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| Original file line number | Diff line number | Diff line change |
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| --- | ||
| title: "Google Summer of Code 2018: Molecular Dynamics" | ||
| categories: News | ||
| author: ghutchis | ||
| date: 2018-08-13 | ||
| --- | ||
|
|
||
| Adarsh Balasubramanian was a strong contributor to Avogadro2 this summer as part of | ||
| [Google Summer of Code](https://summerofcode.withgoogle.com/archive/2018/projects/4861646958755840) | ||
|
|
||
| Adarsh contributed a number of key features: | ||
| - File import for many trajectory formats including: | ||
| - PDB | ||
| - LAMMPS dump files | ||
| - GROMACS trr trajectories | ||
| - DCD trajectory format (CHARMM, OpenMM, NAMD, LAMMPS) | ||
| - VASP OUTCAR | ||
| - Amber mdcrd files | ||
| - LAMMPS Input Generator | ||
| - OpenMM Input Generator | ||
| - Animation / Player tool overhaul | ||
| - Native export to AVI and GIF | ||
| - Molecular dynamics analysis | ||
| - RMSD VTK chart | ||
| - Pair / Radial distribution function chart | ||
| - Rendering force vector arrows | ||
| - Improved residue classes | ||
|
|
||
| His full report is [online](https://gist.github.com/badarsh2/f72c115062154022020ebc57607e31cb) |
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| @@ -0,0 +1,19 @@ | ||
| --- | ||
| title: "Avogadro 1.91.0 Released" | ||
| categories: News | ||
| author: cryos | ||
| date: 2018-08-22 | ||
| --- | ||
|
|
||
| We are very proud to announce the availability of Avogadro 1.91.0, the latest Beta | ||
| for Avogadro 2.0. | ||
|
|
||
| Avogadro 2 is a free, open source, cross-platform molecular editor | ||
| designed for flexible use in computational chemistry, molecular | ||
| modeling, bioinformatics, materials science, and related | ||
| areas. Packages are available for Windows, Linux and Mac OS X. The | ||
| source code source is available under the 3-clause BSD license. | ||
|
|
||
| This release has a lot of new work completed over the last year, including the results of our first Google Summer of Code where two students worked on projects under the program. | ||
|
|
||
| If you use Avogadro or Avogadro 2, please consider citing the Avogadro paper: <http://www.jcheminf.com/content/4/1/17> |
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| @@ -0,0 +1,33 @@ | ||
| --- | ||
| title: "2018 Avogadro UGM Materials" | ||
| categories: News | ||
| author: ghutchis | ||
| date: 2018-08-25 | ||
| --- | ||
|
|
||
|  | ||
|
|
||
| Materials from our first User Group Meeting are available through GitHub: https://github.com/openchemistry/avogadro-ugm2018 | ||
|
|
||
| ## Talks | ||
|
|
||
| - Geoffrey Hutchison, Pitt [Welcome, Intro & Community Feedback](https://github.com/OpenChemistry/avogadro-ugm2018/blob/master/talks/Hutchison-Overview.pdf) | ||
| - Marcus Hanwell, Kitware [Avogadro 2, Open Chemistry](https://github.com/OpenChemistry/avogadro-ugm2018/blob/master/talks/Avogadro2-OpenChemistry.pdf) | ||
| - Patrick Avery, U. Buffalo [Extended Hückel, Solids and Avogadro](https://github.com/OpenChemistry/avogadro-ugm2018/blob/master/talks/avogadroWithYaehmop.pdf) | ||
| - John Keith, Pitt [Quantum chemistry modeling of local solvation effects](https://github.com/OpenChemistry/avogadro-ugm2018/blob/master/talks/Keith-SolvationEchem.pdf) | ||
| - Chris Wilmer, Pitt [The Need for New Tools for Materials Discovery](https://github.com/OpenChemistry/avogadro-ugm2018/blob/master/talks/Wilmer-MaterialsCAD.pdf) | ||
| - Paul Boone, Pitt [Avogadro Plugins](https://github.com/OpenChemistry/avogadro-ugm2018/blob/master/talks/Boone-AvogadroPlugins.pdf) | ||
|
|
||
| ## Tutorials | ||
|
|
||
| - Sending RPC calls: https://github.com/OpenChemistry/avogadro-ugm2018/blob/master/tutorials/JSON-RPC.md | ||
| - Input Generators: https://github.com/OpenChemistry/avogadro-ugm2018/blob/master/tutorials/Generators.md | ||
| - Command Scripts: https://github.com/OpenChemistry/avogadro-ugm2018/blob/master/tutorials/Scripts.md | ||
|
|
||
| ## Example Input Generators | ||
|
|
||
| - https://github.com/OpenChemistry/avogadro-ugm2018/tree/master/generators | ||
|
|
||
| ## Example Command Scripts | ||
|
|
||
| - https://github.com/OpenChemistry/avogadro-ugm2018/tree/master/commands |
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| --- | ||
| title: "Avogadro 1.90.0 Released" | ||
| categories: News | ||
| author: cryos | ||
| date: 2016-12-02 | ||
| --- | ||
|
|
||
| We are very proud to announce the availability of Avogadro 1.90.0, the latest Beta | ||
| for Avogadro 2.0. | ||
|
|
||
| Avogadro 2 is a free, open source, cross-platform molecular editor | ||
| designed for flexible use in computational chemistry, molecular | ||
| modeling, bioinformatics, materials science, and related | ||
| areas. Packages are available for Windows, Linux and Mac OS X. The | ||
| source code source is available under the 3-clause BSD license. | ||
|
|
||
| This release has a lot of new work completed over the last year, including the results of our first Google Summer of Code where two students worked on projects under the program. | ||
|
|
||
| If you use Avogadro or Avogadro 2, please consider citing the Avogadro paper: <http://www.jcheminf.com/content/4/1/17> | ||
|
|
||
| This is a community project and we couldn't have made this release | ||
| without you. Many thanks to all the contributors to Avogadro including | ||
| those of you who submitted feedback, bug reports, and code. We | ||
| acknowledge that the development of Avogadro 2 has been funded in part by a US | ||
| Army SBIR with the Engineering Research Development Center under | ||
| contract (W912HZ-12-C-0005) at Kitware, Inc. |
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| --- | ||
| title: "Avogadro 1.90.0 Released" | ||
| categories: News | ||
| author: cryos | ||
| date: 2016-12-02 | ||
| --- | ||
|
|
||
| We are very proud to announce the availability of Avogadro 1.95.0, the latest Beta | ||
| for Avogadro 2.0. | ||
|
|
||
| More can be found on the [1.94 release page](https://github.com/OpenChemistry/avogadrolibs/releases/tag/1.94.0) including downloads for Mac and Windows. | ||
|
|
||
| As part of the release, we've made it easier to download scripts and data, | ||
| including new input generators, molecule fragments, and build and analysis | ||
| commands. These scripts make it much easier to integrate Avogadro with many | ||
| open source chemistry Python tools, including RDKit, ASE, etc. | ||
|
|
||
| Draft developer documentation can be found at https://two.avogadro.cc | ||
|
|
||
| If you have comments or suggestions, please join us at https://discuss.avogadro.cc | ||
|
|
||
| We anticipate several more releases over the summer and early fall 2021. | ||
|
|
||
| ## Features | ||
|
|
||
| - Bring back "insert framgent" builder from Avogadro v1 @ghutchis (#591) | ||
| - New docs on http://two.avogadro.cc @ghutchis (#568) | ||
| - Remove dependency on MoleQueue @cryos (#596) | ||
| - Initial Flatpak package @kevinsmia1939 | ||
| - Improved download widget @ghutchis (#534) | ||
| - Reorganize menus - fix #474 @ghutchis (#564) | ||
| - Export to SVG @serk12 (#588) | ||
| - Symmetry enhancements @ghutchis (#553) | ||
| - Added yaehmop with band structure calc @psavery (#339) | ||
| - Cp2k input @ghutchis (#383) | ||
| - OpenMM script builder plugin @badarsh2 (#343) | ||
| - Handle drag-and-drop of files to the window @ghutchis | ||
| - Use native message / dialog boxes on Mac @ghutchis | ||
| - Download entries from PDB @ghutchis (#575) | ||
| - Allow manipulate to rotate selected fragments @ghutchis (#594) | ||
| - Add bestFitPlane on Molecule @dvermd (#500) | ||
| - Add centerOfGeometry, centerOfMass and radius methods on Molecule @dvermd (#499) | ||
| - Reset view (camera) @serk12 (#450) | ||
| - Transparent support for ASE "extended XYZ" files @ghutchis (#603) | ||
|
|
||
| ## 🐛 Bug Fixes | ||
|
|
||
| - Switch to using Python 3, fixing #431 @ghutchis (#462) | ||
| - Switch Open Babel calls to use CML and non-local numeric format (#471) | ||
| - Save background color across sessions and set bg alpha for export @ghutchis | ||
| - Add support for cut/copy/clear selected atoms @ghutchis (#510) | ||
| - Label toolbar windows for context menu @ghutchis | ||
| - Make sure to send Extensions the setActiveWidget call @ghutchis | ||
| - Make sure to install Qt image plugins on Mac and Windows @ghutchis | ||
| - Fix #483 through stream-specific locale @ghutchis (#549) | ||
| - Fix a pile of rendering bugs on high-res by saving viewport @ghutchis (#556) | ||
| - Adjust font size for 2D measure labels on hires screens @ghutchis (#548) | ||
| - Make sure to check movie sizes for high-dpi screens @ghutchis (#570) | ||
| - Fixes silent export on save bug #439 @anubh4v (#517) | ||
| - Switch to the navigate tool after pasting coordinates over empty @ghutchis (#593) | ||
| - Fix #571 - ensure we read Gaussian files from file, not stream @ghutchis (#592) | ||
| - Fix symmetry detection with dummy atoms (e.g, ferrocene example) @ghutchis (#595) | ||
|
|
||
| ## 🐍 Python Improvements | ||
|
|
||
| - Add support for a JSON list of selected atoms @ghutchis (#440) | ||
| - Simplify wheel building @psavery (#520) | ||
| - Update example Avogadro RPC script @ghutchis | ||
|
|
||
| ## 🧰 Maintenance | ||
|
|
||
| - Switch to using GitHub actions for continual builds @ghutchis (#461) | ||
| - Translations update from Weblate @weblate | ||
| - Get rid of bits/stdc++ headers - non-portable GCC header @ghutchis (#463) | ||
| - Add fedora patches @ghutchis (#460) | ||
| - Allow use of HDF5 >= 1.12.0 @berquist (#488) | ||
| - Remove exit calls from qtaim code @ghutchis (#475) | ||
| - Switch to include spglib.h with no subdir - fixes build issues @ghutchis (#533) | ||
| - Update residues from LigandExpo @ghutchis (#572) | ||
| - Make VtkPlot more object-oriented @psavery (#379) | ||
|
|
||
| ## Credits | ||
|
|
||
| Thanks to many contributors, including: @Andre870-hub, @ImgBotApp, | ||
| @KovalevArtem, @NathanBnm, @Padanian, | ||
| @Pietro026, @SantosSi, @SoftwareByRedline, @VeryTastyTomato, @Z-Fikar, | ||
| @Zaryob, @adreasnow, @ahmadubuntu, @akyunus, @amandadumi, | ||
| @andhikapangestu29, @anubh4v, @badarsh2, @berquist, @borisfaure, | ||
| @comradekingu, @crlambda, @cryos, @dnandz, @dvermd, @ghutchis, | ||
| @grsousajunior, @hello-malaysia, @imgbot, @joanavieira8, | ||
| @kevinsmia1939, @koffevar, @ludovicobesana, @mirosnik1, @niskala5570, | ||
| @psavery, @rezaalmanda, @serk12, @shivupa, @tacostea, @tiagomalho, | ||
| @udopton, @weblate, @willow88, @yavgech, Alex, Apostol Penkov, Editor | ||
| Do Sonic BR, Irina Puscas, J. Lavoie, Jacque Fresco, Jörg S, Kavin | ||
| Teenakul, Liu Tao, Michalis, My Random Thoughts, Oğuz Ersen, RIDHO | ||
| NURUL ADILLA, Szabolcs Kalapos, Talking Panda, Thomas Koller, Tymofij | ||
| Lytvynenko, fikril Ha, phlostically, rahul bahuguna | ||
|
|
||
|
|
||
| If you use Avogadro or Avogadro 2, please consider citing the Avogadro paper: <http://www.jcheminf.com/content/4/1/17> |
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| --- | ||
| title: "Results from 2021 Community Survey" | ||
| categories: News | ||
| author: ghutchis | ||
| date: 2021-07-28 | ||
| toc: true | ||
| --- | ||
|
|
||
| We recently posted our second "community survey" to gather feedback. | ||
| The survey was highlighted on Twitter and on the | ||
| avogadro mailing lists. | ||
|
|
||
| ## Quick Summary (tldr) | ||
|
|
||
| - Many users find Avogadro from a friend, peer or instructor (~45%) | ||
| - By far, most download binaries (>80%) | ||
| - Many use package managers (42%) | ||
| - Responses were heavily from Linux (71%) and Mac (60%) users, despite most SourceForge downloads from Windows users (66%) | ||
| - Heavily educated, with >90% of responses with at least a graduate degree | ||
| - Many can code: >40% report Python knowledge, >10% report C/C++ knowledge | ||
| - High bias towards research applications | ||
| - Most responses use Avogadro frequently (~57% use at least weekly) | ||
| - Many complaints about stability, crashes, and scalability to large systems | ||
| - Some suggestions to add features that already exist! | ||
| - Over 80% haven't contributed previously |
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| @@ -0,0 +1,82 @@ | ||
| --- | ||
| title: "Avogadro 1.95 Released" | ||
| categories: News | ||
| author: ghutchis | ||
| date: 2021-08-16 | ||
| --- | ||
|
|
||
| We are very proud to announce the availability of Avogadro 1.95.0, the latest Beta | ||
| for Avogadro 2.0. | ||
|
|
||
| More can be found on the [1.95 release page](https://github.com/OpenChemistry/avogadrolibs/releases/tag/1.95.0) including downloads for Mac and Windows. | ||
|
|
||
| Thanks to many for suggestions, bug reports, and discussions. | ||
|
|
||
| This release includes many new features, including new protein ribbon / cartoon renderings and the new "Layer" | ||
| system as part of Google Summer of Code by @serk12. | ||
|
|
||
| Draft developer documentation can be found at https://two.avogadro.cc | ||
|
|
||
| If you have comments or suggestions, please join us at https://discuss.avogadro.cc and as always, help and contributions | ||
| in many forms are very welcome, **particularly if you'd like to help with user documentation.** | ||
|
|
||
|
|
||
| ## ✨ Features | ||
|
|
||
| - New "Layer" system, including custom rendering, locking and hiding parts of the molecule @serk12 (#709) | ||
| - Atom and residue labels @serk12 (#715) | ||
| - New protein cartoon / ribbon display @serk12 (#660 #694 #716) | ||
| - Update render options for Wireframe and Ball-and-Sticks @ghutchis (#700 #720) | ||
| - Use MMTF downloads - more efficient than PDB format @ghutchis (#699) | ||
| - Add back support for importing crystals @ghutchis (#658 #659) | ||
| - Add CJSON support for save/load residues and atom colors @ghutchis (#646) | ||
| - Refactor of Python command and input generators, including tabs @ghutchis (#667) | ||
| - New View => Apply Colors menu @ghutchis (#640 #723) | ||
| - Apply color schemes for residues @ghutchis (#638 #688) | ||
| - Add more selection commands, including select by residue @ghutchis (#632 #634) | ||
| - Render selected atoms in VdW and licorice modes @ghutchis (#702) | ||
| - Detect secondary structure from residues / backbones @ghutchis (#685) | ||
| - Save enabled / disabled state of scene / rendering plugins on quit @ghutchis | ||
| - Should now download and install translations for @ghutchis | ||
|
|
||
| ## 🐛 Bug Fixes | ||
|
|
||
| - Fix Mac builds by turning off COORDGEN library @ghutchis (#606) | ||
| - Fix Windows installer to include all needed files @ghutchis | ||
| - Save projection type on close #682 @ghutchis | ||
| - Add a pass to fix OB plugin library paths on Mac @ghutchis (#627 #628) | ||
| - Fix odd behavior on 'Center' command @serk12 (#728) | ||
| - Fix several crashes with proteins @ghutchis (#724 #726 #727) | ||
| - Fix crash in CJSON reading file without labels @ghutchis (#722) | ||
| - Fix bug deleting selected atoms #650 @ghutchis (#672 #677) | ||
| - Fix "delete last atom" bug @ghutchis (#691) | ||
| - When dragging to create a new atom, use starting coords @ghutchis (#690) | ||
| - Fix #679 - incorrect PDB unit cells @ghutchis (#689) | ||
| - Fixed problems inserting SMILES without coordinates @ghutchis (#661) | ||
| - Fix for transparent widgets @ghutchis (#656) | ||
| - Fix #602 - use Molden order for f-orbitals @ghutchis (#649) | ||
| - If a chain ID is missing / invalid, skip (to read non-standard PDB) @ghutchis (#647) | ||
| - Make sure to reset colors when changing elements @ghutchis (#708) | ||
|
|
||
| ## 🧰 Maintenance | ||
|
|
||
| - Make sure to install crystals directory even when it exists @ghutchis (#613) | ||
| - Replace NULL/0 with nullptr @e-kwsm (#617) | ||
| - Add support for reading partial charge models from obabel @ghutchis (#626) | ||
| - Replace obsolescent `LINK_(PRIVATE|PUBLIC)` with `(PRIVATE|PUBLIC)` @e-kwsm (#629) | ||
| - Refactor Molecules class @serk12 (#648) | ||
| - Don't install cclib script - which was removed @ghutchis (#662 #663) | ||
|
|
||
| ## 📚 Translations | ||
|
|
||
| - Fix fuzzy entry for Nihonium (not Zirconium!) @e-kwsm (#618) | ||
| - Fix all incorrect fuzzy entries #619 @e-kwsm (#643) | ||
| - Remove wrong entries which were fuzzy @e-kwsm (#644) | ||
| - Translations update from Weblate @weblate (#625) | ||
| - Add a workflow which should update the translation template continuously @ghutchis (#624) | ||
|
|
||
| ## Credits | ||
|
|
||
| Thanks to many contributors, including: @12emin34, @GicoProgram, @LihanzUpenn, @NathanBnm, @San4ito, @acunm, @alexrsoares, @danialk03, @dillonschultz93, @e-kwsm, @ghutchis, @grsousajunior, @psavery, @rezaalmanda, @serk12, @tacitcoast, @weblate, Eisuke Kawashima, Jacque Fresco and phlostically | ||
|
|
||
| If you use Avogadro or Avogadro 2, please consider citing the Avogadro paper: <http://www.jcheminf.com/content/4/1/17> |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,25 @@ | ||
| --- | ||
| title: "Google Summer of Code '21: Biomolecular Visualization and Layers" | ||
| categories: News | ||
| author: ghutchis | ||
| date: 2021-09-13 | ||
| --- | ||
|
|
||
| Marc P. Masó was a strong contributor to Avogadro2 this summer as part of | ||
| [Google Summer of Code](https://summerofcode.withgoogle.com/archive/2021/projects/6688823861313536) | ||
|
|
||
| Marc contributed a number of big features including: | ||
| - Protein rendering styles | ||
| - Cartoons | ||
| - Rope | ||
| - Backbone | ||
| - Trace | ||
| - Tube | ||
| - Layers | ||
| - Custom rendering per layer | ||
| - Assigning atoms to layers to hide / lock (e.g., water molecules, etc.) | ||
| - Open / save support in Chemical JSON (CJSON) file format | ||
| - Atom and Residue Labels | ||
| - New tool to create / edit custom labels | ||
|
|
||
| His full report is [online](https://serk12.github.io/gsoc.html) |
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| --- | ||
| title: "New Avogadro2 Development Website" | ||
| categories: News | ||
| author: ghutchis | ||
| date: 2022-01-15 | ||
| --- | ||
|
|
||
| There is now a website to coordinate development on Avogadro2: | ||
|
|
||
| https://two.avogadro.cc/ | ||
|
|
||
| Developer documentation on Avogadro2, including download links for beta releases and nightly | ||
| builds, as well as Python plugin documentation and C++ API are now available. | ||
|
|
||
| We would greatly appreciate help in migrating user documentation from Avgoadro1, | ||
| teaching documents, and translation / internationalization. | ||
|
|
||
| If you can help, please introduce yourself on the [Avogadro forum](https://discuss.avogadro.cc) |