These are prospective packages for the Debichem project, for which an initial packaging effort has already been placed in Git. These packages might just need some polishing to be ready to be uploaded into Debian. They might be a good entry point in helping the Debichem project.
* 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 : 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-mdanalysis Version : Upstream Author : * URL : http://www.mdanalysis.org * License : GPL-2, BSD Programming Lang: Description :
MDAnalysis is an object-oriented python toolkit to analyze molecular dynamics trajectories generated in many popular formats including CHARMM, Gromacs, NAMD, LAMMPS and Amber.
It allows one to read molecular dynamics trajectories and access the atomic coordinates through numpy arrays. This provides a flexible and relatively fast framework for complex analysis tasks. In addition, CHARMM-style atom selection commands are implemented. Trajectories can also be manipulated (for instance, fit to a reference structure) and written out.
* 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 : openmolcas Version : Upstream Author : * URL : https://gitlab.com/Molcas/OpenMolcas * License : LGPL Programming Lang: Description :
(Open)Molcas is a Quantum Chemistry software package developed by scientists to be used by scientists.
The basic philosophy behind Molcas is to develop methods that allow accurate ab initio treatment of very general electronic structure problems for molecular systems in both ground and excited states which is not an easy task. Nowadays, knowledge about how to obtain accurate properties for single-reference dominated ground states is well developed, and Molcas contains a number of codes that can perform such calculations (MP2, CC, CPF, DFT etc). All these methods treat the electron correlation starting from a single determinant (closed or open shell) reference state. Such codes are today’s standard in most Quantum Chemistry program.
However, Molcas is to be able to treat, highly degenerate states, such as those oc- curring in excited states, transition states in chemical reactions, diradicaloid systems, heavy metal systems, as well as other chemically important problems, all at the same level of accuracy. This is a much more difficult problem, since a single-determinant approach does not work well in these cases. The key feature of Molcas is the mul- ticonfigurational approach. Molcas contains codes for general and effective multi- configurational SCF calculations at the Complete Active Space (CASSCF) level, but also employs more restricted MCSCF wave functions such as the Restricted Active Space, RASSCF, and the Generalized Active Space, GASSCF. It is also possible using either CASSCF or RASSCF to employ optimization techniques and obtain equilibrium geometries, transition-state structures, force fields, and vibrational energies using gra- dient techniques.
* Package name : osra Version : 2.0.0 Upstream Author : Igor Filippov <firstname.lastname@example.org> * 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 <email@example.com> * 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.