Avogadro

Latest version: v1.98.1

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1.98.0

🌟 Highlights (tldr)

- Integration with 3Dconnexion input devices on Mac and Windows
- Many thanks to 3Dconnexion and Patryk Skowroński (pskowronskiTDx) for this contribution (1311)
- Improved rendering including ambient occlusion and real-time shadows from aerkiaga
- New template tool for assembly of inorganic complexes and ligands or attaching functional groups (e.g, "click to add phenyl group") from aerkiaga (1075)
- [New forcefield framework](https://discuss.avogadro.cc/t/new-force-field-framework/4921?u=ghutchis) supporting external Python scripts (e.g., XTB, ASE, ANI-2x, etc.) ghutchis (#1370)
- Better perception of bond orders ghutchis
- Align tool (1364) ghutchis
- Manual translate / rotate dialog
- Fetch molecule names from PubChem, including markup
- Commands to create centroid and center-of-mass points
- Improved “fill unit cell” (1375)
- Preview images of insert molecule fragments and import crystals
- Build improvements, including initial support for Qt6 and VTK9 fixes cryos
- Integrated Orca ouputfile support (from Orca-enhanced Avogadro) (1326)
- Add a generic compchem output reader (i.e., should automatically handle `.out` and `.log` files) (1347)
- Initial scripting support (e.g., used to generate preview images through a directory) (1344)
- Several updated toolbar icons

✨ Features

- Reading Gaussian fchk vibrations when present ghutchis (1380)
- Add support for atom labels (e.g., C1, C2, H1…) in the coordinate editor using "L" symbol ghutchis (1362)
- More pybind methods and properties ghutchis (1342)
- Perceive bond orders when requested by Python scripts ghutchis (1211)
- Support for color PLY format spotenza2016 (1177)
- Tweak the edge detection to allow changing the strength too ghutchis (1140)
- Add copy as SMILES / InChI ghutchis (1147)
- Add atoms for selection in wireframe rendering ghutchis (1128)
- Grab the "markup" name from the PubChem JSON response ghutchis (1105)
- Estimate bond distances in template tool aerkiaga (1099)
- Add formal charge combobox to template tool aerkiaga (1090)
- Add support for undo/redo selections, including custom menu text. ghutchis (1056)
- Add initial crystal and space group scripting, including fillUnitCell ghutchis (1374)
- Initial port of align tool from Avogadro 1.x code ghutchis (1364)
- Add a preview panel when PNG images are present for molecules ghutchis (1353)
- Auto-select a format for the user ghutchis (1348)
- Add extension and tool register / handle commands for scripts ghutchis (1320)
- Add an action to create a bond between selected atoms ghutchis (1303)
- Add dialog for manual manipulation ghutchis (1289)
- Read mopac vibrations ghutchis (1239)
- Screen space shading ghutchis (1135)
- Pick a contrasting color (vs. the background) for the text ghutchis (1131)
- Add a copy button for molecular properties ghutchis (1119)
- Fetch molecule names from PubChem PUG interface ghutchis (1103)
- Enable Yaehmop commands - enable if in PATH ghutchis (1100)
- Fix template tool, add more ligands and preview aerkiaga (1097)
- Perceive bond orders ghutchis (1096)
- Add support for polydentate ligand templates aerkiaga (1080)
- Add commands for centroid and center-of-mass atoms ghutchis (1076)
- Initial template tool ghutchis (1075)
- Add default spin multiplicity methods ghutchis (1062)
- Initial support for total charge and spin through CJSON. ghutchis (1058)
- Add AltLoc support to PDB importer aerkiaga (1047)
- Add AltLoc support to MMTF importer aerkiaga (1057)

🐛 Bug Fixes

- Add molden as a possible reader for generic `.out` files ghutchis (1409)
- Fix a few UI / UX issues in the surface dialog ghutchis (1404)
- Fix spurious "change layer" crash with the selection tool (1406) (1408)
- Fix for reading imaginary vibrational frequencies in ORCA outputs. dtelsing (1398)
- Ensure the VTK plot widget has a minimum size cryos (1231)
- Add uncommon "ent" extension for PDB entries ghutchis (1144)
- Put charge / spin in one line with two labels ghutchis (1143)
- By default only enable regular cartoons ghutchis (1141)
- Add VTK auto-init call, which avoids VTK context error message ghutchis (1115)
- Fix some cases where bond order perception gave up ghutchis (1164)
- Fix crash reading non-standard PDB file ghutchis (1161)
- Tweak rendering multiple bonds, rotate 45 degree angle ghutchis (1191)
- Fix a few UI / UX issues in the surface dialog (1404)
- Allow for reading imaginary vibrational frequencies in ORCA outputs. dtelsing (1398)
- Validating filenames before opening files for read / write ghutchis (1367)
- Re-enable CML fragments in case someone has old files ghutchis (1359)
- Don't bond Noble gases ghutchis (1357)
- Fix autodetect for force field with inorganic complexes ghutchis (1337)
- Give better warnings when scripts do not load ghutchis (1336)
- Cleanup label serialize, fixing a potential crash ghutchis (1332)
- Adjust nitrogen valence determination ghutchis (1330)
- Fix 1317 - editor wasn't using the format specification for parsing ghutchis (1327)
- Fix 1179 (finally) setting the colors and transparency of MO ghutchis (1300)
- Add OpenSSL support on Windows ghutchis (1273)
- Update parsing GAMESS coordinates to store the final version ghutchis (1276)
- When deleting an atom, properly adjust the hydrogens of the neighbors ghutchis (1236)
- When removing an atom, remove bonded hydrogens if needed ghutchis (1230)
- Fix atom index labels to start with 1, not zero, as users expect ghutchis (1229)
- Fix POV-Ray mesh export ghutchis (1180)
- Fix requests to the NIH resolver to use new scheme ghutchis (1158)
- Fix editor smooth drag ghutchis (1157)
- Mitigate bright edges in SSAO aerkiaga (1148)
- Fix mis-translated export dialog ghutchis (1133)
- Fix colormap vtk action ghutchis (1145)
- Fix rendering bug that dropped half of the MO rendering ghutchis (1146)
- Fix bug with "combined rows" like Theory / Basis set ghutchis (1136)
- Catch exceptions thrown by mmtf:decode ghutchis (1132)
- Make sure to add / adjust valence in the correct order ghutchis (1112)
- Don't "apply layer" if layer is already zero ghutchis (1108)
- Fix bug to allow editing atom formal charges ghutchis (1091)
- Fix properties menu priorities ghutchis (1079)
- Fix some Edit and Build menu priorities ghutchis (1078)
- Avoid using QWheelEvent::pixelDelta() on X11 aerkiaga (1065)
- Fix bug selecting incorrect angle and torsion atoms ghutchis (1063)

🚀 Performance Improvements

- Switch to (fixed) faster dihedral formula ghutchis (1315)
- Fix editor smooth drag ghutchis (1157)
- Use singleton shaders ghutchis (1156)
- Make sure to cache icons for the LayerModel ghutchis (1152)
- Optimize NeighborPerceiver aerkiaga (1061)

🧰 Maintenance

- Move arc and quad mesh and linestrip convenience classes ghutchis (1068)
- fix typos and punctuation inconsistency (... vs …) e-kwsm (1046)
- Modernize Eigen3, GLEW and OpenGL use as imported targets cryos (1267)
- CMake modernization cryos (1264)
- Remove the ProtoCall code from the repository cryos (1260)
- Remove the MongoChem plugin from the project cryos (1256)
- ImportPQR should not delete the molecule! cryos (1250)
- Port the OpenBabel plugin to work with Qt 6 cryos (1248)
- VTK charts cryos (1247)
- CMake modernization cryos (1246)
- Qt6 porting cryos (1241)
- CMake VTK updates cryos (1228)
- chore: fix typos and spelling inconsistency e-kwsm (1174)
- Make Python bindings build as a standalone project yurivict (1198)
- Switch to using CJSON as the default format with obabel ghutchis (1378)
- Fix the AppImage build for a newer base ubuntu ghutchis (1339)
- CMake: Allow using externally-provided libraries berquist (1286)
- Add arm64 Python wheel builds for Mac ghutchis (1281)
- Now uses notarization for Mac builds ghutchis (1244)
- Now uses a CodeQL scanning workflow ghutchis
- Avoid ambigous definition of mmtf's is\_polymer StefanBruens (1209)
- Turn off deprecated declarations (e.g., Qt 5.15) ghutchis (1142)
- Fix to use "eta" filenames for "C" locale ghutchis (1102)
- Add Dependabot update checks for GitHub actions ghutchis (1083)

📚 Translations

- i18n: fixed \& added russian translations anmorgunov (1137)
- support C locale balducci (1101)
- Many, many translations updates from Hosted Weblate weblate
- Strong translations in English, Esperanto, French, Georgian, German, Hungarian, Japanese, Korean, Portuguese, Serbian, Spanish, and Turkish.

Credits

Thanks to many contributors, including: DDinghoya, DasJott, Lisapple, M3CG, NorwayFun, OfficerBrasidas, SantosSi, StefanBruens, Surajjalpun2002, WilliamBeltranC, Xav83, adityaomar3, aerkiaga, ahenao, anmorgunov, awvwgk, balducci, berquist, comradekingu, cryos, dependabot, dominikflorjan, dtelsing, e-kwsm, ghutchis, github-actions, grsousajunior, hgokhanb, koenr, matterhorn103, mck89, milotype, nbehrnd, nicolazanna, ovari, pskowronskiTDx, salif, simmon-nplob, spotenza2016, tacitcoast, tictactoe101, trollixx, vamsibarnala, weblate, yurivict, Ajith, Alejandro Díaz-Moscoso, Alex B, Eisuke Kawashima, FAN JI, Hugel, Jörg S, Kateryna Golovanvoa, Patryk Skowroński, Shusong Zhang, Weblate Translators, gallegonovato and victor dargallo

1.97

We are pleased to announce the latest release of Avogadro, including piles of bug fixes and many feature enhancements, including contributions from aerkiaga as part of Google Summer of Code.
Thanks to many for suggestions, bug reports, and discussions.

Draft developer documentation can be found at https://two.avogadro.cc

You can download Linux, Windows, and Mac versions at: https://github.com/openchemistry/avogadrolibs/releases/latest

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 or website developement.**

Highlights (tldr)

* Adds molecular surfaces, solvent-accessible, and solvent-excluded surfaces
* Adds support for a range of partial charge models, including coloring electrostatic potentials on surfaces.
* This includes writing Python scripts to assign atomic charges or electrostatic potential
* Adds improved hydrogen-bond, chalcogen, and halogen bond rendering.
* Add improved close-contact and salt-bridge rendering
* Significantly improves interface translation, properly loading translation files, and including a dialog to choose your preferred user interface language (thanks to ovari for significant help)
* Includes English, Hungarian, Serbian, Esperanto, Portuguese, Turkish, German, Georgian, French, and Japanese translations with at least 45% coverage. [Anyone can help via Weblate](https://hosted.weblate.org/engage/avogadro/)
* Now supports VTK-9 and Mac and Windows packages are updated to use Qt 5.15.

✨ Features

- Add tabbed interface to Close Contacts plugin aerkiaga (1026)
- Add "select backbone" and "select sidechain" commands ghutchis (1023)
- Initial salt bridge rendering aerkiaga (1021)
- Implement support for Turbomole coord format (also used by xtb) ghutchis (1012)
- Add ability to choose charge model in Surfaces aerkiaga (1016)
- Color electrostatic mesh aerkiaga (997)
- Add select water, enlarge selection and shrink selection ghutchis (1011)
- Enable editing of atom, bond, angle, torsion properties ghutchis (913)
- Add AM1-BCC charges using `antechamber` ghutchis (999)
- Add Python charge scripts. First example `xtb` GFN2 charges ghutchis (998)
- Enable Open Babel charge models, including caching partial charges ghutchis (984)
- Add arrow key navigation of the periodic table ghutchis (982)
- Assign atom colors by partial charges ghutchis (986)
- Implement basic tabbed interface for NonCovalent rendering aerkiaga (969)
- Implement basic hydrogen bond rendering aerkiaga (926)
- Add "Automatic" resolution, smoothing pass UI, optimization aerkiaga (976)
- Implement Laplacian mesh smoothing aerkiaga (975)
- Implement Solvent Excluded Surfaces aerkiaga (972)
- Initial electrostatics framework ghutchis (970)
- Add molecular surfaces code aerkiaga (897)
- Add missing acceptors and make distance relative (non-covalent) aerkiaga (966)
- Add halogen and chalcogen bonds, tune parameters aerkiaga (949)
- Add electron pair angle check for hydrogen bonds aerkiaga (946)
- Add line widths to the non-covalent / h-bond rendering ghutchis (934)
- Make use of angle tolerance for hole detection aerkiaga (939)
- Rename intensities to IR and add Raman intensities if available ghutchis (938)
- Check for Open Babel CJSON support: use it if available ghutchis (937)

🐛 Bug Fixes

- Clarify error messages of chargeScripts when antechamber or xtb is unavailable e-kwsm (1039)
- Fix input generators (and other scripts) with translation ghutchis (1037)
- Fix crash when layer names are translated (hu_HU right now) ghutchis (1038)
- Fix two minor input generator bugs ghutchis (1033)
- Drop alpha channel in the OpenGL context on Linux to avoid transparent windows
- Fix crashes in Surfaces and Select Backbone aerkiaga (1031)
- Workaround charge models locking up or not running aerkiaga (1020)
- Make sure to process events while rendering an animation ghutchis (1030)
- No longer bundle the "scale" example script - these can be downloaded ghutchis (1029)
- Use single-point calculation for AM1-BCC with Antechamber ghutchis (1002)
- When finding connected atoms, only ignore rings containing the bond ghutchis (1006)
- Fix incorrect hydrogen geometries aerkiaga (980)
- GAMESS-US and NWChem output reader sanity check TiborGY (930)
- Add case-insensitive lookup for file extensions ghutchis (935)


🚀 Performance Improvements

- Optimize mesh smoothing aerkiaga (985)

🧰 Maintenance

- Allow more render plugins to be "layer enabled" ghutchis (1008)
- Modernize using clang tidy fixes ghutchis (1005)
- Use float within Cube instead of double aerkiaga (990)
- Switch to a new clang-tidy script for secure pull-request comments ghutchis (988)
- Fix notarization for Mac M1 builds ghutchis (981)
- Bump Qt version to 5.15.2 (LTS) now that VTK-9 is working ghutchis (977)
- Port vtk9 cryos (973)
- Update source header comments to new format ghutchis (965)
- Fix some inconsistent overrides and headers ghutchis (960)
- Build Mac M1 binaries on self-hosted runner ghutchis (936)
- Fix error when notarizing Mac DMG - use the right working dir ghutchis (927)

📚 Translations

- Fix bug to successfully load translation files
- Automated translation updates
- Fix translation errors with About menu item and 3D View button ghutchis
- Make sure to install qt base translations for Mac and Windows ghutchis
- Make sure that render names in the layer list show up w/ i18n ghutchis (992)
- Translate editor element list ghutchis (964)
- Fix several i18n problems ghutchis (956)
- Make sure to translate menu paths for Python scripts. ghutchis (948)
- Translations update from Hosted Weblate weblate (928)

Credits

Thanks to many contributors, including: NorwayFun, TiborGY, aerkiaga, ahenao, artemmolotov, cryos, e-kwsm, ghutchis, github-actions, matterhorn103, ovari, tacitcoast, usta, weblate, Julen Larrucea, Translator and МАН69К

1.97.0

1.96.0

Not secure
Changes

We are pleased to announce the latest release of Avogadro, including piles of bug fixes and feature enhancements, including contributions from aerkiaga as part of Google Summer of Code.
Thanks to many for suggestions, bug reports, and discussions.

Draft developer documentation can be found at https://two.avogadro.cc

As part of this release, we have an official [AppImage](https://appimage.github.io/apps/) build for Linux, as well as a code-signed release for macOS.

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 or website developement.**

✨ Features

- Insert DNA/RNA dialog ghutchis (909)
- Render close contacts aerkiaga (898)
- Create new layer from selection ghutchis (899)
- Tweak the mesh lighting .. now lights "from the top" ghutchis (880)
- Add an initial config widget to set mesh colors and opacity ghutchis (877)
- Import and retain space group information ghutchis (875)
- Write Gaussian cube files ghutchis (873)
- Add plugin to focus or unfocus selection aerkiaga (868)
- Implement close contact perception logic aerkiaga (862)
- Add formal charge to atom property tables ghutchis (839)
- Add support for formal charges aerkiaga (831)
- Add setting to reverse direction of scroll-to-zoom ghutchis (778)
- Tweak icons for label editor and selection ghutchis (776)
- Add tooltips to tools ghutchis (777)
- Add label editor to create custom labels serk12 (740)
- Add a copy graphics action

🚀 Performance Fixes

- Subgraph rewrite aerkiaga (878)
- Approximate cartoon B-spline from a small local neighborhood aerkiaga (860)
- Bond graph optimization aerkiaga (832)
- Faster bond perception aerkiaga (829)
- Optimize secondary structure aerkiaga (833)

🐛 Bug Fixes

- Add .cjson extension to files if none is present
- Update atomic masses ghutchis (894)
- Fix layer memory crash ghutchis (876)
- Fix memory leak with OpenGL: Detaching and deleting shaders/programs on updates octycs (855)
- Remove call for Core::Molecule rendering to eliminate casting ghutchis (871)
- Fix reading generic file formats with Open Babel ghutchis (848)
- Fix erratic editing behavior aerkiaga (819)
- Solve problems writing files with no extension ghutchis (835)
- Convert 2-letter PDB symbols to appropriate case aerkiaga (830)
- Fix Manipulation and Bond Centric Manipulation tools aerkiaga (825)
- Fall back to Wikipedia method for dihedral angles ghutchis (808)
- Be careful about assign or copy from molecules with no layers ghutchis (806)
- Disable dynamic bonding during animation ghutchis (767)
- Try to use 'python' in the path as a fallback ghutchis (746)

🧰 Maintenance

- Fix Valgrind uninitialized errors aerkiaga (887)
- Add tests using various sanitizers ghutchis (888)
- Make sure to sign and notarize the Mac build ghutchis (893) (885)
- Only build overlayaxes if USE\_OPENGL is enabled ghutchis (879)
- Try using Windows 2019 to build wheels ghutchis (861)
- Create Codacy scans ghutchis (850)
- test ">=0" within machine precision (>-EPS) drew-parsons (813)
- Add defaultBehavior method to render plugins serk12 (807)
- Update setup.py with long description from README.md and URLs ghutchis (750)

📚 Translations

- Translations update from Hosted Weblate weblate
- Automated translation updates github-actions (853)
- Minor tweaks to the automated pull request ghutchis (761)

Credits

Thanks to many contributors, including: HoangTuan110, Lisapple, M3CG, SantosSi, aerkiaga, comradekingu, drew-parsons, ejatjon, ersen0, ghutchis, github-actions, github-actions[bot], milotype, nicolasfella, octycs, ovari, rezaalmanda, serk12, urkawa, weblate, J. Lavoie, Pa, Temuri Doghonadze, phlostically and 刘韬

1.95.1

Not secure
This release fixes several bugs in the recent 1.95.0 release and is recommended for all users.

Thanks to drew-parsons and yurivict for prompt bug reports!

🐛 Bug Fixes

- Fix disabled "Balls and Sticks" rendering on a fresh install serk12 (744)
- Fix for loading settings serk12 (732)
- Add "..." to all input generators to indicate opening a dialog ghutchis (743)
- Fix reference axes menu item ghutchis (705)
- Continue rendering cartoons even if residues aren't found ghutchis (736)
- Enable script formats like cclib to ask for bond perception on read ghutchis (738)

✨ Features

- Initial display-only property tables ghutchis (711)
- Improve selection tool for layers serk12 (729)

🧰 Maintenance

- Make sure to run tests in avogadrolibs (including some fix for test failures) ghutchis (739)

📚 Translations

- Translations update from Weblate weblate (721)

Credits

Thanks to many contributors, including: drew-parsons, ghutchis, mrmrcl, ovari, serk12 yurivict, and weblate

1.95.0

Not secure
Changes

We are pleased to announce the latest release of Avogadro, including piles of bug fixes and feature enhancements.
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.**

We anticipate several more releases over fall 2021 as we finish up our 2.0 release.

✨ 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

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