debichem-0.0.3/0000755000000000000000000000000012112441746010142 5ustar debichem-0.0.3/debian/0000755000000000000000000000000012112442035011354 5ustar debichem-0.0.3/debian/rules0000755000000000000000000000007012111655017012436 0ustar #!/usr/bin/make -f include /usr/share/blends-dev/rules debichem-0.0.3/debian/control.stub0000644000000000000000000000130612111655017013740 0ustar Source: debichem Section: misc Priority: extra Maintainer: Debichem Team Uploaders: Michael Banck , Andreas Tille Build-Depends-Indep: blends-dev (>= 0.6.13) Standards-Version: 3.9.3 Homepage: http://alioth.debian.org/projects/debichem Vcs-Browser: http://svn.debian.org/wsvn/blends/projects/debichem/trunk/debichem/ Vcs-Svn: svn://svn.debian.org/blends/projects/debichem/trunk/debichem/ Package: debichem-tasks Architecture: all Depends: tasksel Description: DebiChem tasks for tasksel This package provides DebiChem tasks in tasksel. . These tasks are described in detail at http://blends.alioth.debian.org/debichem/tasks/ debichem-0.0.3/debian/control0000644000000000000000000000661312112441746012775 0ustar # This file is autogenerated via make -f debian/rules dist. Do not edit! Source: debichem Section: misc Priority: extra Maintainer: Debichem Team Uploaders: Michael Banck , Andreas Tille Build-Depends-Indep: blends-dev (>= 0.6.13) Standards-Version: 3.9.3 Homepage: http://alioth.debian.org/projects/debichem Vcs-Browser: http://svn.debian.org/wsvn/blends/projects/debichem/trunk/debichem/ Vcs-Svn: svn://svn.debian.org/blends/projects/debichem/trunk/debichem/ Package: debichem-tasks Architecture: all Depends: tasksel Description: DebiChem tasks for tasksel This package provides DebiChem tasks in tasksel. . These tasks are described in detail at http://blends.alioth.debian.org/debichem/tasks/ Package: debichem-abinitio Architecture: all Depends: debichem-tasks (= ${binary:Version}) Recommends: abinit, aces3, cp2k, mpqc, nwchem, openmx, psi3, quantum-espresso Description: DebiChem Ab Initio Calculations This metapackage will install packages doing ab initio calculations which might be useful for chemists. Package: debichem-cheminformatics Architecture: all Depends: debichem-tasks (= ${binary:Version}) Recommends: libcdk-java, libopsin-java, openbabel, python-chemfp, python-cinfony, python-fmcs, python-indigo, python-openbabel, python-rdkit Description: DebiChem Cheminformatics This metapackage will install cheminformatics packages useful for chemists. Package: debichem-modelling Architecture: all Depends: debichem-tasks (= ${binary:Version}) Recommends: avogadro, ghemical, pymol Suggests: nmoldyn, python-mmtk Description: DebiChem 3D Molecular Modelling and Visualization This metapackage will install 3D Molecular Modelling and Visualization which might be useful for chemists. Package: debichem-molmech Architecture: all Depends: debichem-tasks (= ${binary:Version}) Recommends: adun.app, avogadro, ghemical, gromacs Suggests: vmd Description: DebiChem Molecular Mechanics This metapackage will install Molecular Mechanics which might be useful for chemists. Package: debichem-polymer Architecture: all Depends: debichem-tasks (= ${binary:Version}) Recommends: lutefisk, massxpert, mmass Description: DebiChem polymer sequence editors and mass spectrometry This metapackage will install packages which enable you to edit polymer sequences so as to perform mass spectrometry simulations and view mass spectra. Package: debichem-semiempirical Architecture: all Depends: debichem-tasks (= ${binary:Version}) Recommends: cp2k, mopac7-bin Description: DebiChem Semi Empirical This metapackage will install Semi Empirical which might be useful for chemists. Package: debichem-view-edit-2d Architecture: all Depends: debichem-tasks (= ${binary:Version}) Recommends: bkchem, chemtool, easychem, gchempaint, xdrawchem Suggests: osra Description: DebiChem 2D structure editors This metapackage will install 2D structure editors which might be useful for chemists. Package: debichem-visualisation Architecture: all Depends: debichem-tasks (= ${binary:Version}) Recommends: adun.app, avogadro, ballview, cclib, drawxtl, gabedit, garlic, gausssum, gcrystal, gdis, gdpc, jmol, kalzium, qutemol, rasmol, raster3d, shelxle, v-sim, viewmol, xbs, xcrysden, xmakemol Description: DebiChem 3D Viewers and Calculation Output Visualization This metapackage will install 3D Viewers and Calculation Output Visualization which might be useful for chemists. debichem-0.0.3/debian/changelog0000644000000000000000000000310312112441724013227 0ustar debichem (0.0.3) unstable; urgency=low [ Michael Banck ] * tasks/visualisation: Added jmol and qutemol. * tasks/visualisation: Added cclib. * tasks/semiempirical: Added cp2k. * tasks/cheminformatics: Added python-indigo. * tasks/visualization: Added shelxle, xcrysden and drawxtl. * tasks/cheminformatics: Added python-fmcs, python-chemfp and libopsin-java. * tasks/visualization: Added gamgi. * tasks/molmech, tasks/visualization, tasks/cheminformatics: Removed some citation data which is already present in the respective debian/upstream files. * tasks/visualization: Added ballview, raster3d and kalzium. [ Daniel Leidert ] * debian/control.stub (Standards-Version): Bumped to 3.9.3. (Vcs-Browser): Adjusted. -- Michael Banck Sun, 24 Feb 2013 16:30:10 +0100 debichem (0.0.2) unstable; urgency=low [ Andreas Tille ] * tasks/modelling: Added python-mmtk and nmoldyn. * tasks/visualisation: Added publication info to rasmol. * tasks/view-edit-2d: Added osra as prospective package. [ Michael Banck ] * tasks/abinitio: Added nwchem, aces3, cp2k and quantum-espresso. * Added and/or updated publication/registration info for adun.app, gromacs, massxpert, mmass, gabedit, rasmol, psi3, abinit, nwchem, aces3 and quantum-espresso. * tasks/cheminformatics: New task. * debian/control: Updated. -- Michael Banck Tue, 01 Nov 2011 23:53:00 +0100 debichem (0.0.1) unstable; urgency=low * Initial release. (Closes: #589042) -- Andreas Tille Mon, 19 Jul 2010 22:44:13 +0200 debichem-0.0.3/debian/compat0000644000000000000000000000000212111655017012557 0ustar 7 debichem-0.0.3/debian/copyright0000644000000000000000000000206112111655017013313 0ustar This package was written by Andreas Tille Mon, 19 Jul 2010 22:44:13 +0200 Upstream Author: Debichem Team Copyright: © 2008-2010 Michael Banck , Andreas Tille License: This package is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; version 2 dated June, 1991. This package is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this package; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301, USA. On Debian GNU/Linux systems, the complete text of the GNU General Public License can be found in `/usr/share/common-licenses/GPL-2'. debichem-0.0.3/tasks/0000755000000000000000000000000012112176504011264 5ustar debichem-0.0.3/tasks/cheminformatics0000644000000000000000000000137312112176504014366 0ustar Task: Cheminformatics Description: DebiChem Cheminformatics This metapackage will install cheminformatics packages useful for chemists. Depends: openbabel Depends: python-openbabel Depends: libcdk-java Published-Title: The Chemistry Development Kit (CDK): An Open-Source Java Library for Chemo- and Bioinformatics Published-Authors: C. Steinbeck, Y. Han, S. Kuhn, O. Horlacher, E. Luttmann and E. L. Willighagen Published-In: J. Chem. Inf. Comput. Sci. 43(2):493-500 Published-Year: 2003 Published-URL: http://pubs.acs.org/doi/abs/10.1021/ci025584y Published-DOI: 10.1021/ci025584y Depends: python-rdkit Depends: python-indigo Depends: python-cinfony Published-In: Chem. Cent. J. 2:24 Depends: python-fmcs Depends: python-chemfp Depends: libopsin-java debichem-0.0.3/tasks/view-edit-2d0000644000000000000000000000252712112176504013415 0ustar Task: 2D Structure Editors Description: DebiChem 2D structure editors This metapackage will install 2D structure editors which might be useful for chemists. Depends: bkchem Depends: chemtool Depends: easychem Depends: gchempaint Depends: xdrawchem Depends: osra Homepage: http://cactus.nci.nih.gov/osra/ License: Creative Commons Pkg-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 (Simplified Molecular Input Line Entry Specification - see http://en.wikipedia.org/wiki/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. . Note that any software designed for optical recognition is unlikely to be perfect, and the output produced might, and probably will, contain errors, so curation by a human knowledgeable in chemical structures is highly recommended. Remark: Packaging was discussed at http://lists.alioth.debian.org/pipermail/debichem-devel/2009-November/002236.html debichem-0.0.3/tasks/polymer0000644000000000000000000000153212112176504012677 0ustar Task: Polymer editors and mass spectrometry Description: DebiChem polymer sequence editors and mass spectrometry This metapackage will install packages which enable you to edit polymer sequences so as to perform mass spectrometry simulations and view mass spectra. Depends: massxpert Published-Title: massXpert 2: a cross-platform software environment for polymer chemistry modelling and simulation/analysis of mass spectrometric data Published-Authors: F. Rusconi Published-In: Bioinformatics 25(20):2741-2742 Published-URL: http://bioinformatics.oxfordjournals.org/content/25/20/2741 Depends: mmass Published-Title: mMass 3: A Cross-Platform Software Environment for Precise Analysis of Mass Spectrometric Data Published-Authors: M. Strohalm, D. Kavan, P. Novak, M. Volny and V. Havlicek Published-In: Anal. Chem. 82(11):4648-4651 Depends: lutefisk debichem-0.0.3/tasks/semiempirical0000644000000000000000000000027612112176504014037 0ustar Task: Semi Empirical Calculations Description: DebiChem Semi Empirical This metapackage will install Semi Empirical which might be useful for chemists. Depends: mopac7-bin Depends: cp2k debichem-0.0.3/tasks/abinitio0000644000000000000000000000656112111655017013015 0ustar Task: Ab Initio Calculations Description: DebiChem Ab Initio Calculations This metapackage will install packages doing ab initio calculations which might be useful for chemists. Depends: mpqc Published-Title: http://www.mpqc.org Published-Authors: The Massively Parallel Quantum Chemistry Program (MPQC), Version 3.0.0 Prerelease, C. L. Janssen, I. B. Nielsen, M. L. Leininger, E. F. Valeev, J. P. Kenny, E. T. Seidl Published-URL: http://www.mpqc.org Depends: psi3 Published-Title: PSI3: an open-source Ab Initio electronic structure package Published-Authors: T. Daniel Crawford, C. David Sherrill, Edward F. Valeev, Justin T. Fermann, Rollin A. King, Matthew L. Leininger, Shawn T. Brown, Curtis L. Janssen, Edward T. Seidl, Joseph P. Kenny and Wesley D. Allen Published-In: J. Comput. Chem. 28(9):1610-1616 Published-Year: 2007 Published-URL: http://onlinelibrary.wiley.com/doi/10.1002/jcc.20573/abstract Published-DOI: 10.1002/jcc.20573 Depends: abinit Published-Title: ABINIT: First-principles approach to material and nanosystem properties Published-Authors: X. Gonze, B. Amadon, P.-M. Anglade, J.-M. Beuken, F. Bottin, P. Boulanger, F. Bruneval, D. Caliste, R. Caracas, M. Côté, T. Deutsch, L. Genovese, Ph. Ghosez, M. Giantomassi, S. Goedecker, D.R. Hamann, P. Hermet, F. Jollet, G. Jomard, S. Leroux, M. Mancini, S. Mazevet, M. J. T. Oliveira, G. Onida, Y. Pouillon, T. Rangel, G.-M. Rignanese, D. Sangalli, R. Shaltaf, M. Torrent, M. J. Verstraete, G. Zerah and J. W. Zwanziger Published-In: Comput. Phys. Commun. 180(12):2582-2615 Published-Year: 2009 Published-URL: http://www.sciencedirect.com/science/article/pii/S0010465509002276 Published-DOI: 10.1016/j.cpc.2009.07.007 Depends: openmx Depends: nwchem Published-Title: NWChem: a comprehensive and scalable open-source solution for large scale molecular simulations Published-Authors: M. Valiev, E.J. Bylaska, N. Govind, K. Kowalski, T.P. Straatsma, H.J.J. van Dam, D. Wang, J. Nieplocha, E. Apra, T.L. Windus and W.A. de Jong Published-In: Comput. Phys. Commun. 181(9):1477-1489 Published-Year: 2010 Published-URL: http://www.sciencedirect.com/science/article/pii/S0010465510001438 Published-DOI: 10.1016/j.cpc.2010.04.018 Depends: aces3 Published-Title: Parallel Implementation of Electronic Structure Energy, Gradient and Hessian Calculations Published-Authors: V. Lotrich, N. Flocke, M. Ponton, A. Yau, A. Perera, E. Deumens and R. J. Bartlett Published-In: J. Chem. Phys. 128:194104 Published-Year: 2008 Published-URL: http://jcp.aip.org/resource/1/jcpsa6/v128/i19/p194104_s1 Published-DOI: 10.1063/1.2920482 Registration: http://www.qtp.ufl.edu/ACES/register.html Depends: cp2k Depends: quantum-espresso Published-Title: QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials Published-Authors: P. Giannozzi, S. Baroni, N. Bonini, M. Calandra, R. Car, C. Cavazzoni, D. Ceresoli, G. L. Chiarotti, M. Cococcioni, I. Dabo, A. Dal Corso, S. Fabris, G. Fratesi, S. de Gironcoli, R. Gebauer, U. Gerstmann, C. Gougoussis, A. Kokalj, M. Lazzeri, L. Martin-Samos, N. Marzari, F. Mauri, R. Mazzarello, S. Paolini, A. Pasquarello, L. Paulatto, C. Sbraccia, S. Scandolo, G. Sclauzero, A. P. Seitsonen, A. Smogunov, P. Umari and R. M. Wentzcovitch Published-In: J. Phys. Condens. Matter 21:395502 Published-Year: 2009 Published-URL: http://iopscience.iop.org/0953-8984/21/39/395502 Published-DOI: 10.1088/0953-8984/21/39/395502 debichem-0.0.3/tasks/visualisation0000644000000000000000000000152712112176504014106 0ustar Task: Output & Visualization Description: DebiChem 3D Viewers and Calculation Output Visualization This metapackage will install 3D Viewers and Calculation Output Visualization which might be useful for chemists. Depends: adun.app Depends: avogadro Depends: cclib Published-Title: cclib: a library for package-independent computational chemistry algorithms Published-Authors: N. M. O'Boyle, A. L. Tenderholt, K. M. Langner Published-In: J. Comput. Chem. 29(5):839-845 Depends: gabedit Depends: garlic Depends: gausssum Depends: gcrystal Depends: gdis Depends: gdpc Depends: jmol Depends: qutemol Depends: rasmol Registration: http://www.rasmol.org/register.shtml Depends: v-sim Depends: viewmol Depends: xbs Depends: xmakemol Depends: shelxle Depends: xcrysden Depends: drawxtl Depends: ballview Depends: raster3d Depends: kalzium debichem-0.0.3/tasks/modelling0000644000000000000000000000233712112176504013166 0ustar Task: Molecular Modelling Description: DebiChem 3D Molecular Modelling and Visualization This metapackage will install 3D Molecular Modelling and Visualization which might be useful for chemists. Depends: avogadro Depends: ghemical Depends: pymol Depends: python-mmtk Homepage: http://dirac.cnrs-orleans.fr/MMTK/ License: CeCILL-C Language: C, Python WNPP: 642586 Responsible: Picca FrĂ©dĂ©ric-Emmanuel Pkg-Description: The molecular modeling toolkit The Molecular Modeling Toolkit (MMTK) is a library for molecular simulation applications. It provides the most common methods in molecular simulations (molecular dynamics, energy minimization, normal mode analysis) and several force fields used for biomolecules (Amber 94, Amber 99, several elastic network models). MMTK also serves as a code basis that can be easily extended and modified to deal with non-standard situations in molecular simulations. Depends: nmoldyn Homepage: http://dirac.cnrs-orleans.fr/plone/software/nmoldyn/ Pkg-Description: interactive analysis program for Molecular Dynamics simulations nMOLDYN is especially designed for the computation and decomposition of neutron scattering spectra, but also computes other quantities. debichem-0.0.3/tasks/molmech0000644000000000000000000000303612111713531012631 0ustar Task: Molecular Mechanics Description: DebiChem Molecular Mechanics This metapackage will install Molecular Mechanics which might be useful for chemists. Depends: adun.app Published-Title: Framework Based Design of a New All-Purpose Molecular Simulation Application: The Adun Simulator Published-Authors: M.A. Johnston, I.F. Galván and J. VillĂ| -Freixa Published-In: J. Comput. Chem. 26(15):1647-1659 Published-Year: 2005 Published-URL: http://www3.interscience.wiley.com/cgi-bin/abstract/112094040/ABSTRACT Published-DOI: 10.1002/jcc.20312 Depends: avogadro Depends: ghemical Depends: gromacs Depends: vmd License: non-free Homepage: http://www.ks.uiuc.edu/Research/vmd/ Vcs-Browser: http://svn.debian.org/wsvn/debichem/wnpp/vmd/ Vcs-Svn: svn://svn.debian.org/svn/debichem/wnpp/vmd/ Responsible: Michael Banck , Steffen Moeller Pkg-Description: presentation of traces of molecular dynamics runs VMD stands for Visual Molecular Dynamics. While text books and even structure databases because of technical problems only present static pictures of proteins or DNA, for the understanding of the properties of those molecules their vibration or their movement in general is important. . The movements itself are calculated by molecular dynamics programs, such as NAMD (by the same group), Rosetta, BALLView or GROMACS. The latter two are already in the distribution. VMD has a series of nice features, from displaying through animation to analysing. It can be scripted, clustered, and runs on all common OS.. debichem-0.0.3/debichem-tasks.desc0000644000000000000000000000504312112441737013667 0ustar Task: debichem-abinitio Section: debichem Description: DebiChem Ab Initio Calculations This metapackage will install packages doing ab initio calculations which might be useful for chemists. Relevance: 10 Key: debichem-abinitio Packages: list mpqc psi3 abinit openmx nwchem aces3 cp2k quantum-espresso Task: debichem-cheminformatics Section: debichem Description: DebiChem Cheminformatics This metapackage will install cheminformatics packages useful for chemists. Relevance: 10 Key: debichem-cheminformatics Packages: list openbabel python-openbabel libcdk-java python-rdkit python-indigo python-cinfony python-fmcs python-chemfp libopsin-java Task: debichem-modelling Section: debichem Description: DebiChem 3D Molecular Modelling and Visualization This metapackage will install 3D Molecular Modelling and Visualization which might be useful for chemists. Relevance: 10 Key: debichem-modelling Packages: list avogadro ghemical pymol Task: debichem-molmech Section: debichem Description: DebiChem Molecular Mechanics This metapackage will install Molecular Mechanics which might be useful for chemists. Relevance: 10 Key: debichem-molmech Packages: list adun.app avogadro ghemical gromacs Task: debichem-polymer Section: debichem Description: DebiChem polymer sequence editors and mass spectrometry This metapackage will install packages which enable you to edit polymer sequences so as to perform mass spectrometry simulations and view mass spectra. Relevance: 10 Key: debichem-polymer Packages: list massxpert mmass lutefisk Task: debichem-semiempirical Section: debichem Description: DebiChem Semi Empirical This metapackage will install Semi Empirical which might be useful for chemists. Relevance: 10 Key: debichem-semiempirical Packages: list mopac7-bin cp2k Task: debichem-view-edit-2d Section: debichem Description: DebiChem 2D structure editors This metapackage will install 2D structure editors which might be useful for chemists. Relevance: 10 Key: debichem-view-edit-2d Packages: list bkchem chemtool easychem gchempaint xdrawchem Task: debichem-visualisation Section: debichem Description: DebiChem 3D Viewers and Calculation Output Visualization This metapackage will install 3D Viewers and Calculation Output Visualization which might be useful for chemists. Relevance: 10 Key: debichem-visualisation Packages: list adun.app avogadro cclib gabedit garlic gausssum gcrystal gdis gdpc jmol qutemol rasmol v-sim viewmol xbs xmakemol shelxle xcrysden drawxtl ballview raster3d kalzium debichem-0.0.3/TODO0000644000000000000000000000125212111655017010627 0ustar Reinstate revision 3133 and parts of revision 3419: * tasks/abinitio: Split up to ... * tasks/molecular-abinitio: ... this and ... * tasks/periodic-abinitio: ... this. * tasks/molmech: Renamed to ... * tasks/molecular-dynamics: ... this. * tasks/molecular-dynamics: Removed ghemical and avogadro, added cp2k and nwchem. * tasks/modelling: Moved nmoldyn to ... * tasks/molecular-dynamics: ... this. * tasks/visualisation: Added cclib. * tasks/crystallography: New task, including shelxle and xcrysden (ITP'd). * tasks/visualisation: Moved gcrystal to ... * tasks/crystallography: ... this. [ Daniel Leidert ] * tasks/crystallography: Added drawxtl. debichem-0.0.3/Makefile0000644000000000000000000000007312111655017011577 0ustar #!/usr/bin/make -f include /usr/share/blends-dev/Makefile