Ycarus Gentoo ebuild

science

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sci-chemistry

GromacsWrapper : Python framework for Gromacs ( http://orbeckst.github.com/GromacsWrapper/ )

NMRdyn : NMR relaxation studies of protein association ( http://sourceforge.net/projects/nmrdyn/ )

acpype : AnteChamber PYthon Parser interfacE ( https://github.com/llazzaro )

ambertools : A suite for carrying out complete molecular mechanics investigations ( http://ambermd.org/#AmberTools" einfo "Go to ${HOMEPAGE} and get AmberTools${PV%_p*}.tar.bz2 )

ball : Biochemical Algorithms Library ( http://www.ball-project.org/ )

burrow-owl : Visualize multidimensional nuclear magnetic resonance (NMR) spectra ( http://burrow-owl.sourceforge.net/ )

camshift : Structure based prediction of protein chemical shifts ( http://www-vendruscolo.ch.cam.ac.uk/camshift/camshift.php )

chimera-bin : An extensible Molecular Modelling System ( http://www.cgl.ucsf.edu/chimera )

chooch : Automatically determine values of the anomalous scattering factors ( http://www.gwyndafevans.co.uk/id2.html )

cnsface : GUI for the Crystallography and NMR System ( http://cnsface.sourceforge.net )

concoord : Protein conformations around a known structure based on geometric restrictions ( http://www.mpibpc.mpg.de/groups/de_groot/concoord/concoord.html )

coot : Crystallographic Object-Oriented Toolkit ( https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/ )

cpmgfit : non-linear least squares fitting of CPMG relaxation dispersion curves ( http://biochemistry.hs.columbia.edu/labs/palmer/software/cpmgfit.html )

cs-rosetta : System for chemical shifts based protein structure prediction using ROSETTA ( http://spin.niddk.nih.gov/bax/software/CSROSETTA/ )

curvefit : Linear and non-linear least squares fitting ( http://cpmcnet.columbia.edu/dept/gsas/biochem/labs/palmer/software/curvefit.html )

dl_poly : a general purpose molecular dynamics simulation package ( http://www.ccp5.ac.uk/DL_POLY/" einfo "Go to ${HOMEPAGE} and download ${A} )

drawxtl : Crystal structure drawings from structural data ( http://www.lwfinger.net/drawxtl/ )

dssp2pdb : convert dssp to pdb ( http://structure.usc.edu/dssp2pdb/ )

erkale : Quantum chemistry program for atoms and molecules ( https://code.google.com/p/erkale/ )

freeon : An experimental suite of programs for linear scaling quantum chemistry ( http://www.freeon.org )

gamess : A powerful quantum chemistry package ( http://www.msg.chem.iastate.edu/GAMESS/GAMESS.html )

gnome-chemistry-utils : Programs and library containing GTK widgets and C++ classes related to chemistry ( http://gchemutils.nongnu.org/ )

hydronmr : Calculation of NMR relaxation of small, quasirigid macromolecules ( http://leonardo.inf.um.es/macromol/programs/hydronmr/hydronmr.htm )

jligand : Java interface which allows links descriptions to be created ( http://www.ysbl.york.ac.uk/mxstat/JLigand/ )

ligplot+ : GUI-based version of LIGPLOT ( http://www.ebi.ac.uk/thornton-srv/software/LigPlus/ )

mage : Mage is a 3D vector display program which shows 'kinemage' graphics ( http://kinemage.biochem.duke.edu/software/mage.php )

mddnmr : Program for processing of NUS multidimensional NMR spectra ( http://www.nmr.gu.se/~mdd/ )

mdsctk : Molecular Dynamics Spectral Clustering Toolkit ( https://github.com/douradopalmares/mdsctk )

mgltools : Software to visualization and analysis of molecular structures ( http://mgltools.scripps.edu/ )

mgltools-autodocktools : MGLTools Plugin -- AutoDockTools ( http://mgltools.scripps.edu )

mgltools-bhtree : MGLTools Plugin -- bhtree ( http://mgltools.scripps.edu )

mgltools-cadd : MGLTools Plugin -- CADD ( http://mgltools.scripps.edu )

mgltools-cmolkit : MGLTools Plugin -- cMolKit ( http://mgltools.scripps.edu )

mgltools-dejavu : MGLTools Plugin -- DejaVu ( http://mgltools.scripps.edu )

mgltools-geomutils : MGLTools Plugin -- geomutils ( http://mgltools.scripps.edu )

mgltools-gle : MGLTools Plugin -- gle ( http://mgltools.scripps.edu )

mgltools-mglutil : MGLTools Plugin -- mglutil ( http://mgltools.scripps.edu )

mgltools-molkit : MGLTools Plugin -- MolKit ( http://mgltools.scripps.edu )

mgltools-networkeditor : MGLTools Plugin -- NetworkEditor ( http://mgltools.scripps.edu )

mgltools-opengltk : MGLTools Plugin -- opengltk ( http://mgltools.scripps.edu )

mgltools-pmv : MGLTools Plugin -- Pmv ( http://mgltools.scripps.edu )

mgltools-pyautodock : MGLTools Plugin -- PyAutoDock ( http://mgltools.scripps.edu )

mgltools-pybabel : MGLTools Plugin -- PyBabel ( http://mgltools.scripps.edu )

mgltools-pyglf : MGLTools Plugin -- pyglf ( http://mgltools.scripps.edu )

mgltools-qslimlib : MGLTools Plugin -- QSlimLib ( http://mgltools.scripps.edu )

mgltools-scenario2 : MGLTools Plugin -- Scenario2 ( http://mgltools.scripps.edu )

mgltools-sff : MGLTools Plugin -- sff ( http://mgltools.scripps.edu )

mgltools-support : MGLTools Plugin -- Support ( http://mgltools.scripps.edu )

mgltools-symserv : MGLTools Plugin -- symserv ( http://mgltools.scripps.edu )

mgltools-utpackages : MGLTools Plugin -- UTpackages ( http://mgltools.scripps.edu )

mgltools-viewer-framework : MGLTools Plugin -- ViewerFramework ( http://mgltools.scripps.edu )

mgltools-vision : MGLTools Plugin -- Vision ( http://mgltools.scripps.edu )

mgltools-visionlib : MGLTools Plugin -- VisionLibraries ( http://mgltools.scripps.edu )

mgltools-volume : MGLTools Plugin -- Volume ( http://mgltools.scripps.edu )

mgltools-webservices : MGLTools Plugin -- WebServices ( http://mgltools.scripps.edu )

mics : Prediction of Protein Structural Motifs from NMR Chemical Shifts ( http://spin.niddk.nih.gov/bax/software/MICS/ )

modelfree : Optimizing Lipari-Szabo model free parameters to heteronuclear relaxation data ( http://www.palmer.hs.columbia.edu/software/modelfree.html )

modeller : Homology or comparative modeling of protein three-dimensional structures ( http://salilab.org/modeller/ )

module2 : Residual dipolar coupling and residual chemical shift analysis software ( http://www.ibs.fr/science-213/scientific-output/software/module/?lang=en" elog "${HOMEPAGE} )

mtz2hkl : Facilitate the transition from refmac5 refinement to shelxh or shelxl refinement ( http://shelx.uni-ac.gwdg.de/~tg/research/programs/conv/mtz2x/mtz2hkl/ )

mtz2sca : Converts CCP4 mtz-files containing anomalous data to Scalepack format ( http://shelx.uni-ac.gwdg.de/~tg/research/programs/conv/mtz2x/mtz2sca/ )

nMOLDYN : nMOLDYN is an interactive analysis program for Molecular Dynamics simulations ( http://dirac.cnrs-orleans.fr/plone/software/nmoldyn/ )

nmrpipe : Spectral visualisation, analysis and Fourier processing ( http://spin.niddk.nih.gov/bax/software/NMRPipe/ )

nmrview : Visualisation and analysis of processed NMR data ( http://www.onemoonscientific.com/nmrview/" einfo "\t${HOMEPAGE} )

nwchem : Delivering High-Performance Computational Chemistry to Science ( http://www.nwchem-sw.org/index.php/Main_Page )

openbabel : Interconverts file formats used in molecular modeling ( http://openbabel.sourceforge.net/ )

openbabel-java : Java bindings for OpenBabel ( http://openbabel.sourceforge.net/ )

openbabel-perl : Perl bindings for OpenBabel ( http://openbabel.sourceforge.net/ )

openbabel-python : Python bindings for OpenBabel (including Pybel) ( http://openbabel.sourceforge.net/ )

openbabel-ruby : Ruby bindings for OpenBabel ( http://openbabel.sourceforge.net/ )

pales-bin : Prediction of alignment from structure ( http://www3.mpibpc.mpg.de/groups/zweckstetter/_links/software_pales.htm )

panav : Probabilistic approach for validating protein NMR chemical shift assignments ( http://link.springer.com/article/10.1007%2Fs10858-010-9407-y/fulltext.html )

pesto : Potential Energy Surface Tools ( http://sourceforge.net/projects/pesto/ )

phenix-bin : Python-based Hierarchical ENvironment for Integrated Xtallography ( http://phenix-online.org/ )

polygon : shows qualitatively if some models parameters are over- or under-refined ( http://www-ibmc.u-strasbg.fr/arn/Site_UPR9002/Polygon/Polygon.html )

pymol : A Python-extensible molecular graphics system ( http://www.pymol.org/ )

pymol-plugins-ezviz : Assistance tool for the difficult to understand user interface of PyMOL ( http://www.rit.edu/cos/ezviz/index.html )

pymol-plugins-psico : Pymol ScrIpt COllection ( https://github.com/speleo3/pymol-psico/ )

pyquante : Quantum chemistry package written in Python ( http://pyquante.sourceforge.net/ )

rosetta : Prediction of protein structures and protein-protein interactions ( http://www.rosettacommons.org/" einfo "Go to ${HOMEPAGE} and get ${A} )

rosetta-tools : Additional scripts for rosetta ( http://www.rosettacommons.org/ http://dylans-biotools.sourceforge.net/ )

shiftx : Prediction of 1H, 13C and 15N chemical shifts for proteins ( http://shiftx.wishartlab.com/ )

shiftx2 : Predicts of backbone and side chain 1H, 13C and 15N CS for proteins ( http://shiftx2.wishartlab.com/ )

smmp : Simple Molecular Mechanics for Proteins ( http://smmp.berlios.de/ )

ssp : Secondary structure propensities ( http://abragam.med.utoronto.ca/software.html )

talosn : Prediction of Protein bb and sc Torsion Angles from NMR Chemical Shifts ( http://spin.niddk.nih.gov/bax/software/TALOS-N/ )

trajng : TrajNG - Trajectory compression library ( http://www.uppmax.uu.se/Members/daniels/trajng-trajectory-compression-library )

unio : Automated NMR Data Analysis ( http://perso.ens-lyon.fr/torsten.herrmann/Herrmann/Software.html" einfo "Please visit ${HOMEPAGE} )

usf-tools : The USF program suite ( http://xray.bmc.uu.se/usf/ )

wxmacmolplt : Chemical 3D graphics program with GAMESS input builder ( http://brettbode.github.io/wxmacmolplt/ )

xplor-nih : Structure determination program which builds on the X-PLOR program ( http://nmr.cit.nih.gov/xplor-nih/" elog "Please visit ${HOMEPAGE} and download ${A} )

Add an ebuild in portage :

The ebuild is now in the portage tree.

You can also use layman : emerge layman then layman -a science

For Paludis use this rsync : rsync://gentoo.zugaina.org/science-portage

If you have a problem : ycarus(-at-)zugaina.org