debichem-0.0.5ubuntu1/0000775000000000000000000000000012443256731011477 5ustar debichem-0.0.5ubuntu1/debichem-tasks.desc0000664000000000000000000000636512443256527015237 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 psi4 elk-lapw ergo 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-crystallography Section: debichem Description: DebiChem crystallography This metapackage will install packages for crystallography which might be useful for chemists. Relevance: 10 Key: debichem-crystallography Packages: list drawxtl gcrystal python-fabio shelxle xcrysden gamgi 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 python-mmtk 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 lammps votca-csg Task: debichem-polymer Section: debichem Description: DebiChem Analytical BioChemistry This metapackage will install packages which enable you to: . - load and convert mass spectrometric data files; - edit biopolymer sequences; - elaborate complex mass spectrometry workflows; - perform protein database searches using tandem-ms data; - view and mine mass spectrometric data; . Relevance: 10 Key: debichem-polymer Packages: list massxpert mmass lutefisk openms libpwiz-tools python-mzml tandem-mass r-cran-maldiquant r-cran-maldiquantforeign r-cran-readbrukerflexdata r-cran-readmzxmldata r-other-curvefdp r-other-nitpick r-cran-mixtools r-other-amsmercury r-other-iwrlars 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 molds 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 gdis gdpc jmol qutemol rasmol v-sim viewmol xbs xmakemol shelxle xcrysden drawxtl ballview kalzium gamgi p4vasp travis debichem-0.0.5ubuntu1/debian/0000775000000000000000000000000012443256732012722 5ustar debichem-0.0.5ubuntu1/debian/control.stub0000664000000000000000000000130612443256466015305 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-0.0.5ubuntu1/debian/copyright0000664000000000000000000000206112443256466014660 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-0.0.5ubuntu1/debian/changelog0000664000000000000000000000542212443256622014575 0ustar debichem (0.0.5ubuntu1) vivid; urgency=medium * Regenerate control file. -- Logan Rosen Sun, 14 Dec 2014 04:49:56 -0500 debichem (0.0.5) unstable; urgency=medium * debian/source/format: Removed. -- Michael Banck Mon, 08 Dec 2014 20:53:53 +0100 debichem (0.0.4) unstable; urgency=medium [ Michael Banck ] * tasks/abinitio: Added psi4. * tasks/crystallography: New task, including shelxle and xcrysden. * tasks/visualisation: Moved gcrystal to ... * tasks/crystallography: ... this. * tasks/crystallography: Added python-fabio. * tasks/molmech: Added lammps. * tasks/semiempirical: Added molds. * tasks/abinitio: Added elk-lapw. * tasks/abinitio: Added ergo. * tasks/visualisation, tasks/crystallography: Added gamgi. * tasks/visualisation: Added p4vasp. * tasks/visualisation: Added travis. * tasks/molmech: Added votca-csg. * tasks/polymer: Changed r-cran-mixtools and r-other-amsmercury Suggests to Depends. * tasks/polymer: Added r-other-iwrlars. [ Daniel Leidert ] * tasks/crystallography: Added drawxtl. [ Andreas Tille ] * d/source/format: 3.0 (native) -- Michael Banck Fri, 05 Dec 2014 16:45:37 +0100 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-0.0.5ubuntu1/debian/rules0000775000000000000000000000007012443256466014003 0ustar #!/usr/bin/make -f include /usr/share/blends-dev/rules debichem-0.0.5ubuntu1/debian/compat0000664000000000000000000000000212443256466014124 0ustar 7 debichem-0.0.5ubuntu1/debian/control0000664000000000000000000001076412443256627014340 0ustar # This file is autogenerated via make -f debian/rules dist. Do not edit! Source: debichem Section: misc Priority: extra Maintainer: Ubuntu Developers XSBC-Original-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 Section: metapackages Architecture: all Depends: debichem-tasks (= ${binary:Version}) Recommends: abinit, aces3, cp2k, elk-lapw, ergo, mpqc, nwchem, openmx, psi3, psi4, 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 Section: metapackages 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-crystallography Section: metapackages Architecture: all Depends: debichem-tasks (= ${binary:Version}) Recommends: drawxtl, gamgi, gcrystal, python-fabio, shelxle, xcrysden Description: DebiChem crystallography This metapackage will install packages for crystallography which might be useful for chemists. Package: debichem-modelling Section: metapackages Architecture: all Depends: debichem-tasks (= ${binary:Version}) Recommends: avogadro, ghemical, pymol, python-mmtk Suggests: nmoldyn 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 Section: metapackages Architecture: all Depends: debichem-tasks (= ${binary:Version}) Recommends: adun.app, avogadro, ghemical, gromacs, lammps, votca-csg Suggests: vmd Description: DebiChem Molecular Mechanics This metapackage will install Molecular Mechanics which might be useful for chemists. Package: debichem-polymer Section: metapackages Architecture: all Depends: debichem-tasks (= ${binary:Version}) Recommends: libpwiz-tools, lutefisk, massxpert, mmass, openms, python-mzml, r-cran-maldiquant, r-cran-maldiquantforeign, r-cran-mixtools, r-cran-readbrukerflexdata, r-cran-readmzxmldata, r-other-amsmercury, r-other-curvefdp, r-other-iwrlars, r-other-nitpick, tandem-mass Suggests: biceps, libmstoolkit, libpwiz-dev Description: DebiChem Analytical BioChemistry This metapackage will install packages which enable you to: . - load and convert mass spectrometric data files; - edit biopolymer sequences; - elaborate complex mass spectrometry workflows; - perform protein database searches using tandem-ms data; - view and mine mass spectrometric data; . Package: debichem-semiempirical Section: metapackages Architecture: all Depends: debichem-tasks (= ${binary:Version}) Recommends: cp2k, molds, mopac7-bin Description: DebiChem Semi Empirical This metapackage will install Semi Empirical which might be useful for chemists. Package: debichem-view-edit-2d Section: metapackages 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 Section: metapackages Architecture: all Depends: debichem-tasks (= ${binary:Version}) Recommends: adun.app, avogadro, ballview, cclib, drawxtl, gabedit, gamgi, garlic, gausssum, gdis, gdpc, jmol, kalzium, p4vasp, qutemol, rasmol, shelxle, travis, v-sim, viewmol, xbs, xcrysden, xmakemol Suggests: raster3d 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-0.0.5ubuntu1/TODO0000664000000000000000000000064312443256466012177 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. debichem-0.0.5ubuntu1/dependency_data/0000775000000000000000000000000012443256731014606 5ustar debichem-0.0.5ubuntu1/dependency_data/debichem_0.0.3.json0000664000000000000000000000262012443256466017764 0ustar {"polymer": {"ignore": [], "suggests": [], "depends": ["massxpert", "mmass", "lutefisk"], "recommends": [], "avoid": []}, "view-edit-2d": {"ignore": [], "suggests": [], "depends": ["bkchem", "chemtool", "easychem", "gchempaint", "xdrawchem", "osra"], "recommends": [], "avoid": []}, "cheminformatics": {"ignore": [], "suggests": [], "depends": ["openbabel", "python-openbabel", "libcdk-java", "python-rdkit", "python-indigo", "python-cinfony", "python-fmcs", "python-chemfp", "libopsin-java"], "recommends": [], "avoid": []}, "molmech": {"ignore": [], "suggests": [], "depends": ["adun.app", "avogadro", "ghemical", "gromacs", "vmd"], "recommends": [], "avoid": []}, "modelling": {"ignore": [], "suggests": [], "depends": ["avogadro", "ghemical", "pymol", "python-mmtk", "nmoldyn"], "recommends": [], "avoid": []}, "visualisation": {"ignore": [], "suggests": [], "depends": ["adun.app", "avogadro", "cclib", "gabedit", "garlic", "gausssum", "gcrystal", "gdis", "gdpc", "jmol", "qutemol", "rasmol", "v-sim", "viewmol", "xbs", "xmakemol", "shelxle", "xcrysden", "drawxtl", "ballview", "raster3d", "kalzium"], "recommends": [], "avoid": []}, "semiempirical": {"ignore": [], "suggests": [], "depends": ["mopac7-bin", "cp2k"], "recommends": [], "avoid": []}, "abinitio": {"ignore": [], "suggests": [], "depends": ["mpqc", "psi3", "abinit", "openmx", "nwchem", "aces3", "cp2k", "quantum-espresso"], "recommends": [], "avoid": []}}debichem-0.0.5ubuntu1/dependency_data/debichem_0.0.4.json0000664000000000000000000000262012443256466017765 0ustar {"polymer": {"ignore": [], "suggests": [], "depends": ["massxpert", "mmass", "lutefisk"], "recommends": [], "avoid": []}, "view-edit-2d": {"ignore": [], "suggests": [], "depends": ["bkchem", "chemtool", "easychem", "gchempaint", "xdrawchem", "osra"], "recommends": [], "avoid": []}, "cheminformatics": {"ignore": [], "suggests": [], "depends": ["openbabel", "python-openbabel", "libcdk-java", "python-rdkit", "python-indigo", "python-cinfony", "python-fmcs", "python-chemfp", "libopsin-java"], "recommends": [], "avoid": []}, "molmech": {"ignore": [], "suggests": [], "depends": ["adun.app", "avogadro", "ghemical", "gromacs", "vmd"], "recommends": [], "avoid": []}, "modelling": {"ignore": [], "suggests": [], "depends": ["avogadro", "ghemical", "pymol", "python-mmtk", "nmoldyn"], "recommends": [], "avoid": []}, "visualisation": {"ignore": [], "suggests": [], "depends": ["adun.app", "avogadro", "cclib", "gabedit", "garlic", "gausssum", "gcrystal", "gdis", "gdpc", "jmol", "qutemol", "rasmol", "v-sim", "viewmol", "xbs", "xmakemol", "shelxle", "xcrysden", "drawxtl", "ballview", "raster3d", "kalzium"], "recommends": [], "avoid": []}, "semiempirical": {"ignore": [], "suggests": [], "depends": ["mopac7-bin", "cp2k"], "recommends": [], "avoid": []}, "abinitio": {"ignore": [], "suggests": [], "depends": ["mpqc", "psi3", "abinit", "openmx", "nwchem", "aces3", "cp2k", "quantum-espresso"], "recommends": [], "avoid": []}}debichem-0.0.5ubuntu1/dependency_data/debichem_0.0.1.json0000664000000000000000000000173412443256466017767 0ustar {"polymer": {"ignore": [], "suggests": [], "depends": ["massxpert", "mmass", "lutefisk"], "recommends": [], "avoid": []}, "view-edit-2d": {"ignore": [], "suggests": [], "depends": ["bkchem", "chemtool", "easychem", "gchempaint", "xdrawchem"], "recommends": [], "avoid": []}, "molmech": {"ignore": [], "suggests": [], "depends": ["adun.app", "avogadro", "ghemical", "gromacs"], "recommends": [], "avoid": []}, "modelling": {"ignore": [], "suggests": [], "depends": ["avogadro", "ghemical", "pymol"], "recommends": [], "avoid": []}, "visualisation": {"ignore": [], "suggests": [], "depends": ["adun.app", "gabedit", "gausssum", "gdpc", "viewmol", "avogadro", "garlic", "gcrystal", "gdis", "rasmol", "v-sim", "xbs", "xmakemol"], "recommends": [], "avoid": []}, "semiempirical": {"ignore": [], "suggests": [], "depends": ["mopac7-bin"], "recommends": [], "avoid": []}, "abinitio": {"ignore": [], "suggests": [], "depends": ["mpqc", "psi3", "abinit", "openmx"], "recommends": [], "avoid": []}}debichem-0.0.5ubuntu1/tasks/0000775000000000000000000000000012443256731012624 5ustar debichem-0.0.5ubuntu1/tasks/modelling0000664000000000000000000000107612443256466014532 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 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-0.0.5ubuntu1/tasks/view-edit-2d0000664000000000000000000000060512443256466014755 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 Remark: Packaging was discussed at http://lists.alioth.debian.org/pipermail/debichem-devel/2009-November/002236.html debichem-0.0.5ubuntu1/tasks/cheminformatics0000664000000000000000000000137312443256466015733 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-0.0.5ubuntu1/tasks/crystallography0000664000000000000000000000041612443256466016004 0ustar Task: Crystallography Description: DebiChem crystallography This metapackage will install packages for crystallography which might be useful for chemists. Depends: drawxtl Depends: gcrystal Depends: python-fabio Depends: shelxle Depends: xcrysden Depends: gamgi debichem-0.0.5ubuntu1/tasks/polymer0000664000000000000000000000153012443256466014242 0ustar Task: Polymer editors and mass spectrometry Description: DebiChem Analytical BioChemistry This metapackage will install packages which enable you to: . - load and convert mass spectrometric data files; - edit biopolymer sequences; - elaborate complex mass spectrometry workflows; - perform protein database searches using tandem-ms data; - view and mine mass spectrometric data; . Depends: massxpert Depends: mmass Depends: lutefisk Depends: openms Depends: libpwiz-tools Suggests: libpwiz-dev Depends: python-mzml Depends: libmstoolkit Depends: tandem-mass Depends: r-cran-maldiquant Depends: r-cran-maldiquantforeign Depends: r-cran-readbrukerflexdata Depends: r-cran-readmzxmldata Depends: biceps Depends: r-other-curvefdp Depends: r-other-nitpick Depends: r-cran-mixtools Depends: r-other-amsmercury Depends: r-other-iwrlars debichem-0.0.5ubuntu1/tasks/semiempirical0000664000000000000000000000031612443256466015377 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 Depends: molds debichem-0.0.5ubuntu1/tasks/molmech0000664000000000000000000000043212443256466014177 0ustar Task: Molecular Mechanics Description: DebiChem Molecular Mechanics This metapackage will install Molecular Mechanics which might be useful for chemists. Depends: adun.app Depends: avogadro Depends: ghemical Depends: gromacs Depends: lammps Depends: vmd Depends: votca-csg debichem-0.0.5ubuntu1/tasks/visualisation0000664000000000000000000000125212443256466015446 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 Depends: gabedit Depends: garlic Depends: gausssum 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 Depends: gamgi Depends: p4vasp Depends: travis debichem-0.0.5ubuntu1/tasks/abinitio0000664000000000000000000000125412443256466014354 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 Depends: abinit Depends: openmx Depends: nwchem Depends: aces3 Registration: http://www.qtp.ufl.edu/ACES/register.html Depends: cp2k Depends: quantum-espresso Depends: psi4 Depends: elk-lapw Depends: ergo debichem-0.0.5ubuntu1/Makefile0000664000000000000000000000007312443256466013144 0ustar #!/usr/bin/make -f include /usr/share/blends-dev/Makefile