * URL : https://xtalopt.github.io * License : GPLv2, LGPLv2 and BSD Programming Lang: C, C++ Description : Evolutionary Crystal Structure Prediction
XtalOpt is a free and truly open source evolutionary algorithm designed to predict crystal structures. It is implemented as an extension to the Avogadro molecular editor. See the list of publications for some of the systems it has been used to explore.
XtalOpt runs on a workstation and supports using GULP, VASP, pwSCF (Quantum ESPRESSO), and CASTEP for geometry optimizations. The calculations can be performed remotely on a cluster running PBS or SGE, or on the workstation if a computing cluster is not available. There is no special set up needed server-side when running on remote queues, just install XtalOpt on the workstation and it’s ready to go!