Commit c093c22a1ec7ae6b79442a6f32809e58bc942902 - debichem

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TODO less more

8	8	nwchem.
9	9	* tasks/modelling: Moved nmoldyn to ...
10	10	* tasks/molecular-dynamics: ... this.
11		* tasks/visualisation: Added cclib.
12		* tasks/crystallography: New task, including shelxle and xcrysden (ITP'd).
13		* tasks/visualisation: Moved gcrystal to ...
14		* tasks/crystallography: ... this.
15
16		[ Daniel Leidert ]
17		* tasks/crystallography: Added drawxtl.

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debian/changelog less more

	0	debichem (0.0.4) unstable; urgency=medium
	1
	2	[ Michael Banck ]
	3	* tasks/abinitio: Added psi4.
	4	* tasks/crystallography: New task, including shelxle and xcrysden.
	5	* tasks/visualisation: Moved gcrystal to ...
	6	* tasks/crystallography: ... this.
	7	* tasks/crystallography: Added python-fabio.
	8	* tasks/molmech: Added lammps.
	9	* tasks/semiempirical: Added molds.
	10	* tasks/abinitio: Added elk-lapw.
	11	* tasks/abinitio: Added ergo.
	12	* tasks/visualisation, tasks/crystallography: Added gamgi.
	13	* tasks/visualisation: Added p4vasp.
	14	* tasks/visualisation: Added travis.
	15	* tasks/molmech: Added votca-csg.
	16	* tasks/polymer: Changed r-cran-mixtools and r-other-amsmercury Suggests to
	17	Depends.
	18	* tasks/polymer: Added r-other-iwrlars.
	19
	20	[ Daniel Leidert ]
	21	* tasks/crystallography: Added drawxtl.
	22
	23	[ Andreas Tille ]
	24	* d/source/format: 3.0 (native)
	25
	26	-- Michael Banck <mbanck@debian.org> Fri, 05 Dec 2014 16:45:37 +0100
	27
0	28	debichem (0.0.3) unstable; urgency=low
1	29
2	30	[ Michael Banck ]

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debian/control less more

19	19	http://blends.alioth.debian.org/debichem/tasks/
20	20
21	21	Package: debichem-abinitio
	22	Section: metapackages
22	23	Architecture: all
23	24	Depends: debichem-tasks (= ${binary:Version})
24		Recommends: abinit, aces3, cp2k, mpqc, nwchem, openmx, psi3, quantum-espresso
	25	Recommends: abinit,
	26	aces3,
	27	cp2k,
	28	elk-lapw,
	29	ergo,
	30	mpqc,
	31	nwchem,
	32	openmx,
	33	psi3,
	34	psi4,
	35	quantum-espresso
25	36	Description: DebiChem Ab Initio Calculations
26	37	This metapackage will install packages doing ab initio calculations which
27	38	might be useful for chemists.
28	39
29	40	Package: debichem-cheminformatics
	41	Section: metapackages
30	42	Architecture: all
31	43	Depends: debichem-tasks (= ${binary:Version})
32		Recommends: libcdk-java, libopsin-java, openbabel, python-chemfp, python-cinfony, python-fmcs, python-indigo, python-openbabel, python-rdkit
	44	Recommends: libcdk-java,
	45	libopsin-java,
	46	openbabel,
	47	python-chemfp,
	48	python-cinfony,
	49	python-fmcs,
	50	python-indigo,
	51	python-openbabel,
	52	python-rdkit
33	53	Description: DebiChem Cheminformatics
34	54	This metapackage will install cheminformatics packages
35	55	useful for chemists.
36	56
37		Package: debichem-modelling
	57	Package: debichem-crystallography
	58	Section: metapackages
38	59	Architecture: all
39	60	Depends: debichem-tasks (= ${binary:Version})
40		Recommends: avogadro, ghemical, pymol
41		Suggests: nmoldyn, python-mmtk
	61	Recommends: drawxtl,
	62	gamgi,
	63	gcrystal,
	64	python-fabio,
	65	shelxle,
	66	xcrysden
	67	Description: DebiChem crystallography
	68	This metapackage will install packages for crystallography which might be
	69	useful for chemists.
	70
	71	Package: debichem-modelling
	72	Section: metapackages
	73	Architecture: all
	74	Depends: debichem-tasks (= ${binary:Version})
	75	Recommends: avogadro,
	76	pymol,
	77	python-mmtk
	78	Suggests: ghemical,
	79	nmoldyn
42	80	Description: DebiChem 3D Molecular Modelling and Visualization
43	81	This metapackage will install 3D Molecular Modelling and Visualization
44	82	which might be useful for chemists.
45	83
46	84	Package: debichem-molmech
	85	Section: metapackages
47	86	Architecture: all
48	87	Depends: debichem-tasks (= ${binary:Version})
49		Recommends: adun.app, avogadro, ghemical, gromacs
50		Suggests: vmd
	88	Recommends: adun.app,
	89	avogadro,
	90	gromacs,
	91	lammps,
	92	votca-csg
	93	Suggests: ghemical,
	94	vmd
51	95	Description: DebiChem Molecular Mechanics
52	96	This metapackage will install Molecular Mechanics
53	97	which might be useful for chemists.
54	98
55	99	Package: debichem-polymer
	100	Section: metapackages
56	101	Architecture: all
57	102	Depends: debichem-tasks (= ${binary:Version})
58		Recommends: lutefisk, massxpert, mmass
59		Description: DebiChem polymer sequence editors and mass spectrometry
60		This metapackage will install packages which enable you to edit
61		polymer sequences so as to perform mass spectrometry simulations and
62		view mass spectra.
	103	Recommends: libpwiz-tools,
	104	lutefisk,
	105	massxpert,
	106	mmass,
	107	openms,
	108	python-mzml,
	109	r-cran-maldiquant,
	110	r-cran-maldiquantforeign,
	111	r-cran-mixtools,
	112	r-cran-readbrukerflexdata,
	113	r-cran-readmzxmldata,
	114	r-other-amsmercury,
	115	r-other-curvefdp,
	116	r-other-iwrlars,
	117	r-other-nitpick,
	118	tandem-mass
	119	Suggests: biceps,
	120	libmstoolkit,
	121	libpwiz-dev
	122	Description: DebiChem Analytical BioChemistry
	123	This metapackage will install packages which enable you to:
	124	.
	125	- load and convert mass spectrometric data files;
	126	- edit biopolymer sequences;
	127	- elaborate complex mass spectrometry workflows;
	128	- perform protein database searches using tandem-ms data;
	129	- view and mine mass spectrometric data;
	130	.
63	131
64	132	Package: debichem-semiempirical
	133	Section: metapackages
65	134	Architecture: all
66	135	Depends: debichem-tasks (= ${binary:Version})
67		Recommends: cp2k, mopac7-bin
	136	Recommends: cp2k,
	137	molds,
	138	mopac7-bin
68	139	Description: DebiChem Semi Empirical
69	140	This metapackage will install Semi Empirical
70	141	which might be useful for chemists.
71	142
72	143	Package: debichem-view-edit-2d
	144	Section: metapackages
73	145	Architecture: all
74	146	Depends: debichem-tasks (= ${binary:Version})
75		Recommends: bkchem, chemtool, easychem, gchempaint, xdrawchem
	147	Recommends: bkchem,
	148	chemtool,
	149	easychem,
	150	gchempaint,
	151	xdrawchem
76	152	Suggests: osra
77	153	Description: DebiChem 2D structure editors
78	154	This metapackage will install 2D structure editors which might be
79	155	useful for chemists.
80	156
81	157	Package: debichem-visualisation
	158	Section: metapackages
82	159	Architecture: all
83	160	Depends: debichem-tasks (= ${binary:Version})
84		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
	161	Recommends: adun.app,
	162	avogadro,
	163	ballview,
	164	cclib,
	165	drawxtl,
	166	gabedit,
	167	gamgi,
	168	garlic,
	169	gausssum,
	170	gdis,
	171	gdpc,
	172	jmol,
	173	kalzium,
	174	p4vasp,
	175	qutemol,
	176	rasmol,
	177	raster3d,
	178	shelxle,
	179	travis,
	180	viewmol,
	181	xbs,
	182	xcrysden,
	183	xmakemol
	184	Suggests: v-sim
85	185	Description: DebiChem 3D Viewers and Calculation Output Visualization
86	186	This metapackage will install 3D Viewers and Calculation Output Visualization
87	187	which might be useful for chemists.

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debian/source/format less more

0

3.0 (native)

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debichem-tasks.desc less more

14	14	aces3
15	15	cp2k
16	16	quantum-espresso
	17	psi4
	18	elk-lapw
	19	ergo
17	20
18	21	Task: debichem-cheminformatics
19	22	Section: debichem

34	37	python-chemfp
35	38	libopsin-java
36	39
	40	Task: debichem-crystallography
	41	Section: debichem
	42	Description: DebiChem crystallography
	43	This metapackage will install packages for crystallography which might be
	44	useful for chemists.
	45	Relevance: 10
	46	Key:
	47	debichem-crystallography
	48	Packages: list
	49	drawxtl
	50	gcrystal
	51	python-fabio
	52	shelxle
	53	xcrysden
	54	gamgi
	55
37	56	Task: debichem-modelling
38	57	Section: debichem
39	58	Description: DebiChem 3D Molecular Modelling and Visualization

44	63	debichem-modelling
45	64	Packages: list
46	65	avogadro
47		ghemical
48	66	pymol
	67	python-mmtk
49	68
50	69	Task: debichem-molmech
51	70	Section: debichem

58	77	Packages: list
59	78	adun.app
60	79	avogadro
61		ghemical
62	80	gromacs
	81	lammps
	82	votca-csg
63	83
64	84	Task: debichem-polymer
65	85	Section: debichem
66		Description: DebiChem polymer sequence editors and mass spectrometry
67		This metapackage will install packages which enable you to edit
68		polymer sequences so as to perform mass spectrometry simulations and
69		view mass spectra.
	86	Description: DebiChem Analytical BioChemistry
	87	This metapackage will install packages which enable you to:
	88	.
	89	- load and convert mass spectrometric data files;
	90	- edit biopolymer sequences;
	91	- elaborate complex mass spectrometry workflows;
	92	- perform protein database searches using tandem-ms data;
	93	- view and mine mass spectrometric data;
	94	.
70	95	Relevance: 10
71	96	Key:
72	97	debichem-polymer

74	99	massxpert
75	100	mmass
76	101	lutefisk
	102	openms
	103	libpwiz-tools
	104	python-mzml
	105	tandem-mass
	106	r-cran-maldiquant
	107	r-cran-maldiquantforeign
	108	r-cran-readbrukerflexdata
	109	r-cran-readmzxmldata
	110	r-other-curvefdp
	111	r-other-nitpick
	112	r-cran-mixtools
	113	r-other-amsmercury
	114	r-other-iwrlars
77	115
78	116	Task: debichem-semiempirical
79	117	Section: debichem

86	124	Packages: list
87	125	mopac7-bin
88	126	cp2k
	127	molds
89	128
90	129	Task: debichem-view-edit-2d
91	130	Section: debichem

117	156	gabedit
118	157	garlic
119	158	gausssum
120		gcrystal
121	159	gdis
122	160	gdpc
123	161	jmol
124	162	qutemol
125	163	rasmol
126		v-sim
127	164	viewmol
128	165	xbs
129	166	xmakemol

133	170	ballview
134	171	raster3d
135	172	kalzium
	173	gamgi
	174	p4vasp
	175	travis
136	176

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dependency_data/debichem_0.0.1.json less more

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{"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": []}}⏎

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dependency_data/debichem_0.0.3.json less more

0

{"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": []}}⏎

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dependency_data/debichem_0.0.4.json less more

0

{"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": []}}⏎

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tasks/abinitio less more

8	8	Published-URL: http://www.mpqc.org
9	9
10	10	Depends: psi3
11		Published-Title: PSI3: an open-source Ab Initio electronic structure package
12		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
13		Published-In: J. Comput. Chem. 28(9):1610-1616
14		Published-Year: 2007
15		Published-URL: http://onlinelibrary.wiley.com/doi/10.1002/jcc.20573/abstract
16		Published-DOI: 10.1002/jcc.20573
17	11
18	12	Depends: abinit
19		Published-Title: ABINIT: First-principles approach to material and nanosystem properties
20		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
21		Published-In: Comput. Phys. Commun. 180(12):2582-2615
22		Published-Year: 2009
23		Published-URL: http://www.sciencedirect.com/science/article/pii/S0010465509002276
24		Published-DOI: 10.1016/j.cpc.2009.07.007
25	13
26	14	Depends: openmx
27	15
28	16	Depends: nwchem
29		Published-Title: NWChem: a comprehensive and scalable open-source solution for large scale molecular simulations
30		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
31		Published-In: Comput. Phys. Commun. 181(9):1477-1489
32		Published-Year: 2010
33		Published-URL: http://www.sciencedirect.com/science/article/pii/S0010465510001438
34		Published-DOI: 10.1016/j.cpc.2010.04.018
35	17
36	18	Depends: aces3
37		Published-Title: Parallel Implementation of Electronic Structure Energy, Gradient and Hessian Calculations
38		Published-Authors: V. Lotrich, N. Flocke, M. Ponton, A. Yau, A. Perera, E. Deumens and R. J. Bartlett
39		Published-In: J. Chem. Phys. 128:194104
40		Published-Year: 2008
41		Published-URL: http://jcp.aip.org/resource/1/jcpsa6/v128/i19/p194104_s1
42		Published-DOI: 10.1063/1.2920482
43	19	Registration: http://www.qtp.ufl.edu/ACES/register.html
44	20
45	21	Depends: cp2k
46	22
47	23	Depends: quantum-espresso
48		Published-Title: QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials
49		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
50		Published-In: J. Phys. Condens. Matter 21:395502
51		Published-Year: 2009
52		Published-URL: http://iopscience.iop.org/0953-8984/21/39/395502
53		Published-DOI: 10.1088/0953-8984/21/39/395502
	24
	25	Depends: psi4
	26
	27	Depends: elk-lapw
	28
	29	Depends: ergo

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tasks/crystallography less more

	0	Task: Crystallography
	1	Description: DebiChem crystallography
	2	This metapackage will install packages for crystallography which might be
	3	useful for chemists.
	4
	5	Depends: drawxtl
	6
	7	Depends: gcrystal
	8
	9	Depends: python-fabio
	10
	11	Depends: shelxle
	12
	13	Depends: xcrysden
	14
	15	Depends: gamgi

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-13

tasks/modelling less more

9	9	Depends: pymol
10	10
11	11	Depends: python-mmtk
12		Homepage: http://dirac.cnrs-orleans.fr/MMTK/
13		License: CeCILL-C
14		Language: C, Python
15		WNPP: 642586
16		Responsible: Picca Frédéric-Emmanuel <picca@synchrotron-soleil.fr>
17		Pkg-Description: The molecular modeling toolkit
18		The Molecular Modeling Toolkit (MMTK) is a library for molecular
19		simulation applications. It provides the most common methods in
20		molecular simulations (molecular dynamics, energy minimization,
21		normal mode analysis) and several force fields used for biomolecules
22		(Amber 94, Amber 99, several elastic network models). MMTK also
23		serves as a code basis that can be easily extended and modified to
24		deal with non-standard situations in molecular simulations.
25	12
26	13	Depends: nmoldyn
27	14	Homepage: http://dirac.cnrs-orleans.fr/plone/software/nmoldyn/

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-23

tasks/molmech less more

3	3	which might be useful for chemists.
4	4
5	5	Depends: adun.app
6		Published-Title: Framework Based Design of a New All-Purpose Molecular Simulation Application: The Adun Simulator
7		Published-Authors: M.A. Johnston, I.F. Galv√°n and J. Vill√\| -Freixa
8		Published-In: J. Comput. Chem. 26(15):1647-1659
9		Published-Year: 2005
10		Published-URL: http://www3.interscience.wiley.com/cgi-bin/abstract/112094040/ABSTRACT
11		Published-DOI: 10.1002/jcc.20312
12	6
13	7	Depends: avogadro
14	8

16	10
17	11	Depends: gromacs
18	12
	13	Depends: lammps
	14
19	15	Depends: vmd
20		License: non-free
21		Homepage: http://www.ks.uiuc.edu/Research/vmd/
22		Vcs-Browser: http://svn.debian.org/wsvn/debichem/wnpp/vmd/
23		Vcs-Svn: svn://svn.debian.org/svn/debichem/wnpp/vmd/
24		Responsible: Michael Banck <mbanck@debian.org>, Steffen Moeller <moeller@debian.org>
25		Pkg-Description: presentation of traces of molecular dynamics runs
26		VMD stands for Visual Molecular Dynamics. While text books
27		and even structure databases because of technical problems only
28		present static pictures of proteins or DNA, for the understanding
29		of the properties of those molecules their vibration or their
30		movement in general is important.
31		.
32		The movements itself are calculated by molecular dynamics programs,
33		such as NAMD (by the same group), Rosetta, BALLView or GROMACS. The
34		latter two are already in the distribution. VMD has a series of
35		nice features, from displaying through animation to analysing.
36		It can be scripted, clustered, and runs on all common OS..
37	16
	17	Depends: votca-csg

+41

-12

tasks/polymer less more

0	0	Task: Polymer editors and mass spectrometry
1		Description: DebiChem polymer sequence editors and mass spectrometry
2		This metapackage will install packages which enable you to edit
3		polymer sequences so as to perform mass spectrometry simulations and
4		view mass spectra.
5
	1	Description: DebiChem Analytical BioChemistry
	2	This metapackage will install packages which enable you to:
	3	.
	4	- load and convert mass spectrometric data files;
	5	- edit biopolymer sequences;
	6	- elaborate complex mass spectrometry workflows;
	7	- perform protein database searches using tandem-ms data;
	8	- view and mine mass spectrometric data;
	9	.
6	10
7	11	Depends: massxpert
8		Published-Title: massXpert 2: a cross-platform software environment for polymer chemistry modelling and simulation/analysis of mass spectrometric data
9		Published-Authors: F. Rusconi
10		Published-In: Bioinformatics 25(20):2741-2742
11		Published-URL: http://bioinformatics.oxfordjournals.org/content/25/20/2741
12	12
13	13	Depends: mmass
14		Published-Title: mMass 3: A Cross-Platform Software Environment for Precise Analysis of Mass Spectrometric Data
15		Published-Authors: M. Strohalm, D. Kavan, P. Novak, M. Volny and V. Havlicek
16		Published-In: Anal. Chem. 82(11):4648-4651
17	14
18	15	Depends: lutefisk
	16
	17	Depends: openms
	18
	19	Depends: libpwiz-tools
	20
	21	Suggests: libpwiz-dev
	22
	23	Depends: python-mzml
	24
	25	Depends: libmstoolkit
	26
	27	Depends: tandem-mass
	28
	29	Depends: r-cran-maldiquant
	30
	31	Depends: r-cran-maldiquantforeign
	32
	33	Depends: r-cran-readbrukerflexdata
	34
	35	Depends: r-cran-readmzxmldata
	36
	37	Depends: biceps
	38
	39	Depends: r-other-curvefdp
	40
	41	Depends: r-other-nitpick
	42
	43	Depends: r-cran-mixtools
	44
	45	Depends: r-other-amsmercury
	46
	47	Depends: r-other-iwrlars

+2

-0

tasks/semiempirical less more

5	5	Depends: mopac7-bin
6	6
7	7	Depends: cp2k
	8
	9	Depends: molds

+0

-18

tasks/view-edit-2d less more

13	13	Depends: xdrawchem
14	14
15	15	Depends: osra
16		Homepage: http://cactus.nci.nih.gov/osra/
17		License: Creative Commons
18		Pkg-Description: Optical Structure Recognition Application
19		OSRA is a utility designed to convert graphical representations of
20		chemical structures, as they appear in journal articles, patent
21		documents, textbooks, trade magazines etc., into SMILES (Simplified
22		Molecular Input Line Entry Specification - see
23		http://en.wikipedia.org/wiki/SMILES) or SD files - a computer
24		recognizable molecular structure format. OSRA can read a document in any
25		of the over 90 graphical formats parseable by ImageMagick - including
26		GIF, JPEG, PNG, TIFF, PDF, PS etc., and generate the SMILES or SDF
27		representation of the molecular structure images encountered within that
28		document.
29		.
30		Note that any software designed for optical recognition is unlikely to
31		be perfect, and the output produced might, and probably will, contain
32		errors, so curation by a human knowledgeable in chemical structures is
33		highly recommended.
34	16	Remark: Packaging was discussed at
35	17	http://lists.alioth.debian.org/pipermail/debichem-devel/2009-November/002236.html

+6

-5

tasks/visualisation less more

7	7	Depends: avogadro
8	8
9	9	Depends: cclib
10		Published-Title: cclib: a library for package-independent computational chemistry algorithms
11		Published-Authors: N. M. O'Boyle, A. L. Tenderholt, K. M. Langner
12		Published-In: J. Comput. Chem. 29(5):839-845
13	10
14	11	Depends: gabedit
15	12
16	13	Depends: garlic
17	14
18	15	Depends: gausssum
19
20		Depends: gcrystal
21	16
22	17	Depends: gdis
23	18

49	44	Depends: raster3d
50	45
51	46	Depends: kalzium
	47
	48	Depends: gamgi
	49
	50	Depends: p4vasp
	51
	52	Depends: travis