https://dindoun.lautre.net/ fr SPIP - www.spip.net https://dindoun.lautre.net/local/cache-vignettes/L128xH128/favicon-68ee1.png?1762285646 https://dindoun.lautre.net/ 128 128 https://dindoun.lautre.net/spip.php?article665 https://dindoun.lautre.net/spip.php?article665 2025-10-08T20:05:44Z text/html fr bruno chimie - <a href="https://dindoun.lautre.net/spip.php?rubrique98" rel="directory">chimie</a> / <a href="https://dindoun.lautre.net/spip.php?mot3" rel="tag">chimie</a> <div class='rss_texte'><div class='spip_document_1494 spip_document spip_documents spip_document_file'> <figure class="spip_doc_inner"> <a href='https://dindoun.lautre.net/IMG/pdf/atomistique_simple.pdf' class=" spip_doc_lien" title='PDF - 65.3 kio' type="application/pdf"><img src='https://dindoun.lautre.net/local/cache-vignettes/L64xH64/pdf-b8aed.svg?1775240275' width='64' height='64' alt='' /></a> </figure> </div></div> https://dindoun.lautre.net/spip.php?article221 https://dindoun.lautre.net/spip.php?article221 2017-09-16T03:22:55Z text/html fr bruno chimie <p>dessins de molécules trixie : apt-get install bkchem chemtool easychem xfig bullseye : apt-get install chemtool easychem xfig bist buster : apt-get install bkchem chemtool easychem xfig bist blender avec import de fichier pdb bkchem : <br class='autobr' /> chemtool <br class='autobr' /> easychem <br class='autobr' /> xfig tracé de polygones/courbes <br class='autobr' /> bist - chemical drawing tool <br class='autobr' /> visualisation de molécules http://www.rcsb.org/ trixie : apt-get install rasmol jmol povray pymol autodock-vina apt-get install rasmol jmol povray gdis ballview (…)</p> - <a href="https://dindoun.lautre.net/spip.php?rubrique44" rel="directory">Physique</a> / <a href="https://dindoun.lautre.net/spip.php?mot3" rel="tag">chimie</a> <div class='rss_texte'><h2 class="spip">dessins de molécules </h2> <p>trixie : <code class='spip_code spip_code_inline' dir='ltr'>apt-get install bkchem chemtool easychem xfig</code><br class='autobr' /> bullseye : <code class='spip_code spip_code_inline' dir='ltr'>apt-get install chemtool easychem xfig bist</code><br class='autobr' /> buster : <code class='spip_code spip_code_inline' dir='ltr'>apt-get install bkchem chemtool easychem xfig bist</code></p> <ul class="spip" role="list"><li> blender avec import de fichier pdb</li></ul><ul class="spip" role="list"><li> bkchem :</li></ul><div class='spip_document_144 spip_document spip_documents spip_document_image spip_documents_center spip_document_center'> <figure class="spip_doc_inner"> <a href='https://dindoun.lautre.net/IMG/png/bkchem.png' class="spip_doc_lien mediabox" type="image/png"> <img src='https://dindoun.lautre.net/IMG/png/bkchem.png?1660413159' width='500' height='260' alt='' /></a> </figure> </div><ul class="spip" role="list"><li> chemtool</li></ul><div class='spip_document_145 spip_document spip_documents spip_document_image spip_documents_center spip_document_center'> <figure class="spip_doc_inner"> <a href='https://dindoun.lautre.net/IMG/png/chemtool.png' class="spip_doc_lien mediabox" type="image/png"> <img src='https://dindoun.lautre.net/IMG/png/chemtool.png?1660413159' width='500' height='220' alt='' /></a> </figure> </div><ul class="spip" role="list"><li> easychem</li></ul><div class='spip_document_146 spip_document spip_documents spip_document_image spip_documents_center spip_document_center'> <figure class="spip_doc_inner"> <img src='https://dindoun.lautre.net/IMG/png/easychem-2.png?1660413159' width='500' height='390' alt='' /> </figure> </div><div class='spip_document_70 spip_document spip_documents spip_document_image spip_documents_center spip_document_center'> <figure class="spip_doc_inner"> <img src='https://dindoun.lautre.net/local/cache-vignettes/L134xH54/easychem-1b6cb.png?1762389479' width='134' height='54' alt='' /> </figure> </div><ul class="spip" role="list"><li> xfig tracé de polygones/courbes</li></ul><div class='spip_document_147 spip_document spip_documents spip_document_image spip_documents_center spip_document_center'> <figure class="spip_doc_inner"> <a href='https://dindoun.lautre.net/IMG/png/xfig.png' class="spip_doc_lien mediabox" type="image/png"> <img src='https://dindoun.lautre.net/IMG/png/xfig.png?1660413159' width='500' height='375' alt='' /></a> </figure> </div><ul class="spip" role="list"><li> bist - chemical drawing tool</li></ul><div class='spip_document_151 spip_document spip_documents spip_document_image spip_documents_center spip_document_center'> <figure class="spip_doc_inner"> <a href='https://dindoun.lautre.net/IMG/png/bist.png' class="spip_doc_lien mediabox" type="image/png"> <img src='https://dindoun.lautre.net/IMG/png/bist.png?1660413159' width='500' height='405' alt='' /></a> </figure> </div><h2 class="spip">visualisation de molécules</h2> <p> <a href="http://www.rcsb.org/" class="spip_url spip_out auto" rel="nofollow external">http://www.rcsb.org/</a><br class='autobr' /> trixie : <code class='spip_code spip_code_inline' dir='ltr'>apt-get install rasmol jmol povray pymol autodock-vina</code><br class='autobr' /> <code class='spip_code spip_code_inline' dir='ltr'>apt-get install rasmol jmol povray gdis ballview pymol</code></p> <ul class="spip" role="list"><li> rasmol-gtk : ouverture de fichiers pdb</li></ul><div class='spip_document_148 spip_document spip_documents spip_document_image spip_documents_center spip_document_center'> <figure class="spip_doc_inner"> <img src='https://dindoun.lautre.net/IMG/png/rasmol-gtk.png?1660413159' width='500' height='518' alt='' /> </figure> </div><ul class="spip" role="list"><li> gdis</li></ul><div class='spip_document_149 spip_document spip_documents spip_document_image spip_documents_center spip_document_center'> <figure class="spip_doc_inner"> <a href='https://dindoun.lautre.net/IMG/png/gdis-2.png' class="spip_doc_lien mediabox" type="image/png"> <img src='https://dindoun.lautre.net/IMG/png/gdis-2.png?1660413159' width='500' height='275' alt='' /></a> </figure> </div><div class='spip_document_71 spip_document spip_documents spip_document_image spip_documents_center spip_document_center'> <figure class="spip_doc_inner"> <img src='https://dindoun.lautre.net/local/cache-vignettes/L136xH100/gdis-05a1b.png?1762389480' width='136' height='100' alt='' /> </figure> </div><ul class="spip" role="list"><li> jmol - Molecular Viewer : export possible vers html avec rotation 3D</li></ul><div class='spip_document_152 spip_document spip_documents spip_document_image spip_documents_center spip_document_center'> <figure class="spip_doc_inner"> <img src='https://dindoun.lautre.net/IMG/png/jmol.png?1660413159' width='500' height='602' alt='' /> </figure> </div><ul class="spip" role="list"><li> ballview - modélisation moléculaire (libre) et outil graphique moléculaire</li></ul><div class='spip_document_153 spip_document spip_documents spip_document_image spip_documents_center spip_document_center'> <figure class="spip_doc_inner"> <a href='https://dindoun.lautre.net/IMG/png/ballview.png' class="spip_doc_lien mediabox" type="image/png"> <img src='https://dindoun.lautre.net/IMG/png/ballview.png?1660413159' width='500' height='375' alt='' /></a> </figure> </div><ul class="spip" role="list"><li> pymol</li></ul><div class='spip_document_156 spip_document spip_documents spip_document_image spip_documents_center spip_document_center'> <figure class="spip_doc_inner"> <a href='https://dindoun.lautre.net/IMG/png/pymol.png' class="spip_doc_lien mediabox" type="image/png"> <img src='https://dindoun.lautre.net/IMG/png/pymol.png?1660413159' width='500' height='420' alt='' /></a> </figure> </div><ul class="spip" role="list"><li> autodock-vina - chargement de petites molécules jusqu'aux protéines : pas réussi à utiliser</li></ul><ul class="spip" role="list"><li> gcrystal - visualiseur léger de structures cristallines : dommage , plante</li></ul><h2 class="spip">tableau périodique des éléments</h2> <p>trixie : <code class='spip_code spip_code_inline' dir='ltr'>apt-get install gperiodic kalzium</code></p> <ul class="spip" role="list"><li> gperiodic ( masse,densité,point de fusion, d'ébullition, rayon atomique, rayon de covalence, rayon ionique, volume atomique, chaleur spécifique, chaleur de fusion, chaleur de vaporisation, conductivité thermique, température de Debye, électronégativité de Pauling, énergie de première ionisation, états d'oxydation, configuration électronique, structure cristalline, apparence ) <div class='spip_document_72 spip_document spip_documents spip_document_image spip_documents_center spip_document_center'> <figure class="spip_doc_inner"> <img src='https://dindoun.lautre.net/local/cache-vignettes/L247xH100/gperiodic-e0d1c.png?1762389480' width='247' height='100' alt='' /> </figure> </div></li></ul><div class='spip_document_150 spip_document spip_documents spip_document_image spip_documents_center spip_document_center'> <figure class="spip_doc_inner"> <img src='https://dindoun.lautre.net/IMG/png/gperiodic-fe.png?1660413159' width='500' height='397' alt='' /> </figure> </div><ul class="spip" role="list"><li> kalzium - periodic table and chemistry tools</li></ul><div class='spip_document_154 spip_document spip_documents spip_document_image spip_documents_center spip_document_center'> <figure class="spip_doc_inner"> <a href='https://dindoun.lautre.net/IMG/png/kalzium.png' class="spip_doc_lien mediabox" type="image/png"> <img src='https://dindoun.lautre.net/IMG/png/kalzium.png?1660413159' width='500' height='375' alt='' /></a> </figure> </div><div class='spip_document_155 spip_document spip_documents spip_document_image spip_documents_center spip_document_center'> <figure class="spip_doc_inner"> <a href='https://dindoun.lautre.net/IMG/png/kalzium-fe.png' class="spip_doc_lien mediabox" type="image/png"> <img src='https://dindoun.lautre.net/IMG/png/kalzium-fe.png?1660413159' width='500' height='368' alt='' /></a> </figure> </div><h2 class="spip">programmes de calcul</h2><ul class="spip" role="list"><li> openbabel - Chemical toolbox utilities (cli) // python-openbabel - Chemical toolbox library (python bindings)</li></ul> <p>contient de nombreux programmes , <br class='autobr' /> par exemple /usr/bin/obenergy /tmp/methane-1.pdb</p> <div class="precode"><pre class='spip_code spip_code_block' dir='ltr' style='text-align:left;'><code>E N E R G Y TOTAL BOND STRETCHING ENERGY = 2.024 kJ/mol TOTAL ANGLE BENDING ENERGY = 0.000 kJ/mol TOTAL TORSIONAL ENERGY = 0.000 kJ/mol TOTAL VAN DER WAALS ENERGY = 0.000 kJ/mol TOTAL ENERGY = 2.02460 kJ/mol </code></pre></div><h2 class="spip">Pas essayés : </h2><ul class="spip" role="list"><li> nwchem - High-performance computational chemistry software</li></ul><ul class="spip" role="list"><li> cclib - Parsers and algorithms for computational chemistry</li><li> python-cclib - Parsers and algorithms for computational chemistry (Python module)</li><li> education-chemistry - Debian Edu chemistry related applications</li><li> science-chemistry - Debian Science Chemistry packages</li><li> debichem-polymer - DebiChem Analytical BioChemistry</li><li> ergo - Quantum chemistry program for large-scale calculations</li><li> indigo-utils - Organic Chemistry Toolkit Utilities</li><li> python-indigo - Organic Chemistry Toolkit (Python module)</li></ul><ul class="spip" role="list"><li> massxpert-data - linear polymer mass spectrometry software - arch-indep data</li><li> mopac7-bin - Semi-empirical Quantum Chemistry Library (binaries)</li><li> mpqc - Massively Parallel Quantum Chemistry Program</li></ul><ul class="spip" role="list"><li> psi4 - Quantum Chemical Program Suite</li><li> psi4-data - Quantum Chemical Program Suite (data files)</li><li> psi3 - Quantum Chemical Program Suite</li><li> python-rdkit - Collection of cheminformatics and machine-learning software</li><li> wims - server for educational content : courses, exercises, and exams</li><li> adun.app - simulateur moléculaire pour GNUstep</li></ul><ul class="spip" role="list"><li> lammps - Molecular Dynamics Simulator</li></ul> <p>et aussi : ghemical libavogadro-dev kalzium mopac7-bin nwchem psi3 avogadro chemps2 cp2k ergo jmol mpqc openmolcas quantum-espresso</p></div>