avogadrolibs
Avogadro libraries provide 3D rendering, visualization, analysis and data processing useful in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. (by OpenChemistry)
openbabel
Open Babel is a chemical toolbox designed to speak the many languages of chemical data. (by openbabel)
avogadrolibs | openbabel | |
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1 | 3 | |
409 | 998 | |
2.4% | 2.5% | |
9.9 | 6.3 | |
2 days ago | about 1 month ago | |
C++ | C++ | |
BSD 3-clause "New" or "Revised" License | GNU General Public License v3.0 only |
The number of mentions indicates the total number of mentions that we've tracked plus the number of user suggested alternatives.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
avogadrolibs
Posts with mentions or reviews of avogadrolibs.
We have used some of these posts to build our list of alternatives
and similar projects.
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What software can you recommend that can extract conformation B from a *.pdb file? Avogadro and Chimera do not appear to work, and surely there exists something better than opening it in Gaussian as a biological unit, selecting chain A and deleting it.
Feel free to track this https://github.com/OpenChemistry/avogadrolibs/issues/846
openbabel
Posts with mentions or reviews of openbabel.
We have used some of these posts to build our list of alternatives
and similar projects.
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Cheaper/free alternatives to ChemDraw?
Perhaps you are aware of openbabel as a converter between files relevant to chemistry (download page, the current documentation), and of the markup language LaTeX. (Maybe more so if you already interact with folks from physical chemistry / spectroscopy.) The official servers compile multiple packages relevant to chemistry (tag cloud chemistry). While the design of organic reactions with a GUI like ChemDraw, ChemDoodle, etc frequently is the most convenient approach (subsequent export as .pdf, or .png), chemobabel is an interesting approach to depict individual molecules for which you "only" have .mol, .sdf file or a descriptive SMILES string. Here, openbabel is working in the background to generate an illustration eventually added to your report (link to the English documentation as pdf).
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Nicely typeset chemical SMILES
``` %% % External assistance to generate "IUPAC traditional name" for SMILES % CC1=C(C(=O)C[C@@H]1OC(=O)[C@@H]2[C@H](C2(C)C)/C=C(\C)/C(=O)OC)C/C=C\C=C % % * converted by openbabel 3.1.1 (https://github.com/openbabel/openbabel) % on the CLI into a mol file % * this mol file was read by chemdoodle (https://web.chemdoodle.com/), % equally possible without an installation on the web on % https://web.chemdoodle.com/demos/iupac-naming % % output string (without the markup chemdoodle provides) used below: % Methyl (E)-3-[(1R,3R)-3-{(S)-3-[(2Z)-2,4-pentadienyl]-2-methyl-4-oxo-2-cyclopenten-1-yloxycarbonyl}-2,2-dimethylcyclopropyl]methacrylate % % With an input of the SMILES into ChemDraw (e.g., on % https://chemdrawdirect.perkinelmer.cloud/js/sample/index.html# ), % the subsequent structure2name function assigns the name % (S)-2-methyl-4-oxo-3-((Z)-penta-2,4-dien-1-yl)cyclopent-2-en-1-yl (1R,3R)-3-((E)-3-methoxy-2-methyl-3-oxoprop-1-en-1-yl)-2,2-dimethylcyclopropane-1-carboxylate % % Setup around longtblr uses the example by FranekW posted in reply to % reddit "Landscape table with code snippets" by 2023-01-16, see % https://www.reddit.com/r/LaTeX/comments/10d0joc/landscape_table_with_code_snippets/ %%
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How do i preview Latex Chemfig snippets in doom emacs?
So keep an eye open on synopses like this one or an other about programs which allow to prepare the drawings and an export as .eps, .png., .svg, etc. in addition to the native file format. On occasion, there are free test sites with (somewhat reduced functionality), too, e.g., chemdraw, or marvin. And if you encounter e.g., a .mol file, openbabel (which equally may export to .png and .svg).
What are some alternatives?
When comparing avogadrolibs and openbabel you can also consider the following projects:
tomviz - Cross platform, open source application for the processing, visualization, and analysis of 3D tomography data
psi4 - Open-Source Quantum Chemistry – an electronic structure package in C++ driven by Python
SFML - Simple and Fast Multimedia Library
OpenCV - Open Source Computer Vision Library
corona - Solar2D Game Engine main repository (ex Corona SDK)
Bitcoin - Bitcoin Core integration/staging tree
Panda3D - Powerful, mature open-source cross-platform game engine for Python and C++, developed by Disney and CMU