[Debichem-devel] List of prospective packages

[Michael Banck]

Hi,

I went through a pile of papers today and added what I believed were
open source projects to PROSPECTIVE_PACKAGES in the debichem subversion
root.  The current list is below, if somebody is intersted in packaging
any of them, let us know.  Even more valuable would be feedback from the
field whether those packages are good or bad - at this point I think we
do not want to package something just because it is open source.

I might package xtalopt and fp-fingerprints in the near future, when I
get around (last time I tried xtalopt, it failed on my notebook, I think
there is a patch in git now, but no new release).

(Andreas, I have not added those package as WNPP for the task pages
because I think that we should only add packages there which we
definitely want to have in wheezy and should get packaged at most
mid-term.  Otherwise, we end up with a couple of dead and misleading
entries on the web sentinel)

Anybody have any other prospective packages?

The packages are: (The first URL is a link to the homepage, the second
to an explanatory paper):

* MOLDY
** http://code.google.com/p/moldy/
** http://www.sciencedirect.com/science/article/pii/S001046551100261X
(also available from http://arxiv.org/abs/1107.2619)
** GPLv2

MOLDY is a parallelised OpenMP short-ranged molecular dynamics program,
first written at Harwell Laboratory in the 1980s. The program is written
in a modular fashion to allow for easy user modification, in particular
the implementation of new interatomic potentials. Using Link Cells and
Neighbour Lists, the code fully exploits the short range of the
potentials, and the slow diffusion expected for solid systems.

* XtalOpt (ITP: #641655)
** http://xtalopt.openmolecules.net/wiki/index.fcgi/
** http://www.sciencedirect.com/science/article/pii/S0010465510003140
** GPL

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!

* ASE (ITP: #602126)
** https://wiki.fysik.dtu.dk/ase/
** GPL/LGPL

The Atomic Simulation Environment (ASE) is the common part of the
simulation tools developed at CAMd. ASE provides Python modules for
manipulating atoms, analyzing simulations, visualization etc.

* TRAVIS
** http://www.uni-leipzig.de/~travis/
** http://pubs.acs.org/doi/abs/10.1021/ci200217w
** GPLv3

TRAVIS is a free tool for analyzing and visualizing trajectories from
all kinds of molecular dynamics or monte carlo simulations.

* chem-fingerprints
** http://code.google.com/p/chem-fingerprints/
** MIT

chemfp is a set of formats and related tools for the storage, exchange,
and search of cheminformatics fingerprint data sets.

* MOIL-opt
** http://clsb.ices.utexas.edu/research/group/index.html
** http://pubs.acs.org/doi/abs/10.1021/ct200360f
** Public Domain

* DL_POLY_CLASSIC
** http://www.cse.scitech.ac.uk/ccg/software/DL_POLY_CLASSIC/index.shtml
** BSD

DL_POLY Classic is a general purpose molecular dynamics simulation
package

* AmberTools
** http://ambermd.org/#AmberTools
** GPLv3 etc.

AmberTools consists of several independently developed packages that
work well by themselves, and with Amber itself. The suite can also be
used to carry out complete (non-periodic) molecular dynamics simulations
(using NAB), with generalized Born solvent models.

* OSRA
** http://cactus.nci.nih.gov/osra/
** GPLv2+

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.

* Coot
** http://biop.ox.ac.uk/coot/
** http://journals.iucr.org/d/issues/2010/04/00/ba5144/
** GPLv3+

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.

* MDAnalysis
** http://code.google.com/p/mdanalysis/
** http://onlinelibrary.wiley.com/doi/10.1002/jcc.21787/abstract
** GPLv2, BSD

MDAnalysis is an object-oriented python toolkit to analyze molecular
dynamics trajectories generated by CHARMM, Gromacs, NAMD, LAMMPS, or
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.

* OpenMM
** https://simtk.org/home/openmm_suite
** http://onlinelibrary.wiley.com/doi/10.1002/jcc.21209/abstract
** MIT, LGPL, other

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.

* PaDEL-Descriptor
** http://padel.nus.edu.sg/software/padeldescriptor/
** http://onlinelibrary.wiley.com/doi/10.1002/jcc.21707/abstract
** AGPLv3+, Apachev2, LGPLv2+, GPLv2/CDDL

A software to calculate molecular descriptors and fingerprints. The
software currently calculates 856 descriptors (722 1D, 2D descriptors
and 134 3D descriptors) and 10 types of fingerprints. The descriptors
and fingerprints are calculated using The Chemistry Development Kit
(CDK) with some additional descriptors and fingerprints. These additions
include atom type electrotopological state descriptors, extended
topochemical atom (ETA) descriptors, McGowan volume, molecular linear
free energy relation descriptors, ring counts, count of chemical
substructures identified by Laggner, and binary fingerprints and count
of chemical substructures identified by Klekota and Roth.

* MATCH
** http://brooks.chem.lsa.umich.edu/index.php?page=match&subdir=articles/resources/software
** http://onlinelibrary.wiley.com/doi/10.1002/jcc.21963/abstract
** Perl license (but download behind dumb registration site,
http://brooks.chem.lsa.umich.edu/downloads/MATCH_RELEASE.tar.gz is the
direct URL)

A toolset of program libraries collectively titled multipurpose
atom-typer for CHARMM (MATCH) for the automated assignment of atom types
and force field parameters for molecular mechanics simulation of organic
molecules. A general chemical pattern-matching engine achieves
assignment of atom types, charges and force field parameters through
comparison against a customizable list of chemical fragments.

* DynamO
** https://www.marcusbannerman.co.uk/index.php/dynamo.html
** http://onlinelibrary.wiley.com/doi/10.1002/jcc.21915/abstract
** GPLv3+

DYNAMics of discrete Objects (DynamO) is a general, event driven
simulation code capable of simulating millions of particles in short
times on commodity computers.

Simple Systems:

 * Smooth or rough hard spheres, square wells, soft cores and all the
   other simple EDMD potentials.
 * Millions of particles for billions of events: Using 500 bytes per
   particle and running at around 75k events a second, even an old
   laptop can run huge simulations with accurate results.
 * Non-Equilibrium Molecular Dynamics (NEMD): DynamO has Lees-Edwards
   boundary conditions for shearing systems, thermalised walls and
   Andersen or rescaling thermostats.
 * Compression dynamics: Need high density systems? DynamO can compress
   any of its systems using isotropic compaction until the pressure
   diverges!
 * Poly-dispersity: All interactions are generalised to fully
   poly-disperse particles.

Granular Systems/Complex Boundaries:

 * Event driven dynamics with gravity: Almost all interactions work in
   the presence of gravity, allowing event driven simulations of
   macroscopic systems.
 * Sleeping particles: In systems where particles come to a rest, the
   sleeping particles algorithm can remove the cost of simulating the
   particles completely.
 * Triangle or sphere meshes: Arbitrary complex boundaries can be
   implemented using triangle meshes imported from CAD drawings.
 * Stepped potentials: Arbitrary stepped potentials may be simulated to
   approximate any soft potential.

Polymeric Systems/Accelerated Dynamics:

 * Parallel tempering/Replica exchange: Run multiple simulations in
   parallel and use this Monte Carlo technique to enhance the sampling
   of phase space.
 * Histogram reweighting: Combine the results from replica exchange
   simulations and extrapolate to temperatures which were not simulated.
 * Multicanonical simulations: Used in conjunction with replica exchange
   techniques, multicanonical simulations greatly enhance the sampling
   of phase space, helping find the true native state of the polymer.

* JGromacs
** http://sbcb.bioch.ox.ac.uk/jgromacs/
** http://pubs.acs.org/doi/abs/10.1021/ci200289s
** GPLv3

JGromacs is a Java library designed to facilitate the development of
cross-platform analysis applications for Molecular Dynamics (MD)
simulations.  The package contains parsers for file formats applied by
GROMACS (GROningen MAchine for Chemical Simulations), one of the most
widely used MD simulation packages. JGromacs provides a multilevel
object-oriented representation of simulation data to integrate and
interconvert sequence, structure and dynamics information. In addititon,
a basic analysis toolkit is included in the package.  The programmer is
also provided with simple tools (e.g. XML-based configuration) to create
applications with a user interface resembling the command-line UI of
Gromacs applications.

* DockoMatic
** http://sourceforge.net/projects/dockomatic/
** http://onlinelibrary.wiley.com/doi/10.1002/jcc.21864/abstract
** LGPLv3+

DockoMatic is a GUI application that is intended to ease and automate
the creation and management of AutoDock jobs for high throughput
screening of ligand/receptor interactions.


Cheers,

Michael